Invited and Poster Abstracts 2009

Invited Presentations


Keynote Session

Daan Frenkel

The future of Simulation is not what it used to be

Berend Smit

Reverse Coarse Graining: Designing Materials that Work



Modeling and Simulation of Biological Systems 

David Baker

From Prediction of Structure to Design of Function

Charles Brooks

Constant pH Molecular Dynamics

Shaoyi Jiang

Molecular Understanding of Protein-surface Interactions



Linking Process Scale Simulation and Molecular Simulation

Linda Broadbelt

Discovery through Complex Reaction Networks

Dion Vlachos

Hierarchical Multiscale Modeling and Control of Nanomaterials



Simulating Rare Events

Baron Peters

Recent Advances in Path Sampling: Accurate Reaction Coordinates, Likelihood Maximization, and Diffusive Barrier Crossing Dynamics

Giovanni Ciccotti

Minimum Free Energy Path by the String Method

Phillip Geissler

Taming and Exploiting Chaos in Order to Effectively Simulate Long Trajectories



Soft Materials and Complex Fluids

J. Ilja Siepmann

Structure, Solvation, and Phase Equilibria in Hydrogen-bonding Systems

Clare McCabe

A Molecular Based Approach to Modeling Complex Fluids

Lev Gelb

Computational Studies of Capillary Phenomena: The Effects of Aerogel Compliance on Adsorptive Behavior



Industrial Applications of Simulation-Based Engineering and Science

Caroline Mellot-Draznieks

Simulation Strategies Versus Experiment in Hybrid Organic-Inorganic Frameworks

Shinichiro Nakamura

Contributions of Computational Science and Simulation in Industrial Research, Focusing on Two Recent Activities: Photonic Molecular Design and NMR Chemical Shift by FMO Method

Herve’ Toulhoat

Applications of DFT to a Better Understanding and Design of Industrial Catalysts in Refining and Petrochemistry


Future and Emerging Computer Architectures for Molecular Simulation: Towards Petascale Simulation

Klaus Schulten

Large-size, Long-time, Molecular Dynamics Simulations on a Budget

David Shaw

Millisecond-Long Molecular Dynamics Simulations of Proteins on the Anton Machine

George Karniadakis

Multiscale Modeling of the Human Arterial Tree



Poster Session I

Poster ID



Simulations of coarse-grained cellulose 1-beta

Antti-Pekka Hynninen, James F. Matthews, Michael F. Crowley, Mark R. Nimlos


Modelling the dissolution of cellulose in ionic liquids

Jussi Polvi, Tommi T. Jarvi, Emppu Salonen, Kai Nordlund


MD Simulations of Ionic Liquids: Relations Between Ion Tranport, Thermodynamics and Ion Size

Oleg Borodin


Static and dynamical properties of ionic liquids

T. Koishi and S. Fujikawa


Molecular Modeling of High and Low Temperature Molten Salts: Melting Points and Other Key Thermophysical Properties

Edward J. Maginn and Saivenkataraman Jayaraman


Modeling the effect of hydrogen bonding for understanding the dissolution of a-quartz surfaces in water

A.A. Skelton, D. J. Wesolowski and  P.T. Cummings


Novel Lubrication Schemes for Silicon-Based Microelectromechanical Devices

Ben Lewis, Jose L. Rivera, Oleg A. Mazyar, Steve Vilt, G. Kane Jennings and Clare McCabe


Molecular Dynamics Studies of Friction in Alkylsilane and Hydroxyalkylsilane Coated MEMs Devices

Jose L. Rivera, Oleg Mazyar, Ben Lewis, G. Kane Jennings and Clare McCabe


Molecular dynamics study for a novel AFM application

Dimitrios Argyris and Alberto Striolo


Dynamics and Energetics of Protein Adsorption Processes

Jason Hower, Yi He, and Shaoyi Jiang


Reversible stretching of a short peptide using parallel adaptive biasing force simulations

K. Minoukadeh, C. Chipot, T. Lelievre


Wetting transition of a nanocluster deposited on a solid surface

Kuniyasu Saitoh, Hisao Hayakawa


Molecular modeling of the cytochrome c on a gold surface

Magdalena Siwko


Molecular Simulation Studies of Low Friction and Biocompatible Zwitterionic Surfaces

Yi He, Rahul Bhowmik and Shaoyi Jiang


Simulation studies of the properties of lung surfactant monolayer-bilayer aggregates

Svetlana Baoukina and D. Peter Tieleman


Computational Simulations of Outer Membrane Proteins of Pseudomonas aeruginosa embedded in Lipopolysaccharide Membranes

Thereza A. Soares, Roberto D. Lins and T.P. Straatsma


Molecular dynamics study of lipid bilayer modeling plasma membrane of normal/leukemic lymphocytes

Yoshimichi Andoh and Susumu Okazaki


Designing Hypothesis of Some 2,4-disubstituted-phenoxy acetic acid derivatives as a CRTH2 Receptor Antagonist: A QSAR Approach

Abhishek Jain, R. K. Agrawal


Algorithmic enhancements to boost the performance of general purpose molecular dynamics on data-parallel architectures

Joshua A. Anderson


Development of numerical integration scheme and application to molecular dynamics simulations

Ikuo Fukuda, Severine Queyroy, and Haruki Nakamura


The self-referential method for calculating crystal free energies

Martin Sweatman


Using an Ensemble of Surrogate Process Approximations (SPAs) to Assist Computing Quantities Depending on Rare Events

Christopher P. Calderon


Collective variables in finding transition pathways

Ruijun Zhao


Modelling beyond manual intervention -- Approach routes to a most useful molecular description

Astrid Maaß, Marco Huelsmann, Thorsten Koeddermann, Dirk Reith


ESPResSo++: Extensible Simulation Package for Research on Soft matter

J. Halverson, A. Arnold, T. Brandes, O. Lenz, D. Reith, A. Schueller, and T. Stuehn


Optimizing Monte Carlo Simulations by Using Transition Probability Data

Charlles R. A. Abreu


Steady-state simulations of homogeneous vapor to liquid nucleation in the grand canonical ensemble "by the intervention of intelligent beings"

Martin Horsch and Jadran Vrabec


Molasses Tail in Two Dimensions

M. Isobe and B. J. Alder


Support Effects on the Catalytic Properties of Pt-Au Bimetallic Nanoparticles: A Multi-Scale Simulation Study

Brian Morrow and Alberto Striolo


A simple potential for graphene-fluid interactions

Xiongce Zhao


Graphene Sheets-Oil Nanocomposites: Equilibrium and Transport Properties from Molecular Simulation

Deepthi Konatham and Alberto Striolo


Atomistic Simulations of CO2 and N2 Diffusion in Siliceous Zeolites

David Selassie, Colin Russell, Henry Heitzer, Lindsey Madison and Daniela Kohen


The Role of Cation Identity and Adsorbate Orientation on the Selective Adsorption of p-Xylene in Faujasite Zeolites

Allison Dickey, David Dubbeldam, John J. Low, Randall Q. Snurr


Investigation of Metal Sites within Metal-Organic Frameworks for Oxidation Catalysis

Patrick Ryan, Linda J. Broadbelt, and Randall Q. Snurr


Pore wall thickness heterogeneity on adsorption in carbons using explicit slit pore model and biased GCMC

Sebastiao M. P. Lucena, Luis F. A. Frutuoso, Pedro F. G. Silvino  and Celio L. Cavalcante Jr.


A molecular simulation study of competitive adsorption of carbon dioxide, propane and butane in porous silica

Sergey M. Melnikov and Andreas Seidel-Morgenstern


Porous Carbon Characterization Experiment and Theory: Top Down and Bottom Up

Alex Balboa, Margaret M. Hurley, John K. Brennan, Keith E. Gubbins, and Jeremy Palmer


Modelling gas adsorption on zeolite-like metal organic frameworks

Javier Perez-Pellitero, Hedi Amrouche, Flor Sipertstein, Carlos Nieto-Draghi, G. Pirngruber, Eric Llido, Sandrine Carl, Delphine Bazer-Bachi, and Nicolas Bats


Evaluation of the BET Method for Determining Surface Areas of Ultra-Microporous MOFs and Zeolites

Youn-Sang Bae, A. Ozgur Yazayd?n, and Randall Q. Snurr


Analysis of Diffusion and Reaction in the Alkylation of Benzene over H-ZSM-5 by Combining Quantum Chemical Calculations, Molecular Simulations and a Continuum  Approach

Niels Hansen, Till Bruggemann, Rajamani Krishna, Frerich J. Keil, Alexis T. Bell


A comparison of DFT calculations and experiments for the rate of a Menschutkin reaction in several solvents

H. Strübing, D. Willitts, P. Karamertzanis, A. Galindo, D. G. Blackmond, E. N. Pistikopoulos, C. S. Adjiman


Stability of non-covalent interactions involving aromatic residues in protein structures: Comparison with conventional hydrogen bonds using molecular dynamics simulations

Alok Jain and Ramasubbu Sankararamakrishnan


Hydrogen abstraction from hydrocarbons: modeling of activation energies and pre-exponential factors

Maarten K. Sabbe, Aaron G. Vandeputte, Marie-Françoise Reyniers, Michel Waroquier, and Guy B. Marin


Ionic Hydration from Born-Oppenheimer Molecular Dynamics Simulations of Clusters

Nuno Galamba


Ab initio modeling of the elementary reactions during thermal decomposition of polysulfides

Aaron G. Vandeputte, Marie-Francoise Reyniers and Guy B. Marin


Thermodynamics and Kinetics of in situ Nitroxide Mediated Polymerization

L. Bentein, M.-F. Reyniers, G.B. Marin


Origins of Autoacceleration in L-proline-assisted Aldol-type Reactions

Ivan A Konstantinov and Linda J. Broadbelt


Applying Computational Quantum Chemistry to Devise a Reaction Mechanism for Use of Morpholine, a Surrogate Biofuel

Phillip R. Westmoreland and Nicole Labbe


Simulation of chemical reaction by the generalized ensemble method

Takehiro Nagasima, Tomoyuki Kinjo, Shi-aki Hyodo


Model Order Reduction and Compressive Sampling

John Sidles


Poster Session II

Poster ID



Bulk and Interfacial Behavior in Polymer-Nanoparticle Melts

Amalie Frischknecht


Entropy stabilized quasicrystalline-like arrangements of spherical micelles

Christopher R. Iacovella, Aaron S. Keys and Sharon C. Glotzer


Molecular dynamics simulation study of the role of nanometer scale structure on interfacial energy

Hao Jiang, Chetana Singh, Pradip K. Ghorai, Jeffrey J. Kuna, Kislon Voitchovsky, Steve Mwenifumbo, Molly M. Stevens, Francesco Stellacci, and Sharon C. Glotzer


SDS Surfactants on Carbon Nanotubes: Aggregate Morphology

Naga Rajesh Tummala and Alberto Striolo


A Molecular Dynamics Study of SDS and C12E6 Surfactants at the Silica-Water and Air-Water Interfaces

Liu Shi, Naga Rajesh Tummala, and Alberto Striolo


Free energy based molecular dynamics study of a spherical micelle - structural stability and solubilization by it

K. Fujimoto, M. Kitabata, N. Yoshii, and S. Okazaki


Characterizing Structure in Particle Systems Using Shape-Matching

Aaron S. Keys, Christopher R. Iacovella and Sharon C. Glotzer


Monte Carlo Simulation of Dense Packings of Hard Tetrahedra

Amir Haji-Akbari, Michael Engel, Aaron S Keys, Xiaoyu Zhang, Rolfe Petschek, Peter Palffy-Muhoray, Sharon C Glotzer


Structure and reactivity of Iron Oxide Nanoparticles

Cynthia Lo


Ordering of Nanoparticles Mediated by End-Functionalized Triblock Copolymers

Rastko Sknepnek, Joshua A. Anderson, Monica H. Lamm, Joerg Schmalian, and Alex Travesset


The Impact of Polydispsersity on the Tethereed Nanosphere Phase Diagram

Carolyn L. Phillips, Christopher R. Iacovella and Sharon C. Glotzer


A new method for developing design strategies for patchy particle self-assembly

Eric Jankowski and Sharon C. Glotzer


Entropic Stabilization of Superstructures with Isotropic Particles

Michael Engel


Liquid State Theory of the Structure and Phase Behavior of Polymer-Tethered Nanoparticles in Dense Suspensions, Melts and Nanocomposites

Arthi Jayaraman


Simulations of the self-assembly of CdTe nanoparticles into large pitch helices

Aaron T. Santos, Sudhanshu Srivastava, Nicholas A. Kotov, and Sharon C. Glotzer


Ordered striped patterns on nanocylinders: A simulation study

Chetana Singh and Sharon C. Glotzer


Assembly of Binary Colloidal Crystals

S. Teich-McGoldrick, J. Kieffer, M.J. Solomon, S. C. Glotzer


Millisecond Time-scale Ligand (Un)binding Event Studied using Accelerated Molecular Dynamics Simulations

Harish Vashisth and Cameron F. Abrams


Molecular simulations of organically modified clays. The cut-sphere model and electrostatics.

Rui P. S. Fartaria and Martin B. Sweatman


Towards developing Mesoscale Models for Organic and Bioorganic Polymers. A Case Study on PMMA and Carbohydrate Polymers

Karl N. Kirschner, Kathrin Heikamp, Dirk Reith, and Astrid Maaß


Mesoscale Modeling of Thermo-Mechanical Response: Constant-Energy Dissipative Particle Dynamics Simulations

John K. Brennan and Martin Lisal


Mulholland Dr. Multiscale molecular modeling of the self-assembly of di/triblock copolymers for drug delivery

Paola Posocco, Maurizio Fermeglia and Sabrina Pricl


A Computationally Efficient Algorithm for Accurate Local Energy Minimization of Crystal Structures Containing Flexible Molecules

A.V. Kazantsev, P.G. Karamertzanis, C.S. Adjiman, C.C. Pantelides


Computational Prediction of Effects of Pressure on Organic Crystal Structure

A.V. Kazantsev, P.G. Karamertzanis, C.S. Adjiman, C.C. Pantelides


Thermodynamic Modeling of the Adsorption of Boric Acid on Fuel Crud Deposit from the Pressurized Water Reactors

Honggang Zhao


A Force Field with Complete Coverage

Huai Sun


A biased Gibbs Ensemble Monte Carlo (GEMC) simulation technique for prediction of vapor liquid equilibria of all atom linear, branched and cyclic molecules with fixed bond length constraints

Jindal K. Shah, Edward J. Maginn


Evaluation of criticality from molecular models using the virial equation of state

Andrew J. Schultz, Katherine R. Schadel, Hye Min Kim, and David A. Kofke


Topological Modeling of Proton Hopping on Hydrogen Bond Network in Liquid Water

Masaomi Hatakeyama, Tomoyuki Kinjo, Shiaki Hyodo.


Accurate Kirkwood-Buff Integrals from Molecular Dynamics Simulations

R. Wedberg, J.P. O'Connell, G.H. Peters, J. Abildskov


Prediction of the fluid phase behavior of the quaternary system ethylene oxide + air by molecular simulation

Yow-Lin Huang, JungHan Kim, Gerhard Herres, and Jadran Vrabec


Computer simulation study of nematic nanodroplets

J. M. Romero-Enrique, L. F. Rull, and A. Fernandez-Nieves


Critical properties of fluids in nanopores: Crossover from 3D to 2D

Jayant K. Singh


Comparison of Wall Models' Effects on Liquid Nanoflows in Planar and Cylindrical Geometries. Application to Nanoinjection.

Nadia Sellami and Dr. Michael M. Micci


Compelling evidence for fluid-solid transition of nanoconfined fluids

Hugh Docherty and Peter T. Cummings


Simulations of Slow Dynamic Processes in Nanoconfined Aqueous Solutions

Lukas Vlcek, Eugene Mamontov, David R. Cole, David J. Wesolowski, and Peter T. Cummings


Monte Carlo simulation of interfacial properties of water and carbon dioxide under confinement

J. M. Miguez, D. Gonzalez-Salgado, J. L. Legido, M. M. Pineiro


Path Sampling Calculation of Methane Diffusivity in Natural Gas Hydrates

Baron Peters, Nils E.R.Zimmermann, Gregg T. Beckham, Jeff W. Tester, and B. L. Trout


Utilization of Molecular Simulations in Aerospace Materials: Molecular Dynamics Simulations of Thermoset Resins

Andrea Robben


Novel Hydrogen-rich Crystalline Compounds for Hydrogen Storage

Maaike C. Kroon, Hugh Docherty, Peter T. Cummings, Cor J. Peters, Geert-Jan Witkamp and Wendy L. Mao


Discontinuous Molecular Simulations for Computing Excess Entropy of Polymer Solutions

Amir Vahid,  Neil H. Gray,  and J. Richard Elliott


Modeling the Folding and Hydrogen Production of Clostridium Acetobutylicum and Clostridium Saccharobutylium Mutants Using Electrostatic Potential Surfaces and Molecular Dynamics

Mark A. Plummer and Scott M. Plummer


The Sound of Silence. Computational/Experimental Investigations of Dendrimer-Based siRNA/DNA Delivery Systems

Sabrina Pricl, Paola Posocco, Giovanni Maria Pavan, Maurizio Fermeglia, Giulio Scocchi1, Anastasia Malek, Marek Maly, Andrea Danani, Carlo Catapano, Ling Peng, Dave K. Smith


Amino acid co-evolution: Evolutive restriction of the structure and function of plant profilin.

Lucio Montero Valenzuela, Gabriel Guillen, Federico Sanchez.


Velocity inversion in a cylindrical Couette flow

Sangrak Kim


Intelligent Design of Energetic Materials

Margaret Hurley


Rational Organic Semiconductors Materials Design One Screensaver at a Time

Roel S. Sanchez-Carrera, Joshua Schrier, Sule Atahan, Leslie Vogt, Roberto Amaya-Olivares, and Alan Aspuru-Guzik


Atomistic Modeling of Tin Surface and Grain Boundary Diffusion

Michael S. Sellers, Andrew J. Schultz, Cemal Basaran, and David A. Kofke


Simulation of Epitaxial Regrowth of Doped Silicon

Scott Dunham, Haoyu Lai, Joo-Chul Yoon

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