Publications

Daniel Staros, Abdulgani Annaberdiyev, Kevin Gasperich, Anouar Benali, Panchapakesan Ganesh, And Brenda Rubenstein (2025). A many-body characterization of the fundamental gap in monolayer CrI3.

Bibo ’Noah’ Feng, Ava J. Marks, Faith Kim, Mandar Naik, Tannin A. Schmidt, Khaled A. Elsaid, Gregory D. Jay, Brenda Rubenstein (2025). Lubricin’s Mucin Domain Has Strong Polyproline Type-II Helical Character.

Flavia Maria Galeazzi, Gabriel Monteiro Da Silva, Pablo Ricardo Arantes, Iz Varghese, Ananya Shukla, Brenda Marilyn Rubenstein (2025). FastConformation: A Standalone ML-Based Toolkit for Modeling and Analyzing Protein Conformational Ensembles at Scale.

Michał Gabruk, Mateusz Łuszczyński, Katarzyna Szafran, Wiktoria Ogrodzińska, Brenda M. Rubenstein, And Gabriel Monteiro Da Silva (2025). Mobility of Four Isostructural Regions Drives Isoform-Specific Properties of Plant LPOR.

Annette Lopez, Cody A. Melton, Jeonghwan Ahn, Brenda M. Rubenstein, Jaron T. Krogel (2025). Identifying Band Inversions in Topological Materials Using Diffusion Monte Carlo. JCTC.

Yash M. Lokare, Dingding Wei, Lucas Chan, Brenda Rubenstein, J. B. Marston (2024). Steady-State Statistics of Classical Nonlinear Dynamical Systems from Noisy Intermediate-Scale Quantum Devices.

Gopal Iyer, Noah Whelpley, Juha Tiihonen, Paul R.C. Kent, Jaron T. Krogel, Brenda Rubenstein (2024). Force-free identification of minimum-energy pathways and transition states for stochastic electronic structure theories. Journal of Chemical Theory and Computation.

Abid Khan, Prateek Vaish, Yaoqi Pang, Nikhil Kowshik, Michael S. Chen, Clay H. Batton, Grant M. Rotskoff, J. Wayne Mullinax, Bryan K. Clark, Brenda M. Rubenstein, And Norm M. Tubman (2024). Quantum Hardware-Enabled Molecular Dynamics via Transfer Learning.

Daniel Wines, Jeonghwan Ahn, Anouar Benali, Paul R. C. Kent, Jaron T. Krogel, Yongkyung Kwon, Lubos Mitas, Fernando A. Reboredo, Brenda Rubenstein, Kayahan Saritas, Hyeondeok Shin, Ivan Štich, Can Ataca (2024). Towards improved property prediction of two-dimensional (2D) materials using many-body Quantum Monte Carlo methods.

Gabriel Monteiro Da Silva, Kyle Lam, David C. Dalgarno, Brenda Rubenstein (2024). Compound Mutations in the Abl1 Kinase Cause Inhibitor Resistance by Shifting DFG Flip Mechanisms and Relative State Populations.

Tong Shen, Hatem Barghathi, Adrian Del Maestro, Brenda Rubenstein (2024). Disentangling the Physics of the Attractive Hubbard Model via the Accessible and Symmetry-Resolved Entanglement Entropies. Phys. Rev. B 109, 195119 (2024).

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Tilas Kabengele, Yash M. Lokare, J. B. Marston, Brenda Rubenstein (2024). Modeling Stochastic Chemical Kinetics on Quantum Computers.

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Gabriel Monteiro Da Silva, Jennifer Cui, David Dalgarno, George Lisi, Brenda Rubenstein (2024). High-Throughput Prediction of Protein Conformational Distributions with Subsampled AlphaFold2. Nature Communications, 15: 2464 (2024).

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Edgar Josue Landinez-Borda, Kenneth Berard, Annette Lopez, Brenda Rubenstein (2024). Gaussian Processes for Finite Size Extrapolation of Many-Body Simulations. Faraday Discussion (2024) arXiv:2112.10334.

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Gopal Iyer, Brenda Rubenstein (2024). Atomistic Descriptor Optimization Using Complementary Euclidean and Geodesic Distance Information. Molecular Physics.

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Mengqi Shen, Amir Afshar, Nathan Sinai, Huanqin Guan, Cooro Harris, Brenda Rubenstein, Shouheng Sun (2023). Enabling Pd Catalytic Selectivity via Engineering Intermetallic Core@Shell Structure. ACS Nano. 18(1): 178-185 (2024).

David Wolpert, Jan Korbel, Christopher Lynn, Farita Tasnim, Joshua Grochow, Gülce Kardeş, James Aimone, Vijay Balasubramanian, Eric De Giuli, David Doty, Nahuel Freitas, Matteo Marsili, Thomas E. Ouldridge, Andrea Richa, Paul Riechers, Édgar Roldán, Brenda Rubenstein, Zoltan Toroczkai, Joseph Paradiso (2023). Is stochastic thermodynamics the key to understanding the energy costs of computation?. Proceedings of the National Academy of Sciences.

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Daniel Nader, Brenda Rubenstein (2023). VMC Optimization of Ultra-Compact Explicitly-Correlated Wave Functions of the Li Isoelectronic Sequence in Its Lowest 1s2s2p Quartet State. Chemical Physics Letters. 838: 141091 (2024). arXiv:2310.00916.

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Carlos Baiz, Robert Berger, Kelling Donald, Julio De Paula, Stephen Fried, Brenda Rubenstein, Grace Stokes, Kana Takematsu, Casey Londergran (2023). Lowering Activation Barriers to Success in Physical Chemistry (LABSIP): A Community Project. Journal of Physical Chemistry A. 128(1): 3-9 (2024).

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Selahaddin Gumus, Dana Biechele-Speziale, Katherine Manz, Kurt Pennell, Brenda Rubenstein, J. Rosenstein (2023). Repurposing Waste Chemicals for Sustainable and Durable Molecular Data Storage. ACS Omega, 9: 18, 19904–19910 (2024)..

Daniel Staros, Brenda Rubenstein, Panchapakesan Ganesh (2023). A First-Principles Study of Bilayer 1T'-WTe2/CrI3: A Candidate Topological Spin Filter. npj Spintronics: 2, 4 (2024). arXiv:2308.06415.

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Sushree Jagriti Sahoo, Qimen Xu, Xiangyun Lei, Daniel Staros, Gopal Iyer, Brenda Rubenstein, Phanish Suryanarayana, Andrew Medford (2023). Self-Consistent Convolutional Density Functional Approximations: Formulation and Application to Adsorption at Metal Surfaces. ChemPhysChem (2024); arXiv:2308.05310.

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Tong Shen, H. Barghathi, J. Yu, A. Del Maestro, Brenda Rubenstein (2023). Stable Recursive Auxiliary Field Quantum Monte Carlo Algorithm in the Canonical Ensemble: Applications to Thermometry and the Hubbard Model. Phys. Rev. E. 107, 055302 (2023). arXiv:2212.08654.

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M. F. DiScala, Daniel Staros, A. De La Torre, Annette Lopez, D. Wong, C. Schulz, M. Bartkowiak, Brenda Rubenstein, K. W. Plumb (2023). Dimensionality dependent electronic structure of the exfoliated van der Waals antiferromagnet NiPS3. Advanced Physics Research. 2300096. arXiv:2302.07910.

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A. Agiza, K. Oakley, J. Rosenstein, Brenda Rubenstein, E. Kim, M. Riedel, S. Reda (2023). Digital Circuits and Neural Networks Based on Acid-Base Chemistry Implemented by Robotic Fluid Handling. Nature Communications. 14(496) (2023).

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C. Huang, Brenda Rubenstein (2022). Machine Learning Diffusion Monte Carlo Forces. Journal of Physical Chemistry A. 127(1): 339-355 (2023). arXiv:2211.07103.

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J. Lai, J. Yang, E. Uzun, Brenda Rubenstein, I. N. Sarkar (2022). LYRUS: A Machine Learning Model for Predicting the Pathogenicity of Missense Variants. Bioinformatics Advances, 2(1): vbab045.

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Gopal Iyer, Brenda Rubenstein (2022). Error Cancellation in Diffusion Monte Carlo Calculations of Surface Chemistry. J. Phys. Chem. A. 126(28): 4636-4646 (2022). arXiv:2206.00729.

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S. Li, J. Patel, J. Yang, A. Crabtree, Brenda Rubenstein, P. Lund-Andersen, F. Ytreberg, P. Rowley (2022). Defining the HIV Capsid Binding Site of Nucleoporin 153. mSphere. 7(5) (2022). biorxiv: 10.1101/2022.05.06.490988v1.

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Gabriel Monteiro Da Silva, J. Yang, B. Leang, J. Huang, D.M. Weinreich, Brenda Rubenstein (2022). Covalent Docking and Molecular Dynamics Simulations Reveal the Specificity-Shifting Mutations Ala237Arg and Ala237Lys in TEM Beta-Lactamase. PLoS Comput. Biol. 18(6): e1009944.

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W. S. Tang, Gabriel Monteiro Da Silva, H. Kirveslahti, E. Skeens, B. Feng, T. Sudijono, K. Yang, S. Mukherjee, Brenda Rubenstein, L. Crawford (2022). A Topological Data Analytic Approach for Discovering Biophysical Signatures in Protein Dynamics. PLoS Comput Biol. 18(5): e1010045.

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Daniel Staros, G. Hu, R. Nanguneri, J. Krogel, M.C. Bennett, O. Heinonen, P. Ganesh, Brenda Rubenstein (2022). A Combined First Principles Study of the Structural, Magnetic, and Phonon Properties of Monolayer CrI3. J. Chem. Phys. 156, 014707.

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Benjamin-Foulon, K. Ray, C. Kim, Y. Liu, Brenda Rubenstein, V. Lordi (2022). 1/w Electric-Field Noise in Surface Ion Traps from Correlated Adsorbate Dynamics. Phys. Rev. A, 105, 013107.

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E. Kennedy, J. Geiser, C. Arcadia, P. Weber, C. Rose, Brenda Rubenstein, J. Rosenstein (2021). Secret Messaging with Endogenous Chemistry. Scientific Reports, 11, 13960.

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M.S. Church, Brenda Rubenstein (2021). Real Time Dynamics of Correlated Fermions via Auxiliary Field Quantum Monte Carlo. J. Chem. Phys., 154, 184103.

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C. Arcadia, A. Dombroski, K. Oakley, S.-L. Chen, H. Tann, C. Rose, E. Kim, S. Reda, Brenda Rubenstein, J. Rosenstein (2021). Leveraging Autocatalytic Reactions for Chemical-Domain Image Classification. Chemical Science.

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A. Dombroski, K. Oakley, C. Arcadia, F. Nouraei, S.L. Chen, C. Rose, Brenda Rubenstein, J. Rosenstein, S.Reda, E. Kim (2021). Implementing Parallel Arithmetic via Acetylation and Its Application to Chemical Image Processing. Proceedings of the Royal Society A, 477, 2248.

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J. Yang, N. Naik, J. S. Patel, C. S. Wylie, W. Gu, J. Huang, F. M. Ytreberg, M. T. Naik, D. M. Weinreich, Brenda Rubenstein (2020). Predicting the Viability of Beta-Lactamase: How Folding and Binding Free Energies Correlate with Beta-Lactamase Fitness. PLOS One. 15(5), e0233509.

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P. R. C. Kent, A. Annaberdiyev, A. Benali, M. Chandler Bennett, E. J. Landinez Borda, P. Doak, K. D. Jordan, J. T. Kogel, I. Kylanpaa, J. Lee, Y. Luo, F. D. Malone, C. A. Melton, L. Mitas, M. A. Morales, E. Neuscamman, F. A. Reboredo, Brenda Rubenstein, K. Saritas, S. Upadhyay, H. Hao, G. Wang, S. Zhang, L. Zhao (2020). QMCPACK: Advances in the Development, Efficiency, and Application of Auxiliary Field and Real-Space Variational and Diffusion Quantum Monte Carlo. Selected as the Editor’s Pick by the Journal of Chemical Physics. 152 (17): 174105 (2020).

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Y. Liu, Tong Shen, H. Zhang, Brenda Rubenstein (2020). Unveiling the Finite Temperature Physics of Hydrogen Chains via Auxiliary Field Quantum Monte Carlo. Journal of Chemical Theory and Computation. 16 (7), 4298-4314.

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J. Rosenstein, C. Rose, S. Reda, P. M. Weber, E. Kim, J. Sello, J. Geiser, E. Kennedy, C. Arcadia, A. Dombroski, K. Oakley, S.-L. Chen, H. Tann, Brenda Rubenstein (2020). Principles of Information Storage in Small-Molecular Mixtures. Accepted for IEEE Transactions on Nanobioscience.

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D. Yuan, Y. Liu, C.-H. Qian, G. S. Kocheril, Y.-R. Zhang, Brenda Rubenstein, L.-S. Wang (2020). Polarization of Valence Orbitals by the Intramolecular Electric Field from a Diffuse Dipole-Bound Electron. J. Phys. Chem. Lett.1 (18),7914–7919.

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Y. Liu, G.-Z. Zhu, D.-F. Yuan, C.-H. Qian, Y.-R. Zhang, Brenda Rubenstein, L.-S. Wang (2020). Observation of a Symmetry-Forbidden Excited Quadrupole-Bound State. JACS, 142 (47), 20240-20246.

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D. Yuan, Y. Liu, C.-H. Qian, Y.-R. Zhang, Brenda Rubenstein, L.-S. Wang (2020). Observation of a Pi-Type Dipole-Bound State in Molecular Anions. Phys. Rev. Lett. 125, 073003.

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C. E. Arcadia, E. Kennedy, J. Geiser, A. Dombroski, K. Oakley, S.-L. Chen, L. Sprague, M. Ozmen, J. Sello, P. M. Weber, S. Reda, C. Rose, E. Kim, Brenda Rubenstein, J. Rosenstein (2020). Multicomponent Molecular Memory. Nature Communications.

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H. Hao, A. Georges, A. Millis, Brenda Rubenstein, Q. Han, H. Shi (2020). Metal-Insulator and Magnetic Phase Diagram of Ca2RuO4 from Auxiliary Field Quantum Monte Carlo and Dynamical Mean Field Theory. Physical Review B, 101, 235110.

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R. Cong, R. Nanguneri, Brenda Rubenstein, V. Mitrovic (2020). First Principles Calculations of the EFG Tensors of Ba2NaOsO6, a Mott Insulator with Strong Spin Orbit Coupling. Journal of Physics.: Condensed Matter, 100, 245141.

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Tong Shen, Y. Liu, Y. Yu, Brenda Rubenstein (2020). Finite Temperature Auxiliary Field Quantum Monte Carlo in the Canonical Ensemble. J. Chem. Phys. 153, 204108.

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K.G. Ray, Brenda Rubenstein, W. Gu, V. Lordi (2019). vdW-Corrected Density Functional Study of Electric Field Noise Heating in Ion Traps Caused by Electrode Surface Adsorbates. New J. Phys.

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L. Sprague, C. Huang, J.-P. Song, Brenda Rubenstein (2019). Maximizing Thermoelectric Figures of Merit by Uniaxially Straining Indium Selenide. Journal of Physical Chemistry C.

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R. Cong, R. Nanguneri, Brenda Rubenstein (2019). First Principles Calculations of the EFG Tensors of Ba2NaOsO6, a Mott Insulator with Strong Spin Orbit Coupling. Accepted for Physical Review B, 100, 245141.

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E. Kennedy, C. Arcadia, J. Geiser, P. M. Weber, C. Rose, Brenda Rubenstein, J. Rosenstein (2019). Encoding Information in Synthetic Metabolomes. PLOS One.

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H. Hao, Brenda Rubenstein, H. Shi (2019). Auxiliary Field Quantum Monte Carlo for Multiband Hubbard Models: Controlling the Sign and Phase Problems to Capture Hund's Physics. Phys. Rev. B.

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Benjamin-Foulon, Y. Liu, J. Rosenstein, Brenda Rubenstein (2019). A Language for Molecular Computation. Chem.

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T. Cai, H. Yang, K. Hills-Kimball, J.-P. Song, H. Zhu, E. Hofamn, W. Zheng, Brenda Rubenstein, O. Chen (2018). Synthesis of All-Inorganic Cd-Doped CsPbCl3 Perovskite Nanocrystals with Dual-Wavelength Emission. Journal of Chemical Physics Letters.

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Jeongnim Kim, Andrew D Baczewski, Todd D Beaudet, Anouar Benali, M Chandler Bennett, Mark a Berrill, Nick S Blunt, Edgar Josué Landinez Borda, Michele Casula, David M Ceperley, Simone Chiesa, Bryan K Clark, Raymond C Clay III, Kris T Delaney, Mark Dewing, Kenneth P Esler, Hongxia Hao, Olle Heinonen, Paul R C Kent, Jaron T Krogel, Ilkka Kylänpää, Ying Wai Li, M Graham Lopez, Ye Luo, Fionn D Malone, Richard M Martin, Amrita Mathuriya, Jeremy McMinis, Cody a Melton, Lubos Mitas, Miguel a Morales, Eric Neuscamman, William D Parker, Sergio D Pineda Flores, Nichols a Romero, Brenda Rubenstein, Jacqueline a R Shea, Hyeondeok Shin, Luke Shulenburger, Andreas F Tillack, Joshua P Townsend, Norm M Tubman, Brett Van Der Goetz, Jordan E Vincent, D ChangMo Yang, Yubo Yang, Shuai Zhang, Luning Zhao (2018). QMCPACK: An Open Source Ab Initio Quantum Monte Carlo Package for the Electronic Structure of Atoms, Molecules, and Solids. Journal of Physics: Condensed Matter, 30, 195901.

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H. Zhu, T. Cai, M. Que, J.-P. Song, Brenda Rubenstein, Z. Wang, O. Chen (2018). Pressure-Induced Phase Transformation and Band-Gap Engineering of Formamidinium Lead Iodide Perovskite Nanocrystals. Journal of Physical Chemistry Letters, 9(15), 4199.

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C. Arcadia, H. Tann, A. Dombroski, K. Ferguson, S.-L. Chen, E. Kim, C. Rose, Brenda Rubenstein, S. Reda, J. Rosenstein (2018). Parallelized Linear Classification with Volumetric Chemical Perceptrons. Accepted to Proceedings of the International Conference on Rebooting Computing.

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Brenda Rubenstein, J. Rosenstein, E. Kim, S. Reda, J.D. Geiser, P.M. Weber, C. Rose, J. Sello (2018). Methods of Chemical Computation. Patent Application (Provisional 2018, Full 2019).

Y. Liu, M. Cho, Brenda Rubenstein (2018). Finite Temperature Ab Initio Auxiliary Field Quantum Monte Carlo. Journal of Chemical Theory and Computation.

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Brenda Rubenstein, J. Rosenstein (2018). Encoding Information in Synthetic Metabolomes and Molecular Mixtures. Provisional Patent Application.

H. Hao, J. Shee, S. Upadhyay, C. Ataca, K. Jordan, Brenda Rubenstein (2018). Accurate Predictions of Electron Binding Energies of Dipole-Bound Anions via Quantum Monte Carlo Methods. Journal of Chemical Physics Letters.

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E. Schwegler, Brenda Rubenstein, S. Libby (2017). Symposium in Honor of Dr. Berni Alder's 90th Birthday. Advances in the Computational Sciences. World Scientific.

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M. Gulian, H. Yang, Brenda Rubenstein (2017). Fractional Path Integral Monte Carlo. Submitted to JCP.

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Brenda Rubenstein (2016). Introduction to the variational Monte Carlo method in quantum chemistry and physics. Variational Methods in Molecular Modeling, ed. Jianzhong Wu.

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C.-C. Chang, Brenda Rubenstein, M.A. Morales-Silva (2016). Auxiliary-field based trial wave functions in quantum Monte Carlo calculations. Physical Review B (Rapid). 94, 235144.

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Brenda Rubenstein (2013). Novel Quantum Monte Carlo Approaches for Quantum Liquids. Ph.D. Thesis (Columbia University).

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Brenda Rubenstein, S. Zhang, D.R. Reichman (2012). Finite-temperature auxiliary-field quantum Monte Carlo technique for Bose-Fermi mixtures. Physical Review A. 86, 053606.

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Brenda Rubenstein, I. Coluzza, M.A. Miller (2012). Controlling the folding and substrate-binding of proteins using polymer brushes. Physical Review Letters. 108, 208104.

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Brenda Rubenstein, J.E. Gubernatis, J.D. Doll (2010). Comparative Monte Carlo efficiency by Monte Carlo analysis. Physical Review E. 82, 036701.

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Brenda Rubenstein, L. J. Kaufman (2008). The role of extracellular matrix in glioma invasion: A cellular Potts model approach. Biophysical Journal. 95(12): 5661.

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Brenda Rubenstein (2008). Protein Folding and Binding Amidst Entropy Sources. M.Phil. Thesis (University of Cambridge).

Brenda Rubenstein (2007). Complex Structure, Complex Dynamics: The Dynamics of Liquid Crystals in the Nematic Phase. Sc.B. Thesis (Brown University).