Bulletin of the American Physical Society
2006 APS March Meeting
Monday–Friday, March 13–17, 2006; Baltimore, MD
Session N10: Focus Session: Frontiers in Computational Chemical Physics III |
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Sponsoring Units: DCP Chair: Jeffrey Saven, University of Pennsylvania Room: Baltimore Convention Center 302 |
Wednesday, March 15, 2006 8:00AM - 8:36AM |
N10.00001: Development of effective models for vectorial biological processes Invited Speaker: Progress towards understanding vectorial processes in biological systems using theoretical and computational approaches will be discussed. The specific problems of interest include mechanochemical coupling in the molecular motor myosin and vectorial proton pumping in cytochrome c oxidase. Several related methodological developments will be discussed, which include boundary potential for QM/MM simulations, effective QM methods for treating long-range proton transfers and phosphate chemistry, and coarse-grained models for describing large-scale motions in biomolecules. Quantitative benchmark calculations of these methods have been carried out using both model and realistic biological systems. The application of these methods to myosin and cytochrome c oxidase will be briefly presented. [Preview Abstract] |
Wednesday, March 15, 2006 8:36AM - 8:48AM |
N10.00002: Hierarchical Coarse-Grained Models for Polymer Simulations Sheng D. Chao Structural and thermodynamic properties of industrial and bioengineering materials can be better investigated using atomistic simulations. However, current large-scale atomistic simulations remain computationally demanding. It is thus desirable to seek alternatives to perform efficient and informative mesoscopic simulations. We have developed a coarse-grained intermolecular force (CGIF) model for polymer nanostructures and nanocomposites. This model can effectively capture the stereochemical response to anisotropic long-range interactions. The coarse-graining procedure forms the basis to perform a hierarchy of simulations starting with the quantum-chemistry calculations to coarse-grained molecular dynamics toward continuum modeling. We have applied this procedure to several cases from alkane to benzene to fullerene. For liquid methane, molecular dynamics simulations using the CGIF model reproduce the structural properties calculated using the atomistic force field. The coarse-grained energetics of benzene clusters has well reproduced the results using electronic structure calculations. The subtle anisotropy in the interaction potential of fullerene dimer is also well represented by the CGIF model and is consistent with that calculated using the Brenner force field. [Preview Abstract] |
Wednesday, March 15, 2006 8:48AM - 9:00AM |
N10.00003: Dynamic Phase Transitions in Coupled Motor Proteins Anatoly Kolomeisky, Eugene Stukalin The effect of interactions on dynamics of coupled motor proteins is investigated theoretically. A simple stochastic discrete model, that allows to calculate explicitly the dynamic properties of the system, is developed. It is shown that there are two dynamic regimes, depending on the interaction between the particles. For strong interactions the motor proteins move as one tight cluster, while for weak interactions there is no correlation in the motion of the proteins, and the particle separation increases steadily with time. The boundary between two dynamic phases is specified by a critical interaction that has a non-zero value only for the coupling of the asymmetric motor proteins, and it depends on the temperature and the transitions rates. At the critical interaction there is a change in a slope for the mean velocities and a discontinuity in the dispersions of the motor proteins as a function of the interaction energy. [Preview Abstract] |
Wednesday, March 15, 2006 9:00AM - 9:12AM |
N10.00004: Reduced-Dimensional Models for Chemical Dynamics in Complex Environments Rigoberto Hernandez, Alex V. Popov, Eli Hershkovits Nonstationary Langevin models have been developed that are capable of capturing feedback between complex environments and the underlying molecular constructs which in turn collectively comprise the environment. Although initial justifications for this formalism were heuristic and phenomenological, in recent work we have shown that in some cases it arises as the projection of a simple model of a chemical system bilinearly coupled to a harmonic bath with a time-dependent coupling. Moreover, the stochastic model can be used to surmise the diffusion of a tagged particle in a colloidal suspension which swells or shrinks with time. Alternatively, a liquid crystal, modelled as a colloidal suspension of orientable bodies, can also exhibit driven (time-dependent) behavior by way of the rotation of a magnetic field. Once again, the diffusion of a tagged particle under such time-dependence, can be surmised by the stochastic model. Thus these models allow for a substantial reduction of the dimensionality of a complex environment while retaining its multiple-time-scale features. [Preview Abstract] |
Wednesday, March 15, 2006 9:12AM - 9:24AM |
N10.00005: Structure of Alzheimer's 10-35 $\beta$ peptide from replica-exchange molecular dynamics simulations in explicit water Andriy Baumketner, Joan-Emma Shea We report a replica-exchange molecular dynamics study of the 10-35 fragment of Alzheimer's disease amyloid $\beta$ peptide, A$\beta$10-35, in aqueous solution. This fragment was previously seen~[J. Str. Biol. 130 (2000) 130] to possess all the most important amyloidogenic properties characteristic of full-length A$\beta$ peptides. Our simulations attempted to fold A$\beta$10-35 from first principles. The peptide was modeled using all-atom OPLS/AA force field in conjunction with the TIP3P explicit solvent model. A total of 72 replicas were considered and simulated over 40 ns of total time, including 5 ns of initial equilibration. We find that A$\beta$10-35 does not possess any unique folded state, a 3D structure of predominant population, under normal temperature and pressure. Rather, this peptide exists as a mixture of collapsed globular states that remain in rapid dynamic equilibrium with each other. This conformational ensemble is seen to be dominated by random coil and bend structures with insignificant presence of $\alpha$-helical or $\beta$-sheet structure. We find that, overall, the 3D structure of A$\beta$10-35 is shaped by salt bridges formed between oppositely charged residues.Of all possible salt bridges, K28-D23 was seen to have the highest formation probability, totaling more than 60\% of the time. [Preview Abstract] |
Wednesday, March 15, 2006 9:24AM - 9:36AM |
N10.00006: Orbital Energetics and Molecular Recognition Aaron George, Rebecca Harris, Vishali Mogallapu, Yonas Abraham, Roberto Car, Jeffrey Schmitt We present data demonstrating that orbital eigenenergy fluctuation recorded in the course of ab initio molecular dynamics calculations contains information relevant in determining molecular behavior and recognition. A simple scheme is presented that maps these data to molecular descriptors. Using computational drug design as the context, these descriptors are compared with previous electronic eigenvalue descriptor methods with encouraging results. Finally we discuss further methods of mapping electronic structure based molecular dynamics trajectories to Quantitative Structure Activity Relationships (QSAR). [Preview Abstract] |
Wednesday, March 15, 2006 9:36AM - 9:48AM |
N10.00007: Unrestricted Hartree-Fock Investigation of the Electron Distribution on the Heme System in Azidohemoglobin-$^{57m}$Fe and $^{14}$N Hyperfine Interactions. Archana Dubey, H.P. Saha, Lee Chow, R.H. Scheicher, N. Sahoo, R.H. Pink, Dip N. Mahato, M.B. Huang, T.P. Das* We have a program of investigations in progress on the electronic structure of azidohemoglobin by the first-principles Unrestricted Hartree-Fock procedure to understand the substantial amount of magnetic (g-tensor), magnetic hyperfine, and nuclear quadrupole interaction, data available [1] from electron paramagnetic resonance, Mosbauer and electron-nuclear double resonance measurements. Earlier semi-empirical Self-Consistent Charge Extended Huckel investigations have provided semiquantitative results [2] with different degrees of agreement for the available properties and suggested the need for more accurate and quantitative investigations. Results of our investigations will be presented for the $^{57m}$Fe and $^{14}$N nuclear quadrupole and magnetic hyperfine interaction properties and compared with experimental data. *Also UCF Orlando [1] See Refs. 2-4 listed in Ref.[2]. [2] Santosh K. Mishra, J.N. Roy, K.C. Mishra and T.P. Das, Theo. Chim. Acta 75, 195(1989). [Preview Abstract] |
Wednesday, March 15, 2006 9:48AM - 10:00AM |
N10.00008: Polymer dynamics and the folding rates of fast folding proteins John Portman In recent years, minimal models of fast folding proteins has enabled considerable agreement between computation, theory, and experiment. The assumptions associated with most simple models of fast folding proteins (Go-models) give rather robust results in terms of coarse grained description of the transition state ensemble. One aspect of the folding mechanism that has received less attention is describing the conformational dynamics responsible for the folding rate prefactor, $k_0$. Here, we consider the distribution of prefactors of fast folding proteins: does local dynamics influence $k_0$, or can one reasonably expect that $k_0$ is essentially the same regardless of contact order or mean structure of the transition state ensemble. We address this question by considering the folding routes of a wide variety of fast folding proteins using a polymer based model in which structural ensembles are parameterized by the degree of localization about the native structure. [Preview Abstract] |
Wednesday, March 15, 2006 10:00AM - 10:12AM |
N10.00009: A United Atom Model for Simulation of DNA from Angstroms to Microns in Length Thomas Knotts IV, Nitin Rathore, Juan de Pablo For several years, single molecule pulling experiments have given insights into the stability of DNA. Many descriptions of DNA, from atomistic to continuum, have proven successful at reproducing observed behavior.~ We have found, however, that there is no suitable model for several problems of interest, including viral packaging of DNA and microarray interactions, where the size of the molecules prohibits atomistic representations, but continuum and linear bead-spring models do not contain the required molecular level of detail.~ Emerging technologies require that mesoscopic models of DNA be developed, capable of describing length scales in the 5 to 500 nm range. One of the main challenges is to preserve a coupling between the phenomena seen at longer length scales (e. g.~ a persistence length of 50 nm) while incorporating the features needed for smaller scales (e. g. charge effects, geometry, and base specificity).~ We have developed a coarse grain description of DNA which reduces the complexity of a nucleotide to three interaction sites.~ The model is capable of describing sequence information, bubble formation, and salt effects in simulations of DNA up to a few microns in length.~ The predictions are in remarkable, quantitative agreement with experiment, and shed light into the coupling of multiple length scales and interactions to yield unique behaviors and functions. [Preview Abstract] |
Wednesday, March 15, 2006 10:12AM - 10:24AM |
N10.00010: Diffusion Monte Carlo applied to weak interactions - hydrogen bonding and aromatic stacking in (bio-)molecular model systems M. Fuchs, J. Ireta, M. Scheffler, C. Filippi Dispersion (Van der Waals) forces are important in many molecular phenomena such as self-assembly of molecular crystals or peptide folding. Calculating this nonlocal correlation effect requires accurate electronic structure methods. Usual density-functional theory with generalized gradient functionals (GGA-DFT) fails unless empirical corrections are added that still need extensive validation. Quantum chemical methods like MP2 and coupled cluster are more accurate, yet limited to rather small systems by their unfavorable computational scaling. Diffusion Monte Carlo (DMC) can provide accurate molecular total energies and remains feasible also for larger systems. Here we apply the fixed-node DMC method to (bio-)molecular model systems where dispersion forces are significant: (dimethyl-) formamide and benzene dimers, and adenine-thymine DNA base pairs. Our DMC binding energies agree well with data from coupled cluster (CCSD(T)), in particular for stacked geometries where GGA-DFT fails qualitatively and MP2 predicts too strong binding. [Preview Abstract] |
Wednesday, March 15, 2006 10:24AM - 10:36AM |
N10.00011: Computational Methods for Enhanced Conformational Kinetics Ioan Andricioaei We present and analyze two general method to calculate time-correlation functions from molecular dynamics on scaled potentials or from molecular dynamics with artificial momenta distributions. They are useful for complex systems whose simulations are affected by broken ergodicity. Depending on the value of the scaling factor or of the details of the momentum distributions, correlation functions can be accurately calculated for times that can be orders of magnitude longer than those accessible to current molecular dynamics simulations. We show that the exact value of the correlation functions of the original system can be obtained, in principle, using an action-reweighting scheme based on a stochastic path-integral formalism. Tests on model systems and peptides are exemplified. We also show that free energy profiles using Jarzynski's identity can be more effectively calculated within this scheme. [Preview Abstract] |
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