Program Book

4047-P os B oard #B775 EFFECTS OF DIACYLGLYCEROLS (DAGS) AND ARACHIDONIC ACID (AA) ON THE PHYSICAL PROPERTIES OF MODEL LIPID BILAYERS: A MOLECULAR DYNAMICS SIMULATIONS STUDY. Ioannis Beis , Matti Weckström, André Juffer, Marja Hyvönen 4048-P os B oard #B776 MOLECULAR DYNAMICS SIMULATIONS OF COLLOIDS IN SINGLE SOLID-STATE NANOPORES. Nazar Ileri , Matthew Davenport, Sonia E. Letant, Joseph W. Tringe 4049-P os B oard #B777 EXPLORING DYNAMIC EVENTS OF BACTERIAL MICROCOMPARTMENT SHELL PORES. Sunny Chun , Jiyong Park, Michael C. Thompson, Changsun Eun, J Andrew McCammon, Kendall N. Houk, Todd O. Yeates 4050-P os B oard #B778 ALL-ATOMS MD SIMULATION OF PROTEIN TRANSLOCATION THROUGH α -HEMOLYSIN NANOPORE: IMPLICATIONS FOR PROTEIN SEQUENCE/STRUCTURAL ANALYSES. Daniele Di Marino , Anna Tramontano, Mauro Chinappi 4051-P os B oard #B779 COARSE-GRAINED MODELING OF DNA-VESICLE SYSTEMS WITH THE MARTINI FORCE FIELD. Jaakko Uusitalo , Helgi I. Ingólfsson, Parisa Akhshi, D. Peter Tieleman, Bert Poolman, Andreas Herrmann, Siewert J. Marrink 4052-P os B oard #B780 REFINEMENT OF MULTISITE ION MODEL THROUGH SIMULATION OF OSMOTIC PRESSURE: APPLICATIONS ON ION-MEDIATED CALCULATIONS OF SSRNA. Akansha Saxena , Angel E. Garcia 4053-P os B oard #B781 A MOLECULAR DYNAMICS SIMULATION STUDY ON THE EFFECT OF ENDOGENOUS MOLECULES ON SIRNA POLYPLEXES. Deniz Meneksedag , Tian Tang, Hasan Uludag 4054-P os B oard #B782 NOVEL COARSE-GRAINED MODEL FOR MOLECULAR DYNAMICS SIMULATIONS OF DNA. Aleksandra Karolak , Arjan van der Vaart 4055-P os B oard #B783 INVESTIGATING THE FOLDING DYNAMICS OF RNA PSEUDOKNOT STRUCTURAL MOTIF VIA MASSIVELY PARALLEL MOLECULAR DYNAMICS. Amethyst Radcliffe , Samantha Cao, Benjamin Pham, Phuc La, Richard Wang, Eric Sorin 4056-P os B oard #B784 HIERARCHICAL FOLDING OF THE RRNA IN THE EARLY ASSEMBLY OF THE E. COLI RIBOSOMAL SMALL SUBUNIT. Jonathan Lai , Ke Chen, Hajin Kim, Taejkip Ha, Zaida Luthey-Schulten  Computational Methods II (Boards #B785–#B816) 4057-P os B oard #B785 LIGAND BINDING PATHWAYS AND TRANSITIONS IN A GLUTAMATE RECEPTOR. Alvin Yu , Albert Lau 4058-P os B oard #B786 A THERMODYNAMIC DISCRIMINATION OF EFFICACY OF GPCR LIGANDS USING ABSOLUTE BINDING FREE ENERGY CALCULATIONS. Hui Sun Lee , Wonpil Im

4059-P os B oard #B787 SIMULATING CURRENT-VOLTAGE RELATIONSHIPS FOR A SIMPLE ION CHANNEL WITH ALL-ATOM RESOLUTION USING THE WEIGHTED ENSEMBLE METHOD. Joshua L. Adelman , Michael Grabe 4060-P os B oard #B788 PRINCIPAL COMPONENT ANALYSIS OF GLUTAMATE RECEPTOR LIGAND BINDING DOMAINS. John Belcher , Yongneng Yao, Anthony J. Berger, Mark L. Mayer, Albert Lau 4061-P os B oard #B789 QUANTITATIVE CHARACTERIZATION OF MEMBRANE PROTEIN-LIPID INTERACTIONS. Soohyung Park , Wonpil Im 4062-P os B oard #B790 EFFECT OF SEROTONIN ON MEMBRANES PROPERTIES STUDIED BY MOLECULAR DYNAMICS SIMULATIONS. Hubert Santuz, Slim Azouzi, Pascal Amireault, Catherine Etchebest 4063-P os B oard #B791 international travel awardee ANALYSIS OF MEMBRANE TRANSLOCATION SIMULATIONS USING DIMENSIONALITY REDUCTION. Begum Alaybeyoglu , Elif Ozkirimli 4064-P os B oard #B792 COMPUTATIONAL APPROACHES TO UNDERSTANDING THE ROLE OF OXIDIZED TRI-ACLYGLYCEROLS IN SUPPRESSION OF ANTIGEN CROSS-PRESENTATION IN CANCER. Dariush Mohammadyani , Vladimir A. Tyurin, Andrew A. Amoscato, Dmitry I. Gabrilovich, Judith Klein-Seetharaman, Valerian E. Kagan 4065-P os B oard #B793 A SOFTWARE PLATFORM FOR FINITE ELEMENT SIMULATION OF ION PERMEATION IN ION CHANNEL SYSTEMS. Benzhuo Lu 4066-P os B oard #B794 HETEROGENEITY OF THREADLIKE SHAPE OF DNA-STABI- LIZED SILVER FLUORESCENT CLUSTERS. Ruslan R. Ramazanov , Alexei I. Kononov 4067-P os B oard #B795 IN SILICO SINGLE-MOLECULE MANIPULATION OF CHROMATIN FIBRES WITH GAME ENGINES. Pascal Carrivain, Maria Barbi, Jean-Marc Victor 4068-P os B oard #B796 INTERPOLATION OF POTENTIAL ENERGY SURFACES FOR NONADIABATIC SIMULATIONS OF BIOLOGICAL SYSTEMS. Jae Woo Park , Young Min Rhee 4069-P os B oard #B797 MIXED QUANTUM-CLASSICAL STUDY OF THE NONADIABATIC DYNAMICS IN PHOTOSYNTHETIC SYSTEMS. Hyun Woo Kim , Young Min Rhee 4070-P os B oard #B798

COMPUTATIONAL STUDIES OF THE CATALYTIC MECHANISM OF THE STAPHYLOCOCCUS AUREUS SORTASE A ENZYME. Pooja Shrestha , Jeff Wereszczynski 4071-P os B oard #B799 INVESTIGATIONS OF MODEL PROTON-COUPLED ELECTRON TRANSFER REACTIONS FROM A MIXED QUANTUM-CLASSICAL LIOUVILLE PERSPECTIVE. Farnaz Shakib, Gabriel Hanna

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Biophysical Society 58 th Annual Meeting, San Francisco, California