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Publications
Bythell, B. J.; Hendrickson, C. L.; Marshall, A. G. , . Relative Stability of Peptide Sequence Ions Generated by Tandem Mass Spectrometry . Journal: J. Am. Soc. Mass Spectrom. , pages 644-654, 2012. B. J. Bythell, To Jump or Not To Jump? Cα Hydrogen Atom Transfer in Post-cleavage Radical-Cation Complexes. Journal: J. Phys. Chem. A , pages DOI:10.102, 2012. Abstract [+]: Conventionally, electron capture or transfer to a polyprotonated peptide ion produces an initial radical-cation intermediate which dissociates “directly” to generate complementary cn′ and zm• sequence ions (or ions and neutrals). Alternatively, or in addition, the initial radical-cation intermediate can undergo H• migration to
produce cn• (or cn − H•) and zm′ (or zm• + H•) species prior to complex separation (“nondirect”). This reaction significantly complicates spectral interpretation, creates
ambiguity in peak assignment, impairs effective algorithmic processing (reduction of the spectrum to solely 12C m/z values), and reduces sequence ion signal-to-noise. Experimental evidence indicates that the products of hydrogen atom transfer reactions are substantially less prevalent for higher charge state precursors. This effect is generally rationalized on the basis of decreased complex lifetime. Here, we present a theoretical study of these reactions in post N−Cα bond cleavage radical-cation complexes as a function of size and precursor charge state. This approach provides a computational estimate of the barriers associated with these processes for highly charged peptides with little charge solvation. The data indicate
that the H• migration is an exothermic process and that the barrier governing this reaction rises steeply with precursor ion charge state. There is also some evidence for immediate product separation following N−Cα bond cleavage at higher charge state.
Schenkel, B., An Analysis of the Impacts of Western North Pacific Tropical Cyclones on Their Local And Large Scale Environment. Dissertation/Thesis 2012. Abstract [+]: The following study examines the spatiotemporal response of the local scale and large scale environment to tropical cyclone (TC) passage. The research presented here is broken up into three chapters that can be separated into two parts. Given that the analysis of the environmental response to TC passage heavily relies upon the use of atmospheric reanalysis datasets, the first half of this dissertation (Chapter 2) will examine the fidelity of TC intensity, position, and intensity life cycle within five reanalyses to determine what reanalyses can be used for when studying TCs. The results of this analysis show an underestimation of reanalysis TC intensity beyond what can be attributed to the coarse grid resolution of reanalyses. Moreover, the mean life cycle of normalized TC intensity within reanalyses exhibits an underestimation of pre-peak intensification rates as well as a delay in the timing of peak TC intensity relative to the Best Track. Significant discrepancies between reanalysis and Best-Track TC position are noted to exist particularly in regions that are observation deficient. Of the five reanalyses examined, the NCEP Climate Forecast System Reanalysis (CFSR) and JMA 25-yr Japanese Reanalysis (JRA-25) have the most robust representation of TCs particularly within the North Atlantic (NATL) and Western North Pacific (WPAC).
The second half of this study examines the local scale (Chapter 3) and large scale (Chapter 4) impacts of WPAC TCs upon their environment using storm-relative composites. On local scales, TCs are found to cool sea surface temperatures (SSTs) for at least a month following TC passage. The feedbacks from the SST cold wake combined with an initial net flux divergence of energy from the column yields a significant cooling and drying of the atmosphere that is strongest in the lower troposphere. Restoration of the environment is eventually achieved through a return of SSTs to climatology and a net flux convergence of potential energy aloft.
The large scale response of the environment is primarily associated with an anomalous drying of the lower and middle tropospheric atmospheric environment to the west and southwest of the TC. The drying appears to be caused by upper level convergence resulting from the interaction of the TC outflow with its environment. On the western side of the TC, both the upper level flow from the anticyclone of the Asian monsoon and the increasing inertial stability with latitude due to the meridional gradient of planetary vorticity limit the ventilation to the west of the TC yielding upper level convergence and subsidence. The area of anomalous drying to the southwest is associated with the convergent upper level flow from the right exit region of the anticyclonically curved equatorward outflow jet of the
TC. Lastly, the meridional transport of total energy by TCs results in a substantial cross hemispheric export of dry static energy nearly 4000 km southwards as result of the upper level outflow jet of the TC. The meridional dry static energy transports by TCs appear to comprise a substantial portion of the total atmospheric dry static energy transports at the equator during late summer and early fall. In their totality, these results suggest that TCs may significantly impact their environment both on long temporal scales and large spatial scales with potentially significant aggregate climate impacts in the WPAC given the high frequency of TC occurrence.
Click here for more informationGeoffery Miller, Parametric Uncertainty Analysis of Uranium Transport Surface Complexation Models. Dissertation/Thesis 2011. Abstract [+]: Parametric uncertainty analysis of surface complexation modeling (SCM) has been studied using linear and nonlinear analysis. A computational SCM model was developed by Kohler et al. (1996) to simulate the breakthrough of Uranium(VI) in a column of quartz. Calibration of parameters which describe the reactions involved during reactive-transport simulation has been found to fit experimental data well. Further uncertainty analysis has been conducted which determines the predictive capability of these models. It was concluded that nonlinear analysis results in a more accurate prediction interval coverage than linear analysis. An assumption made by both linear and nonlinear analysis is that the parameters follow a normal distribution. In a preliminary study, when using Monte Carlo sampling a uniform distribution among a known feasible parameter range, the model exhibits no predictive capability. Due to high parameter sensitivity, few realizations exhibit accuracy to the known data. This results in a high confidence of the calibrated parameters, but poor understanding of the parametric distributions. This study first calibrates these parameters using a global optimization technique, multi-start quasi-newton BFGS method. Second, a Morris method (MOAT) analysis is used to screen parametric sensitivity. It is seen from MOAT that all parameters exhibit nonlinear effects on the simulation. To achieve an approximation of the sim- ulated behavior of SCM parameters without the assumption of a normal distribution, this study employs the use of a Covariance-Adaptive Monte Carlo Markov chain algorithm. It is seen from posterior distributions generated from accepted parameter sets that the parameters do not neces- sarily follow a normal distribution. Likelihood surfaces confirm the calibration of the models, but shows that responses to parameters are complex. This complex surface is due to a nonlinear model and high correlations between parameters. The posterior parameter distributions are then used to find prediction intervals about an experiment not used to calibrate the model. The predictive capability of Adaptive MCMC is found to be better than that of linear and non-linear analysis, showing a better understanding of parametric uncertainty than previous study.
Click here for more informationSteven C. Chan, Vasubandhu Misra, Dynamic downscaling of the North American Monsoon with the NCEP-Scripps Regional Spectral Model from the NCEP CFS global model. Journal: Journal of Climate, pages 21, 2011. Abstract [+]: The June-September (JJAS) 2000-2007 NCEP coupled Climate Forecasting System (CFS) global hindcasts are downscaled over the North and South American continents with the NCEP-Scripps Regional Spectral Model (RSM) with anomaly nesting (AN) and without bias correction (control). A diagnosis of the North American Monsoon (NAM) in CFS and RSM hindcasts is presented here. RSM reduces errors caused by coarse resolution, but is unable to address larger scale CFS errors even with bias correction. CFS has relatively weak Great Plains and Gulf of California low-level jets. Low-level jets are strengthened from downscaling, especially after AN bias correction. The RSM NAM hydroclimate shares similar flaws with CFS with problematic diurnal and seasonal variability. Flaws in both diurnal and monthly variability are forced by erroneous convection-forced divergence outside the monsoon core region in eastern and southern Mexico. NCEP Reanalysis shows significant seasonal variability errors, and AN shows little improvement in regional scale flow errors. Our results suggest extreme caution must be taken when the correction is applied relative to reanalyses. Analysis also shows North American Regional Reanalysis NAM seasonal
16 variability has benefited from precipitation data assimilation, but many questions remain concerning NARR’s representation of NAM.
Click here for more informationSteven C. Chan, Vasubandhu Misra, and Henry Smith, A modeling study of the interaction between the Atlantic Warm Pool, the tropical Atlantic easterlies, and the Lesser Antilles. Journal: Journal of Geophysical Research - Atmospheres, pages , 2011. Abstract [+]: The European Centre for Medium-Range Forecasts Reanalysis-40 and National Centers for Environmental Prediction (NCEP)/Department of Energy reanalyses are downscaled over the eastern Caribbean and Lesser Antilles using the NCEP-Scripps Regional Spectral Model for Augusts when the Atlantic Warm Pool (AWP) area is the most anomalous. The simulations show a two-way influence between the Lesser Antilles and the AWP: the islands modulate the regional atmospheric circulation, and AWP variations modulate the interannual variabilities of the islands. The Lesser Antilles introduce diurnal variations and drag to the easterlies. The presence of the islands modulates the prevalent easterlies as a result of the daytime heating of the islands and the consequent boundary layer expansion. The modulations are sensitive to the islands' size and topography. Small and flat islands act as thermal plumes, but the modulations of large and hilly islands are during the daytime as their boundary layer expands. The manifestation of the atmospheric response to the sea surface temperature (SST) anomalies over the islands is sensitive to the island orography. For most islands, the atmospheric response to the SST anomalies is reflected only during the daytime. For all 1-grid-point islands and Antigua, nighttime and dawn minimum temperatures are modulated to the same degree as the daytime maximum. For island rainfall, downscaling reduces the gross overestimations of rainfall in the reanalyses. However, our downscaling results suggest that there is room for improvement in simulating the marine surface diurnal cycle.
Keola Wierschem and Efstratios Manousakis, Simulation of melting of two-dimensional Lennard-Jones solids. Journal: Physical Review B, Vol. 83, pages 214108, 2011. Abstract [+]: We study the nature of melting of a two-dimensional (2D) Lennard-Jones solid using large-scale Monte Carlo simulation. We use systems of up to 102 400 particles to capture the decay of the correlation functions associated with translational order (TO) as well as the bond-orientational (BO) order. We study the role of dislocations and disclinations and their distribution functions. We computed the temperature dependence of the second moment of the TO parameter (ΨG) as well as of the order parameter Ψ6 associated with BO order. By applying finite-size scaling of these second moments, we determined the anomalous dimension critical exponents η(T) and η6(T) associated with power-law decay of the ΨG and Ψ6 correlation functions. We also computed the temperature-dependent distribution of the order parameters ΨG and Ψ6 on the complex plane that supports a two-stage melting with a hexatic phase as an intermediate phase. From the correlation functions of ΨG and Ψ6, we extracted the corresponding temperature-dependent correlation lengths ξ(T) and ξ6(T). The analysis of our results leads to a consistent picture strongly supporting a two-stage melting scenario as predicted by the Kosterlitz, Thouless, Halperin, Nelson, and Young (KTHNY) theory where melting occurs via two continuous phase transitions, first from solid to a hexatic fluid at temperature Tm, and then from the hexatic fluid to an isotropic fluid at a critical temperature Ti. We find that ξ(T) and ξ6(T) have a distinctly different temperature dependence, each diverging at different temperature, and that their finite-size scaling properties are consistent with the KTHNY theory. We also used the temperature dependence of η and η6 and their theoretical bounds to provide estimates for the critical temperatures Tm and Ti, which can also be estimated using the Binder ratio. Our results are within error bars, the same as those extracted from the divergence of the correlation lengths.
Click here for more informationVolha Abramkina and Alexander Volya, Quadrupole collectivity in the two-body random ensemble. Journal: Physical Review C, pages 024322-024, 2011. Abstract [+]: We conduct a systematic investigation of the nuclear collective dynamics that emerges in systems with two-body
random interactions. We explore the development of the mean field and study its geometry. We investigate
multipole collectivities in the many-body spectra and their dependence on the underlying two-body interaction
Hamiltonian. The quadrupole-quadrupole interaction component appears to be dynamically dominating in the
two-body random ensemble. This quadrupole coherence leads to rotational spectral features and thus suggests
the formation of the deformed mean-field of a specific geometry.
Click here for more informationW.R. Deskins, G. Brown, S.H. Thompson, P.A. Rikvold, Kinetic Monte Carlo simulations of a model for heat-assisted magnetization reversal in ultrathin films. Journal: Physical Review B Vol. 84, pages 094431, 2011. Abstract [+]: To develop practically useful systems for ultra-high-density information recording with densities above terabits per square centimeter, it is necessary to simultaneously achieve high thermal stability at room temperature and high recording rates. One method that has been proposed to reach this goal is heat-assisted magnetization reversal (HAMR). In this method, the magnetic orientation is assigned to a high-coercivity material by temporarily reducing the coercivity during the writing process through localized heating. Here we present kinetic Monte Carlo simulations of a model of HAMR for ultrathin films, in which the temperature in the central part of the film is momentarily increased above the critical temperature, for example by a laser pulse. We observe that the speed-up achieved by this method, relative to the switching time at a constant, subcritical temperature, is optimal for an intermediate strength of the writing field. This effect is explained using the theory of nucleation-induced magnetization switching in finite systems. Our results should be particularly relevant to recording media with strong perpendicular anisotropy, such as ultrathin Co/Pt or Co/Pd multilayers.
Click here for more informationTjipto Juwono, Ibrahim Abou Hamad, Per Arne Rikvold, Sanwu Wang, Parameter estimation by Density Functional Theory for a lattice-gas model of Br and Cl chemisorption on Ag(100). Journal: Journal of Electroanalytical Chemistry Vol 662, pages 130-136, 2011. Abstract [+]: We study Bromine and Chlorine chemisorption on a Ag (1 0 0) surface, using a lattice-gas model and the quantum-mechanical Density Functional Theory (DFT) method. In this model the Br and Cl ions adsorb at the fourfold hollow sites of the Ag (1 0 0) surface, which can be represented by a square lattice of adsorption sites. Five different coverages were used for each kind of adsorbate. For each adsorbate and coverage, we obtained the minimum-energy configuration, its energy, and its charge distribution. From these data we calculated dipole moments, lateral interaction energies, and binding energies. Our results show that for Br the lateral interactions obtained by fitting to the adsorption energies obtained from the DFT calculation are consistent with long-range dipole–dipole lateral interactions obtained using the dipole moments calculated from the DFT charge distribution. For Cl we found that, while the long-range dipole–dipole lateral interactions are important, short-range attractive interactions are also present. Our results are overall consistent with parameter estimates previously obtained by fitting room-temperature Monte Carlo simulations to electrochemical adsorption isotherms [I. Abou Hamad, et al., J. Electroanal. Chem. 554 (2003) 211; Electrochim. Acta 50 (2005) 5518].
Click here for more informationSchenkel, B., and R. Hart, Conference Notebook: Potential Implications of Tropical Cyclone Passage. Journal: Bulletin of the American Meteorological Society, pages 1282-1283, 2011. Click here for more informationFierst, J.L. and T.F. Hansen, Genetic architecture in postzygotic reproductive isolation: Evolution of bateson-dobzhansky-muller incompatibilities in a polygenic model. Journal: Evolution, pages 19, 2010. Abstract [+]: The Bateson–Dobzhansky–Muller model predicts that postzygotic isolation evolves due to the accumulation of incompatible epistatic interactions, but few studies have quantified the relationship between genetic architecture and patterns of reproductive divergence. We examined how the direction and magnitude of epistatic interactions in a polygenic trait under stabilizing selection influenced the evolution of hybrid incompatibilities. We found that populations evolving independently under stabilizing selection experienced suites of compensatory allelic changes that resulted in genetic divergence between populations despite the maintenance of a stable, high-fitness phenotype. A small number of loci were then incompatible with multiple alleles in the genetic background of the hybrid and the identity of these incompatibility loci changed over the evolution of the populations. For F1 hybrids, reduced fitness evolved in a window of intermediate strengths of epistatic interactions, but F2 and backcross hybrids evolved reduced fitness across weak and moderate strengths of epistasis due to segregation variance. Strong epistatic interactions constrained the allelic divergence of parental populations and prevented the development of reproductive isolation. Because many traits with varying genetic architectures must be under stabilizing selection, our results indicate that polygenetic drift is a plausible hypothesis for the evolution of postzygotic reproductive isolation.
Click here for more informationAbdulkader Baroudi, Justin Mauldin and Igor V. Alabugin, Conformationally Gated Fragmentations and Rearrangements Promoted by Interception of the Bergman Cyclization through Intramolecular H-Abstraction: A Possible Mechanism of Auto-Resistance to Natural.... Journal: Journal of the American Chemical Society, pages 967–979, 2010. Abstract [+]: A variety of fragmentations and rearrangements can follow Bergman cyclization in enediynes equipped with acetal rings mimicking the carbohydrate moiety of natural enediyne antibiotics of the esperamicine and calchiamicine families. In the first step of all these processes, intramolecular H-atom abstraction efficiently intercepts the p-benzyne product of the Bergman cyclization through a six-membered
TS and transforms the p-benzyne into a new more stable radical. Depending on the substitution pattern and reaction conditions, this radical follows four alternative paths: (a) abstraction of an external hydrogen atom, (b) O-neophyl rearrangement which transposes O- and C-atoms of the substituent, (c) fragmentation of the O-C bond in the acetal ring, or (d) fragmentation with elimination of the appended acetal moiety as a whole. Experiments with varying concentrations of external H-atom donor (1,4-cyclohexadiene) were performed to gain further insight into the competition between intermolecular H-abstraction and the fragmentations. The Thorpe-Ingold effect in gem-dimethyl substituted enediynes enhances the efficiency
of fragmentation to the extent where it cannot be prevented even by a large excess of external H-atom donor. These processes provide insight into a possible mechanism of unusual fragmentation of esperamicin A1 upon its Bergman cycloaromatization and lay foundation for a new approach for the conformational control of reactivity of these natural antitumor antibiotics. Such an approach, in conjunction with supramolecular constraints, may provide a plausible mechanism for resistance to enediyne antibiotics by the enediyne-producing microorganisms.
Morey, S.L., D. S. Dukhovskoy, and C. Cooper, Measurements and modeling of topographically trapped waves along the Sigsbee Escarpment. 2010. Abstract [+]: Observations of strong currents with wave-like behavior have been documented from specific sites near the sea floor along the Sigsbee Escarpment (SE) in the northern Gulf of Mexico. The strongest of these currents reached 100 cm/s, with currents exceeding 40 cm/s observed multiple times. These currents tend to occur when the Loop Current or its separated eddies are in the vicinity, typically to the east of the SE. The currents are oriented dominantly along isobaths with fluctuations of roughly 10-day periods, are decoupled from the upper ocean flow, and appear intensified over the lower part of the water column. These traits are generally consistent with Topographic Rossby Waves. Observational and numerical modeling efforts were funded in 2008 by DeepStar to better understand these events and their dynamics. This paper summarizes the observations, as well as numerical model hindcasts and process studies. Several events of moderately intense currents with quasi-periodic fluctuations were observed in early 2009 while the Loop Current was positioned to the east of the SE. Results show that the model hindcasts are capable of replicating many of the characteristics of the deep currents along the SE. Analysis of the model data show that the energy for these strong deep currents along the SE may originate over the Mississippi Fan to the east of the SE under the strongest part of the Loop Current when it is fully extended over the region.
Ye, M., MMA: A computer code for multimodel analysis. Journal: Ground Water, pages 48(1), 9-1, 2010. Ye, M., K.F. Pohlmann, J.B. Chapman, G.M. Pohll, and D.M. Reeves, A model-averaging method for assessing groundwater conceptual model uncertainty. Journal: Ground Water, pages doi:10.111, 2010. Abstract [+]: This study evaluates alternative groundwater models with different recharge and geologic components at the
northern Yucca Flat area of the Death Valley Regional Flow System (DVRFS), USA. Recharge over the DVRFS
has been estimated using five methods, and five geological interpretations are available at the northern Yucca
Flat area. Combining the recharge and geological components together with additional modeling components that
represent other hydrogeological conditions yields a total of 25 groundwater flow models. As all the models are
plausible given available data and information, evaluating model uncertainty becomes inevitable. On the other
hand, hydraulic parameters (e.g., hydraulic conductivity) are uncertain in each model, giving rise to parametric
uncertainty. Propagation of the uncertainty in the models and model parameters through groundwater modeling
causes predictive uncertainty in model predictions (e.g., hydraulic head and flow). Parametric uncertainty within
each model is assessed using Monte Carlo simulation, and model uncertainty is evaluated using the model
averaging method. Two model-averaging techniques (on the basis of information criteria and GLUE) are discussed.
This study shows that contribution of model uncertainty to predictive uncertainty is significantly larger than that of
parametric uncertainty. For the recharge and geological components, uncertainty in the geological interpretations
has more significant effect on model predictions than uncertainty in the recharge estimates. In addition, weighted
residuals vary more for the different geological models than for different recharge models. Most of the calibrated
observations are not important for discriminating between the alternative models, because their weighted residuals
vary only slightly from one model to another.
Beerli, P., M. Palczewski, Unified Framework to Evaluate Panmixia and Migration Direction Among Multiple Sampling Locations.. Journal: Genetics, pages , 2010. Abstract [+]: For many biological investigations, groups of individuals are genetically sampled from several geographic locations. These sampling locations often do not reflect the genetical population structure. We describe a framework using marginal likelihoods to compare and order structured population models, such as testing whether the sampling locations belong to the same randomly mating population or comparing unidirectional and multidirectional gene flow models. In the context of inferences employing Markov chain Monte Carlo methods, the accuracy of the marginal likelihoods depends heavily on the approximation method used to calculate the marginal likelihood. Two methods, modified thermodynamic integration and a stabilized harmonic mean estimator, are compared. With finite Markov chain Monte Carlo run lengths, the harmonic mean estimator may not be consistent. Thermodynamic integration, in contrast, delivers considerably better estimates of the marginal likelihood. The choice of prior distributions does not influence the order and choice of the better models when the marginal likelihood is estimated using thermodynamic integration, whereas with the harmonic mean estimator the influence of the prior is pronounced and the order of the models changes. The approximation of marginal likelihood using thermodynamic integration in MIGRATE allows the evaluation of complex population genetic models; not only of whether sampling locations belong to a single panmictic population, but also of competing complex structured population models.
P.A. Rikvold, Degree correlations in a dynamically generated model food web. Journal: Physics Procedia, pages Vol. 3, pp, 2010. Abstract [+]: We explore aspects of the community structures generated by a simple predator-prey model of biological coevolution, using large-scale kinetic Monte Carlo simulations. The model accounts for interspecies and intraspecies competition for resources, as well as adaptive foraging behavior. It produces a metastable low-diversity phase and a stable high-diversity phase. The structures and joint indegree-outdegree distributions of the food webs generated in the latter phase are discussed.
Click here for more informationYongye, A.; Giulianotti, M. A.; Nefzi, A.; Houghten, R. A.; Martinez-Mayorga, K., Conformational ladscape of platinum(II)-tetraamine complexes: DFT and NBO studies. Journal: Journal of Computer Aided Molecular Design, pages 225-235, 2010. Abstract [+]: The potential energy surfaces of chiral tetraamine Pt(II) coordination complexes were computed at the B3LYP/LANL2DZ level of theory by a systematic variation of two dihedral angles: C12–C15–C34–C37 (phi) and C24–C17–C31–C48 (psi) employing a grid resolution of 30 degrees. Potential energy surfaces calculated using density functional theory methods and Boltzmann-derived populations revealed strong preference for one diasteromer of each series studied. In addition, natural bond orbital analysis show that the minima are stabilized predominantly by a combination of electronic interactions between two phenyl groups, the phenyl groups and the Pt2+ ion, as well as with the amine groups. Additional experimental characterization of the diasteroisomers studied here is in progress and will permit further molecular modeling studies with the appropriate stereochemistry.
Thompson, S.H.; Brown, G.; Rikvold, P.A. and Novotny, M.A., Two modes of magnetization switching in a simulated iron nanopillar in an obliquely oriented field. Journal: Journal of Physics: Condensed Matter, Vol. 22, pages 236001, 2010. Abstract [+]: Finite-temperature micromagnetics simulations are employed to study the magnetization-switching dynamics driven by a field applied at an angle to the long axis of an iron nanopillar. A bimodal distribution in the switching times is observed, and evidence for two competing modes of magnetization-switching dynamics is presented. For the conditions studied here, temperature T = 20.2 K and the reversal field 3260 Oe at an angle of 75° to the long axis, approximately 60% of the switches involve unstable decay (no free-energy barrier) and 40% involve metastable decay (a free-energy barrier is crossed). The latter are indistinguishable from switches that are constrained to start at a metastable free-energy minimum. Competition between unstable and metastable decay may not be confined to the temperature studied in this paper, and could greatly complicate applications involving magnetization switching near the coercive field.
Click here for more informationBeerli, P and M. Palczewski, Unified Framework to Evaluate Panmixia and Migration Direction Among Multiple Sampling Locations. Journal: Genetics, pages 185: 313-3, 2010. Abstract [+]: For many biological investigations, groups of individuals are genetically sampled from several geographic
locations. These sampling locations often do not reflect the genetic population structure. We describe a framework using marginal likelihoods to compare and order structured population models, such as testing whether the sampling locations belong to the same randomly mating population or comparing unidirectional and multidirectional gene flow models. In the context of inferences employing Markov chain Monte Carlo methods, the accuracy of the marginal likelihoods depends heavily on the approximation method used to calculate the marginal likelihood. Two methods, modified thermodynamic integration and a stabilized harmonic mean estimator, are compared. With finite Markov chain Monte Carlo run lengths, the harmonic mean estimator may not be consistent. Thermodynamic integration, in contrast, delivers considerably better estimates of the marginal likelihood. The choice of prior distributions does not influence the order and choice of the better models when the marginal likelihood is estimated using thermodynamic integration, whereas with the harmonic mean estimator the influence of the prior is pronounced and the order of the models changes. The approximation of marginal likelihood using thermodynamic integration in MIGRATE allows the evaluation of complex population genetic models, not only of whether sampling locations belong to a single panmictic population, but also of competing complex structured population models.
Click here for more informationClark Evans, Russ S. Schumacher, and Thomas J. Galarneau, Jr., The overland reintensification of North Atlantic Tropical Cyclone Erin (2007): physical and dynamical characteristics. 2010. Abstract [+]: North Atlantic Tropical Cyclone Erin (2007) is perhaps best remembered for its brief yet dramatic reintensification period over western and central Oklahoma early on 19 August 2007. During this period of time, or approximately two and a half days after landfall, the cyclone acquired an eye-like structure and regained tropical storm strength with maximum 1-minute sustained winds estimated at over 25 m s-1 at peak intensity. The study of Arndt et al. (2009, BAMS) details further observations of the cyclone during the reintensification period and briefly discusses potential mechanisms behind the reintensification itself.
The focus of this presentation is upon the recreation of the observed evolution using a mesoscale modeling approach and upon identifying the physical and dynamical mechanisms behind the overland reintensification. As noted in the companion presentation (Schumacher et al.), the simulated and observed reintensification process occurs as intense convective development occurs immediately to the east of the simulated cyclone center. Vorticity budgets suggest that this convection tilts and stretches ambient buoyancy-generated horizontal relative vorticity; after this occurs, axisymmeterization of vertical relative vorticity elements about the broad center of the cyclone results in the formation of an intense, nearly axisymmeteric ring of relative vorticity in the boundary layer. Similar evolutions are noted between reintensifying and non-reintensifying cases with differences lying in the vigor of the convective activity and thus the vertical relative vorticity generation and axisymmeterization process. The location of the cyclone with respect to the left exit region of the lower tropospheric jet appears to focus this convection close enough to the center for this axisymmeterization process to occur.
Connections will be drawn within the presentation between Erin's reintensification and developing tropical cyclones and continental mesoscale convective vortices to attempt to conclusively determine the proper taxonomy for the remnant Erin circulation over Oklahoma on 19 August 2007.
Click here for more informationSchenkel, B. and R. Hart, Fidelity of Tropical Cyclone Intensity and Structure within Reanalyses. Poster: Workshop on Evaluation of Reanalyses – Developing an Integrated Earth System Analysis (IESA) Capab, 2010. Abstract [+]: The emergence of atmospheric reanalysis datasets has provided a tool of great utility with regards to climate scale studies. The recent use of these datasets for studies involving TCs has renewed interest in determining how truthfully these extreme events are depicted within reanalyses. With this thought in mind, the following study seeks to critically examine TC intensity and structure within 5 members of the current generation of reanalyses. Using positions derived from the manual tracking of TCs (Manning and Hart 2007), 3-D storm relative composites of anomalies are constructed to facilitate the examination of how closely TC structure agrees with observations and the degree to which TCs are significantly anomalous within each dataset.
The results of this study show substantial variability of TC representation among basins as well as among reanalyses. Of the three basins examined, North Atlantic TCs exhibit the most robust composite structure, possibly due to the increased density and quality of the observations within this basin. In contrast to this, Eastern Pacific TCs exhibit the poorest representation, possibly due to a number of possible factors including deficiencies in the observing system and smaller overall TC size. With regards to the inter dataset differences, the reanalyses that use supplement observations or vortex relocation for TCs during the data assimilation cycle (JRA-25 and CFSR, respectively) yield TCs with the strongest warm cores. More interestingly, there is dramatically decreased difference in TC structure among the ERA-40, ERA-Interim, and MERRA. The relative uniformity of structure among these latter reanlayses, when compared to the much stronger strcuture in JRA25 and CFSR, might suggest that the inclusion of partially synthetic approaches can be most influential in changing TC representation. The results of this study confirm prior studies suggesting reanalyses have not yet become sufficient for analyzing historical TC trends. Nonetheless, the reanalyses may be useful for other climate scale applications such as evaluating TC-environment interactions.
Click here for more informationSchenkel, B. and R. Hart, The Fidelity of Tropical Cyclone Representation in Atmospheric Reanalysis Datasets. Poster: 29th Conference on Hurricanes and Tropical Meteorology, 2010. Abstract [+]: Atmospheric reanalysis datasets have been notorious for under representing tropical cyclone (TC) structure due to their coarse spatial resolution. With regards to studies utilizing these datasets in studying TCs, reanalyses have only been practical for evaluating the large scale effects of TCs. With the release of several new reanalyses including the JMA's JRA (Onogi and coauthors 2005) and NASA's MERRA (Bosilovich et al. 2006) and the impending release of the ECMWF's ERA Interim (Simmons and coauthors 2006) and NCEP's CFSRR (Saha and Pan 2008) comes the hope of a more truthful depiction of TCs. The following work will determine the extent to which TCs are represented realistically in reanalyses.
Using the methodology of Manning and Hart (2007), this study will evaluate the structure of TCs within three atmospheric datasets: the ERA40 (Uppala and coauthors 2005), the JRA, and the MERRA. TCs from the period 1982-2001 are manually tracked from three basins: the North Western Pacific, North Eastern Pacific, and North Atlantic. Absolute errors in track in comparison to the NHC best track (Jarvinen 1984) are made. Metrics used for evaluating TC structure are drawn from the cyclone phase space (Hart 2003) in addition to the use of more traditional fields such as minimum sea level pressure and 10 m surface winds. Additionally, Student's t-tests are used to determine whether the differences between TCs within basins, between basins, and amid the datasets are statistically significant.
Click here for more informationSchenkel, B. and R. Hart, The Evolution of Tropical Cyclone Climate Memory in the Atmosphere-Ocean System. Poster: 29th Conference on Hurricanes and Tropical Meteorology, 2010. Abstract [+]: Knowledge of the role of tropical cyclones (TCs) in the climate is crucial towards predicting their future frequency and intensity in a warming world. Hart et al. (2007) provided the first attempt at quantifying the TC-induced stabilization of the atmospheric-oceanic system that occurs due to the cooling of the ocean and warming of the atmosphere. Following in the footsteps of this prior work, this study will serve as an extension to Hart et al. (2007) in both time and space. The impact of TCs upon the climate is evaluated using standard atmosphere and ocean metrics as well as maximum potential intensity (MPI; Emanuel 1987). Anomalies are computed relative to climatology and composited by TC intensity, latitude, ocean basin, and time of year. The sensitivity of these results to the use of different atmospheric reanalysis datasets is also evaluated.
The spatial extent of the positive local MPI anomaly is found to be primarily influenced by the cooling of the ocean whose slow dynamic response allows for the oceanic memory of TCs to be longer. Storm relative sea surface temperature (SST) spatial anomalies, rotated to account for storm motion, show maximum SST cooling to the right of track on day 4 relative to TC passage with SST anomalies lasting up to 60 days or more. The restoration timescale of the SST anomaly was found to be longer than was previously stated in Hart et al. (2007). Positive storm relative atmospheric thickness anomalies are maximized on day 0 with areal coverage that is more symmetric and temporally transient than the oceanic anomalies. Pre-storm anomalies will be examined in an attempt to understand the large scale mechanisms responsible for genesis as it pertains to creating a warmer atmosphere-ocean system prior to TC passage.
Click here for more informationSchenkel, B. and R. Hart, Fidelity of Tropical Cyclone Intensity and Structure within Reanalyses. Poster: 5th Annual Thelassic Symposium, 2010. Abstract [+]: The emergence of atmospheric reanalysis datasets has provided a tool of great utility with regards to climate scale studies. The recent use of these datasets for studies involving TCs has renewed interest in determining how truthfully these extreme events are depicted within reanalyses. With this thought in mind, the following study seeks to critically examine TC intensity and structure within 5 members of the current generation of reanalyses. Using positions derived from the manual tracking of TCs (Manning and Hart 2007), 3-D storm relative composites of anomalies are constructed to facilitate the examination of how closely TC structure agrees with observations and the degree to which TCs are significantly anomalous within each dataset. The results of this study show substantial variability of TC representation among basins as well as among reanalyses. Of the three basins examined, North Atlantic TCs exhibit the most robust composite structure, possibly due to the increased density and quality of the observations within this basin. In contrast to this, Eastern Pacific TCs exhibit the poorest representation, possibly due to a number of possible factors including deficiencies in the observing system and smaller overall TC size. With regards to the inter dataset differences, the reanalyses that use supplement observations or vortex relocation for TCs during the data assimilation cycle (JRA-25 and CFSR, respectively) yield TCs with the strongest warm cores. More interestingly, there is dramatically decreased difference in TC structure among the ERA-40, ERA-Interim, and MERRA. The relative uniformity of structure among these latter reanlayses, when compared to the much stronger strcuture in JRA25 and CFSR, might suggest that the inclusion of partially synthetic approaches can be most influential in changing TC representation. The results of this study confirm prior studies suggesting reanalyses have not yet become sufficient for analyzing historical TC trends. Nonetheless, the reanalyses may be useful for other climate scale applications such as evaluating TC-environment interactions.
Click here for more informationNaureen Ahsan and Alexander Volya, Quantum tunneling and scattering of a composite object reexamined. Journal: Physical Review C, pages 064607(19), 2010. Abstract [+]: This work presents an extensive exploration of scattering and tunneling involving composite objects with intrinsic degrees of freedom. We aim at exact solutions to such scattering problems. Along this path we demonstrate solutions to model Hamiltonians and develop different techniques for addressing these complex reaction-physics problems, discuss their applicability, and investigate the relevant convergence issues. As examples, we study the scattering of two-constituent deuteron-like systems either with an infinite set of intrinsic bound states or with a continuum of states that allows for breakup. We show that the internal degrees of freedom of the projectile and its virtual excitation in the course of reactions play an important role in shaping the S-matrix and related observables, giving rise to enhanced or reduced tunneling in various situations.
Click here for more informationO'Donnell J, Taylor KA, Chapman MS., Adeno-associated virus-2 and its primary cellular receptor-Cryo-EM structure of a heparin complex.. Journal: Virology, pages 434-443, 2009. Abstract [+]: Adeno-associated virus serotype 2 (AAV-2) is a leading candidate vector for gene therapy. Cell entry starts with attachment to a primary receptor, Heparan Sulfate Proteoglycan (HSPG) before binding to a co-receptor. Here, cryo-electron microscopy provides direct visualization of the virus-HSPG interactions. Single particle analysis was performed on AAV-2 complexed with a 17 kDa heparin fragment at 8.3 A resolution. Heparin density covers the shoulder of spikes surrounding viral 3-fold symmetry axes. Previously implicated, positively charged residues R(448/585), R(451/588) and R(350/487) from another subunit cluster at the center of the heparin footprint. The footprint is much more extensive than apparent through mutagenesis, including R(347/484), K(395/532) and K(390/527) that are more conserved, but whose roles have been controversial. It also includes much of a region proposed as a co-receptor site, because prior studies had not revealed heparin interactions. Heparin density bridges over the viral 3-fold axes, indicating multi-valent attachment to symmetry-related binding sites.
Click here for more informationS. H. Thompson, G. Brown, A. Kuhnle, P. A. Rikvold, and M. A. Novotny, Resolution-dependent Mechanisms for Bimodal Switching-time Distributions in Simulated Fe Nanopillars. Journal: Physical Review B, Vol. 79, pages 024429, 2009. Abstract [+]: We study the magnetization-switching statistics following reversal of the applied field for three separate computational models representing the same physical system: an iron nanopillar. The primary difference between the models is the resolution of the computational lattice and, consequently, the intrinsic parameters that must be rescaled to retain similarity to the physical system. Considering the first-passage time to zero for the magnetization component in the longitudinal (easy-axis) direction, we look for applied fields that result in bimodal distributions of this time for each computational system and compare the results to the experimental system. We observe that the relevant fluctuations leading to bimodal distributions are different for each lattice resolution and result in magnetization-switching behavior that is unique to each computational model. Correct model resolution is thus essential for obtaining reliable numerical results for the system dynamics.
Click here for more information# Sanbo Qin and
Sanbo Qin and Huan-Xiang Zhou, Dissection of the high rate constant for the binding of a ribotoxin to the ribosome. Journal: Proc Natl Acad Sci U S A, pages 6974-6979, 2009. Abstract [+]: Restrictocin belongs to a family of site-specific ribonucleases that kill cells by inactivating the ribosome. The restrictocin-ribosome binding rate constant was observed to exceed 10(10) M(-1) s(-1). We have developed a transient-complex theory to model the binding rates of protein-protein and protein-RNA complexes. The theory predicts the rate constant as k(a) = k(a0) exp(-DeltaG(el)*/k(B)T), where k(a0) is the basal rate constant for reaching the transient complex, located at the outer boundary of the bound state, by random diffusion, and DeltaG(el)* is the average electrostatic interaction free energy of the transient complex. Here, we applied the transient-complex theory to dissect the high restrictocin-ribosome binding rate constant. We found that the binding rate of restrictocin to the isolated sarcin/ricin loop is electrostatically enhanced by approximately 300-fold, similar to results found in other protein-protein and protein-RNA complexes. The ribosome provides an additional 10,000-fold rate enhancement because of two synergistic mechanisms afforded by the distal regions of the ribosome. First, they provide additional electrostatic attraction with restrictocin. Second, they reposition the transient complex into a region where local electrostatic interactions of restrictocin with the sarcin/ricin loop are particularly favorable. Our calculations rationalize a host of experimental observations and identify a strategy for designing proteins that bind their targets with high speed.
Click here for more informationAustin Yongye, Yangmei Li, Marc Giulianotti, Yongping Yu, Richard Houghten, Karina Martinez-Mayorga, Modeling of Peptides Containing D-Amino Acids: Implications on Cyclization. Journal: Journal of Computer-Aided Molecular Design, pages DOI 10.100, 2009. Abstract [+]: Cyclic peptides are therapeutically attractive due to their high bioavailability, potential selectivity, and scaffold novelty. Furthermore, the presence of D-residues induces conformational preferences not followed by peptides consisting of naturally abundant L-residues. Therefore, comprehending how amino acids induce turns in peptides, subsequently facilitating cyclization, is significant in peptide design. Here, we performed 20-ns explicit-solvent molecular dynamics simulations for three diastereomeric peptides with stereochemistries: LLLLL, LLLDL, and LDLDL. Experimentally LLLLL and LDLDL readily cyclize, whereas LLLDL cyclize in low yield. Simulations at 310 K produced conformations with inter-terminal hydrogen bonds that correlated qualitatively with the experimental cyclization trend. Energies obtained for representative structures from quantum chemical (B3LYP/PCM/cc-pVTZ//HF/6-31G*) calculations predicted pseudo-cyclic and extended conformations as the most stable for LLLLL and LLLDL, respectively, in agreement with the experimental data. In contrast, the most stable conformer predicted for peptide LDLDL was not a pseudo-cyclic structure. Moreover, D-residues preferred the experimentally less populated αL rotamers even when simulations were performed at higher temperature and with strategically selected starting conformations. Energies calculated with molecular mechanics were consistent only with peptide LLLLL. Thus, the conformational preferences obtained for the all L-amino acid peptide were in agreement with the experimental observations. Moreover, refinement of the force field is expected to provide far-reaching conformational sampling of peptides containing D-residues to further develop force field-based conformational-searching methods.
Jianhua Lu & Ming Cai, Quantifying contributions to polar warming amplification in an idealized coupled general circulation model. Journal: Springer-Verlag 2009, pages 19, 2009. Abstract [+]: An idealized coupled general circulation model
is used to demonstrate that the surface warming due to the
doubling of CO2 can still be stronger in high latitudes than
in low latitudes even without the negative evaporation
feedback in low latitudes and positive ice-albedo feedback
in high latitudes, as well as without the poleward latent
heat transport. The new climate feedback analysis method
formulated in Lu and Cai (Clim Dyn 32:873–885, 2009)
is used to isolate contributions from both radiative and
non-radiative feedback processes to the total temperature
change obtained with the coupled GCM. These partial
temperature changes are additive and their sum is convergent
to the total temperature change. The radiative energy
flux perturbations due to the doubling of CO2 and water
vapor feedback lead to a stronger warming in low latitudes
than in high latitudes at the surface and throughout the
entire troposphere. In the vertical, the temperature changes
due to the doubling of CO2 and water vapor feedback are
maximum near the surface and decrease with height at all
latitudes. The simultaneous warming reduction in low
latitudes and amplification in high latitudes by the
enhanced poleward dry static energy transport reverses the
poleward decreasing warming pattern at the surface and in
the lower troposphere, but it is not able to do so in the
upper troposphere. The enhanced vertical moist convection
in the tropics acts to amplify the warming in the upper
troposphere at an expense of reducing the warming in the
lower troposphere and surface warming in the tropics. As a
result, the final warming pattern shows the co-existence of
a reduction of the meridional temperature gradient at the
surface and in the lower troposphere with an increase of the
meridional temperature gradient in the upper troposphere.
In the tropics, the total warming in the upper troposphere is stronger than the surface warming.
Arbic, B.K., Karsten, R.H., and C. Garrett, On tidal resonance in the global ocean and the back effect of coastal tides upon open-ocean tides. Journal: Atmosphere-Ocean, pages 239-266, 2009. Abstract [+]:
Click here for more informationS. F.Vasilevsky, T. F. Mikhailovskaya, V. I. Mamatyuk, G. A. Bogdanchikov, M. Manoharan, I. V. Alabu, Tuning Selectivity of Anionic Cyclizations: Competition between 5-Exo and 6-Endo-dig Closures of Hydrazides of o-Acetylenyl Benzoic Acids and Based-catalyzed Fragmentation/Recyclization of the Initial. Journal: Joutnal of Organic Chemistry, pages 8106–811, 2009. Abstract [+]: Depending on the reaction conditions and the nature of substituents at the triple bond, anionic cyclizations of hydrazides of o-acetylenyl benzoic acids can be selectively directed along three alternative paths, each of which provides efficient access to a different class of nitrogen heterocycles. The competition between 5-exo and 6-endo cyclizations of the “internal” nitrogen nucleophile is controlled by the nature of alkyne substituents under the kinetic control conditions. In the presence of KOH, the initially formed 5-exo products undergo a new rearrangement that involves a ring-opening followed by recyclization to the formal 6-exo-products and rendered irreversible by a prototropic isomerization. DFT computations provide insight into the nature of factors controlling relative rates of 5-exo, 6-endo, and 6-exo cyclization paths, ascertain the feasibility of direct 6-exo closure and relative stability for the anionic precursor for this process, provide, for the first time, the benchmark data for several classes of anionic nitrogen cyclizations, and dissect stereoelectronic effects controlling relative stability of cyclic anionic intermediates and influencing reaction stereoselectivity. We show that the stability gain due transformation of a weak π-bond into a stronger σ-bond (the usual driving force for the cyclizations of alkynes) is offset in this case by the transformation of a stable nitrogen anion into an inherently less stable carbanionic center. As a result, the cyclizations are much more sensitive to external conditions and substituents than similar cyclizations of neutral species. However, the exothermicity of such anionic cyclizations is increased dramatically upon prototropic isomerization of the initially formed carbanions into the more stable N-anions. Such tautomerizations are likely to play the key role in driving such cyclizations to completion but may also prevent future applications of such processes as the first step in domino cyclization processes.
Click here for more informationP.A. Rikvold, Complex Dynamics in Models of Biological Coevolution with Ratio-dependent Functional Response. Journal: Ecological Complexity, pages 443-452, 2009. Abstract [+]: We explore the complex dynamical behavior of two simple predator–prey models of biological coevolution that on the ecological level account for interspecific and intraspecific competition, as well as adaptive foraging behavior. The underlying individual-based population dynamics are based on a ratio-dependent functional response [Getz, W.M., 1984. Population dynamics: a per capita resource approach. J. Theor. Biol. 108, 623–643]. Analytical results for fixed-point population sizes in some simple communities are derived and discussed. In long kinetic Monte Carlo simulations we find quite robust, approximate 1/f noise in species diversity and population sizes, as well as power-law distributions for the lifetimes of individual species and the durations of periods of relative evolutionary stasis. Adaptive foraging enhances coexistence of species and produces a metastable low-diversity phase and a stable high-diversity phase.
Click here for more informationG. M. Buendía, E. Machado, and P. A. Rikvold, Effect of CO Desorption and Coadsorption with O on the Phase Diagram of a Ziff-Gulari-Barshad Model for the Catalytic Oxidation of CO. Journal: Journal of Chemical Physics, pages 184704, 2009. Abstract [+]: We study the effect of coadsorption of CO and O on a Ziff–Gulari–Barshad model with CO desorption for the reaction CO+O-->CO2 on a catalytic surface. Coadsorption of CO at a surface site already occupied by an O is introduced by an Eley–Rideal-type mechanism that occurs with probability p, 0<=p<=1. We find that besides the well-known effect of eliminating the second-order phase transition between the reactive state and an O-poisoned state, the coadsorption step has a profound effect on the transition between the reactive state and the CO-poisoned state. The coexistence curve between these two states terminates at a critical value kc of the desorption rate k, which now depends on p. Our Monte Carlo simulations and finite-size scaling analysis indicate that kc decreases with increasing values of p. For p=1, there appears to be a sharp phase transition between the two states only for k at (or near) zero.
Click here for more informationDeng, H., M. Ye, M. G. Schaap, and R. Khaleel, Quantification of uncertainty in pedotransfer function-based parameter estimation for unsaturated flow modeling. Journal: Water Resources Research, pages doi:10.102, 2009. Abstract [+]: While pedotransfer functions (PTFs) have long been applied to estimate soil hydraulic
parameters for unsaturated flow and solute transport modeling, the uncertainty associated
with the estimates is often ignored. The objective of this study is to evaluate uncertainty
of the PTF-estimated soil hydraulic parameters and its effect on numerical simulation
of moisture flow. Contributing to the parameter estimation uncertainty are (1) the PTF
intrinsic uncertainty caused by limited data used for PTF training and (2) the PTF input
uncertainty in pedotransfer variables (i.e., PTF inputs). The PTF intrinsic uncertainty is
assessed using the bootstrap method by generating multiple bootstrap realizations
of the soil hydraulic parameters; the realizations follow normal or lognormal distributions.
The PTF input variables (i.e., bulk density and soil texture) are obtained using the
cokriging technique. The PTF input uncertainty is quantified by assuming that the
cokriging estimates follow a normal distribution. Our results show that the PTF input
uncertainty dominates over the PTF intrinsic uncertainty and determines the spatial
distribution of the PTF parameter estimation uncertainty. When the parameter estimation
uncertainty is included, the spatial variability of the measured soil hydraulic parameters is
better captured. This is also the case for the observed moisture contents, whose spatial
variability is well bracketed by the prediction intervals. However, this is only possible
after the PTF input uncertainty is considered. These results suggest that additional
sample acquisition for the PTF input variables would have a more favorable impact on
reduction of the parameter estimation uncertainty than collecting additional soil hydraulic
parameter measurements for PTF development.
Ye, M., C.A. Cooper, J.B. Chapman, D. Gillespie, and Y. Zhang, A geologically based Markov chain model for simulating tritum transport with uncertain conditions in a nuclear-stimulated natural gas reservoir. Journal: SPE Reservoir Evaluation & Engineering, pages 12(6), 974, 2009. Leslaw Kwasniewski, Jeff Siervogel, Cezary Bojanowski, Jerry W. Wekezer, Krzysztof Cichocki, "Crash and Safety Assessment Program for Paratransit Buses". Journal: International Journal of Impact Engineering, pages Vol. 36, I, 2009. Abstract [+]: This paper describes an assessment program for paratransit buses concerning their crashworthiness and safety of passengers. The program developed by the authors was approved by the Transit Office of the Florida Department of Transportation as a part of the Florida Vehicle Procurement Program (FVPP) in August 2007. Several valuable, worldwide vehicle safety standards were adopted in it with modifications addressing the bus construction process and relevance of particular structural components in crash events. Passenger compartment structure, which needs to be protected against the most dangerous accidents such as a side impact and a rollover, is a major area of concern in the standard. Lack of such standards may result in poor crashworthiness characteristics of the bus structure and in severe injuries and possible passenger fatalities. Either full-scale experiments or numerical standardized simulations were proposed as equivalent approval methods for paratransit buses. Selected results for partially validated Finite Element (FE) models and the nonlinear explicit dynamic code LS-DYNA were used to demonstrate a numerical approach for a bus structure approval. The FE models can also be used to assist the bus manufacturer in an effort to improve the crashworthiness of the new bus designs. The procedure described in this paper was implemented to monitor crashworthiness resistance of the paratransit buses distributed and operated in the state of Florida.
Click here for more informationChristopher R. Harden, Real Time Computing with the Parareal Algorithm, Solving time-dependent differential equations with increased speed. VDM Verlag Dr. Müller, 2009. Abstract [+]: This work presents and evaluates a particular algorithm used for the real time computations of time dependent ordinary and partial differential equations which employs a parallelization strategy over the temporal domain. We also discuss the coupling of this method with another popular technique used for real time computations, model reduction, which will be shown to provide more gains than either method alone. In particular, we look at reduced order modeling based on proper orthogonal decompositions. We present some applications in terms of solving time dependent nonlinear partial differential equations and solving these equations with a coupled approach of combining model reduction and the parareal algorithm . The performance of this method, both numerically and computationally, is discussed in terms of the gains in speedup and efficiency, and in terms of the scalability of the parallelization of the temporal domain on a larger and larger set of compute nodes or processors.
Click here for more informationTan, Y. H., Chen, Y. M., Ye, X., Lu, Q., Tretyachenko-Ladokhina, V., Yang, W., Senear, D. F., and Lu, Molecular mechanisms of functional rescue mediated by p53 tumor.. Journal: Biophys. Chem. 145, pages 37-44, 2009. Ye, X., Yang, W., Luo, R., Roles of boundary conditions in DNA simulations: Analysis of ion distributions with the finite-difference Poisson-Boltzmann method. Journal: Biophys. J. 97,, pages 554-562, 2009. Chen, M. and Yang, W., On-the-path random walk to efficiently optimize minimum free energy path. Journal: J. Comp. Chem. 30, pages 1649-1653, 2009. Zheng, L., Chen, M., and Yang, W., ). Simultaneous escaping of explicit and hidden free energy barriers: Application of the orthogonal space random walk strategy in generalized ensemble conformational sampling. Journal: J. Chem. Phys. 130, pages 234105, 2009. Nguyen, L. T., Yang, W., Wang, Q., and Hirst, L. S., Molecular dynamics simulation of F-actin: Studying the mechanisms for semi-flexible filament assembly reveals the role of cross-linkers.. Journal: Soft Matter 5, pages 2033-2036, 2009. Myunggi Yi, Timothy A. Cross, Huan-Xiang Zhou, Conformational heterogeneity of the M2 proton channel and a structural model for channel activation.. Journal: Proceedings of the National Academy of Sciences of the United States of America, pages 13311-1331, 2009. Abstract [+]: The M2 protein of influenza virus A is a proton-selective ion channel activated by pH. Structure determination by solid-state and solution NMR and X-ray crystallography has contributed significantly to our understanding, but channel activation may involve conformations not captured by these studies. Indeed, solid-state NMR data demonstrate that the M2 protein possesses significant conformational heterogeneity. Here, we report molecular dynamics (MD) simulations of the M2 transmembrane domain (TMD) in the absence and presence of the antiviral drug amantadine. The ensembles of MD conformations for both apo and bound forms reproduced the NMR data well. The TMD helix was found to kink around Gly-34, where water molecules penetrated deeply into the backbone. The amantadine-bound form exhibited a single peak ≈10° in the distribution of helix-kink angle, but the apo form exhibited 2 peaks, ≈0° and 40°. Conformations of the apo form with small and large kink angles had narrow and wide pores, respectively, around the primary gate formed by His-37 and Trp-41. We propose a structural model for channel activation, in which the small-kink conformations dominate before proton uptake by His-37 from the exterior, and proton uptake makes the large-kink conformations more favorable, thereby priming His-37 for proton release to the interior.
Click here for more informationGopinath Subramanian and Sachin Shanbhag, Self-Diffusion in Binary Blends of Cyclic and Linear Polymers. Journal: Macromolecules, pages 7239–724, 2008. Abstract [+]: A lattice model is used to estimate the self-diffusivity of entangled cyclic and linear polymers in blends of varying compositions. To interpret simulation results, we suggest a minimal constraint release model for the motion of a cyclic polymer infiltrated by neighboring linear chains. Both the simulation and recently reported experimental data on entangled DNA solutions support the simple model over a wide range of blend compositions, concentrations, and molecular weights.
Click here for more informationNylander, J. A., J.C. Wilgenbusch, D. L. Warren, D. L. Swofford, AWTY (Are We There Yet): a system for graphical exploration of MCMC convergence in Bayesian phylogenetics. Journal: Bioinformatics, pages 581–583, 2008. Abstract [+]: A key element to a successful Markov chain Monte Carlo (MCMC) inference is the programming and run performance of the Markov chain. However, the explicit use of quality assessments of the MCMC simulations, convergence diagnostics, in phylogenetics is still uncommon. Here we present a simple tool that uses the output from MCMC simulations and visualizes a number of properties of primary interest in a Bayesian phylogenetic analysis, such as convergence rates of posterior split probabilities and branch lengths. Graphical exploration of the output from phylogenetic MCMC simulations gives intuitive and often crucial information on the success and reliability of the analysis. The tool presented here complements convergence diagnostics already available in other software packages primarily designed for other applications of MCMC. Importantly, the common practice of using trace-plots of a single parameter or summary statistic, such as the likelihood score of sampled trees, can be misleading for assessing the success of a phylogenetic MCMC simulation.
Click here for more informationVan Dyke, Donald F., COAPS/FSU Real Time Gulf of Mexico 4 km WRF-ARW Atmospheric Model. Dissertation/Thesis 2008. Abstract [+]: There are several goals of these simulations, and the web page will see new graphics and features over time. The primary goal is to attempt to address the continuing struggle that current operational numerical models have with the correct prediction of the moisture content of the return flow airmass over the Gulf of Mexico after a cold-air outbreak during the cool season (Nov-Mar). Cold-air outbreaks are associated with significant changes in the sea surface temperature over a wide region of the Gulf of Mexico. This cooling of the sea surface temperature by as much as several degrees relative to the initial temperature field should be reflected in differences in the air-sea fluxes of latent and sensible heat, which then may be manifested in different boundary layer temperature and humidity structures. Errors in forecasted surface winds and the use of non-varying sea surface temperatures are identified as possible influences on the incorrect moisture forecast (Lewis 2007). Thus, it is speculated that the inclusion of this variation in sea surface temperature will influence the nature of the return flow airmass. As such, the ultimate goal is to work toward a fully coupled high resolution WRF/HYCOM (HYbrid Coordinate Ocean Model) atmosphere/ocean modeling system over the Gulf of Mexico.
Click here for more informationClemens Lakner, Paul van der Mark, John P. Huelsenbeck, Bret Larget, and Fredrik Ronquist, Efficiency of Markov Chain Monte Carlo Tree Proposals in Bayesian Phylogenetics. Journal: Systematic Biology, 57(1), pages 86-103, 2008. Henry R. Winterbottom, Eric P. Chassignet, and Carol Anne Clayson, HYCOM North Atlantic Ocean Basin Forecasts. Dissertation/Thesis 2008. Abstract [+]: This page provides experimental 1-2 times daily (0000 UTC and 1200 UTC) high resolution HYbrid Coordinate Ocean Model (HYCOM) real-time WRF-ARW atmospheric forcing forecasts
for the North Atlantic basin.
Click here for more informationIsabel SanMartin, Paul van der Mark, and Fredrik Ronquist, Inferring dispersal: a Bayesian approach to phylogenetic-based island biogeography, with special reference to the Canary islands. Journal: Journal of Biogeography, 35, pages 428-449, 2008. Haidao Lin and Xiaolei Zou, Can geosynchronous imaging Fourier transform spectrometer capture vertical and temporal variability of a convective atmosphere?. Journal: J. Appl. Remote Sens., Vol. 2, 023534 (2008); DOI:10.1117/1.2980331, pages 19, 2008. Abstract [+]: Insufficient high vertical and temporal resolution data have limited the precipitation forecast skill of convective initiation. The Geosynchronous Imaging Fourier Transform Spectrometer (GIFTS), a new hyperspectral geostationary satellite measurement system, could provide top-of-atmosphere (TOA) radiances across two broad spectral regions with high-resolutions in spectral, horizontal and temporal spaces within a fixed domain. A set of modeled and observed vertical profiles of atmospheric moisture and temperature during a convective initiation (CI) event within the observing period of the International H2O Project (IHOP_2002) are used to assess the potential values of GIFTS measurements to convective precipitation forecast. First, it is shown that the model simulation captures reasonably well the movement of the precipitation bands and the gradient structures of temperature and water vapor of the convectively initiated storm. Second, the observed vertical and temporal variability of water vapor during the CI period is shown to be quite significant in the lower troposphere. The differences between observations and model simulation are also noticed. Using both the observed and the model-predicted profiles as input to GIFTS radiative transfer model (RTM), it is finally shown that the simulated GIFTS radiance could capture the high vertical and temporal variability of the real and modeled atmosphere prior to the CI, as well as the differences between observations and model forecasts. The study suggests the potential for GIFTS to make important contributions to the improvement of the forecast skill of convective precipitation.
Click here for more information Harianto Tjong and Huan-Xiang Zhou, Accurate Calculations of Binding, Folding, and Transfer Free Energies by a Scaled Generalized Born Method. Journal: Journal of Chemical Theory and Computation, pages , 2008. Abstract [+]: The Poisson−Boltzmann (PB) equation is widely used for modeling solvation effects. The computational cost of PB has restricted its applications largely to single-conformation calculations. The generalized Born (GB) model provides an approximation at substantially reduced cost. Currently the best GB methods reproduce PB results for electrostatic solvation energies with errors at ~5 kcal/mol. When two proteins form a complex, the net electrostatic contributions to the binding free energy are typically of the order of 5 to 10 kcal/mol. Similarly, the net contributions of individual residues to protein folding free energy are <5 kcal/mol. Clearly in these applications the accuracy of current GB methods is insufficient. Here we present a simple scaling scheme that allows our GB method, GBr6, to reproduce PB results for binding, folding, and transfer free energies with high accuracy. From an ensemble of conformations sampled from molecular dynamics simulations, five were judiciously selected for PB calculations. These PB results were used for scaling GBr6. Tests on the binding free energies of the barnase-barstar, GTPase-WASp, and U1A-U1hpII complexes and on the folding free energy of FKBP show that the effects of point mutations calculated by scaled GBr6 are accurate to within 0.3 kcal/mol of PB results. Similar accuracy was also achieved for the free energies of transfer for ribonuclease Sa and insulin from the crystalline phase to the solution phase at various pHs. This method makes it possible to thoroughly sample the transient-complex ensemble in predicting protein binding rate constants and to incorporate conformational sampling in electrostatic modeling (such as done in the MM-GBSA approach) without loss of accuracy.
Myunggi Yi, Hugh Nymeyer, Huan X Zhou, Test of the Gouy-Chapman Theory for a Charged Lipid Membrane against Explicit-Solvent Molecular Dynamics Simulations. Journal: Physical Review Letters Vol. 101, No. 3, pages , 2008. Abstract [+]: A wealth of experimental data has verified the applicability of the Gouy-Chapman (GC) theory to charged lipid membranes. Surprisingly, a validation of GC by molecular dynamics (MD) simulations has been elusive. Here, we report a test of GC against extensive MD simulations of an anionic lipid bilayer solvated by water at different concentrations of NaCl or KCl. We demonstrate that the ion distributions from the simulations agree remarkably well with GC predictions when information on the adsorption of counterions to the bilayer is incorporated.
Click here for more informationMyunggi Yi, Timothy A. Cross, and Huan-Xiang Zhou, A Secondary Gate As a Mechanism for Inhibition of the M2 Proton Channel by Amantadine. Journal: Journal of Physical Chemistry B Vol. 112, No. 27, pages 7977-7979, 2008. Abstract [+]: Abstract: The mechanism of inhibition of the influenza A virus M2 proton channel by the antiviral drug amantadine has been under intense investigation. The importance of a mechanistic understanding is heightened by the prevalence of amantadine-resistant mutations. To gain mechanistic insight at the molecular level, we carried out extensive molecular dynamics simulations of the tetrameric M2 proton channel in both apo and amantadine-bound forms in a lipid bilayer. The simulation of the apo form revealed that Val27 from the four M2 subunits can form a secondary gate near the channel entrance and break the water wire in the channel pore. This gate arises from physical occlusion and the elimination of hydrogen-bonding partners for water molecules. In the presence of amantadine, the secondary gate formed by Val27 and the drug molecule lying just below form an extended blockage, which breaks the water wire throughout the simulation. The location and orientation of amantadine inside of the channel pore as found in our simulation are supported by a host of experimental observations. Our study suggests a novel role for Val27 in the inhibition of the M2 proton channel by amantadine.
Click here for more informationMyunggi Yi, Harianto Tjong, and Huan-Xiang Zhou, Spontaneous conformational change and toxin binding in a7 acetylcholine receptor: Insight into channel activation and inhibition. Journal: Proc. Natl. Acad. Sci Vol 105, No. 34, pages 8280-8285, 2008. Abstract [+]: Nicotinic AChRs (nAChRs) represent a paradigm for ligand-gated ion channels. Despite intensive studies over many years, our understanding of the mechanisms of activation and inhibition for nAChRs is still incomplete. Here, we present molecular dynamics (MD) simulations of the α7 nAChR ligand-binding domain, both in apo form and in α-Cobratoxin-bound form, starting from the respective homology models built on crystal structures of the acetylcholine-binding protein. The toxin-bound form was relatively stable, and its structure was validated by calculating mutational effects on the toxin-binding affinity. However, in the apo form, one subunit spontaneously moved away from the conformation of the other four subunits. This motion resembles what has been proposed for leading to channel opening. At the top, the C loop and the adjacent β7-β8 loop swing downward and inward, whereas at the bottom, the F loop and the C terminus of β10 swing in the opposite direction. These swings appear to tilt the whole subunit clockwise. The resulting changes in solvent accessibility show strong correlation with experimental results by the substituted cysteine accessibility method upon addition of acetylcholine. Our MD simulation results suggest a mechanistic model in which the apo form, although predominantly sampling the “closed” state, can make excursions into the “open” state. The open state has high affinity for agonists, leading to channel activation, whereas the closed state upon distortion has high affinity for antagonists, leading to inhibition.
Click here for more informationHarianto Tjong and Huan-Xiang Zhou, Prediction of Protein Solubility from Calculation of Transfer Free Energy. Journal: Biophysical Journal Vol 95, pages 2601-2609, 2008. Abstract [+]: Solubility plays a major role in protein purification, and has serious implications in many diseases. We studied the effects of pH and mutations on protein solubility by calculating the transfer free energy from the condensed phase to the solution phase. The condensed phase was modeled as an implicit solvent, with a dielectric constant lower than that of water. To account for the effects of pH, the protonation states of titratable side chains were sampled by running constant-pH molecular dynamics simulations. Conformations were then selected for calculations of the electrostatic solvation energy: once for the condensed phase, and once for the solution phase. The average transfer free energy from the condensed phase to the solution phase was found to predict reasonably well the variations in solubility of ribonuclease Sa and insulin with pH. This treatment of electrostatic contributions combined with a similar approach for nonelectrostatic contributions led to a quantitative rationalization of the effects of point mutations on the solubility of ribonuclease Sa. This study provides valuable insights into the physical basis of protein solubility.
Click here for more informationHarianto Tjong and Huan-Xiang Zhou, On the Dielectric Boundary in Poisson-Boltzmann Calculations. Journal: J. Chem. Theory Comput Vol. 4, No. 3, pages 507-514, 2008. Abstract [+]: In applying the Poisson-Boltzmann (PB) equation for calculating the electrostatic free energies of solute molecules, an open question is how to specify the boundary between the low-dielectric solute and the high-dielectric solvent. Two common specifications of the dielectric boundary, as the molecular surface (MS) or the van der Waals (vdW) surface of the solute, give very different results for the electrostatic free energy of the solute. With the same atomic radii, the solute is more solvent-exposed in the vdW specification. One way to resolve the difference is to use different sets of atomic radii for the two surfaces. The radii for the vdW surface would be larger in order to compensate for the higher solvent exposure. Here we show that radius reparametrization required for bringing MS-based and vdW-based PB results to agreement is solute-size dependent. The difference in atomic radii for individual amino acids as solutes is only 2-5% but increases to over 20% for proteins with ~200 residues. Therefore two sets of radii that yield identical MS-based and vdW-based PB results for small solutes will give very different PB results for large solutes. This finding raises issues about two common practices. The first is the use of atomic radii, which are parametrized against either experimental solvation data or data obtained from explicit-solvent simulations on small compounds, for PB calculations on proteins. The second is the parametrization of vdW-based generalized Born models against MS-based PB results.
Click here for more informationHugh Nymeyer and Huan-Xiang Zhou, A Method to Determine Dielectric Constants in Nonhomogeneous Systems: Application to Biological Membranes. Journal: Biophysical Journal Vol 94, pages 1185-1193, 2008. Abstract [+]: Continuum electrostatic models have had quantitative success in describing electrostatic-mediated phenomena on atomistic scales; however, there continues to be significant disagreement about how to assign dielectric constants in mixed, nonhomogeneous systems. We introduce a method for determining a position-dependent dielectric profile from molecular dynamics simulations. In this method, the free energy of introducing a test charge is computed two ways: from a free energy perturbation calculation and from a numerical solution to Poisson's Equation. The dielectric profile of the system is then determined by minimizing the discrepancy between these two calculations simultaneously for multiple positions of the test charge. We apply this method to determine the dielectric profile of a lipid bilayer surrounded by water. We find good agreement with dielectric models for lipid bilayers obtained by other approaches. The free energy of transferring an ion from bulk water to the lipid bilayer computed from the atomistic simulations indicates that large errors are introduced when the bilayer is represented as a single slab of low dielectric embedded in the higher-dielectric solvent. Significant improvement results from introducing an additional layer of intermediate dielectric (~3) on each side of the low dielectric core extending from ~12 Å to 18 Å. A small dip in transfer free energy just outside the lipid headgroups indicates the presence of a very high dielectric. These results have implications for the design of implicit membrane models and our understanding of protein-membrane interactions.
Click here for more informationSanbo Qin and Huan-Xiang Zhou, Prediction of Salt and Mutational Effects on the Association Rate of U1A Protein and U1 Small Nuclear RNA Stem/Loop II. Journal: J. Phys. Chem. B Vol 112, N o. 19, pages 5955-5960, 2008. Abstract [+]: We have developed a computational approach for predicting protein-protein association rates (Alsallaq and Zhou, Structure 2007, 15, 215). Here we expand the range of applicability of this approach to protein-RNA binding and report the first results for protein-RNA binding rates predicted from atomistic modeling. The system studied is the U1A protein and stem/loop II of the U1 small nuclear RNA. Experimentally it was observed that the binding rate is significantly reduced by increasing salt concentration while the dissociation changes little with salt concentration, and charges distant from the binding site make marginal contribution to the binding rate. These observations are rationalized. Moreover, predicted effects of salt and charge mutations are found to be in quantitative agreement with experimental results.
Click here for more informationPing Zhu, Hanspeter Winkler, Kenneth A. Taylor, and Kenneth H. Roux., Cryoelectron tomography of HIV-1 envelope spikes: further evidence for tripod-like legs. Journal: PLoS Pathogens, pages (in press), 2008. Jason O'Donnel, Kenneth A. Taylor & Michael S. Chapman., Adeno-Associated Virus-2 and its primary cellular receptor ? cryo-EM structure of a heparin complex. Journal: J. Virology, pages submitted, 2008. Donghong Min and Wei Yang, A divide-and-conquer strategy to improve diffusion sampling in generalized ensemble simulations. Journal: The Journal of Chemical Physics Vol. 128, No. 9, pages , 2008. Abstract [+]: Generalized ensemble simulations generally suffer from the associated diffusion-sampling problem; the increased entropic barrier can greatly abolish sampling efficiency, in particular, with the increase of number of degrees of freedom in the target conformational space. Taking advantage of the recent simulated scaling method, we formulate a divide-and-conquer sampling strategy to solve this problem so as to robustly improve the sampling efficiency in generalized ensemble simulations. In the present method, the target conformational space sampling enhancement is decomposed to the sampling enhancements of several subconformational regions, and multiple independent SS simulations are performed to establish the individual sampling enhancement for each of the subconformational regions; in order to realize the global importance sampling, structure exchanges among these replicas are performed based on the Monte Carlo acceptance/rejection procedure. As demonstrated in our studies, the present divide-and-conquer sampling algorithm, named by us as “simulated scaling based variant Hamiltonian replica exchange method,” has superior sampling capability so as to possibly play an essential role in dealing with the present bottleneck of generalized ensemble method developments: the system size limitations
Click here for more informationDonghong Min, Hongzhi Li, Guohui Li, Bernd A Berg, Marcia O Fenley, Wei Yang, fficient sampling of ion motions in molecular dynamics simulations on DNA: Variant Hamiltonian replica exchange method. Journal: Chemical Physics Letters Volume 454, Issues 4-6, pages 391-395, 2008. Abstract [+]: Counterions play an important role in biomolecular functions. Although molecular dynamics simulations have been applied on various nucleic acids, accurate and efficient descriptions of ion motions around DNA or RNA are still challenging, largely due to ions' slow mobility. Here, a variant Hamiltonian replica exchange method was developed to achieve efficient sampling of ion motions. Based on the present approach, the results from our model study on classical Drew-Dickerson B-DNA dodecamer show remarkable agreements with experimental measurements and nonlinear Poisson-Boltzmann predictions. Due to the employment of this variant Hamiltonian replica exchange method, these amazing agreements can be achieved within a short simulation time (900 ps).
Click here for more informationDonghong Min and Wei Yang, Energy difference space random walk to achieve fast free energy calculations. Journal: The Journal of Chemical Physics Vol. 128, No. 19, pages , 2008. Abstract [+]: A method is proposed to efficiently obtain free energy differences. In the present algorithm, free energy calculations proceed by the realization of an energy difference space random walk. Thereby, this algorithm can greatly improve the sampling of the regions in phase space where target states overlap
Click here for more informationLianqing Zheng and Wei Yang, Essential energy space random walks to accelerate molecular dynamics simulations: Convergence improvements via an adaptive-length self-healing strategy. Journal: The Journal of Chemical Physics Vol. 129, No. 1, pages , 2008. Abstract [+]: Recently, accelerated molecular dynamics (AMD) technique was generalized to realize essential energy space random walks so that further sampling enhancement and effective localized enhanced sampling could be achieved. This method is especially meaningful when essential coordinates of the target events are not priori known; moreover, the energy space metadynamics method was also introduced so that biasing free energy functions can be robustly generated. Despite the promising features of this method, due to the nonequilibrium nature of the metadynamics recursion, it is challenging to rigorously use the data obtained at the recursion stage to perform equilibrium analysis, such as free energy surface mapping; therefore, a large amount of data ought to be wasted. To resolve such problem so as to further improve simulation convergence, as promised in our original paper, we are reporting an alternate approach: the adaptive-length self-healing (ALSH) strategy for AMD simulations; this development is based on a recent self-healing umbrella sampling method. Here, the unit simulation length for each self-healing recursion is increasingly updated based on the Wang–Landau flattening judgment. When the unit simulation length for each update is long enough, all the following unit simulations naturally run into the equilibrium regime. Thereafter, these unit simulations can serve for the dual purposes of recursion and equilibrium analysis. As demonstrated in our model studies, by applying ALSH, both fast recursion and short nonequilibrium data waste can be compromised. As a result, combining all the data obtained from all the unit simulations that are in the equilibrium regime via the weighted histogram analysis method, efficient convergence can be robustly ensured, especially for the purpose of free energy surface mapping.
Click here for more informationLianqing Zheng, Irina O. Carbone and Alexey Lugovskoy, Bernd A. Berg, and Wei Yang, A hybrid recursion method to robustly ensure convergence efficiencies in the simulated scaling based free energy simulations. Journal: The Journal of Chemical Physics Vol. 129, No. 3, pages , 2008. Abstract [+]: Recently, we developed an efficient free energy simulation technique, the simulated scaling (SS) method [H. Li et al., J. Chem. Phys. 126, 024106 (2007)], in the framework of generalized ensemble simulations. In the SS simulations, random walks in the scaling parameter space are realized so that both phase space overlap sampling and conformational space sampling can be simultaneously enhanced. To flatten the distribution in the scaling parameter space, in the original SS implementation, the Wang–Landau recursion was employed due to its well-known recursion capability. In the Wang–Landau recursion based SS free energy simulation scheme, at the early stage, recursion efficiencies are high and free energy regions are quickly located, although at this stage, the errors of estimated free energy values are large; at the later stage, the errors of estimated free energy values become smaller, however, recursions become increasingly slow and free energy refinements require very long simulation time. In order to robustly resolve this efficiency problem during free energy refinements, a hybrid recursion strategy is presented in this paper. Specifically, we let the Wang–Landau update method take care of the early stage recursion: the location of target free energy regions, and let the adaptive reweighting method take care of the late stage recursion: the refinements of free energy values. As comparably studied in the model systems, among three possible recursion procedures, the adaptive reweighting recursion approach is the least favorable one because of its low recursion efficiency during free energy region locations; and compared to the original Wang–Landau recursion approach, the proposed hybrid recursion technique can be more robust to guarantee free energy simulation efficiencies
Click here for more informationD. Min, H. Josephine, H. Li, C. Lakner, I. Macpherson, G. Naylor, D. Swofford, L. Hedstrom, W. Yang, An Enzymatic Atavist Revealed in Dual Pathways for Water Activation. Journal: PLoS Biology, Vol. 6, No. 8, pages , 2008. Abstract [+]: Inosine monophosphate dehydrogenase (IMPDH) catalyzes an essential step in the biosynthesis of guanine nucleotides. This reaction involves two different chemical transformations, an NAD-linked redox reaction and a hydrolase reaction, that utilize mutually exclusive protein conformations with distinct catalytic residues. How did Nature construct such a complicated catalyst? Here we employ a “Wang-Landau” metadynamics algorithm in hybrid quantum mechanical/molecular mechanical (QM/MM) simulations to investigate the mechanism of the hydrolase reaction. These simulations show that the lowest energy pathway utilizes Arg418 as the base that activates water, in remarkable agreement with previous experiments. Surprisingly, the simulations also reveal a second pathway for water activation involving a proton relay from Thr321 to Glu431. The energy barrier for the Thr321 pathway is similar to the barrier observed experimentally when Arg418 is removed by mutation. The Thr321 pathway dominates at low pH when Arg418 is protonated, which predicts that the substitution of Glu431 with Gln will shift the pH-rate profile to the right. This prediction is confirmed in subsequent experiments. Phylogenetic analysis suggests that the Thr321 pathway was present in the ancestral enzyme, but was lost when the eukaryotic lineage diverged. We propose that the primordial IMPDH utilized the Thr321 pathway exclusively, and that this mechanism became obsolete when the more sophisticated catalytic machinery of the Arg418 pathway was installed. Thus, our simulations provide an unanticipated window into the evolution of a complex enzyme.
Click here for more informationZheng, L. and Yang, W, On the simulated scaling based free energy simulations: Adaptive optimization of the scaling parameter. Journal: The Journal of Chemical Physics, pages (in press), 2008. Mrinal K Biswas and T N Krishnamurti, Modulation of African waves from the advection of upper level moisture from the Tropical Easterly Jet. Poster: AMS 28th Conference on Hurricanes and Tropical Meteorology, 2008. Abstract [+]: Many Atlantic hurricanes develop from African waves and moves westward over the Atlantic Ocean. The impact of upper level moisture from the Asian summer monsoon region on the African waves is addressed in this study. Sensitivity experiments were done with the PSU/NCAR MM5 model to see the impact of upper level moisture from the Tropical Easterly Jet on the African waves. The integration domain spanned the whole of Africa and run with 5 km resolution. Results show that reducing the moisture at the eastern African boundary decreases the rainfall over Africa and modulates the amplitude of the African waves. Forecasts from the FSU Global Spectral model was used to compute the kinetic energy of the African waves. Numerical experiments were separately performed when the monsoonal upper level moisture is low and then compared when it is high. The kinetic energy and the magnitude of the waves were more when the upper level moisture was greater. Our studies indicate that the growth and development of the African waves is modulated by the advection of moisture from the Asian summer monsoon. The study clearly shows the connection between the Asian summer monsoon and African waves and thus affecting the hurricanes in the Atlantic.
Click here for more informationBenjamin A. Schenkel and T.N. Krishnamurti, Conversion from Shear to Curvature Vorticity and Hurricane Evolution. Dissertation/Thesis 2008. Benjamin A. Schenkel and T.N. Krishnamurti, Conversion from Shear to Curvature Vorticity, Organization of Convection, and Hurricane Genesis. Poster: Tropical Meteorology Special Symposium, 2008. Abstract [+]: This study examines the exchange between shear and curvature vorticity and the resulting organization of convection that is central to the formation of tropical cyclones from African Waves. Horizontal shear instability results in a strong transfer of shear vorticity into curvature vorticity, which implies a small radius of curvature of flow or an “organization of convection.” As curvature is maximized and convection organizes, convective heat release based baroclinic processes start to dominate in the genesis of the storm. This study uses high-resolution satellite data in combination with model data for Hurricane Nate (2005) and a non-developing African Easterly Wave to show that vorticity conversions are responsible for the organization of convection. Cloud liquid water is calculated from brightness temperatures using the algorithm given by Wentz (1997) from AQUA, the DMSP series, and TRMM at resolutions of 0.25º. These datasets are used to show that convection is organizing by displaying a time series of the growth of the power of the azimuthal wavenumber structure of cloud liquid water. Shear to curvature vorticity ratios are then computed from the MM5 at a resolution of 0.03º using the equations given by Bell and Keyser (1993). Contributions to vorticity exchanges from barotropic, baroclinic, and diabatic processes will be examined using a modified version of the MM5.
Click here for more informationDukhovskoy, D.S., S.L. Morey, P.J. Martin, J.J. O’Brien, C. Cooper, Application of a vanishing, quasi-sigma, vertical coordinate for simulation of high-speed, deep currents over the Sigsbee Escarpment in the Gulf of Mexico. Journal: Ocean Modelling, pages , 2008. Abstract [+]: Recent observations over the Sigsbee Escarpment in the Gulf of Mexico have revealed extremely energetic deep currents (near 1 m s-1), which are trapped along the escarpment. Both scientific interest and engineering needs demand dynamical understanding of these extreme events. A primary objective of this study is to develop an appropriate model of the Sigsbee Escarpment region that will be used to study the ocean dynamics in the region, aid in analysis of the observational data, and suggest possible mechanisms of the phenomenon. The very steep slope of the Sigsbee Escarpment (0.05 - 0.1) limits the application of ocean models with traditional terrain-following (sigma) vertical coordinates, which may represent the very complicated topography in the region adequately, can result in large truncation errors during calculation of the horizontal pressure gradient. A new vertical coordinate system, termed a vanishing quasi-sigma coordinate, is implemented in the Navy Coastal Ocean Model for application to the Sigsbee Escarpment region. Vertical coordinate surfaces for this grid have noticeably gentler slopes than a traditional sigma grid, while still following the terrain near the ocean bottom. The new vertical grid is tested with a suite of numerical experiments and compared to a classical sigma-layer model. The numerical error is substantially reduced in the model with the new vertical grid. A one-year, realistic, numerical simulation is performed to simulate strong, deep currents over the Escarpment using a very-high-resolution nested modeling approach. The model results are analyzed to demonstrate that the deep ocean currents in the simulation replicate the prominent dynamical features of the observed intense currents in the region.
Ye, M., and R. Khaleel, A Markov chain model for characterizing medium heterogeneity and sediment layering structure. Journal: Water Resources Research, pages doi:10.102, 2008. Abstract [+]: By leveraging use of ‘‘soft’’ data (e.g., initial moisture content, qi), this study applies
the transition probability (TP) based Markov chain (MC) model to sediment textural
classes for characterizing the medium heterogeneity and sediment layering structure. The
TP/MC method is evaluated by simulating the vadose zone moisture movement at a
field site, where the stratigraphy consists of imperfectly stratified soil layers. Soil
heterogeneity is characterized via spatial variability of the geometry of soil textural
classes. When the qi measurements, which carry signature about medium heterogeneity
and stratigraphy, are not included in the TP/MC model, it is not possible to identify the
horizontal TP. The qi measurements, when transformed into soil classes, are necessary in
mapping the soil layering structure prevalent at the site. The soil hydraulic parameters
for each soil class are treated deterministically and are estimated on the basis of core
samples. To evaluate uncertainty in characterizing geometry of the soil classes, multiple
conditional realizations of the soil classes are generated. A Monte Carlo simulation
shows that the simulated mean moisture contents agree well with corresponding field
observations. The observed splitting of the moisture plume in a coarse sand layer that is
sandwiched between two fine-textured layers, the southeastward movement of the plume
during the redistribution period, and the near-zero fluid flux below the bottom fine layer
are adequately simulated. Spatial variability of the field-measured moisture content is
sufficiently captured by the 95% confidence intervals calculated from the Monte Carlo
simulations. Investigating the effect of data conditioning on the simulated results shows
that a reduction of conditioning data does not necessarily deteriorate simulation results if
other conditioning data exist within the mean length of the soil classes. The TP/MC
method is flexible so that other types of site characterization data (e.g., geophysical data)
can be incorporated as they become available.
Ye, M., P.D. Meyer, and S.P. Neuman, On model selection criteria in multimodel analysis. Journal: Water Resources Research, pages doi:10.102, 2008. Abstract [+]: Hydrologic systems are open and complex, rendering them prone to multiple
conceptualizations and mathematical descriptions. There has been a growing tendency to
postulate several alternative hydrologic models for a site and use model selection criteria
to (1) rank these models, (2) eliminate some of them, and/or (3) weigh and average
predictions and statistics generated by multiple models. This has led to some debate
among hydrogeologists about the merits and demerits of common model selection (also
known as model discrimination or information) criteria such as AIC, AICc, BIC, and KIC
and some lack of clarity about the proper interpretation and mathematical representation of
each criterion. We examine the model selection literature to find that (1) all published
rigorous derivations of AIC and AICc require that the (true) model having generated the
observational data be in the set of candidate models; (2) though BIC and KIC were
originally derived by assuming that such a model is in the set, BIC has been rederived by
Cavanaugh and Neath (1999) without the need for such an assumption; and (3) KIC
reduces to BIC as the number of observations becomes large relative to the number of
adjustable model parameters, implying that it likewise does not require the existence of a
true model in the set of alternatives. We explain why KIC is the only criterion accounting
validly for the likelihood of prior parameter estimates, elucidate the unique role that the
Fisher information matrix plays in KIC, and demonstrate through an example that it
imbues KIC with desirable model selection properties not shared by AIC, AICc, or BIC.
Our example appears to provide the first comprehensive test of how AIC, AICc, BIC, and
KIC weigh and rank alternative models in light of the models’ predictive performance
under cross validation with real hydrologic data.
Cezary Bojanowski, Leslaw Kwasniewski, Jerry Wekezer, "Safety Assessment of Wheelchair Occupants in Paratransit Buses". Journal: International Journal of Human Modeling and Simulation, pages Vol. 1, No, 2008. Abstract [+]: Safety assessment of passengers with disabilities travelling in their wheelchairs in paratransit buses is presented. Computational mechanics and LS-DYNA non-linear finite element code were used as tools in this study. All finite element models were partially validated using data available from experimental sled tests. The validated dummy-wheelchair-bus system, which was developed, allowed for quantitative assessment of injury criteria in several accident scenarios. Although backward seating was found beneficial in reducing severity of injuries during accidents, the outcome is sensitive to imperfect initial conditions during accidents. Material presented allows for detailed assessment of benefits and shortcomings of each configuration considered.
Hongyi Li, Leslaw Kwasniewski, Jerry W. Wekezer, "Dynamic Response of a Highway Bridge Subjected to Moving Trucks". Journal: ASCE Journal of Bridge Engineering, pages pp. 439-44, 2008. Abstract [+]: Several full-scale load tests were performed on a selected Florida highway bridge. The bridge was dynamically excited by two fully loaded trucks, and the strain, acceleration, and displacement at selected points were recorded for the investigation of the bridge's dynamic response. Experimental data were compared with simplified vehicle and bridge finite-element models. The vehicle was represented as a three-dimensional mass–spring–damper system with 11 degrees of freedom, and the bridge was modeled as a combination of plate and beam elements that characterize the slab and girders, respectively. The equations of motion were formulated with physical components for the vehicle and modal components for the bridge. The coupled equations were solved using a central difference method. It was found that the numerical analysis matched well with the experimental data and was used to successfully explain critical dynamic phenomena observed during the testing. Impact factors for this tested bridge were thoroughly investigated by using these models.
Click here for more informationZheng, L., Chen, M., and Yang, W, Random walk in orthogonal space. 2008. Min, D., Josephine, H., Li, H., Lakner, C., Swofford, D., Naylor, G. P.,Hedstrom, L.*, and Yang, W., An enzymatic atavist revealed in dual. Journal: PLoS Biology 6, pages 1802-1810, 2008. Zheng, L. and Yang, W., On the simulated scaling based free energy simulations: Adaptive optimization of the scaling parameter intervals. Journal: Chem. Phys. 129, pages 124107, 2008. Zheng, L. and Yang, W., Essential energy space random walks to accelerate molecular dynamics simulations: Convergence improvements via an adaptive-length self-healing strategy.. Journal: J. Chem. Phys. 129, pages 014105, 2008. Zheng, L., I. O. Carbone, Berg, B. A., and Yang, W., A hybrid recursion method to robustly ensure efficiency in the simulated scaling based free energy simulations.. Journal: J. Chem. Phys. 129, pages 034105, 2008. Min, D. and Yang, W, Energy difference space random walk to achieve fast free energy calculations. Journal: J. Chem. Phys. (Communication) 128, pages 19102, 2008. Min, D., Li, H., Berg, B. A., Fenley, M. O., and Yang, W., Efficient sampling of ion motions in molecular dynamics simulations on DNA: Variant Hamiltonion replica exchange strategy. Journal: Chem. Phys. Lett. 454, pages 391-395, 2008. Paul van der Mark, Daniel R. Voss, and Jeff E. McDonald, High Performance Computing at FSU. Poster: SuperComputing 07, 2007. Click here for more informationMikolai I. Fajer, Hongzhi Li, Wei Yang, and Piotr G. Fajer, Mapping Electron Paramagnetic Resonance Spin Label Conformations by the Simulated Scaling Method. Journal: Journal of the American Chemical Society Vol. 129, No. 45, pages 13840-1384, 2007. Abstract [+]: In order to efficiently simulate spin label behavior when attached to the protein backbone we developed a novel approach that enhances local conformational sampling. The simulated scaling (SS) approach (Li, H., et al. J. Chem. Phys. 2007, 126, 24106) couples the random walk of a potential scaling parameter and molecular dynamics in the framework of hybrid Monte Carlo. This approach allows efficient barrier crossings between conformations. The method retains the thermodynamic detailed balance allowing for determination of relative free energies between various conformations. The accuracy of our method was validated by comparison with the recently resolved X-ray crystal structure of a spin labeled T4 lysozyme in which the spin label was in the interior of the protein. Consistent potentials of mean force (PMF) are obtained for the spin label torsion angles to illustrate their behavior in various protein environments: surface, semiburied, and buried. These PMFs reflect the experimentally observed trends and provide the rationale for the spin label dynamics. We have used this method to compare an implicit and explicit solvent model in spin label modeling. The implicit model, which is computationally faster, was found to be in excellent agreement with the explicit solvent treatment. Based on this collection of results, we believe that the presented approach has great potential in the general strategy of describing the behavior of the spin label using molecular modeling and using this information in the interpretation of EPR measurements in terms of protein conformation and dynamics.
Click here for more informationJin Wang, Xiliang Zheng, Yongliang Yang, Dale Drueckhammer, Wei Yang, and Gennardy Verkhi, Quantifying Intrinsic Specificity: A Potential Complement to Affinity in Drug Screening. Journal: Physical Review Letters Vol. 99, No. 19, pages , 2007. Abstract [+]: We report here the investigation of a novel description of specificity in protein-ligand binding based on energy landscape theory. We define a new term, intrinsic specificity ratio (ISR), which describes the level of discrimination in binding free energies of the native basin for a protein-ligand complex from the weaker binding states of the same ligand. We discuss the relationship between the intrinsic specificity we defined here and the conventional definition of specificity. In a docking study of molecules with the enzyme COX-2, we demonstrate a statistical correspondence between ISR value and geometrical shapes of the small molecules binding to COX-2. We further observe that the known selective (nonselective) inhibitors of COX-2 have higher (lower) ISR values. We suggest that intrinsic specificity ratio may be a useful new criterion and a complement to affinity in drug screening and in searching for potential drug lead compounds.
Click here for more informationBernd A. Berg and Wei Yang, Numerical calculation of the combinatorial entropy of partially ordered ice. Journal: The Journal of Chemical Physics Vol. 127, No. 22, pages , 2007. Abstract [+]: Using a one-parameter case as an example, we demonstrate that multicanonical simulations allow for accurate estimates of the residual combinatorial entropy of partially ordered ice. For the considered case, corrections to an (approximate) analytical formula are found to be small, never exceeding 0.5%. The method allows one as well to calculate combinatorial entropies for other systems
Click here for more informationMark F. Horstemeyer, Hongyi Li, Jeff Siervogel, Leslaw Kwasniewski, Jerry W. Wekezer, Brian Christia, "Material and Structural Crashworthiness Characterization of Paratransit Buses". Journal: International Journal of Crashworthiness, pages pp. 509-52, 2007. Abstract [+]: A comprehensive experimental material characterization and full-scale testing of structural connections of paratransit buses is presented in this paper. Structure-property relations were quantified for the constitutive material models used for finite element simulation-based crashworthiness research of paratransit buses. Several structural materials used by the paratransit bus industry were identified, and coupon size specimens were tested. A dynamic wall panel test with an impact hammer provided validation data for the finite element simulations. In addition, quasi-static laboratory tests of standard connections between the walls, floor, and the roof of a selected paratransit bus were performed. In addition to FE model validation, the connection testing allowed for thorough qualitative assessment of connection design, which resulted in improved crashworthy connection details. The experimental materials characterization and validation protocol described in this paper is consistent with the draft of the crash and safety standard for structural assessment of paratransit buses in the state of Florida. This roadmap is intended to be used for crashworthiness evaluation of future paratransit buses.
Click here for more informationKrzysztof Cichocki, Jerry W. Wekezer, "Structural Response of Paratransit Buses in Rollover Accidents". Journal: International Journal of Crashworthiness, pages Vol. 12,, 2007. Abstract [+]: Existing crashworthiness standards in the United States are focused primarily on passenger cars and school buses, while paratransit buses are not required to meet these codes. The main objective of this research was to develop a finite element (FE) model of the Champion Challenger paratransit bus in order to perform the crashworthiness evaluation during the rollover test using computational mechanics. The FE model was developed based on technical description and AutoCAD files of the bus structure supplied by Champion, the producer of the Challenger bus.
In the absence of U.S. crashworthiness standards applicable to paratransit buses, the FE model of Champion Challenger bus was used for computational mechanics study of the rollover test according to ECE Regulation 66. All numerical analyses were carried out using LS-DYNA, a nonlinear, explicit code. Experimental validation of assumed material models, mesh density, and contact definition was performed through a simple pendulum impact test of the bus sidewall panels [1].
Click here for more informationJerzy Malachowski, Hongyi Li, Jerry W. Wekezer, Leslaw Kwasniewski, "Numerical Assessment of Dynamic Response of Highway Bridges Subjected to Heavy Vehicles". Journal: Advances in Transportation Studies, An International Journal, pages Issue XII,, 2007. Abstract [+]: This paper presents results of the Finite Element (FE) analyses of dynamic interaction between heavy
vehicles and selected group of smaller, typical Florida highway bridges. Computational mechanics and LSDYNA,
3-D explicit, dynamic, non-linear FE code were used as primary research tools to investigate vehicle
– bridge interaction. One selected vehicle-bridge configuration was thoroughly validated by conducting
actual dynamic testing on a highway bridge on US 90 in Northern Florida. Collected experimental data,
which included time histories of strains, displacements, and accelerations of selected points on the bridge
and the truck, were found to be well correlated with computational mechanics analysis. Dynamic impact
factors were calculated for over thirty vehicle-bridge cases based on FE models of one heavy truck, three
cranes and four bridges. Influence of vehicle mass, their speed, bridge span lengths, and deck surface
imperfections on bridge dynamic response was investigated using bridge and vehicle FE models developed.
These validated models can be used for follow-up studies for other vehicle-bridge combinations in the future.
It is expected that extrapolating results of FE analysis on a broad class of heavy vehicles and bridges will
enable formulation of practical recommendations for management decisions regarding dynamic impact
factors, speed limits, or permissible weight of the heavy vehicles for highway bridges.
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