Publications by authors named "Brenda M Rubenstein"

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Weighted Ensemble Simulations With the Drude Polarizable Model.
Marcelo D Polêto, Gabriel Monteiro da Silva, Brenda M Rubenstein, Justin A Lemkul

J Comput Chem· November 2025

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Identifying Band Inversions in Topological Materials Using Diffusion Monte Carlo.
Annette Lopez, Cody A Melton, Jeonghwan Ahn, Brenda M Rubenstein, Jaron T Krogel

J Chem Theory Comput· August 2025

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FastConformation: A Standalone ML-Based Toolkit for Modeling and Analyzing Protein Conformational Ensembles at Scale.
Flavia Maria Galeazzi, Gabriel Monteiro da Silva, Pablo Arantes, Iz Varghese, Ananya Shukla, Brenda M Rubenstein

bioRxiv· May 2025

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Mobility of four structural regions drives isoform-specific properties of photoenzyme LPOR in plants.
Michał Gabruk, Mateusz Łuszczyński, Katarzyna Szafran, Wiktoria Ogrodzińska, Brenda M Rubenstein

J Biol Chem· March 2025

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Force-Free Identification of Minimum-Energy Pathways and Transition States for Stochastic Electronic Structure Theories.
Gopal R Iyer, Noah Whelpley, Juha Tiihonen, Paul R C Kent, Jaron T Krogel, Brenda M Rubenstein

J Chem Theory Comput· September 2024

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Repurposing Waste Chemicals for Sustainable and Durable Molecular Data Storage.
Selahaddin Gumus, Dana Biechele-Speziale, Katherine E Manz, Kurt D Pennell, Brenda M Rubenstein

ACS Omega· May 2024

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Author Correction: High-throughput prediction of protein conformational distributions with subsampled AlphaFold2.
Gabriel Monteiro da Silva, Jennifer Y Cui, David C Dalgarno, George P Lisi, Brenda M Rubenstein

Nat Commun· April 2024

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High-throughput prediction of protein conformational distributions with subsampled AlphaFold2.
Gabriel Monteiro da Silva, Jennifer Y Cui, David C Dalgarno, George P Lisi, Brenda M Rubenstein

Nat Commun· March 2024

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Predicting Relative Populations of Protein Conformations without a Physics Engine Using AlphaFold 2.
Gabriel Monteiro da Silva, Jennifer Y Cui, David C Dalgarno, George P Lisi, Brenda M Rubenstein

bioRxiv· December 2023

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Predicting Relative Populations of Protein Conformations without a Physics Engine Using AlphaFold2.
Gabriel Monteiro da Silva, Jennifer Y Cui, David C Dalgarno, George P Lisi, Brenda M Rubenstein

ArXiv· July 2023

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Stable recursive auxiliary field quantum Monte Carlo algorithm in the canonical ensemble: Applications to thermometry and the Hubbard model.
Tong Shen, Hatem Barghathi, Jiangyong Yu, Adrian Del Maestro, Brenda M Rubenstein

Phys Rev E· May 2023

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Machine Learning Diffusion Monte Carlo Forces.
Cancan Huang, Brenda M Rubenstein

J Phys Chem A· January 2023

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Digital circuits and neural networks based on acid-base chemistry implemented by robotic fluid handling.
Ahmed A Agiza, Kady Oakley, Jacob K Rosenstein, Brenda M Rubenstein, Eunsuk Kim

Nat Commun· January 2023

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Defining the HIV Capsid Binding Site of Nucleoporin 153.
Shunji Li, Jagdish Suresh Patel, Jordan Yang, Angela Marie Crabtree, Brenda Marilyn Rubenstein

mSphere· October 2022

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Finite-Size Error Cancellation in Diffusion Monte Carlo Calculations of Surface Chemistry.
Gopal R Iyer, Brenda M Rubenstein

J Phys Chem A· July 2022

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Covalent docking and molecular dynamics simulations reveal the specificity-shifting mutations Ala237Arg and Ala237Lys in TEM beta-lactamase.
Gabriel Monteiro da Silva, Jordan Yang, Bunlong Leang, Jessie Huang, Daniel M Weinreich, Brenda M Rubenstein

PLoS Comput Biol· June 2022

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LYRUS: a machine learning model for predicting the pathogenicity of missense variants.
Jiaying Lai, Jordan Yang, Ece D Gamsiz Uzun, Brenda M Rubenstein, Indra Neil Sarkar

Bioinform Adv· December 2021

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Secret messaging with endogenous chemistry.
Eamonn Kennedy, Joseph Geiser, Christopher E Arcadia, Peter M Weber, Christopher Rose, Brenda M Rubenstein

Sci Rep· July 2021

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Real-time dynamics of strongly correlated fermions using auxiliary field quantum Monte Carlo.
Matthew S Church, Brenda M Rubenstein

J Chem Phys· May 2021

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Leveraging autocatalytic reactions for chemical domain image classification.
Christopher E Arcadia, Amanda Dombroski, Kady Oakley, Shui Ling Chen, Hokchhay Tann, Brenda M Rubenstein

Chem Sci· March 2021

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Observation of a Symmetry-Forbidden Excited Quadrupole-Bound State.
Yuan Liu, Guo-Zhu Zhu, Dao-Fu Yuan, Chen-Hui Qian, Yue-Rou Zhang, Brenda M Rubenstein

J Am Chem Soc· November 2020

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Finite temperature auxiliary field quantum Monte Carlo in the canonical ensemble.
Tong Shen, Yuan Liu, Yang Yu, Brenda M Rubenstein

J Chem Phys· November 2020

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Polarization of Valence Orbitals by the Intramolecular Electric Field from a Diffuse Dipole-Bound Electron.
Dao-Fu Yuan, Yuan Liu, Chen-Hui Qian, G Stephen Kocheril, Yue-Rou Zhang, Brenda M Rubenstein

J Phys Chem Lett· September 2020

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Predicting the viability of beta-lactamase: How folding and binding free energies correlate with beta-lactamase fitness.
Jordan Yang, Nandita Naik, Jagdish Suresh Patel, Christopher S Wylie, Wenze Gu, Brenda M Rubenstein

PLoS One· August 2020

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Observation of a π-Type Dipole-Bound State in Molecular Anions.
Dao-Fu Yuan, Yuan Liu, Chen-Hui Qian, Yue-Rou Zhang, Brenda M Rubenstein

Phys Rev Lett· August 2020

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