## Current MolSSI Fellows

## Samragni Banerjee

*The Ohio State University*

*2020-A Seed, 2020-B Investment*

**Adviser:** Alexander Y. Sokolov

**MolSSI Software Mentor:** Jessica A. Nash, Susi Lehtola

*“Efficient Implementation of Algebraic Diagrammatic Construction Theory for Accurate Simulations of Electron Ionization and Attachment”*

## Madison Berger

*University of North Texas*

*2020-B Investment*

**Adviser:** Andres Cisneros

**MolSSI Software Mentor:** Jessica A. Nash

*“Implementation of advanced potentials for QM/MM calculations and application to mutation impacts in protein complexes.”*

## Tucker Burgin

*University of Michigan*

*2019-A Seed, 2020-A Investment*

**Adviser:** Heather B. Mayes

**MolSSI Software Mentor:** Sam Ellis

*“Building software tools for understanding and evolving enzymes in silico guided by unbiased, all-atom simulations”*

## Brandon Butler

*University of Michigan*

*2021-A Seed*

**Adviser:** Sharon C. Glotzer

**MolSSI Software Mentor:** Taylor Barnes

*None*

## Matthew Chan

*University of Illinois at Urbana-Champagne*

*2021-A Seed*

**Adviser:** Diwakar Shukla

**MolSSI Software Mentor:** Doaa Altarawy, Sina Mostafanejad

*“Transfer learning to elucidate protein sequence-structure-function relationships”*

## Victor Chavez

*Purdue University*

*2020-A Seed, 2020-B Investment*

**Adviser:** Adam Wasserman

**MolSSI Software Mentor:** Taylor Barnes

*“Development and implementation of Partition DFT”*

## Yunsie Chung

*Massachusetts Institute of Technology*

*2021-A Seed*

**Adviser:** William H. Green

**MolSSI Software Mentor:** Sina Mostafanejad

*“Development of an automatic liquid phase kinetic modeling tool with solvation-corrected kinetic rates and thermochemistry”*

## Jennifer Clark

*North Carolina State University*

*2019-B Seed, 2020-A Investment*

**Adviser:** Erik Santiso

**MolSSI Software Mentor:** Andrew Abi-Mansour

*“Developing the first open-source application for thermodynamic calculations for the Statistical Associating Fluid Theory equation of state and associated coarse-graining method”*

## Bradley Dice

*University of Michigan*

*2019-B Investment*

**Adviser:** Sharon C. Glotzer

**MolSSI Software Mentor:** Doaa Altarawy

*“Developing powerful, parallel analysis tools for studies of soft matter, nanoparticles, and colloidal self-assembly”*

## Sebastian Dick

*Stony Brook University*

*2019-A Seed, 2020-A Investment*

**Adviser:** Marivi Fernandez-Serra

**MolSSI Software Mentor:** Sam Ellis

*“Improving electronic structure calculations with the help of machine learning”,”Development of an open source library for machine learned density functionals”*

## Heta A. Gandhi

*University of Rochester*

*2020-A Investment*

**Adviser:** Andrew D. White

**MolSSI Software Mentor:** Jessica A. Nash

*“Extending machine learning software to coarse-grained molecular dynamics”*

## Igor Gayday

*Marquette University*

*2020-B Investment*

**Adviser:** Dmitri Babikov

**MolSSI Software Mentor:** Jonathan Moussa

*“A program for calculation of coupled rotational-vibrational energy levels and their respective lifetimes of three-atomic (and, potentially, tetra-atomic) systems in hyper-spherical (APH) coordinates.”*

## James R. Gayvert

*Boston University*

*2020-A Seed, 2020-B Investment*

**Adviser:** Ksenia Bravaya

**MolSSI Software Mentor:** Andrew Abi-Mansour

*“Development of an open-source library for the description of metastable electronic states in molecules”*

## Jason Gibson

*University of Florida*

*2021-A Seed*

**Adviser:** Richard Hening

**MolSSI Software Mentor:** Jessica A. Nash

*“Database and API development of proven machine learning models to accelerate material simulations”*

## Samuel Greene

*University of Chicago*

*2019-B Seed, 2020-A Investment*

**Adviser:** Jonathan Weare, Timothy Berkelbach

**MolSSI Software Mentor:** Ben Pritchard

*“Developing randomized linear algebra libraries for efficient quantum chemistry calculations”*

## Dr. Rachel Kurchin

*Carnegie Mellon University*

*2021-A Seed*

**Adviser:** Venkat Viswanathan

**MolSSI Software Mentor:** Sam Ellis, Sina Mostafanejad

*“Next-generation graph-based models as computationally inexpensive surrogates for first-principles quantum calculations”*

## Dr. Pascal T. Merz

*Unviersity of Colorado, Boulder*

*2020-A Investment*

**Adviser:** Michael R. Shirts

**MolSSI Software Mentor:** Eliseo Marin-Rimoldi

*“Enhancement of GROMACS to provide an extensible high-performance hybrid MC/MD framework”*

## Anupam Ojha

*University of California, San Diego*

*2021-A Seed*

**Adviser:** Rommie Amaro

**MolSSI Software Mentor:** Eliseo Marin-Rimoldi

*“Developing a Multiscale Milestoning Simulation Approach for Efficient Protein-Ligand Binding and Unbinding Kinetics”*

## Heejune Park

*University of California, Davis*

*2021-A Seed*

**Adviser:** Lee-Ping Wang

**MolSSI Software Mentor:** Susi Lehtola

*“Development of reaction path finding and optimization methods and implementation into the QCArchive Infrastructure”*

## John Russo

*Oregon Health & Science University*

*2021-A Seed*

**Adviser:** Daniel D. Zuckerman

**MolSSI Software Mentor:** Levi N. Naden

*“Enhancing the WESTPA weighted ensemble simulation tool by implementing recent methodological advances in analysis for improved rate constant estimation”*

## Nicholas Stair

*Emory University*

*2019-B Seed, 2020-A Investment*

**Adviser:** Francesco Evangelista

**MolSSI Software Mentor:** Jonathan Moussa

*“Development of a self-contained quantum computer simulator with reference implementations of quantum algorithms for strongly correlated electronic structure problems”*

## Rithwik Tom

*Carnegie Mellon University*

*2021-A Seed*

**Adviser:** Noa Marom

**MolSSI Software Mentor:** Jonathan Moussa

*“Crystal structure prediction of molecular co-crystals”*

## Bryce M. Westheimer

*Iowa State University*

*2020-B Investment*

**Adviser:** Mark S. Gordon

**MolSSI Software Mentor:** Taylor Barnes

*“Development of a high-performance, open source library for fragment-based ab initio quantum chemistry simulations.”*

## Yuan Yao

*Cornell University*

*2020-A Seed, 2020-B Investment*

**Adviser:** Cyrus Umrigar

**MolSSI Software Mentor:** Ben Pritchard

*“Improving basis set convergence in the semistochastic heatbath configuration interaction (SHCI) method”*

## Dr. Patricia Vindel Zandbergen

*Rutgers University*

*2021-A Seed*

**Adviser:** Neepa T. Maitra

**MolSSI Software Mentor:** Sina Mostafanejad

*“Implementation and development of mixed quantum classical methods to study laser driven molecular dynamics within the framework of the Exact Factorization approach”*

## MolSSI Fellow Alumni

## Adam S. Abbott

*University of Georgia*

*2018-A Phase I*

**Adviser:** Fritz Schaefer

**MolSSI Software Mentor:** Daniel G. A. Smith, Doaa Altarawy

*Generalized software interface between quantum chemistry packages and neural network algorithms to facilitate the construction of potential energy surfaces*

## Patrick Avery

*University at Buffalo*

*2017-B Phase I*

**Adviser:** Eva Zurek

**MolSSI Software Mentor:** Daniel G. A. Smith

*“Algorithms for molecular crystal structure prediction and their implementation in XtalOpt, an open-source evolutionary algorithm”*

## Caitlin Bannan

*University of California, Irvine*

*2018-A Phase I, 2018-B Phase II*

**Adviser:** David L. Mobley

**MolSSI Software Mentor:** Jessica A. Nash

*“Development of an open source tool using Bayesian inference to automatically sample chemical perception for parameterization of molecular mechanics force fields”*

## Giuseppe Barbalinardo

*University of California, Davis*

*2019-B Investment*

**Adviser:** Davide Donadio

**MolSSI Software Mentor:** Doaa Altarawy

*“Development of an open source framework to model heat transport at the nanoscale”*

## Dr. Hannah Bruce Macdonald

*Sloan Kettering Cancer Center*

*2019-B Investment*

**Adviser:** John Chodera

**MolSSI Software Mentor:** Sam Ellis

*“Free energy calculations with adaptive sampling, using a Bayesian Bandit framework”*

## Emiliano Deustua

*Michigan State University*

*2018-B Phase I, 2019-A Phase II*

**Adviser:** Piotr Piecuch

**MolSSI Software Mentor:** Jonathan Moussa

*“Coupled-cluster software using moment expansions and stochastic wave function sampling”*

## Ryan J. DiRisio

*University of Washington*

*2020-B Seed*

**Adviser:** Anne McCoy

**MolSSI Software Mentor:** Jonathan Moussa

*“Development of an open source, general-purpose Diffusion Monte Carlo software suited for high-performance computing environments to study vibrational problems.”*

## Nadav Geva

*Massachusetts Institute of Technology*

*2017-B Phase I*

**Adviser:** Troy Van Voorhis

**MolSSI Software Mentor:** Daniel G. A. Smith

*“Energy transfer between organic semiconductors and emerging low dimensionality materials”*

## Dr. Alon Grinberg Dana

*Massachusetts Institute of Technology*

*2020-A Seed*

**Adviser:** William H. Green

**MolSSI Software Mentor:** Matthew Welborn

*“A standardized open infrastructure for conveniently storing and obtaining theoretical chemical information of relevance for kinetic computations”*

## Mojtaba Haghighatlari

*University at Buffalo*

*2018-B Phase I, 2019-A Phase II*

**Adviser:** Johannes Hachmann

**MolSSI Software Mentor:** Doaa Altarawy

*“Advancing Machine Learning Methodology and Software for Data-Driven Discovery in Chemistry”*

## Jennifer Hays

*University of Virginia*

*2018-B Phase I, 2019-A Phase II*

**Adviser:** Peter Kasson

**MolSSI Software Mentor:** Ben Pritchard

*“Development of methods and software to integrate complex, multi-modal experimental data into molecular dynamics simulations”*

## Dr. Alex Holehouse

*Washington University in St. Louis*

*2019-A Seed*

**Adviser:** Rohit V. Pappu

**MolSSI Software Mentor:** Jessica A. Nash

*“Development of computational tools to explore and understand bimolecular phase separation of intrinsically disordered proteins”*

## Dr. M. Eric Irrgang

*University of Virginia *

*2018-A Phase I, 2018-B Phase II*

**Adviser:** Peter Kasson

**MolSSI Software Mentor:** Jessica A. Nash

*“Development of a GROMACS extension API and Python module for scalable complex workflows”*

## Monika Kodrycka

*Auburn University*

*2019-A Seed*

**Adviser:** Konrad Patkowski

**MolSSI Software Mentor:** Levi N. Naden

*“The development of a massively parallel framework for computing dispersion energies using explicitly correlated methods”*

## Lauren Koulias

*University of Washington*

*2019-B Investment*

**Adviser:** Xiaosong Li

**MolSSI Software Mentor:** Daniel G. A. Smith, Jonathan Moussa

*“Development of time-dependent equation-of-motion coupled-cluster methods with a focus on relativistic effects”*

## Dr. James M. Krieger

*University of Pittsburgh*

*2020-B Seed*

**Adviser:** Ivet Bahar

**MolSSI Software Mentor:** Andrew Abi-Mansour

*“I will be applying a multi-component computational approach to the coronavirus spike protein, which will provide a greater understanding of how the virus enters host cells and therefore will help identify drugs that interfere with such mechanisms.”*

## Kate Lebold

*Penn State University*

*2017-B Phase I, 2018-A Phase II*

**Adviser:** William Noid

**MolSSI Software Mentor:** Eliseo Marin-Rimoldi

*“Thermodynamic state point transferability of coarse-grained models through the force-, pressure-, and energy-matching methodologies”*

## Sebastian Lee

*California Institute of Technology*

*2019-A Seed, 2019-B Investment*

**Adviser:** Thomas Miller

**MolSSI Software Mentor:** Taylor Barnes

*“Creation of a general, open-sourced implementation the projection-based wavefunction- in-DFT embedding method to provide a general framework for application studies using wide-ranging codes and for quantum embedding method developments”*

## Nathan Lim

*University of California, Irvine*

*2018-B Phase I, 2019-A Phase II*

**Adviser:** David L. Mobley

**MolSSI Software Mentor:** Eliseo Marin-Rimoldi

*“Development of an enhanced sampling toolkit for molecular dynamics simulations in OpenMM”*

## Fang Liu

*Massachusetts Institute of Technology*

*2019-A Seed, 2019-B Investment*

**Adviser:** Heather J. Kulik

**MolSSI Software Mentor:** Daniel G. A. Smith

*“Improving the interoperability of quantum chemistry packages and enabling in-situ automated analysis and control of simulations”*

## Aaron L. Mahler

*Duke University*

*2017-B Phase I, 2018-A Phase II*

**Adviser:** Weitao Yang

**MolSSI Software Mentor:** Taylor Barnes

*“Theory and implementation of a localized orbital scaling correction to generate improved functionals”*

## Dr. Sriramvignesh Mani

*University of Chicago*

*2020-B Seed*

**Adviser:** Gregory A. Voth

**MolSSI Software Mentor:** Andrew Abi-Mansour

*“Development of Multiscale Ultra-Coarse-Graining (UCG) Computational Framework for Simulating Biochemical Reaction Networks”*

## Dr. James D. McClain

*California Institute of Technology*

*2018-A Phase I*

**Adviser:** Garnet Chan

**MolSSI Software Mentor:** Daniel G. A. Smith, Taylor Barnes

*“Advancing the solid-state electronic structure capabilities of the open-source PySCF package”*

## Sina Mostafanejad

*Florida State University*

*2019-B Seed, 2020-A Investment*

**Adviser:** Albert Eugene DePrince III

**MolSSI Software Mentor:** Sam Ellis, Matthew Welborn

*“Accurate Reduced-Density Matrix-Based Methods for Strongly-Correlated Systems”*

## Ankita J. Mukhtyar

*Cornell University*

*2020-A Seed*

**Adviser:** Fernando A. Escobedo

**MolSSI Software Mentor:** Eliseo Marin-Rimoldi

*“Developing a pattern recognition based framework to characterize order in materials, with a focus on block copolymer self assembly”*

## Srinivas Mushnoori

*Rutgers University*

*2017-B Phase I, 2018-A Phase II*

**Adviser:** Meenakshi Dutt

**MolSSI Software Mentor:** Ben Pritchard, Doaa Altarawy

*“Development and extension of a flexible, scalable Replica Exchange framework”*

## Dominique Nocito

*University of California, Riverside*

*2018-B Phase I*

**Adviser:** Gregory Beran

**MolSSI Software Mentor:** Taylor Barnes

*“Developing algorithms to make numerically robust polarizable force field simulations more computationally tractable for chemical systems of interest.”*

## Mariya Popova

*University of North Carolina, Chapel Hill*

*2019-A Seed*

**Adviser:** Alexander Tropsha

**MolSSI Software Mentor:** Levi N. Naden

*“Deep Learning toolkit for computational chemistry and drug design”*

## Justin Provazza

*Boston University*

*2018-A Phase I, 2018-B Phase II*

**Adviser:** David Coker

**MolSSI Software Mentor:** Ben Pritchard

*“Development of a modular quantum dynamics and spectroscopy package for the computation of nonlinear spectroscopic signals and time-dependent observables in open quantum systems”*

## Dr. Yudong Qiu

*University of California, Davis*

*2018-B Phase I*

**Adviser:** Lee-Ping Wang

**MolSSI Software Mentor:** Daniel G. A. Smith, Doaa Altarawy

*“Development of a web application for automatic and reproducible force field parameterization.”*

## Joshua A. Rackers

*Washington University in St. Louis*

*2018-A Phase I*

**Adviser:** Jay W Ponder

**MolSSI Software Mentor:** Daniel G. A. Smith

*“Working to make the next generation of the AMOEBA force field more accurate and more widely available”*

## Farhad Ramezanghorbani

*University of Florida*

*2020-A Seed*

**Adviser:** Adrian Roitberg

**MolSSI Software Mentor:** Levi N. Naden, Matthew Welborn

*“Development of neural network architectures for multi-task learning of QM energies and forces to enhance drug discovery”*

## Dhiman Ray

*University of California Irvine*

*2020-B Seed*

**Adviser:** Ioan Andricioaei

**MolSSI Software Mentor:** Eliseo Marin-Rimoldi

*“Development and Implementation of the Weighted Ensemble Milestoning (WEM) Scheme for Studying Rare Events in Molecular Biophysics”*

## Marc Riera-Riambau

*University of California, San Diego*

*2017-B Phase I, 2018-A Phase II*

**Adviser:** Francesco Paesani

**MolSSI Software Mentor:** Daniel G. A. Smith

*“Development and application of many-body potential energy functions in a user friendly software interface”*

## Dr. Joao Rodrigues

*Stanford University School of Medicine*

*2020-A Seed*

**Adviser:** Michael Levitt

**MolSSI Software Mentor:** Levi N. Naden

*“Developing an open-source library to characterize the chemistry and energetics of protein interfaces”*

## Iliya Sabzevari

*The University of Colorado at Boulder*

*2020-B Seed*

**Adviser:** Sandeep Sharma

**MolSSI Software Mentor:** Levi N. Naden

*“My goal is to develop a systematically improvable approach to challenging chemical problems using Quantum Monte Carlo”*

## Dr. Janos Sarka

*Texas Tech University *

*2019-B Seed*

**Adviser:** Bill Poirier

**MolSSI Software Mentor:** Eliseo Marin-Rimoldi

*“Development of exact rovibrational spectroscopy codes to solve the time independent, nuclear-motion Schrödinger equation on massively parallel high-performance computing clusters”*

## Kutay Sezginel

*University of Pittsburgh*

*2018-B Phase I*

**Adviser:** Christopher E. Wilmer

**MolSSI Software Mentor:** Jessica A. Nash

*“Computational design of artificial molecular machines”*

## Dr. Xuecheng Shao

*Rutgers University – Newark*

*2020-B Investment*

**Adviser:** Michele Pavanello

**MolSSI Software Mentor:** Levi N. Naden

*“Development of multi-scale modeling software in Python based on embedding”*

## Tongtong Shen

*Purdue University*

*2020-B Seed*

**Adviser:** Alejandro Strachan

**MolSSI Software Mentor:** Jessica A. Nash

*“Polymer Crystal Structure Generator and Analysis Software (PolymerXtal)”*

## Dr. Hythem Sidky

*University of Chicago*

*2018-B Phase I*

**Adviser:** Andrew L. Ferguson

**MolSSI Software Mentor:** Eliseo Marin-Rimoldi, Doaa Altarawy

*“Combining machine learning, collective variable discovery, and free energy sampling in an OpenMM-accelerated framework”*

## James Smith

*University of Colorado, Boulder*

*2018-B Phase I, 2019-A Phase II*

**Adviser:** Sandeep Sharma

**MolSSI Software Mentor:** Taylor Barnes

*“Calculating nuclear energy gradients and response properties of SHCI wavefunctions.”*

## Chaya Stern

*Tri-Institutional PhD Program in Chemical Biology*

*2018-B Phase I, 2019-A Phase II*

**Adviser:** John Chodera

**MolSSI Software Mentor:** Daniel G. A. Smith

*“Improving molecular models via generating chemically relevant quantum mechanics data to remove bias in data, and quantifying parameter uncertainty due to force field fitting errors”*

## Torin F. Stetina

*University of Washington*

*2020-B Seed*

**Adviser:** Xiaosong Li

**MolSSI Software Mentor:** Ben Pritchard

*“An efficient implementation of effective QED configuration interaction for high accuracy heavy element chemistry”*

## Jocelyn Sunseri

*University of Pittsburgh*

*2018-A Phase I*

**Adviser:** David Koes

**MolSSI Software Mentor:** Doaa Altarawy, Jessica A. Nash

*“Novel algorithms for improving generalization and performance of machine learning models of molecular binding”*

## Dr. Tyler Takeshita

*University of California, Berkeley*

*2018-A Phase I, 2018-B Phase II*

**Adviser:** Eran Rabani

**MolSSI Software Mentor:** Daniel G. A. Smith

*“Stochastic electronic structure techniques for large-scale molecular systems”*

## Ruslan Tazhigulov

*Boston University*

*2018-A Phase I*

**Adviser:** Ksenia Bravaya

**MolSSI Software Mentor:** Doaa Altarawy

*“A web application for robust identification, mapping, and visualization of electron/hole transfer channels in proteins and protein families”*

## Erik Thiede

*University of Chicago*

*2017-B Phase I, 2018-A Phase II*

**Adviser:** Aaron Dinner, Jonathan Weare

**MolSSI Software Mentor:** Eliseo Marin-Rimoldi

*“Protein dynamics in the absence of collective variables through dynamics-dependent statistics and the study of partial differential equations”*

## Oanh Vu

*Vanderbilt University*

*2017-B Phase I, 2018-A Phase II*

**Adviser:** Jens Meiler

**MolSSI Software Mentor:** Doaa Altarawy

*“Machine-learning models used for drug discovery through local similarity-based descriptors with traditional autocorrelation descriptors”*

## Dr. Zhi Wang

*Washington University in St. Louis*

*2019-B Seed*

**Adviser:** Jay W Ponder

**MolSSI Software Mentor:** Andrew Abi-Mansour

*“GPU-accelerated library of the next-generation force fields and enhanced sampling methods for molecular dynamics simulations”*

## Michael D. Ward

*Washington University School of Medicine*

*2020-B Seed*

**Adviser:** Gregory R. Bowman

**MolSSI Software Mentor:** Sina Mostafanejad

*“Deep learning to identify the mechanistic basis for biochemical differences between protein variants.”*

## Geemi P. Wellawatte

*University of Rochester*

*2020-B Seed*

**Adviser:** Andrew D. White

**MolSSI Software Mentor:** Eliseo Marin-Rimoldi

*“Development of an automated, complete coarse-grained simulation model”*

## David Williams-Young

*University of Washington*

*2017-B Phase I, 2018-A Phase II*

**Adviser:** Xiaosong Li

**MolSSI Software Mentor:** Ben Pritchard

*“High-performance and scalable relativistic electronic structure methods for the ab initio prediction of molecular properties”*

## Dr. Chuck Witt

*Princeton University*

*2019-B Seed*

**Adviser:** Emily Carter

**MolSSI Software Mentor:** Doaa Altarawy, Matthew Welborn

*“New horizons for orbital-free density functional theory”*

## Haoyang Oscar Wu

*Massachusetts Institute of Technology*

*2020-B Seed*

**Adviser:** William H. Green

**MolSSI Software Mentor:** Sina Mostafanejad

*“Self-improving software that automatically predicts the chemical stability and model the radical oxidative degradation kinetics of active pharmaceutical ingredients in the solution.”*

## Jing Yang

*University of Pennsylvania*

*2018-A Phase I*

**Adviser:** Andrew Rappe

**MolSSI Software Mentor:** Taylor Barnes

*“Development of a ‘multi-functional’ optimized pseudopotential generator for accurate prediction of solids properties in density functional theory simulations”*

## Victor Yu

*Duke University*

*2019-A Seed, 2019-B Investment*

**Adviser:** Volker Blum

**MolSSI Software Mentor:** Jonathan Moussa

*“Open source software interface bridging electronic structure code to high-performance eigensolvers and density matrix solvers”*

## Boyi Zhang

*University of Georgia*

*2017-B Phase I, 2018-A Phase II*

**Adviser:** Fritz Schaefer

**MolSSI Software Mentor:** Doaa Altarawy, Taylor Barnes

*“A unified software platform that effectively implements various adaptive Quantum Mechanics/Molecular Mechanics (QM/MM) methods”*

## Dr. Jun Zhang

*University of Illinois*

*2017-B Phase I*

**Adviser:** So Hirata

**MolSSI Software Mentor:** Ben Pritchard

*“Ab initio quantum chemical calculations of periodic solids using Monte Carlo algorithms”*

## Ivy Zhang

*Memorial Sloan Kettering Cancer Center*

*2020-B Seed*

**Adviser:** John Chodera

**MolSSI Software Mentor:** Levi N. Naden

*“Design of SARS-CoV-2 antibodies using free energy calculations”*