'Md simulations' diaporamas de présentation

Basics of molecular dynamics simulations

Reduction of the quantum problem to a classical one Parameterization of force fields Boundaries, energy minimization, integration algorithms Analysis of trajectory data Lecture notes are at : www.physics.usyd.edu.au/~serdar/ws. Basics of molecular dynamics simulations.

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V5: Exploring energy landscapes for protein folding: by all-atom MD simulations

V5: Exploring energy landscapes for protein folding: by all-atom MD simulations. The folded state. How do you characterize the folded state of a protein?. Combining experiment with simulations.

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First-principle MD studies on the reaction pathways at T=0K and at finite temperatures

First-principle MD studies on the reaction pathways at T=0K and at finite temperatures. Artur Michalak a,b and Tom Ziegler a a Department of Chemistry, University of Calgary, Calgary, Alberta, Canada b Department of Theoretical Chemistry Jagiellonian University Cracow, Poland.

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Structure and function of transporters from molecular dynamics simulations Serdar Kuyucak

Structure and function of transporters from molecular dynamics simulations Serdar Kuyucak University of Sydney. Transporter families. Two major families: Primary active transporters use the energy from ATP (e.g. Na-K pump, ABC transporters)

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Statistical Mechanics of Proteins

Statistical Mechanics of Proteins. Ioan Kosztin. Department of Physics & Astronomy University of Missouri - Columbia. Equilibrium and non-equilibrium properties of proteins Free diffusion of proteins Coherent motion in proteins: temperature echoes Simulated cooling of proteins.

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Molecular Dynamics

Molecular Dynamics.

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Applications of relative free energy calculations

Relative free energies are useful in two contexts: 1. Calculation of the free energy of binding of a ligand relative to bulk. This is the most common application. The simplest examples are binding of ions. As the ligand gets more complex, it becomes less accurate.

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De sktop G rids for I nternational S cientific Co llaboration

De sktop G rids for I nternational S cientific Co llaboration. APPLICATION OF DESKTOP GRID TECHNOLOGY IN MATERIAL SCIENCE. A.Gatsenko , A.Baskova , Yu.Gordienko G.V.Kurdyumov Institute for Metal Physics, National Academy of Sciences of Ukraine, Kiev, Ukraine.

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Rare events: classical and quantum

Rare events: classical and quantum. Roberto Car, Princeton University. Croucher ASI, Hong Kong, Dec. 9 2005. Reaction Pathways. FPMD simulations are currently limited to time scales of tens of ps

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Giant fluctuations at a granular phase separation threshold

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Sumanth J.V, David R. Swanson and Hong Jiang University of Nebraska-Lincoln

Scheduling Many-Body Short Range MD Simulations on a Cluster of Workstations and Custom VLSI Hardware. Sumanth J.V, David R. Swanson and Hong Jiang University of Nebraska-Lincoln. We thank ONR, RCF and SDI(NSF 0091900) for funding this research and

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Cholesterol Structure in Lipid Rafts

Cholesterol Structure in Lipid Rafts. Laura Toppozini CAP Congress 2014 June 19, 2014. Cholesterol in Lipid Membranes. Mosaic model: Lipids, cholesterol, and proteins homogeneously mixed. Singer and Nicholson, 1972. Lipid raft model: Cholesterol-rich domains. Simons, 1997.

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Molecular Dynamics simulations

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(d)

Catalyzed Nucleation and Growth of Semiconductor Nanowires Wei Cai , Stanford University, DMR 0907642.

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Introduction

Steven Neshyba 1 *, Will Pfalzgraff 1,2 , and Martina Roeselova 2 1 University of Puget Sound, Tacoma, WA 2 Institute of Organic Chemistry and Biochemistry, Prague, Czech Republic. *nesh@pugetsound.edu. Introduction

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Proteins in Bionanotechnology Computational Studies

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REFERENCES [1] S. A. Hassan, F. Guarnieri and E. L. Mehler, J. Phys. Chem. 104 , 6478 (2000)

A FAST AND GENERAL CONTINUUM APPROACH FOR DESCRIBING ELECTROSTATIC EFFECTS IN MOLECULAR DYNAMICS SIMULATIONS OF BIOMOLECULES. Sergio A. Hassan , Daqun Zhang, Ernest L. Mehler and Harel Weinstein, Department of Physiology and Biophysics, Mount Sinai School of Medicine, New York, New York 10029.

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