Journal of Chemical Theory and Computation Journal

Overview

publication venue for

• Assessing the Accuracy and Efficiency of Free Energy Differences Obtained from Reweighted Flow-Based Probabilistic Generative Models. 2024
• Replica Exchange of Expanded Ensembles: A Generalized Ensemble Approach with Enhanced Flexibility and Parallelizability. 2024
• Toward Linear Scaling Auxiliary-Field Quantum Monte Carlo with Local Natural Orbitals 2023
• Accurate Force Fields for Atomistic Simulations of Oxides, Hydroxides, and Organic Hybrid Materials up to the Micrometer Scale 2023
• Development and Benchmarking of Open Force Field 2.0.0: The Sage Small Molecule Force Field 2023
• Alchemical Metadynamics: Adding Alchemical Variables to Metadynamics to Enhance Sampling in Free Energy Calculations 2023
• Relativistic Semistochastic Heat-Bath Configuration Interaction 2023
• Fast Exchange with Gaussian Basis Set Using Robust Pseudospectral Method 2022
• Folding Coarse-Grained Oligomer Models with PyRosetta 2022
• Improving Force Field Accuracy by Training against Condensed-Phase Mixture Properties 2022
• Open Force Field Evaluator: An Automated, Efficient, and Scalable Framework for the Estimation of Physical Properties from Molecular Simulation 2022
• Bond-Valence Parameterization for the Accurate Description of DFT Energetics 2022
• CHARMM-GUI Nanomaterial Modeler for Modeling and Simulation of Nanomaterial Systems 2022
• Development and Benchmarking of Open Force Field v1.0.0-the Parsley Small-Molecule Force Field 2021
• Expanded Ensemble Methods Can be Used to Accurately Predict Protein-Ligand Relative Binding Free Energies 2021
• Using a Coarse-Grained Modeling Framework to Identify Oligomeric Motifs with Tunable Secondary Structure 2021
• Accurate and Compatible Force Fields for Molecular Oxygen, Nitrogen, and Hydrogen to Simulate Gases, Electrolytes, and Heterogeneous Interfaces 2021
• Taming the Sign Problem in Auxiliary-Field Quantum Monte Carlo Using Accurate Wave Functions 2021
• Externally Corrected CCSD with Renormalized Perturbative Triples (R-ecCCSD(T)) and the Density Matrix Renormalization Group and Selected Configuration Interaction External Sources 2021
• Efficient Evaluation of Two-Center Gaussian Integrals in Periodic Systems 2021
• Statistical Mechanical Approximations to More Efficiently Determine Polymorph Free Energy Differences for Small Organic Molecules 2020
• Capturing Subdiffusive Solute Dynamics and Predicting Selectivity in Nanoscale Pores with Time Series Modeling 2020
• Modified Single Iteration Synchronous-Transit Approach to Bound Diffusion Barriers for Solid-State Reactions 2020
• Statistically Optimal Continuous Free Energy Surfaces from Biased Simulations and Multistate Reweighting 2020
• Toward Learned Chemical Perception of Force Field Typing Rules 2019
• Improved Speed and Scaling in Orbital Space Variational Monte Carlo 2018
• Escaping Atom Types in Force Fields Using Direct Chemical Perception 2018
• Thermal Gradient Approach for the Quasi-harmonic Approximation and Its Application to Improved Treatment of Anisotropic Expansion 2018
• Configuration-Sampling-Based Surrogate Models for Rapid Parameterization of Non-Bonded Interactions 2018
• One-Step Treatment of Spin-Orbit Coupling and Electron Correlation in Large Active Spaces 2018
• Cheap and Near Exact CASSCF with Large Active Spaces 2017
• Multistate Complete-Active-Space Second-Order Perturbation Theory Based on Density Matrix Renormalization Group Reference States 2017
• Semistochastic Heat-Bath Configuration Interaction Method: Selected Configuration Interaction with Semistochastic Perturbation Theory 2017
• Combining Internally Contracted States and Matrix Product States To Perform Multireference Perturbation Theory 2017
• Effects of a More Accurate Polarizable Hamiltonian on Polymorph Free Energies Computed Efficiently by Reweighting Point-Charge Potentials 2016
• Comparison of Methods To Reweight from Classical Molecular Simulations to QM/MM Potentials 2016
• Rapid Computation of Thermodynamic Properties over Multidimensional Nonbonded Parameter Spaces Using Adaptive Multistate Reweighting 2016
• Linear Basis Function Approach to Efficient Alchemical Free Energy Calculations. 2. Inserting and Deleting Particles with Coulombic Interactions 2015
• Correction to Small Molecule Hydration Free Energies in Explicit Solvent: An Extensive Test of Fixed-Charge Atomistic Simulations. 2015
• Correction to Small Molecule Hydration Free Energies in Explicit Solvent: An Extensive Test of Fixed-Charge Atomistic Simulations (vol 5, pg 350, 2009) 2015
• Linear Basis Function Approach to Efficient Alchemical Free Energy Calculations. 1. Removal of Uncharged Atomic Sites 2014
• Using Multistate Reweighting to Rapidly and Efficiently Explore Molecular Simulation Parameters Space for Nonbonded Interactions 2013
• Effects of Temperature Control Algorithms on Transport Properties and Kinetics in Molecular Dynamics Simulations 2013
• Simple Quantitative Tests to Validate Sampling from Thermodynamic Ensembles 2013
• OpenMM 4: A Reusable, Extensible, Hardware Independent Library for High Performance Molecular Simulation 2013
• A Benchmark Test Set for Alchemical Free Energy Transformations and Its Use to Quantify Error in Common Free Energy Methods 2011
• Small Molecule Hydration Free Energies in Explicit Solvent: An Extensive Test of Fixed-Charge Atomistic Simulations 2009
• Improved Methods for Side Chain and Loop Predictions via the Protein Local Optimization Program:  Variable Dielectric Model for Implicitly Improving the Treatment of Polarization Effects 2007
• Improved methods for side chain and loop predictions via the protein local optimization program: Variable dielectric model for implicitly improving the treatment of polarization effects 2007
• Multiscale optimization of a truncated Newton minimization algorithm and application to proteins and protein-ligand complexes 2007

Research

keywords

• 0307 Theoretical and Computational Chemistry, 0803 Computer Software, 0601 Biochemistry and Cell Biology