Bulletin of the American Physical Society
2009 APS March Meeting
Volume 54, Number 1
Monday–Friday, March 16–20, 2009; Pittsburgh, Pennsylvania
Session P40: Theoretical and Computational Biophysics |
Hide Abstracts |
Sponsoring Units: DBP Chair: Sonya Bahar, University of Missouri--St. Louis Room: 412 |
Wednesday, March 18, 2009 8:00AM - 8:12AM |
P40.00001: Noise-Optimized Speciation in a Simple Evolutionary Model Nathan Dees, Sonya Bahar A simple computational model for Darwinian evolution is constructed based on three minimal requirements: inheritance, variability, and overpopulation. The fitness of organisms is based on their position in a two-dimensional fitness landscape which is changed periodically either by random fluctuations, or via a feedback mechanism based on the number of organisms in close proximity. The clustering of organisms in a morphospace overlaid on this landscape is considered an analog of speciation and is investigated as a function of the degree of variability, or ``noise'', allowed in the morphology of new (children) organisms with respect to their parents. We find that a maximum number of species are formed at an intermediate value of this noise parameter, suggesting a stochastic resonance-like effect. We also address the spread of inherited traits through the overall population, finding an ``all or none'' effect in which the properties of a traced organism either die out completely or percolate through the entire population, leading to what might be considered as ``homologous'' traits even in species widely separated in morphospace. [Preview Abstract] |
Wednesday, March 18, 2009 8:12AM - 8:24AM |
P40.00002: Cyclic Process as a Tool for Considering Evolution Victor Bondarenko Evolution is the process. The primary question is which tools we use to consider the process. In this work, basing on the original results of investigation of the intrinsic bistability in quantum systems, the concept of the cyclic process is developed for qualitative and quantitative consideration of processes as following: Everything that happens is the process of changing; the process is the cyclic process of ``... $\to $ seed $\to $ plant $\to $ seed $\to $...'' type; the cyclic process is formed by two complement phase transitions of ``seed $\to $ plant'' and ``plant $\to $ seed'' type; the cyclic process is the manifestation of self-consistent interaction of interdependent two-state system, environment, and radiation, so that the whole Universe is involved in each process; the cyclic process can be described qualitatively and quantitatively by a real cubic equation with four generalized dimensionless real parameters, provided that one of the parameters undertakes cyclic change of its value and all four parameters belong to limited interdependent intervals to maintain cyclic process. Using the cyclic process approach as a powerful tool a variety of issues is considered. Preference of evolution, extinction, adaptation, and relation between microscopic structure and macroscopic behavior of the system are addressed. Seeing the evolution is the most transcending seeing of existence. The cyclic process approach is suggested to be a corner stone for scientific approach to seeing evolution. [Preview Abstract] |
Wednesday, March 18, 2009 8:24AM - 8:36AM |
P40.00003: Stepping in the bacterial flagellar motor Thierry Mora, Howard Yu, Ned S. Wingreen Many bacteria swim by virtue of tiny rotary motors that drive rotation of helical flagella. These motors are powered by a proton flux that is converted into torque by a mechanism which remains largely unknown. Recently, it has been reported that at low speed, the bacterial flagellar motor proceeds by steps. To account for these steps, we propose a physical model in which the stator drives a ``bumpy'' rotor through a viscous medium. Our model is consistent with most of the available data, and allows us to make testable predictions, in particular on the speed and diffusion properties of the rotor. [Preview Abstract] |
Wednesday, March 18, 2009 8:36AM - 8:48AM |
P40.00004: Actin-Polymerization-Driven Motility with Site Specific Tethering Edward Banigan, Andrea Liu A recent numerical simulation by Lee and Liu (2008) has demonstrated a new possible mechanism for actin-polymerization-driven motility. The simulation is a physically consistent version of the Brownian dynamics formulation of the dendritic nucleation model. The model shows that motility can indeed be achieved with the constituent proteins of the dendritic nucleation model, but that motility arises from a mechanism completely different from those proposed before. In the simulations, the build-up of F-actin behind the moving surface drives the surface forwards if the surface has a net repulsion with actin. In this work, we extend the model to include a site specific tethering interaction between the moving surface and actin, to imitate, for example, the effects the ActA or N-Wasp protein. We study the effects of varying binding strength and binding site coverage. [Preview Abstract] |
Wednesday, March 18, 2009 8:48AM - 9:00AM |
P40.00005: FKBP binding free energies obtained via non-equilibrium simulation F. Marty Ytreberg We discuss the advantages and disadvantages of estimating binding free energies (i.e., absolute binding affinities) via non-equilibrium unbinding simulations. The study utilizes the FKBP protein bound to two different ligands as a model system. The non-equilibrium methodology utilized is straight-forward, requiring little or no modification to modern molecular simulation packages, and is trivially parallelizable. The approach makes use of a physical pathway, eliminating the need for complicated alchemical decoupling schemes. [Preview Abstract] |
Wednesday, March 18, 2009 9:00AM - 9:12AM |
P40.00006: Computational Research Needs for Renewable and Alternative Energy: Studies of Natural and Artificial Photosynthesis Victor Batista The atomspheric oxygen that sustains life on earth has been generated by plants during the light period of photosynthesis. At the molecular level, the reaction involves catalytic water splitting into dioxygen, protons and electrons in the subunit D1 of photosystem II (a transmembrane complex of about 20 proteins found in the thylakoid membranes of green plant chloroplasts). Both the reaction mechanism and the structure of the catalytic center responsible for this important reaction remain poorly understood. This talk will present recent advances in experimental and computational studies towards the development of rigorous models of the oxomangenese catalytic complex and the catalytic cycle responsible for oxygen evolution, as well as recent progress on studies of biomimetic systems for artificial photosynthesis. [Preview Abstract] |
Wednesday, March 18, 2009 9:12AM - 9:24AM |
P40.00007: Systematic Coarse-Graining of Peptides to Understand their Effective Molecular Interactions Luca Larini, Gregory A. Voth The process of building reliable coarse-grained models is a major challenge for both theory and simulation. Force matching is a systematic method to produce quantitatively accurate coarse-grained potentials from atomistic simulation data. This method provides a sound theoretical background that can also be used to gain deeper insight into the system under examination. In this way, force matching can be employed as a tool for analysis. Application to a simple biological molecule will be described in order to gain a better understanding of the effective forces acting on the system. [Preview Abstract] |
Wednesday, March 18, 2009 9:24AM - 9:36AM |
P40.00008: Rigorous treatment of electrostatics for spatially varying dielectrics: how far can one go using energy minimization? Yi-Kuo Yu, Oleg Obolensky, Rajarshi Ray, T. Doerr A novel energy minimization formulation of electrostatics that allows computation of the electrostatic energy and forces to any desired accuracy in a system with arbitrary dielectric properties is presented. An integral equation for the scalar charge density is derived from an energy functional of the polarization vector field. This energy functional represents the true energy of the system even in non-equilibrium states. Arbitrary accuracy is achieved by solving the integral equation for the charge density via a series expansion in terms of the equation's kernel, which depends only on the geometry of the dielectrics. The streamlined formalism operates with volume charge distributions only, not resorting to introducing surface charges by hand. Therefore, it can be applied to arbitrary spatial variation of the dielectric susceptibility. The simplicity of application of the formalism to real problems is shown with three examples. [Preview Abstract] |
Wednesday, March 18, 2009 9:36AM - 9:48AM |
P40.00009: Ab-Initio Based Computation of Rate Constants of Spin Forbidden Transitions in (Bio)inorganic Complexes and Metalloproteins Abdullah Ozkanlar, Jorge H. Rodriguez Some (bio)chemical reactions are non-adiabatic processes whereby the total spin angular momentum, before and after the reaction, is not conserved. These are named spin- forbidden reactions. The application of spin density functional theory (SDFT) to the prediction of rate constants is a challenging task of fundamental and practical importance. We apply non-adiabatic transition state theory in conjunction with SDFT to predict the rate constant of the spin- forbidden dihydrogen binding to iron tetracarbonyl. To model the surface hopping probability between singlet and triplet states, the Landau-Zener formalism is used. The lowest energy point for singlet-triplet crossing, known as minimum energy crossing point (MECP), was located and used to compute, in a semi-quantum approach, reaction rate constants at 300 K. The predicted rates are in good agreement with experiment. In addition, we present results which are relevant to the ligand binding reactions of metalloproteins. This work is supported in part by NSF via CAREER award CHE-0349189 (JHR). [Preview Abstract] |
Wednesday, March 18, 2009 9:48AM - 10:00AM |
P40.00010: Electrostatic properties of two finite width charged dielectric slabs in water Y.S. Jho, M. Kanduc, A. Naji, M.W. Kim, R. Podgornik, F.L.H. Brown, P.A. Pincus We study the electrostatic interaction between two like-charged membranes of finite thickness embedded (composed of five parallel dielectric interfaces) in a medium of higher dielectric constant. A generalized SC theory is applied along with extensive Monte-Carlo simulations which applied numerical algorithm based on the image charge method to calculate accurate electrostatic potential or forces. We found the dielectric discontinuity is important in a SC regime. They drive strong counterion crowding in the central region of the inter-surface space upon increasing the solvent/membrane dielectric mismatch and change the membrane interactions from attractive to repulsive at small separations. [Preview Abstract] |
Wednesday, March 18, 2009 10:00AM - 10:12AM |
P40.00011: Electronic Structure Analysis for Proteins on the FMO Method Tomoki Kobori, Shinji Tsuneyuki, Keitaro Sodeyama, Kazuto Akagi, Kiyoyuki Terakura, Hidetoshi Fukuyama The enormity and complexity of proteins have rendered their electronic structure calculation very costly. Although recently established Fragment Molecular Orbital (FMO) method enables us to calculate total energy of a huge protein precisely based on quantum mechanics, the method does not refer to one-electron orbitals and one-electron energy spectrum. In this paper we propose a method of analyzing electronic structure of a protein based on first principles calculation with reasonable accuracy and CPU cost. We construct one- electron Hamiltonian of proteins by assembling the output of the FMO method: fragment orbitals are determined by fragment monomer calculation, while interaction and overlap between fragment orbitals in different fragments are obtained from dimer calculation. After one-electron Hamiltonian matrix of the whole system is fabricated with the fragment orbital basis, one- electron energy spectrum is obtained by its diagonalization. If the matrix dimension is too large, unimportant orbitals are eliminated from the matrix so that the diagonalization of the Hamiltonian becomes feasible. The method is applicable to both the Hartree-Fock method and the density functional theory. In this paper, validity of the method is verified by some test calculations of small peptides. [Preview Abstract] |
Wednesday, March 18, 2009 10:12AM - 10:24AM |
P40.00012: Helical secondary structure of polyalanine peptides in vacuo: Ac-Ala$_n$-LysH$^+$ ($n$=5,10,15), experiment and theory Mariana Rossi, Volker Blum, Peter Kupser, Gert von Helden, Frauke Bierau, Gerard Meijer, Matthias Scheffler The presence of a solvent is often viewed as indispensable to explain the structure of peptides and proteins. However, well defined \emph{secondary} structure motifs (helices, sheets, ...) also exist \emph{in vacuo}, offering a unique ``clean room'' condition to quantify the stabilizing interactions. We here unravel the structure of LysineH$^+$ capped polyalanine peptides Ac-Ala$_n$-LysH$^+$ ($n$-5,10,15), by combining experimental multi-photon IR spectra obtained using the FELIX free-electron laser at room-temperature with van der Waals-corrected all-electron density-functional theory (DFT) in the generalized gradient approximation in the FHI-aims code [1]. Earlier ion mobility studies of these molecules indicate helical structure [2], which we here demonstrate quantitatively. For $n$=5, we find a close energetic competition of different helix motifs ($\alpha$, 3$_{10}$), with similar and good agreement between measured and calculated vibrational spectra. We show how the LysH$^+$ termination acts to induce helices also for longer peptides, and how vibrational modes develop with helix length ($n$=10,15), yielding, e.g., a softening of collective modes towards the infinite helix limit. [1] V. Blum \emph{et al}, Comp. Phys. Comm. (2008), accepted. [2] M. Kohtani \emph{et al.}, JACS 120, 12975 (1998). [Preview Abstract] |
Wednesday, March 18, 2009 10:24AM - 10:36AM |
P40.00013: Hofmeister effect and the phase diagram of lysozyme Steven Lettieri, Xiaofei Li, James Gunton The phase diagrams for lysozyme are calculated for two different precipitant salts, NaCl and NaSCN, using a potential of mean force that takes into account contributions from ion-dispersion forces (J.Phys.Chem.B, 110, 24757). Our results are consistent with a recent perturbation theory calculation (J.Phys.Chem.B, 110, 24757) in that the phase diagram for lysozyme with NaCl is quite different than for lysozyme with NaSCN for the same molar concentration (0.2M). However, in contrast to the perturbation theory calculation, we find that the lysozyme phase diagram with NaCl has a metastable fluid-fluid coexistence curve and that the metastability gap in the case of NaSCN is much larger than predicted by perturbation theory. [Preview Abstract] |
Wednesday, March 18, 2009 10:36AM - 10:48AM |
P40.00014: Infrared Spectroscopy with ab initio molecular dynamics simulations : gas phase floppy peptides of increasing size and complexity, in relation with IR-MPD experiments Marie-Pierre Gaigeot We present finite temperature DFT-based Car-Parrinello molecular dynamics (MD) simulations for the calculation of infrared spectra of complex molecular systems, either in the gas phase or in the condensed phase. We will review the fundamentals of the method, as well as the applicability and originality of finite temperature MD simulations for the purpose of modeling infrared spectra. Illustrations are taken from the infrared spectroscopy of alanine peptides of increasing size and complexity (from dipeptides to an octo-peptide) in the gas phase, in relation with IR-MPD (Infrared Multi Photon Dissociation) experiments : 300-400 K gas-phase action spectroscopy as devised on the CLIO platform at the University of Orsay-France or on the platform developed in the group of L. Snoek at Oxford-UK. A special emphasis on vibrational anharmonicities and how they can be extracted from molecular dynamics simulations will be put forward. Furthermore, band assignments in terms of atomic movements from MD is challenging and we have introduced a general method for obtaining effective normal modes of molecular systems from MD simulations. [Preview Abstract] |
Wednesday, March 18, 2009 10:48AM - 11:00AM |
P40.00015: Linear irreversible thermodynamics, efficiency and coefficient of performance of a thermal Brownian motor in tight coupling Mulugeta Bekele, Anteneh Getachew, Arun Jayannavar We analytically study a thermal Brownian motor and calculate the Onsager's coefficients near a \textit{finite} stall force in the spirit of recent development in non-equilibrium steady state thermodynamics. We show that the reciprocity relation holds and the determinant of the Onsager's matrix vanishes \textit{when heat leakage is neglected}. This condition implies that the device is built with tight coupling and hence Carnot's efficiency can be achieved for the quasi-static process. We also show that the efficiency at maximum power to be exactly half of Carnot's efficiency. Under similar condition we explore the coefficient of performance when our model works as a refrigerator. [Preview Abstract] |
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