Publications by authors named "Brenda 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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Lubricin's Mucin Domain Has Strong Polyproline Type-II Helical Character.
Bibo 'Noah' Feng, Ava J Marks, Faith Kim, Mandar Naik, Tannin A Schmidt, Brenda Rubenstein

bioRxiv· June 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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Gaussian processes for finite size extrapolation of many-body simulations.
Edgar Josué Landinez Borda, Kenneth O Berard, Annette Lopez, Brenda Rubenstein

Faraday Discuss· November 2024

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Stochastic and low-scaling techniques/extended systems: general discussion.
Ali Alavi, Kemal Atalar, Timothy C Berkelbach, George H Booth, Ji Chen, Brenda Rubenstein

Faraday Discuss· November 2024

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Is stochastic thermodynamics the key to understanding the energy costs of computation?
David H Wolpert, Jan Korbel, Christopher W Lynn, Farita Tasnim, Joshua A Grochow, Brenda Rubenstein

Proc Natl Acad Sci U S A· November 2024

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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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Self-Consistent Convolutional Density Functional Approximations: Application to Adsorption at Metal Surfaces.
Sushree Jagriti Sahoo, Qimen Xu, Xiangyun Lei, Daniel Staros, Gopal R Iyer, Brenda Rubenstein

Chemphyschem· May 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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Lowering Activation Barriers to Success in Physical Chemistry (LABSIP): A Community Project.
Carlos R Baiz, Robert F Berger, Kelling J Donald, Julio C de Paula, Stephen D Fried, Brenda Rubenstein

J Phys Chem A· January 2024

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Enabling Pd Catalytic Selectivity via Engineering Intermetallic Core@Shell Structure.
Mengqi Shen, Amir Afshar, Nathan Sinai, Huanqin Guan, Cooro Harris, Brenda Rubenstein

ACS Nano· January 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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A topological data analytic approach for discovering biophysical signatures in protein dynamics.
Wai Shing Tang, Gabriel Monteiro da Silva, Henry Kirveslahti, Erin Skeens, Bibo Feng, Brenda Rubenstein

PLoS Comput Biol· May 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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