Chemical Computing Group Excellence Award for Graduate Students

Up to Five $1,150 Chemical Computing Group Excellence Student Travel Award Stipends Available for the ACS National Meeting

Chemical Computing Group, Inc. (CCG) Research Excellence student travel award stipends are available for the Fall 2024  ACS National Meeting. The CCG Excellence Awards have been created to stimulate graduate student participation in ACS COMP Division activities (symposia and poster sessions) at ACS National Meetings. Those eligible for a CCG Excellence Award are graduate students in good standing who present work within the COMP program. Winners receive $1,150 to apply toward their travel expenses, as well as a copy of CCG's MOE (Molecular Operating Environment) software with a one-year license. They are also honored during a ceremony at the meeting.

Up to 5 awardees will be chosen on the basis of the quality and significance of the research to be presented, as well as the strength of the supporting letter and other materials. All graduate students of the Americas (North, South or Central) are encouraged to submit applications. Awards will be given only to those individuals making presentations, not co-authors. There is a limit of one CCG award application per research lab (PI). Previous winners of an ACS CCG graduate student award (given by any division) are not eligible to apply. Applicants must be a current member of the ACS COMP Division, see the Join COMP page.

To apply for an award for the Fall ACS National Meeting in Washington, DC, do the following: 

1. Submit your abstract to the "CCG Poster Session" symposium on the ACS MAPS system.  For this meeting, the award presentations will be held as poster presentations. Check the ACS MAPS deadline in case it is earlier than the COMP awards deadline. Abstracts cannot be submitted to ACS MAPS after the ACS deadline.

2. Fill out the application form (CLICK HERE) , which also explains how to submit a single pdf document containing the following items:  title, authors/affiliations and extended abstract of the work (no more than 2 pages), a 1-2 page CV, and a 1-page personal statement. Please ensure that your list of publications in your CV includes only peer-reviewed articles that have been accepted or published. If you wish to include manuscripts in preparation or under review, you must create a separate section of your CV. Likewise, presentations and non-reviewed publications should be included in separate sections.

3. Have your research mentor submit a letter of recommendation (see the form for details).

The deadline for completing both of these items 11:59 PM March 31, 2025, Time Zone AoE. 

Posters not selected for the CCG Excellence Award for Graduate Students will automatically be placed in to the regular COMP Poster Session. 

For additional information, contact:

ACS COMP Division Awards Committee

acs.comp.awards_AT_gmail.com

The Spring 2025 Winners 

1. Lexin Chen; Department of Chemistry, University of Florida, USA; Ramon Miranda Quintana, mentor; MDANCE: flexible and versatile n-ary clustering package

2. Anika Friedman; Chemical and Biological Engineering, University of Colorado Boulder, USA; Michael Shirts, mentor; Analysis of the Conformational Ensemble and Free Energy Landscape of Flexible Protein Complexes

3. Robert Lavroff; Department of Chemistry and Biochemistry, University of California, Los Angeles, USA; Anastassia Alexandrova, mentor; Aperiodic fragments in periodic solids: Achieving the thermodynamic limit of solid-state defect calculations with hundreds to thousands times speedup

4. Jiashu Liang; Department of Chemistry, University of California, Berkeley, USA; Martin Head-Gordon, mentor; Gold-Standard Chemical Database (GSCDB138) and Carefully Optimized and Appropriately Constrained (COAC) Hybrid Density Functional

5. Qianzhen Shao; Department of Chemistry, Vanderbilt University, USA; Zhongyue J. Yang, mentor; EnzyHTP: High-throughput enzyme modeling platform enables new ways to understand and engineer enzymes

The Fall 2024 Winners 

1. Montgomery Gray; Ohio State University, Department of Chemistry and Biochemistry; John M. Herbert, mentor; Using quantum mechanics to understand noncovalent interactions

2. David Kastner; Massachusetts Institute of Technology, Department of Chemical Engineering; Heather Kulik, mentor; Blueprints of C-H Bond Activation Across Iron-Containing High-Valent Metalloenzymes

3.  Jordy Homing Lam; University of Southern California, Department of Computational Biology and Bioinformatics; Vsevolod Katritch, mentor; Anisotropic Vibrational Modes in Biomolecules with Millions of Atoms

4. Xuenan Mi; University of Illinois Urbana-Champaign, Center for Biophysics and Quantitative Biology; Diwakar Shukla, mentor; Computational Characterization of Substrate Preferences of RiPP Biosynthetic Enzymes

5. Ernest Opoku; Auburn University, Department of Chemistry and Biochemistry; J. V. Ortiz, mentor; Novel Electron-Propagator Methods for Computing Molecular Electron-Binding Energies and Dyson Orbitals

Previous Winners: Chemical Computing Group Excellence Award for Graduate Students 

The Fall 2021 Winners 

Isuru Ariyarathna, Auburn University; Department of Chemistry and Biochemistry; Evangelos Miliordos, mentor

Ground and excited electronic structures of metal-ammonia superatoms and how to design novel 2D– and 3D–materials from them

Matthew Du, University of California, San Diego; Department of Chemistry and Biochemistry; Joel Yuen-Zhou, mentor

Nonequilibrium models for thermally activated electron transfer under vibrational strong coupling

Croix Laconsay, University of California, Davis; Department of Chemistry; Dean Tantillo, mentor

Mechanistic Interrogation of Reactions Involving Dirhodium Complexes: Effects of Solvent Coordination

Arkajit Mandal, University of Rochester; Department of Chemistry; Pengfei Huo, mentor

On-the-fly Quantum Dynamics Simulation with Quasi-Diabatic Propagation Scheme

Hannah Wayment-Steele, Stanford University; Department of Chemistry; Rhiju Das, mentor

Stabilizing mRNA therapeutics through computational design

The Spring 2021 Winners 

Sarah Alamdari

University of Washington, Chemical Engineering; Jim Pfaendtner, mentor

Detailed Exploration of Peptoid Folding Thermodynamics with Metadynamics

Marcos Felipe Calegari Andrade

Princeton University, Chemistry Department; Annabella Selloni, mentor

Free Energy of Proton Transfer at the Water-TiO2 Interface from Ab Initio Deep Potential Molecular Dynamics

Kevin Carter-Fenk

The Ohio State University, Department of Chemistry and Biochemistry; John Herbert, mentor

Building an Alternative to the Hunter-Sanders Model of π-π Interactions

Yeongsu Cho

Columbia University, Department of Chemistry; Timothy Berkelbach, mentor

Optical Properties of the Layered Perovskites Derived from Properties of the Bulk Perovskites

Rimsha Mehmood

Massachusetts Institute of Technology, Department of Chemistry; Heather J. Kulik, mentor

Revealing Substrate Positioning Dynamics in Non-Heme Fe(II)/Alpha-Ketoglutarate Dependent Halogenases Through Spectroscopically-Guided Simulation

The Fall 2020 Winners (Virtual Meeting)

Julia Rogers, University of California Berkeley, Department of Chemistry (Phillip Geissler advisor), Constructing a framework to understand the molecular mechanisms of lipid transfer proteins using simulation and theory

Justin Seffernick, Ohio State University, Department of Chemistry and Biochemistry (Steffen Lindert advisor), Computational prediction of protein complex structure using data from surface-induced dissociation and cryo-electron microscopy

Nandhini Rajagopal, Syracuse University, Department of Biomedical and Chemical Engineering (Shikha Nangia advisor), Generating Potential Energy Landscapes for Membrane Proteins

Jiangyan Feng, University of Illinois at Urbana-Champaign, Department of Chemical and Biomolecular Engineering (Diwakar Shukla advisor), Predicting protein alternative conformations using machine learning and coevolution

Luis Angel Martinez Martinez, University of California San Diego, Department of Chemistry and Biochemistry (Joel Yuen-Zhou advisor), Variational open-quantum-system description of electroluminescence in the polariton regime.

The Spring 2020 Winners (Philadelphia, PA)

Alex Chew, Department of Chemical and Biological Engineering, University of Wisconsin-Madison. Adviser: Reid C. Van Lehn, "Solvent Screening for Biomass Conversion Reactions Using Molecular Dynamics Simulations"

Phillip Hudson, Department of Chemistry, University of South Florida and Laboratory of Computational Biology, National Heart, Lung and Blood Institute, National Institutes of Health. Adviser: H. Lee Woodcock, "Failure of the Interaction Energy Approximation"

Ga Young Lee, Department of Chemistry and Biochemistry, University of California, Los Angeles. Advisers: Ken Houk and Ellen M. Sletten, "Investigating Arene-perfluoroarene Interactions in Solution using Computation and Experiment"

Viki Prasad, Department of Chemistry, The University of British Columbia. Adviser: Gino A. DiLabio, "Fast and accurate electronic structure modeling of large molecular systems using atom-centered potentials"

Yuan Liu, Department of Chemistry, Brown University. Adviser: Brenda Rubenstein,, "Probing Metal-Insulator Phase Transitions in Realistic Solids via Ab Initio Finite Temperature Auxiliary Field Quantum Monte Carlo"

The Fall 2019 Winners (San Diego, CA)

Ruijie Darius Teo, Duke University, Department of Chemistry (David N. Beratan, advisor), Unraveling functional hole hopping pathways in the [4Fe4S]-containing DNA primase

Diptarka Hait, University of California, Berkeley, Department of Chemistry (Martin Head-Gordon, advisor), Development of excited state quantum chemistry methods capable of describing photodissociation of single bonds

Jon Paul Janet, Massachusetts Institute of Technology, Department of Chemical Engineering (Heather Kulik, advisor), Multifidelity methods for the design of transition metal complexes

Kalli Kappel, Stanford University, Biophysics Program (Rhiju Das, advisor), Rapid RNA structure determination through cryo-EM, high-throughput biochemistry, and computational modeling

Jaehyeok Jin, University of Chicago, Department of Chemistry (Gregory A. Voth, advisor), High Fidelity Ultra-Coarse-Graining of Soft Matter Systems

The Spring 2019 Winners (Orlando, FL)

Vinicius Cruzeiro, University of Florida, Department of Chemistry (Adrian E. Roitberg, advisor), GPU-accelerated constant pH and redox potential molecular dynamics with multidimensional replica exchange simulations in Amber

Ryan DeFever, Clemson University, Department of Chemical and Biomolecular Engineering (Sapna Sarupria, advisor), Rare events in complex systems: Methods and applications

Hongxia Hao,  Brown University, Department of Chemistry (Brenda M. Rubenstein, advisor), Accurate predictions of electron binding energies of dipole-bound anions via Quantum Monte Carlo methods

Joonho Lee,  University of California, Berkeley, Department of Chemistry (Martin P. Head-Gordon, advisor), Open-Shell Coupled-Cluster Valence-Bond Theory Augmented with an Independent Amplitude Approximation for Three-Pair Correlations: Application to a Model Oxygen-Evolving Complex and Single Molecular Magnet

Fang-Yu Lin, University of Maryland School of Pharmacy, Department of Pharmaceutical Sciences (Alexander D. MacKerell, advisor), Optimization of the Drude Polarizable Protein Force Field

The Fall 2018 Winners (Boston, MA)

Gabriel dos Passos Gomes (Igor V. Alabugin, advisor); Florida State University; Department of Chemistry and Biochemistry, ”Drawing Catalytic Power from Charge Separation: Stereoelectronic and Zwitterionic Assistance in the Au(I)-Catalyzed Bergman Cyclization”

Victor Fung (De-en Jiang, advisor); University of California, Riverside; Department of Chemistry, ”The nature of oxygen-adsorbate chemical bonding on transition metal oxides”

Rajat Maji (Steven E Wheeler, advisor); Texas A&M University; Department of Chemistry, “Importance of Electrostatic effects in the stereoselectivity of NHC-Catalyzed Kinetic Resolutions”

Qing Zhao (Heather J. Kulik, advisor); Massachusetts Institute of Technology, Department of Chemical Engineering, Mechanical Engineering ; “Density localization and scaling relations in the solid state: Understanding divergent behavior for hybrids and DFT+U”

Hongyu Zhou (Peng Tao, advisor); Southern Methodist University; Department of Chemistry, “Unravel protein allostery mechanism” 

The Spring 2018 Winners (New Orleans, LA)

Stephanie Hare (Dean J. Tantillo, advisor), University of California Davis, Chemistry, A Pummerer-Like Rearrangement: Effects of Solvent on a Post-Transition State Bifurcation 

John Karnes (Ilan Benjamin, advisor), University of California, Santa Cruz, Chemistry and Biochemistry, Mixing oil and water: The thermodynamics and mechanism of water transferring into oil 

Michiel Niesen (Thomas F. Miller III, advisor), California Institute of Technology, Chemistry & Chemical Engineering, Forces on nascent polypeptides during membrane insertion and translocation via the Sec translocon

Alice Walker (G. Andres Cisneros, advisor), University of North Texas, Chemistry, Unfolding pathways of hen egg white lysozyme in ethanol; insights from IMS-MS and molecular dynamics

Tzuhsiung Yang (John F. Berry, advisor), University of Wisconsin-Madison, Chemistry, Enabling and accelerating Hessian calculations with numerical nuclear second derivatives on computing grid

The Fall 2017 Winners (Washington, DC)

Evgenii Fetisov (J. Ilja Siepmann, advisor), University of Minnesota, First principles Monte Carlo simulations of reactive phase and sorption equilibria

Hoshin Kim (Yaroslava G. Yingling, advisor), North Carolina State University, Role of graphene oxidation on physisorption of biomolecules using computational modeling

Daniel Nascimento  (A. Eugene DePrince III, advisor), Florida State University, Broadband absorption spectra from time-dependent coupled-cluster theory

David Williams-Young (Xiaosong Li, advisor), University of Washington, Novel model reduction algorithm for the efficient evaluation of molecular response properties

Zhongyue Yang (Kendall N. Houk, advisor), University of California, Los Angeles, Environment-Perturbed transition state sampling and its applications in chemical and biochemical reactions in condensed media

The Spring 2017 Winners (San Francisco, CA)

Fiona Kearns, University of South Florida (Lee Woodcock, advisor), QM-NEW: An efficient and accurate QM/MM free energy estimator and its application to pKa predictions

Patrick Lestrange, University of Washington (X. Li, advisor), Controlling coherent electron transfer in bi-nuclear platinum complexes

Elvira Sayfutyarova, Princeton University (G. Chan, advisor), Automatic and systematic construction of active spaces from the atomic valence orbitals

Kayla Sprenger, University of Washington (J. Pfaendtner, advisor), Molecular simulations provide crucial insights into the mechanisms of biocatalysis in ionic liquids

Mingzhen Zhang, University of Akron (J. Zheng, advisor), Oncogenic mutations differentially affect bax monomer, dimer, and oligomeric pore formation in the membrane

The Fall 2016 Winners (Philadelphia, PA)

Saeed Izadi, Biomedical Engineering and Mechanics, Virginia Tech (Alexey Onufriev, advisor), Optimal Point Charge Approximation, from 3-atom Water Molecule to Million-Atom Chromatin Fiber

Hector Corzo, Auburn University (J.V. Ortiz, advisor), Design of New Theoretical and Computational Methods Through The Development of Computer Algebra Systems

Wenjuan Jiang, Syracuse University (Shika Nangia, advisor), Multiscale Approach to Designing Drug-Specific Nanocarriers for Anticancer Drug Delivery

Xubin Li, Florida State University (Wei Yang, advisor), Predictive Sampling of Long-Timescale Protein Functional Motions in Explicit Solvent

Arkajyoti Sengupta, Indiana University (K. Raghavachari, advisor), Digging Deep: A Combined SAPT and NBO Study towards the Fundamental Origin of CH...X– and NH...X– Interactions in Receptor–Anion Complexes

The Spring 2016 Winners (San Diego, CA)

Jacob Faucheaux, University of Illinois at Urbana-Champaign (So Hirata, advisor), High-Order Diagrammatic Vibrational Coupled-Cluster Theory

Joshua Goings, University of Washington (Xiaosong Li, advisor), Towards a Real-Time Description of Magnetic Systems with Applications to Magnetic Circular Dichroism Spectroscopy

Tyler Hughes, Washington University in Saint Louis (S. Joshua Swamidass, advisor), Modeling Reactivity to Soft, Hard, and Biological Targets with a Deep Learning Network

Hedieh Torabifard, Wayne State University (G. Andrés Cisneros, advisor), Insights on TET2 activity for DNA Demethylation from MD Simulations

Michael Webb, California Institute of Technology (Thomas Miller III, advisor), Chemically Specific Dynamic Bond Percolation Model for Computational Screening of Polymer Electrolytes

The Fall 2015 Winners (Boston, MA)

Ruibin Liang, Department of Chemistry, University of Chicago (w/Greg Voth), Theoretical Multiscale simulation reveals a multifaceted mechanism of proton permeation through the influenza A M2 proton channel

Rebecca Carlson, Department of Chemistry, University of Minnesota (w/Laura Gagliardi), Catalysis in Metal Organic Frameworks: Ethylene Oligomerization and Methane to Methanol Conversion

Bo Peng, Department of Chemistry, University of Washington (w/Xiaosong Li), Equation of Motion Coupled-Cluster Calculations of K-edge X-ray Absorption Spectra

Ka Un Lao, Department of Chemistry and Biochemistry, The Ohio State University (w/John Herbert), Accurate, efficient, and insightful quantum chemistry calculations of non-covalent interactions for large systems

Daniel Smith, Department of Chemistry and Biochemistry, Auburn University (w/Konrad Patkowski), Psi4NumPy: A Hybrid C++/Python Interpreted Quantum Chemistry Programming Environment

The Spring 2015 Winners (Denver, CO)

Vivek Bharadwaj, Department of Chemical and Biological Engineering, Colorado School of Mines, Theoretical Investigations of the Fumarate Addition Reaction: Implications for the Biological Stability of Future Fuels and Opportunities for Bioremediation of Hydrocarbon Contaminated Areas

Feizhi Ding, Department of Chemistry, University of Washington, Time-Dependent Non-equilibrium Dynamics in QM/continuum approaches

Nan Li, Department of Materials Science and Engineering, North Carolina State University, Simulations of the self-assembly of polyelectrolyte block copolymers using dissipative particle dynamics with an implicit solvent ionic strength (ISIS) method 

Gregory Medders, Department of Chemistry and Biochemistry, University of California, San Diego, Sum Frequency Generation Spectra of the Air/Water Interface from First Principles Based Models

Heather Wiebe, Department of Chemistry, Simon Fraser University, MD-Generated Volume Profiles as a Tool for Probing Transition States of Conformational Changes

The Fall 2014 Winners (San Francisco, CA)

Ara Abramyan, Department of Chemistry and Biochemistry, University of the Sciences, Computational studies of aromatic foldamer helices: molecular encapsulation and handedness inversion

Symon Gathiaka, Department of Chemistry and Biochemistry, Auburn University, Mechanism and product specificity of PRMT1: Implications from QM and MD simulations

Eric Lai, Graduate Program in Biochemistry and Structural Biology, Stony Brook University, Rational modulations of inhibitor binding kinetics

Heather Mayes, Dept. of Chemical and Biological Engineering, Northwestern University, Why pucker sugar? Computational chemistry investigations into carbohydrate ring distortion for enzymatic action

Christopher Roberts, Department of Chemistry, University of California Riverside, Effects of spatial organization and molecular scaffoldings on the diffusive activity of substrates in enzyme nanstructures 

The Spring 2014 Winners (Dallas, Texas)

Laura Albrecht, Department of Chemistry, Dalhousie University, Investigating local stability in water clusters using atomic energies

Peng Bai, Department of Chemical Engineering and Materials Science, University of Minnesota, Understanding solution-phase adsorption of complex molecules in zeolites by molecular simulation

Allison Dzubak, Department of Chemistry, Chemical Theory Center, and Supercomputing Institute, University of Minnesota, Exploiting under-coordinated metal sites in porous materials for unique reactivity and novel gas separations

Jason Goodpaster, Department of Chemistry and Chemical Engineering, California Institute of Technology, Accurate and Robust Wavefunction Embedding Methodologies

Melek Nihan Ucisik, Department of Chemistry, University of Florida, Insights into the Structure and Dynamics of the Cu(I) Binding Proteins CusB and CusF

The Fall 2013 Winners (Indianapolis, Indiana)

Joseph W May, Department of Chemistry, University of Washington, Theoretical investigation of ion diffusion pathways in II-VI semiconductor nanocrystals

Yipu Miao, Department of Chemistry, University of Florida, Acceleration of ab initio quantum chemistry calculation on GPUs

Sally R Ellingson, Genome Science & Technology, University of Tennessee, Knoxville and Oak Ridge National Laboratory, Center for Molecular Biophysics, Oak Ridge, Tennessee, Multi-receptor high-throughput virtual docking on supercomputers with VinaMPI

Sai Lakshmana Vankayala, Department of Chemistry, University of South Florida, Unlocking the binding and reaction mechanism of hydroxyurea as a biological nitric oxide donor

Chern-Hooi Lim, Chemical & Biological Engineering, University of Colorado at Boulder, Mechanism of Homogeneous Reduction of CO2 by Pyridine: Proton Relay in Aqueous Solvent and Aromatic Stabilization

The Spring 2013 Winners (New Orleans, Louisiana)

Kyle E Hart, Department of Materials Science and Engineering, Penn State University, Toward effective C02/CH4 separations by sulfur-containing PIMs: Insight from molecular simulations

Marie L Laury, Department of Chemistry, University of North Texas, Examining the 4d transition metals and the lower p-block with a pseudopotential-based composite method: Atomic and molecular applications of rp-ccCA

Iffat H Nayyar, Los Alamos National Laboratory, University of Central Florida, Effect of trans and cis conformational defects on the localization of electronic excitations in π-conjugated organic polymers

Yanxin Liu, Department of Physics, University of Illinois at Urbana-Champaign, Fast protein refolding observed in pressure-jump molecular dynamics simulations

Raghunath O Rambhadran, Department of Chemistry, Indiana University, Development and Application of the generalized Connectivity-Based Hierarchy: Accurate Thermochemistry for Organic molecules

The Fall 2012 Winners (Philadelphia, Pennsylvania)

Sean Fischer, Department of Chemistry, University of Washington, Surface hoping with Ehrenfest Excited Potential: Towards accurate and affordable non-adiabatic dynamics for large systems

Brian Gold, Department of Chemistry and Biochemistry, Florida State University, Selective transition state stabilization in the design of fast and tunable non-catalyzed click reactions

Emilie Guidez , Department of Chemistry, Kansas State University, Development of a charge-perturbed particle in a sphere model for electronic structure calculations of ligand-protected gold nanoparticles

Nikolay Plotnikov , Department of Chemistry, University of Southern California, Validation of Linear Response Approximation of the Free Energy Perturbation while moving from the reference potential to the ab initio QM/MM potential

Yue Shi , Department of Biomedical Engineering, University of Texas at Austin, Thermodynamic Effects of Conformational constraints in protein-ligand interactions

The Spring 2012 Winners (San Diego, California)

Adrian W. Lange, Department of Chemistry, The Ohio State University, Recent developments and progress with polarizable continuum models

Chris MacDermaid, Department of Chemistry, University of Pennsylvania, Computational Design of a Protein Crystal Structure

Cong Liu, Department of Chemistry, University of North Texas, Computational studies on CO2 activation using transition metal catalysts: In consideration of homogeneous and heterogeneous catalysis

Garrett B. Goh, Department of Chemistry, University of Michigan, Novel explicit solvent pH molecular dynamics methods for RNA

Jason A. Wallace, Department of Chemistry and Biochemistry, University of Oklahoma, Unraveling the pH-dependence of spider dragline silk formation

The Fall 2011 Winners (Denver, Colorado)

Wenkel Liang, Department of Chemistry, University of Washington, Efficient First-Principles Electronic Dynamics

Yi Shang, Department of Chemistry, Stony Brook University, Simulations of Spin-labeled HIV-1 Protease Exhibit Diverse Flap Dynamics Due To Sequence Polymorphism

Falgun Shah, Department of Medicinal Chemistry, The University of Mississippi, Design and Development of Novel Cysteine Protease Inhibitors of Malaria Parasite Plasmodium falciparum: Virtual Screening, Denovo Design, and Combinatorial Library Synthesis

John Faver, Department of Chemistry, University of Florida, Estimation of Error in Energy Functions for Large Molecular Systems

Maria P. Frushicheva, Department of Chemistry, University of Southern California, Using Computational Enzyme Design to Study the Promiscuous Activities of Phosphotriesterase

The Spring 2011 Winners (Anaheim, California)

Bin Zhang, Department of Chemistry and Chemical Engineering, California Institute of Technology, Hydrophobically stabilized open state for the lateral gate of the Sec translocon

Christina Bergonzo, Department of Chemistry, Stony Brook University, Selective destabilization of lesions leads to divergent base flipping pathways by a DNA glycosylase

Justin M Spiriti, Department of Chemistry and Biochemistry and Center for Biological Physics, Arizona State University, Intrinsic bending flexibility of bare and protein-bound DNA by adaptive umbrella sampling on roll angles

Ramu Anandakrishnan, Department of Computer Science, Virginia Polytechnic Institute and State University, N Log N generalized Born approximation

Sudipto Mukherjee, Department of Applied Mathematics & Statistics, Stony Brook University, Development of the SB2010 testset to evaluate docking

The Fall 2010 Winners (Boston, Massachusetts)

Bonnie A. Merchant, Department of Chemistry & Biochemistry, Duquesne University, Computational investigation of the transport mechanism for monoamine transporters

Qin Cai, Department of Biomedical Engineering, University of California, Biomolecular dynamics simulations based on the finite-difference Poisson-Boltzmann method

Roberto Olvares-Amaya, Department of Chemistry & Chemical Biology, Harvard University, Quantum chemistry calculations for arbitrarily complex electrostatic environments: Benzene anion stabilization

Scott Johnson, Department of Chemistry & Biochemistry, UCLA, Filtering and ranking enzyme designs using EDGE

Yat T. Tang, Department of Biochemistry & Molecular Biophysics, Washington University in St. Louis, Virtual screening targeting the PhoP response regulator to inhibit bacterial virulence

The Spring 2010 Winners (San Francisco, California)

Trent Balius, SUNY Stony Brook (Advisor: Robert Rizzo), Computational prediction of fold resistance in EGFR drug resistance

Mehmed Ertem, University of Minnesota (Advisor: Chris Cramer), Water Oxidation Mechanisms of Ru-Hbpp, cis-Ru(bpy)2(OH2)2 and Ru(DAMP)(bpy) Catalysts

Katrina Lexa, University of Michigan (Advisor: Heather Carlson), Mapping protein surfaces for druggable hot spots: Mixed-solvent molecular dynamics (MixMD)

Pansy Patel, University of Central Florida (Advisor: Artëm E. Masunov), Prediction of Properties of Diarylethene Photochromic Compounds for use as Nonvolatile Optical Data Storage Devices: A Density Functional Theory Study

Jason Swails, University of Florida (Advisor: Adrian Roitberg), Effect of pH on Protein Conformation and Function in GM2-Activator Protein

The Fall 2009 Winners (Washington, DC)

Sourav Das, Rensselaer Polytechnic Institute (Advisor: Curt Breneman), Pair-wise Property-Encoded Shape Distributions: Binding affinity prediction of protein-ligand complexes

Fangyu Ding, SUNY Stony Brook (Advisor: Carlos Simmerling), Drug Pressure Induced Mutations in HIV-1 Protease alter Flap Conformations

James Fells, University of Memphis (Advisor: Abby Parrill), Binary QSAR study for identifying selective LPA3 antagonists

Kiumars Shahrokh, University of Utah (Advisor: Tom Cheatham), A first set of QM-coupled AMBER ff99 compatible heme parameters for the P450 catalytic cycle

Lai Xu, UCLA (Advisor: Ken Houk), Dynamics of 1,3-dipolar cycloadditions of diazonium betaines to acetylene and ethylene: Bending vibrations facilitate reaction

The Spring 2009 Winners (Salt Lake City, Utah)

Jiahao Chen, University of Illinois at Urbana Champaign (Advisor: Todd Martinez), Investigations into the properties of a new water model capable of polarization and intermolecular charge transfer

Wenxun Gan, University of Chicago (Advisor: Benoit Roux), Using Markov model to estimate transition rate and free energy profile of Src kinase activation

Dian Jiao, University of Texas at Austin (Advisor: Pengyu Ren), Free Energy simulation of Protein-Ligand Binding via a Polarizable Potential

Kelly Lancaster, Georgia Institute of Technology (Advisor: Jean-Luc Brédas), Intramolecular Electron Transfer in Two- and Three-Center Mixed-Valence Triarylamines

Yilin Meng, University of Florida (Advisor: Adrian Roitberg), Constant pH replica exchange molecular dynamics simulation in biomolecules

The Fall 2008 Winners (Philadelphia, PA)

Satyender Goel, University of Central Florida (Advisor: ), Pairwise spin-contamination correction and application to 3-D transition metal hydrides from BS-DFT

Lucius E. Johnson, University of Louisville (Advisor: ), Mechanism of electronic stabilization of cyclopropenylidene by amino-substitution

In Suk Joung, University of Utah(Advisor: ), Determination of alkali and halide monovalent ion parameters for use in explicitly solvated biomolecular simulations

Laveena Muley, University at Buffalo (Advisor: ), Binding affinity awarded for hydrophobic bonding in scoring functions needs to be context dependent

Somisetti V Sambasivarao, Auburn University (Advisor: Orlando Acevedo), Systematic development of OPLS-AA force field parameters for ionic liquid simulations

The Spring 2008 Winners (New Orleans, Louisiana)

Jeff Hammond, Pacific Northwest National Laboratory, Coupled-cluster theory on supercomputers

Jean-François Truchon, Université de Montreal, Considering a treatment of induced electronic polarization based on the Poisson equation

Pablo Englebienne, McGill University, FORECASTER: A new platform for drug discovery

Sapna Sarupria, Rensselaer Polytechnic Institute, Using computer simulations to explore pressure effects on proteins

Hanning Chen, University of Utah, Hydrophobic Interaction in Acidic Aqueous Solutions

The Fall 2007 Winners (Boston, Massachusetts)

Kai Zhu, Columbia University, Improving generalized Born model in protein side chain and loop prediction

Raed Khashan, University of North Carolina, Development of scoring functions for protein-ligand binding based on frequent geometric and chemical patterns of inter-atomic interactions at their interfaces

James S. M. Anderson, McMaster University, Novel basis-set free approaches to solving the electronic-Schrödinger equation

Christina R. Crecca, Florida University, How much experimental data is needed to predict a protein's structure?

Lauren Wickstrom, Stony Brook University, To be native or not to be native, that is the question: Studies of the unfolded state structure of the Villin Headpiece Helical Subdomain

The Spring 2007 Winners (Chicago, Illinois)

Billy Griffin, University of Arkansas, Neural network and ab initio studies of metal hydride nanoparticles

Maricris Lodriguito, Michigan State University, Externally corrected coupled-cluster methods employing method of moments of coupled-cluster equations and multireference perturbation theory

Salma B. Rafi, Stony Brook University, Molecular dynamic simulations help capture TB-drugdesign’s most wanted: Mechanism of active site loop ordering

Sigifredo Sanchez-Carrera, Georgia Institute of Technology, Electron-photon coupling in organic semiconductors: A DFT-based approach

Laura Thomas, Yale University, Monte Carlo investigations of fundamental properties of organic molecules in the gas and liquid phases

The Fall 2006 Winners (San Francisco, California)

Ying Wei, Northeastern University, High-recall, high-precision prediction of protein binding sites from 3D structure

Sara E. Nichols, Yale University, Shrinking residues for enhanced Monte Carlo sampling for proteins

Timothy H. Click, University of Oklahoma, Locating alpha-helices and beta-strands using recently-developed protocols

Johannes Hachmann, Cornell University, Quadratic Scaling Multireference Correlation in Polyenes and Long Molecules with the Local Density Matrix Renormalization Group

Zhi Wang, Emory University, Quantum Chemical Molecular Dynamics Study of Catalyst-Free SWNT Growth from SiC-derived Carbon

The Spring 2006 Winners (Atlanta, Georgia)

Xhua Chen, New York University, MFCC-DM with pairwise interaction correction for quantum chemical study of proptein

Xuhui Huang, Columbia University, Hydrophobic-Aided Replica Exchange: an efficient algorithm for sampling biological systems in explicit solvent

Casey P. Kelly, University of Minnesota, Calculation of acid dissociation constants by the SM6 quantum mechanical implicit solvation model

Valerie McCarthey, University of Pittsburgh, Stability of H2 Clathrates vs Cavity Occupancy

Devina Pillay, The University of Texas at Austin, Role of Oxygen Vacancies on Growth of 1B (Au, Ag and Cu) Particles on TiO2(110)

The Fall 2005 Winners (Washington, D.C.)

Manoj V. Athawale, Rensselaer Polytechnic Institute, Osmolyte (TMAO) effects on the strength of hydrophobic interactions: Origin of osmolyte compatibility

Barun Bhhatarai, Clarkson University, Digging the past for a clue: A novel in-silico approach for new leads on 4-OH-pyran-2-ones HIV protease inhibitors

Elaine R. Chan, University of Michigan, Multiscale modeling and simulation of polymertethered silsesquioxane assemblies

Jun Cu, University of Pittsburgh, Accurate calculations of interaction energies of H-bonded clusters

Jason DeChancie, University of California, Los Angeles, Origins of the high affinity binding of the biotin-(strept)avidin complex

Christopher B. Harrison, University of Notre Dame, Unraveling the role of (6-4) Photolyase in DNA repair through homology modeling, consensus docking, and MD simulations

Benjamin Mintz, University of North Texas, Reduction of computational requirements and trends for high accuracy description of molecular properties

Jeremy M. Moix, Georgia Institute of Technology, A phenomenological model for surface diffusion: Diffusive dynamics across stochastic potentials

Kun Song, Stony Brook University, A simulation study of the binding modes of formamidopyrimidine bound to DNA containing 8-oxo guanine

Nicholas J. Wright, University of Illinois, Forwardbackward semiclassical dynamics

The Spring 2005 Winners (San Diego)

Anastassia Alexandrova, Utah State University, ab Initio Genetic Algorithm-based Elucidation of Multiply Aromatic Clusters

Biggi Albrecht, University of Oxford, Uncovering Networks within Protein Structure

Dechuan Zhuang, Rensselaer Polytechnic Institute, Consensus Descriptor Selection under Multiple Objectives using Linear Support Vector Regression

Hanbin Liu, University of Pittsburgh, On the Convergence of a Hybrid Parallel Tempering Tsallis Statistics Monte Carlo Algorithm

John Mongan, University of California, San Diego, Discrete State Constant pH Molecular Dynamics in Generalized Born Implicit Solvent

Matt Sundling, Rensselaer Polytechnic Institute, PEST vs CoMFA: A Comparative Study of two 3D QSAR Technologies

Melinda Harrison, Duquesne University, A QM/QM Approach to Modeling the Zn(II)/Cu(I) Core of a Protein

Scott Yockel, University of North Texas, Denton, Structures and Energetics of Small Third-Row Molecules with Correlation-Consistent Basis Sets

Xianlong Vincent Wang, Bryn Mawr College, ab Initio Studies of Methyl and t-Butyl Group Internal Rotation in Aromatic Molecular Crystals

Zunnan Huang, University of Oklahoma, Trajectory randomized Replica Canonical and Microcanonical Ensembles Simulations and Limitations of MD simulations

The Fall 2004 Winners (Philadelphia)

Raphaël Geney, State University of New York, Stony Brook, Investigations of Salt Bridge Strength in the Generalized Born Water Solvation Model

Rajarshi Guha, Pennsylvania State University, Using Similarity and Classification Methods to Determine Applicability of QSAR Models to Query Set Compounds

David J. Harriman, University of New Brunswick, Canada, Reverse Docking’ as a Computational Tool for the Study of Asymmetric Organocatalysis

Linnan He, Pennsylvania State University, Can a QSAR Model Reliably Predict a Query Compound’s Activity

Christopher Hixson, University of Oklahoma, Filling the Gap between Conventional and ‘Mean-Field’ Molecular Dynamics the Exact Approximation

Devleena Mazumder Shivakuma, University of California, Santa Barbara, Computational Study of Hyperthermophilic Indole Glycerol Phosphate Synthase: Structural Alterations at the Active Site with Temperature

Scott Oloff, University of North Carolina, Chapel Hill, COLIBRI: A Novel Method for the Prediction of Complementary Ligands Based on Receptor Information and its Application to Database Screening

Somianarayanan Rajamani, Rensselaer Polytechnic University, Molecular Level Studies of Water-Mediated Interactions Between Ions and their Relevance to Biomolecular Interactions

Michael Shirts, Stanford University, Directly Calculated Ligand Binding Free Energies using Folding@Home

Shuxing (King) Zhang, University of North Carolina, Chapel Hill, ALL-QSAR: A Novel Automated Lazy Learning QSAR Approach and its Application to Experimental Datasets

The Spring 2004 Winners (Anaheim)

Xiaolin Cheng, Stony Brook University,  Molecular Dynamics Simulations of 8-oxoguanine: A mismatch DNA

Alexander Perryman, University of California at San Diego, HIV-1 Protease Molecular Dynamics of a Wild-Type and of the V82F/I84V Mutant: Possible Contributions to Drug Resistance and a Potential New Target Site for Drugs

Asif Ladiwala, Rensselaer Polytechnic Institute, Prediction of Protein Affinity in Hydrophobic Interaction Chromatography using Quantitative Structure-Retention Relationship (QSRR) Models

Asim Okur, Stony Brook University, Multiple pathways in beta-hairpin folding and unfolding simulations

Jessica Swanson, University of California, Revisiting Free Energy Calculations: One Step Closer to Rigorous Scoring Functions and One Step beyond MM/PBSA

Ivan Tubert-Brohman, Yale University, Improved Semiempirical Methods: Parameterization of PDDG/PM3 for Sulfur

Sarah A. Mueller Stein, Duquesne University, The Influence of Steric Congestion on the Dynamics and Geometry of DNA

(David) Wei Deng, Rensselaer Polytechnic Institute, Predicting Protein-Ligand Binding Affinities using Transferable Atom Equivalent (TAE) Techniques And Machine-Learning Methods

Andreas Bender, University of Cambridge, Similarity Searching using Atom Environments, Information Gain based Feature Selection and the Naive Bayesian Classifier

Anne E. Loccisano, Duquesne University, Development of New CHARMM Force Field Parameters for Novel DNA Bending Agents

The Fall 2003 Winners (New York)

Tuhin Ghosh, Rensselaer Polytechnic Institute (Advisor: Sekhar Garde), Proteins Under Stress: Molecular Studies of Pressure Effects on Proteins

Jason Thompson, University of Minnesota (Advisor: Christopher J Cramer), Predicting Aqueous Solubility: A Fundamental Approach

Marina Udier-Blagovic, Yale University (Advisor: William L. Jorgensen), Validation of A Model for the Complex of HIV-1 Reverse Transcriptase with Non-Nucleoside Inhibitor TMC125

Brian Mattioni, Pennsylvania State University (Advisor: Peter C. Jurs), Classifying the Mutagenicity of Two Diverse Sets of Organic Compounds Using Ames Test Data for Salmonella Typhimurium TA100 and TA98

Nitin Rathore, University of Wisconsin (Advisor: Juan J. de Pablo), Density of States Simulations of Proteins in a Continuum

Min Shen, University of North Carolina, Chapel Hill (Advisor: Alex Tropsha), Discovery and Experimental Validation of Novel Functionalized Amino Acid Anticonvulsant Compounds: A Success Story of QSAR-Based Database Mining

Dong-Qi Wang, University of Hong Kong (Advisor: David Lee Phillips), A DFT Investigation of the Remarkable Reactivity of the Gem-Dizinc Carbenoid (IZn) 2CHI as a Cyclopropanation Reagent with Ethylene Compared to its Mono Zinc Carbenoid IZnCHI2

Yudong Wu, Princeton University (Advisor: Roberto Car), Application of a Coarse-Grained Dynamical Method to Explore the Conformational Space of Small Molecules

Ling-Ling Shen, Rensselaer Polytechnic Institute (Advisor: Curt M. Breneman), Modeling the mu-opiod receptor affinity of synthetic 8-aminocyclazocine analogues using TAE, PEST and PAD descriptors and machine-learning methods

Sarah Tschampel, University of Georgia (Advisor: Robert J. Woods), Rational Development of a Lone Pair Inclusive Force Field

The Spring 2003 Winners (New Orleans)

Christine Aikens, Iowa State University (Advisor: Mark S. Gordon), Molecular Electronic Structure and Magnetic Properties of Y2Ti(?-X)2TiY2(X,Y=H,F,Cl,Br) Isomers

Nicolae-Viorel Buchete, Boston University (Advisor: John E. Straub), The Effect of Relative Side Chain Orientations on the Ability of Statistical Potentials to Identify Native-Like Structures of Proteins

Guanglei Cui, SUNY at Stony Brook (Advisor: Carlos Simmerling), The Complicated Folding of a Simple Peptide Studied by Multiple Folding Simulations and Replica Exchange Approach

Haitao Dong, The University of Oklahoma (Advisor: Ralph A. Wheeler), Quasiharmonic Vibrations of Water, Water Clusters, and Liquid Water from Principal Component Analysis of Quantum or QM/MM Trajectories

Ivaylo N. Ivanov, University of Pennsylvania (Advisor: Michael L. Klein), Relative pKs from First Principles Molecular Dynamics: The Case of Histidine Deprotonation

William B. Katt, Rensselaer Polytechnic Institute (Advisor: Curt M. Breneman), Optimization of Molecular Properties Through Structural Mutation and Virtual Screening with QSAR Models

Bethany Kormos, University of Minnesota (Advisor: Christopher J. Cramer), Utilizing Density Functional Theory to Study Nucleophilic Substitution Reactions: Optimization of an Adiabatic Connection Method and its Application

Bentley Strockbine, Stony Brook University (Advisor: Carlos Simmerling), Advances in Structure Prediction Techniques

Min Wu, New York University (Advisor: Suse Broyde), Structural Studies of an Environmental Carcinogen within a Y Family Bypass DNA Polymerase

Zhigang Zhou, Duquesne University (Advisor: Jeffrey D. Madura), Resistant Effect Exploring of HIV-1 RT Mutation by Molecular Dynamics

The Fall 2002 Winners (Boston)

Srikanth Kidambi, University of Michigan, Quantum chemical calculations of cadmium chemical shielding tensors in biologically relevant molecules

Qiong Luo, Rensselaer Polytechnic Institute, Prediction of Glass Transition Temperatures for Polymers Using TAE/RECON Method

Nathan R. McElroy, Pennsylvania State University, Classification of Cytogenetic Toxicity of Organic Compounds from Molecular Structure

Suhas J. Patankar, Pennsylvania State University, Classification of HIV Protease Inhibitors and Prediction of Their Antiviral Potency from Molecular Structure

Minghu Song, Rensselaer Polytechnic Institute, Prediction of Protein Retention Times in Anion-exchange System using Support Vector Machine Regression

Shixiang Yan, New York University, Molecular dynamics simulation and free energy analysis of polycyclic aromatic carcinogen-damaged DNA: accurate representation and        

new insights

The Spring 2002 Winners (Orlando)

Thomas Dick, Duquesne University (Advisor: Jeffry Madura), Computational Modeling of Brine to aid CO2 Sequestration Research

Benoit Leblanc, Institut Francais du Petrole in Reueil-Malmaison, France (Advisors: Herve Toulhoat, Bertrand Braunsweig & Evelyne Lutton), Mixing Monte Carlo moves more efficiently with an evolutionary algorithm

Viera Lukacova, North Dakota State University (Advisor: Stefan Balaz), Implementation of Multiple Binding Modes in CoMFA

Sabine Schefzick, Indiana University-Purdue University-Indianapolis (IUPUI) (Advisor: Kenny Lipkowitz), Theoretical Ligand Distortions in Chiral Catalysts: Can molecular deformations enhance a catalyst's chirality content?

Xuelin Wang, University of North Texas (Advisor: Angela K. Wilson), Error Analysis in Density Functional Theory: Atomization Energies

The Fall 2001 Winners (Chicago)

Caterina Bissantz, Swiss Federal Institute of Technology, Zurich (Advisor: Gerd Folkers), Virtual Screening of Chemical Databases: Application of G-protein Coupled Receptors

Catherine Check, Northern Illinois University (Advisors: Thomas M. Gilbert and Lee S. Sunderlin), Augmentation of the LANL2DZ Basis Set Under B3LYP and MP2 Models to Improve Calculated Results for p Block Elements

Norge Cruz Hernandez, University of Seville, Spain (Advisor: Javier Fernandez Sanz), DFGT and Molecular Dynamic Study of ScN, TiN, and VN Materials

Ohyun Kwon, Auburn University (Advisor: Michael L. McKee), Theoretical Studies of Main-Group Metallocenes

Nelaine Mora-Diez, Dalhousie University, Halifax, Nova Scotia (Advisor: Russell J. Boyd), Theoretical Calculations in Atmospheric Chemistry: OH and NO Hydrogen-Abstraction Reactions from Aldehydes