oksupercompsymp2006 talk tummala

Information about oksupercompsymp2006 talk tummala

Published on December 30, 2007

Author: Sabatini

Source: authorstream.com

Content

Molecular Dynamics Study of Aqueous Solutions in Heterogeneous Environments: Water Traces in Organic Media:  Molecular Dynamics Study of Aqueous Solutions in Heterogeneous Environments: Water Traces in Organic Media Naga Rajesh Tummala and Alberto Striolo School of Chemical, Biological and Materials Engineering University of Oklahoma OUTLINE :  Importance of confined water Experiments used to study confined water Motivation for doing simulations Simulation details Findings from simulation study OUTLINE CONFINED WATER:  CONFINED WATER Where do we find ? protein hydration various biochemical processes ionic channels Differences we expect compared to bulk water Slow hydrogen bond dynamics (time scales ?) Slow reorientation times 1 http://www.lsbu.ac.uk/water/protein.html Experiments:  Experiments Femto second mid-infrared pump-probe measurements Water in Dimethylsulfoxide Water in acetone/carbon tetrachloride Vibrational Echo Spectroscopy for HOD in H2O Ultra-fast Infrared Spectroscopy to study OH stretch vibration of HOD/H2O in D2O FTIR spectroscopy to study hydroxyl and librational modes of confined water in reverse micelles Output of experiments is usually a spectra, and in most cases it is absorbance VS frequency, and dynamics are studied from the absorbance VS delay (signal) Approachable time scales: Generally pico (10-12) seconds Sometimes 50-100 femto (10-15) seconds depending upon the duration of probe pulses. Slide5:  Experiments with small traces of water in heterogeneous organic solutions.2 (1:10:40) ratio of water, acetone and carbon tetrachloride Assuming that water disperses homogenously in solution 2 Dynamics of confined water molecules, Gilijamse et al, PNAS 2005, 102, 3202-3207 Typical output from femto second mid-infrared pump-probe measurements2:  Typical output from femto second mid-infrared pump-probe measurements2 Absorbance VS frequency ln(T/To) VS delay Experimentally it was found that the energy transfer in confined water is more than 20 times slower than bulk water MOTIVATION:  MOTIVATION To answer following questions Do traces of water completely disperse in acetone/carbon tetrachloride system ? Influence of water-water hydrogen bonds on dynamics of trapped water ? Influence of water-acetone hydrogen bonds on dynamics of confined water ? Molecular Dynamics:  Molecular Dynamics Solving time dependent Newton’s equations of motion of all the particles in the system. We use LAMMPS (Large-scale Atomic/Molecular Massively Parallel Simulator ) developed by Steve Plimpton and his group of Sandia National Laboratories1. LAMMPS employs spatial decomposition to load balance on the number of processors used. Forces Computed: Inter-molecular (Van der Waal’s forces, Coulombic forces) Intra-molecular (bond, angle, dihedral and improper forces) 1 “Large-scale Atomic/Molecular Massively Parallel Simulator” , “Fast Parallel Algorithms for Short- Range Molecular Dynamics”, S. J. Plimpton, J. Comp. Phys. 1995, 117, 1-19 . http://www.cs.sandia.gov/~sjplimp/lammps.html Simulation Details:  Simulation Details Water modeled with extended simple point charge (SPC/E) potential. Carbon tetrachloride with a fully flexible, non-polarizable five site model. Acetone was modeled using united atom for methyl atoms and carbonyl (-C=O) group was explicitly modeled. Ratio of water : acetone : carbon tetrachloride was maintained at 1:10:40 to mimic experimental conditions. Initially 12 water molecules are used and all molecules were placed in a lattice. ‘H’, effectively zero radius and charge of + 0.4238 each ‘O’, Radius of 3.166 Ao and charge of -0.8476 Slide10:  1 ns at 1000 K Cooling at 100 K every 300 ps Equilibration for 1.5 ns at 300 K NVT (constant (# of atoms, volume and temperature)) simulation NPT (constant (# of atoms, pressure and temperature)) simulation Simulation box replicated twice in X,Y and Z directions Equilibration for 375 ps at 300 K Production phase for 300 ps at 300 K with output every 100 fs for only water and acetone time step 1 fs SIMULATION METHODOLOGY (1:10:40) Energy Curve ( indication to equilibrium):  Energy Curve ( indication to equilibrium) Transformation from NVT to NPT ensemble with 12 water molecules in simulation box:  Transformation from NVT to NPT ensemble with 12 water molecules in simulation box Movie of 96 water molecules in the simulation box:  Movie of 96 water molecules in the simulation box Computational Expenses:  Computational Expenses System with 12 water molecules takes ~8 hrs on 20 processors to simulate 300ps (2916 atoms) System with 96 water molecules takes ~2days on 80 processors to simulate 300 ps (23328 atoms) Performance comparison of “SEABORG” and “TOPDAWG”:  Performance comparison of “SEABORG” and “TOPDAWG” Results: I. Equilibrium structure:  Results: I. Equilibrium structure Population distribution of cluster sizes at 300 K Visualization of temporal breaking and forming of H-bonds:  Visualization of temporal breaking and forming of H-bonds Slide18:  Probability P for one water molecule of being hydrogen bonded to nw water molecules and na acetone molecules Slide19:  Probability (P) of finding the water molecule hydrogen bonded to ‘na’ acetone molecules within the system of molecular composition (1:120:480). Results II. Hydrogen Bond Dynamics:  Results II. Hydrogen Bond Dynamics Intermittent auto correlation functions for water-acetone hydrogen bonds. HB ACF OH-reorientational dynamics:  OH-reorientational dynamics OH reorientation ACF Pl is the legendre polynomial of order l OH-reorientation ACF Relaxation time constants:  Relaxation time constants ** * @ experimental value is 1.33 ps Conclusions:  Conclusions Do traces of water completely disperse in acetone/carbon tetrachloride system ? NO Influence of water-water hydrogen bonds on dynamics of trapped water. MORE RESPONSIBLE FOR SLOW DYNAMICS Influence of water-acetone hydrogen bonds on dynamics of confined water. ~ EQUIVALENT TO BULK WATER We cannot neglect water-water hydrogen bonds which are responsible for slow dynamics of trapped water. Acknowledgements:  Acknowledgements Dr. Henry Neeman OSCER, University of Oklahoma NERSC, Berkeley, CA Oklahoma State Reagents for Higher Education Department of Energy QUESTIONS ? :  QUESTIONS ?

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