<h1>Miller, Thomas F.</h1> <h2>Combined from <a href="https://authors.library.caltech.edu">CaltechAUTHORS</a></h2> <ul> <li>Qiao, Zhuoran and Nie, Weili, el al. (2024) <a href="https://authors.library.caltech.edu/records/rhxkg-vj009">State-specific protein–ligand complex structure prediction with a multiscale deep generative model</a>; Nature Machine Intelligence; <a href="https://doi.org/10.1038/s42256-024-00792-z">10.1038/s42256-024-00792-z</a></li> <li>Mai, Huanghao and Zimmer, Matthew H., el al. (2023) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20230209-988069100.19">Exploring PROTAC Cooperativity with Coarse-Grained Alchemical Methods</a>; Journal of Physical Chemistry B; Vol. 127; No. 2; 446-455; PMCID PMC9869335; <a href="https://doi.org/10.1021/acs.jpcb.2c05795">10.1021/acs.jpcb.2c05795</a></li> <li>Dommer, Abigail and Casalino, Lorenzo, el al. (2023) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20221017-15547800.39">#COVIDisAirborne: AI-enabled multiscale computational microscopy of delta SARS-CoV-2 in a respiratory aerosol</a>; International Journal of High Performance Computing Applications; Vol. 37; No. 1; 28-44; PMCID PMC9527558; <a href="https://doi.org/10.1177/10943420221128233">10.1177/10943420221128233</a></li> <li>Cheng, Lixue and Sun, Jiace, el al. (2022) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20221110-414654600.1">Molecular-orbital-based machine learning for open-shell and multi-reference systems with kernel addition Gaussian process regression</a>; Journal of Chemical Physics; Vol. 157; No. 15; Art. No. 154105; <a href="https://doi.org/10.1063/5.0110886">10.1063/5.0110886</a></li> <li>Lawniczak, James J. and Zhang, Xinglong, el al. (2022) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20221011-128968500.22">Solution-Phase Conformational/Vibrational Anharmonicity in Comonomer Incorporation Polyolefin Catalysis</a>; Journal of Physical Chemistry A; Vol. 126; No. 39; 6858-6869; <a href="https://doi.org/10.1021/acs.jpca.2c04038">10.1021/acs.jpca.2c04038</a></li> <li>Qiao, Zhuoran and Nie, Weili, el al. (2022) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20221221-004659742">Dynamic-Backbone Protein-Ligand Structure Prediction with Multiscale Generative Diffusion Models</a>; <a href="https://doi.org/10.48550/arXiv.2209.15171">10.48550/arXiv.2209.15171</a></li> <li>Sun, Jiace and Cheng, Lixue, el al. (2022) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20221010-454096500.3">Molecular dipole moment learning via rotationally equivariant derivative kernels in molecular-orbital-based machine learning</a>; Journal of Chemical Physics; Vol. 157; No. 10; Art. No. 104109; <a href="https://doi.org/10.1063/5.0101280">10.1063/5.0101280</a></li> <li>Cheng, Lixue and Sun, Jiace, el al. (2022) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20220517-214308613">Accurate Molecular-Orbital-Based Machine Learning Energies via Unsupervised Clustering of Chemical Space</a>; Journal of Chemical Theory and Computation; Vol. 18; No. 8; 4826-4835; <a href="https://doi.org/10.1021/acs.jctc.2c00396">10.1021/acs.jctc.2c00396</a></li> <li>Shoshani, Manar M. and Xiong, Shuoyan, el al. (2022) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20220720-918328000">Phosphine-Phenoxide Nickel Catalysts for Ethylene/Acrylate Copolymerization: Olefin Coordination and Complex Isomerization Studies Relevant to the Mechanism of Catalysis</a>; Organometallics; Vol. 41; No. 15; 2119-2131; <a href="https://doi.org/10.1021/acs.organomet.2c00241">10.1021/acs.organomet.2c00241</a></li> <li>Qiao, Zhuoran and Christensen, Anders S., el al. (2022) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20210831-203900979">Informing geometric deep learning with electronic interactions to accelerate quantum chemistry</a>; Proceedings of the National Academy of Sciences; Vol. 119; No. 31; Art. No. e2205221119; PMCID PMC9351474; <a href="https://doi.org/10.1073/pnas.2205221119">10.1073/pnas.2205221119</a></li> <li>Lu, Fenris and Cheng, Lixue, el al. (2022) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20220721-8916000">Fast Near Ab Initio Potential Energy Surfaces Using Machine Learning</a>; Journal of Physical Chemistry A; Vol. 126; No. 25; 4013-4024; <a href="https://doi.org/10.1021/acs.jpca.2c02243">10.1021/acs.jpca.2c02243</a></li> <li>Sun, Jiace and Cheng, Lixue, el al. (2022) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20220707-204130247">Molecular Dipole Moment Learning via Rotationally Equivariant Gaussian Process Regression with Derivatives in Molecular-orbital-based Machine Learning</a>; <a href="https://doi.org/10.22002/D1.1177">10.22002/D1.1177</a></li> <li>Begušić, Tomislav and Tao, Xuecheng, el al. (2022) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20220223-214612882">Equilibrium–nonequilibrium ring-polymer molecular dynamics for nonlinear spectroscopy</a>; Journal of Chemical Physics; Vol. 156; No. 13; Art. No. 131102; <a href="https://doi.org/10.1063/5.0087156">10.1063/5.0087156</a></li> <li>Jacobson, Daniel and Miller, Thomas F., III (2022) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20220428-212257386">Compact-to-Dendritic Transition in the Reactive Deposition of Brownian Particles</a>; <a href="https://doi.org/10.48550/arXiv.2204.01173">10.48550/arXiv.2204.01173</a></li> <li>Xiong, Shuoyan and Shoshani, Manar M., el al. (2022) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20220714-215129425">Mechanistic studies of P,O-chelated nickel complexes targeting functional polyolefin synthesis</a></li> <li>Carmody, Patrick J. and Zimmer, Matthew H., el al. (2021) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20210312-124533397">Coordination of -1 programmed ribosomal frameshifting by transcript and nascent chain features revealed by deep mutational scanning</a>; Nucleic Acids Research; Vol. 49; No. 22; 12943-12954; PMCID PMC8682741; <a href="https://doi.org/10.1093/nar/gkab1172">10.1093/nar/gkab1172</a></li> <li>Turner, Andrew C. and Korol, Roman, el al. (2021) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20210507-093059787">Experimental and theoretical determinations of hydrogen isotopic equilibrium in the system CH₄-H₂-H₂O from 3 to 200°C</a>; Geochimica et Cosmochimica Acta; Vol. 314; 223-269; <a href="https://doi.org/10.1016/j.gca.2021.04.026">10.1016/j.gca.2021.04.026</a></li> <li>Christensen, Anders S. and Sirumalla, Sai Krishna, el al. (2021) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20210831-203931813">OrbNet Denali: A machine learning potential for biological and organic chemistry with semi-empirical cost and DFT accuracy</a>; Journal of Chemical Physics; Vol. 155; No. 20; Art. No. 204103; <a href="https://doi.org/10.1063/5.0061990">10.1063/5.0061990</a></li> <li>Dommer, Abigail and Casalino, Lorenzo, el al. (2021) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20220208-947187000">#COVIDisAirborne: AI-Enabled Multiscale Computational Microscopy of Delta SARS-CoV-2 in a Respiratory Aerosol</a>; PMCID PMC8609898; <a href="https://doi.org/10.1101/2021.11.12.468428">10.1101/2021.11.12.468428</a></li> <li>Rawlings, Dakota and Lee, Dongwook, el al. (2021) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20210830-230029193">Li⁺ and Oxidant Addition To Control Ionic and Electronic Conduction in Ionic Liquid-Functionalized Conjugated Polymers</a>; Chemistry of Materials; Vol. 33; No. 16; 6464-6474; <a href="https://doi.org/10.1021/acs.chemmater.1c01811">10.1021/acs.chemmater.1c01811</a></li> <li>Ma, Emily and Kim, Jeongmin, el al. (2021) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20210830-230029026">Stern and Diffuse Layer Interactions during Ionic Strength Cycling</a>; Journal of Physical Chemistry C; Vol. 125; No. 32; 18002-18014; <a href="https://doi.org/10.1021/acs.jpcc.1c04836">10.1021/acs.jpcc.1c04836</a></li> <li>Li, Bo and Zhang, Xinglong, el al. (2021) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20210721-172302557">Electronic Structure of Superoxidized Radical Cationic Dodecaborate-Based Clusters</a>; Journal of Physical Chemistry A; Vol. 125; No. 28; 6141-6150; <a href="https://doi.org/10.1021/acs.jpca.1c03927">10.1021/acs.jpca.1c03927</a></li> <li>Ma, Emily and Ohno, Paul E., el al. (2021) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20210412-101224507">A New Imaginary Term in the Second-Order Nonlinear Susceptibility from Charged Interfaces</a>; Journal of Physical Chemistry Letters; Vol. 12; No. 24; 5649-5659; <a href="https://doi.org/10.1021/acs.jpclett.1c01103">10.1021/acs.jpclett.1c01103</a></li> <li>Zimmer, Matthew H. and Niesen, Michiel J. M., el al. (2021) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20201021-082852041">Force transduction creates long-ranged coupling in ribosomes stalled by arrest peptides</a>; Biophysical Journal; Vol. 120; No. 12; 2425-2435; <a href="https://doi.org/10.1016/j.bpj.2021.03.041">10.1016/j.bpj.2021.03.041</a></li> <li>Xiong, Shuoyan and Shoshani, Manar M., el al. (2021) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20210430-120931834">Efficient Copolymerization of Acrylate and Ethylene with Neutral P, O-Chelated Nickel Catalysts: Mechanistic Investigations of Monomer Insertion and Chelate Formation</a>; Journal of the American Chemical Society; Vol. 143; No. 17; 6516-6527; <a href="https://doi.org/10.1021/jacs.1c00566">10.1021/jacs.1c00566</a></li> <li>Magdău, Ioan-Bogdan and Miller, Thomas F., III (2021) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20200914-111809398">Machine Learning Solvation Environments in Conductive Polymers: Application to ProDOT-2Hex with Solvent Swelling</a>; Macromolecules; Vol. 54; No. 7; 3377-3387; <a href="https://doi.org/10.1021/acs.macromol.0c02132">10.1021/acs.macromol.0c02132</a></li> <li>Lee, Sebastian J. R. and Husch, Tamara, el al. (2021) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20210119-161656738">Analytical gradients for molecular-orbital-based machine learning</a>; Journal of Chemical Physics; Vol. 154; No. 12; Art. No. 124120; <a href="https://doi.org/10.1063/5.0040782">10.1063/5.0040782</a></li> <li>Kim, Jeongmin and Savoie, Brett M., el al. (2021) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20210119-101412986">Interfacial Electron Transfer and Ion Solvation in the Solid Electrolyte Interphase</a>; Journal of Physical Chemistry C; Vol. 125; No. 8; 4614-4622; <a href="https://doi.org/10.1021/acs.jpcc.0c11194">10.1021/acs.jpcc.0c11194</a></li> <li>Jiang, Hongyan and Tao, Xuecheng, el al. (2021) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20210218-150439555">Small Nuclear Quantum Effects in Scattering of H and D from Graphene</a>; Journal of Physical Chemistry Letters; Vol. 12; No. 7; 1991-1996; <a href="https://doi.org/10.1021/acs.jpclett.0c02933">10.1021/acs.jpclett.0c02933</a></li> <li>Husch, Tamara and Sun, Jiace, el al. (2021) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20201110-142606934">Improved accuracy and transferability of molecular-orbital-based machine learning: Organics, transition-metal complexes, non-covalent interactions, and transition states</a>; Journal of Chemical Physics; Vol. 154; No. 6; Art. No. 064108; <a href="https://doi.org/10.1063/5.0032362">10.1063/5.0032362</a></li> <li>Nicolaus, Felix and Metola, Ane, el al. (2021) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20200929-122616290">Residue-by-residue analysis of cotranslational membrane protein integration in vivo</a>; eLife; Vol. 10; Art. No. e64302; <a href="https://doi.org/10.7554/eLife.64302">10.7554/eLife.64302</a></li> <li>Rosa-Raíces, Jorge L. and Sun, Jiace, el al. (2021) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20201203-151032238">A generalized class of strongly stable and dimension-free T-RPMD integrators</a>; Journal of Chemical Physics; Vol. 154; No. 2; Art. No. 024106; PMCID PMC7796824; <a href="https://doi.org/10.1063/5.0036954">10.1063/5.0036954</a></li> <li>Qiao, Zhuoran and Ding, Feizhi, el al. (2020) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20201203-151028849">Multi-task learning for electronic structure to predict and explore molecular potential energy surfaces</a>; <a href="https://doi.org/10.48550/arXiv.2011.02680">10.48550/arXiv.2011.02680</a></li> <li>Das, Pratyusha and Zayat, Billal, el al. (2020) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20201021-121820625">Dihexyl-Substituted Poly(3,4-Propylenedioxythiophene) as a Dual Ionic and Electronic Conductive Cathode Binder for Lithium-Ion Batteries</a>; Chemistry of Materials; Vol. 32; No. 21; 9176-9189; <a href="https://doi.org/10.1021/acs.chemmater.0c02601">10.1021/acs.chemmater.0c02601</a></li> <li>Ferguson, Andrew L. and Hachmann, Johannes, el al. (2020) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20201105-152206460">The Journal of Physical Chemistry A/B/C Virtual Special Issue on Machine Learning in Physical Chemistry</a>; Journal of Physical Chemistry B; Vol. 124; No. 44; 9767-9772; <a href="https://doi.org/10.1021/acs.jpcb.0c09206">10.1021/acs.jpcb.0c09206</a></li> <li>Ferguson, Andrew L. and Hachmann, Johannes, el al. (2020) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20201105-152206567">The Journal of Physical Chemistry A/B/C Virtual Special Issue on Machine Learning in Physical Chemistry</a>; Journal of Physical Chemistry A; Vol. 124; No. 44; 9113-9118; <a href="https://doi.org/10.1021/acs.jpca.0c09205">10.1021/acs.jpca.0c09205</a></li> <li>Ferguson, Andrew L. and Hachmann, Johannes, el al. (2020) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20201105-152206366">The Journal of Physical Chemistry A/B/C Virtual Special Issue on Machine Learning in Physical Chemistry</a>; Journal of Physical Chemistry C; Vol. 124; No. 44; 24033-24038; <a href="https://doi.org/10.1021/acs.jpcc.0c09208">10.1021/acs.jpcc.0c09208</a></li> <li>Mead, Griffin and Lin, Haw-Wei, el al. (2020) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20200909-152203413">Sum-Frequency Signals in 2D-Terahertz-Terahertz-Raman Spectroscopy</a>; Journal of Physical Chemistry B; Vol. 124; No. 40; 8904-8908; <a href="https://doi.org/10.1021/acs.jpcb.0c07935">10.1021/acs.jpcb.0c07935</a></li> <li>Qiao, Zhuoran and Welborn, Matthew, el al. (2020) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20200818-095759329">OrbNet: Deep learning for quantum chemistry using symmetry-adapted atomic-orbital features</a>; Journal of Chemical Physics; Vol. 153; No. 12; Art. No. 124111; <a href="https://doi.org/10.1063/5.0021955">10.1063/5.0021955</a></li> <li>Chapovetsky, Alon and Liu, Jeffrey J., el al. (2020) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20200901-095615539">Electronically Modified Cobalt Aminopyridine Complexes Reveal an Orthogonal Axis for Catalytic Optimization for CO₂ Reduction</a>; Inorganic Chemistry; Vol. 59; No. 18; 13709-13718; <a href="https://doi.org/10.1021/acs.inorgchem.0c02086">10.1021/acs.inorgchem.0c02086</a></li> <li>Stauber, Julia M. and Schwan, Josef, el al. (2020) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20200713-085326752">A Super-Oxidized Radical Cationic Icosahedral Boron Cluster</a>; Journal of the American Chemical Society; Vol. 142; No. 30; 12948-12953; <a href="https://doi.org/10.1021/jacs.0c06159">10.1021/jacs.0c06159</a></li> <li>Chen, Leanne D. and Lawniczak, James J., el al. (2020) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20200526-141455955">Embedded Mean-Field Theory for Solution-Phase Transition-Metal Polyolefin Catalysis</a>; Journal of Chemical Theory and Computation; Vol. 16; No. 7; 4226-4237; <a href="https://doi.org/10.1021/acs.jctc.0c00169">10.1021/acs.jctc.0c00169</a></li> <li>Jiang, Hongyan and Tao, Xuecheng, el al. (2020) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20210929-230209364">Nuclear Quantum Effects in Scattering of H and D from Graphene</a>; <a href="https://doi.org/10.48550/arXiv.2007.03372">10.48550/arXiv.2007.03372</a></li> <li>Harrington, Haley R. and Zimmer, Matthew H., el al. (2020) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20191003-111416580">Cotranslational Folding Stimulates Programmed Ribosomal Frameshifting in the Alphavirus Structural Polyprotein</a>; Journal of Biological Chemistry; Vol. 295; No. 20; 6798-6808; PMCID PMC7242702; <a href="https://doi.org/10.1074/jbc.RA120.012706">10.1074/jbc.RA120.012706</a></li> <li>Werner, Hans-Joachim and Knowles, Peter J., el al. (2020) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20200413-101102938">Molpro quantum chemistry package</a>; Journal of Chemical Physics; Vol. 152; No. 14; Art. No. 144107; <a href="https://doi.org/10.1063/5.0005081">10.1063/5.0005081</a></li> <li>Tao, Xuecheng and Shushkov, Philip, el al. (2020) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20200303-084230635">Microcanonical rates from ring-polymer molecular dynamics: Direct-shooting, stationary-phase, and maximum-entropy approaches</a>; Journal of Chemical Physics; Vol. 152; No. 12; Art. No. 124117; <a href="https://doi.org/10.1063/1.5144307">10.1063/1.5144307</a></li> <li>Niesen, Michiel J. M. and Zimmerman, Michael H., el al. (2020) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20200304-160026575">Dynamics of Co-translational Membrane Protein Integration and Translocation via the Sec Translocon</a>; Journal of the American Chemical Society; Vol. 142; No. 12; 5449-5460; <a href="https://doi.org/10.1021/jacs.9b07820">10.1021/jacs.9b07820</a></li> <li>Korol, Roman and Rosa-Raíces, Jorge L., el al. (2020) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20191216-155842954">Dimension-free path-integral molecular dynamics without preconditioning</a>; Journal of Chemical Physics; Vol. 152; No. 10; Art. No. 104102; <a href="https://doi.org/10.1063/1.5134810">10.1063/1.5134810</a></li> <li>Eldridge, Daniel L. and Korol, Roman, el al. (2019) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20191029-105305218">Comparison of Experimental vs Theoretical Abundances of ¹³CH₃D and ¹²CH₂D₂ for Isotopically Equilibrated Systems from 1 to 500 °C</a>; ACS Earth and Space Chemistry; Vol. 3; No. 12; 2747-2764; <a href="https://doi.org/10.1021/acsearthspacechem.9b00244">10.1021/acsearthspacechem.9b00244</a></li> <li>Cheng, Lixue and Kovachki, Nikola B., el al. (2019) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20191023-150600399">Regression-clustering for Improved Accuracy and Training Cost with Molecular-Orbital-Based Machine Learning</a>; Journal of Chemical Theory and Computation; Vol. 15; No. 12; 6668-6677; <a href="https://doi.org/10.1021/acs.jctc.9b00884">10.1021/acs.jctc.9b00884</a></li> <li>Davis, Victoria K. and Munoz, Stephen, el al. (2019) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20191024-130308856">Fluoride-ion solvation in non-aqueous electrolyte solutions</a>; Materials Chemistry Frontiers; Vol. 3; No. 12; 2721-2727; <a href="https://doi.org/10.1039/c9qm00512a">10.1039/c9qm00512a</a></li> <li>Rosa-Raíces, Jorge L. and Zhang, Bin, el al. (2019) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20191029-104519003">Path-accelerated stochastic molecular dynamics: Parallel-in-time integration using path integrals</a>; Journal of Chemical Physics; Vol. 151; No. 16; Art. No. 164120; <a href="https://doi.org/10.1063/1.5125455">10.1063/1.5125455</a></li> <li>Shushkov, Philip and Miller, Thomas F., III (2019) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20191002-094950660">Real-time density-matrix coupled-cluster approach for closed and open systems at finite temperature</a>; Journal of Chemical Physics; Vol. 151; No. 13; Art. 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(2015) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20150925-142236374">Design of next-generation polymer electrolytes: A site network model for ion transport from mechanistic insight</a></li> <li>Lee, Joonho and Miyamoto, Kaito, el al. (2015) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20150916-160908247">Embedded mean-field theory: Toward a large-scale ab-initio molecular dynamics</a></li> <li>Webb, Michael A. and Jung, Yukyung, el al. (2015) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20150724-073254175">Systematic Computational and Experimental Investigation of Lithium-Ion Transport Mechanisms in Polyester-Based Polymer Electrolytes</a>; ACS Central Science; Vol. 1; No. 4; 198-205; PMCID PMC4827473; <a href="https://doi.org/10.1021/acscentsci.5b00195">10.1021/acscentsci.5b00195</a></li> <li>Bennie, Simon J. and Stella, Martina, el al. (2015) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20150720-080707412">Accelerating wavefunction in density-functional-theory embedding by truncating the active basis set</a>; Journal of Chemical Physics; Vol. 143; No. 2; Art. No. 024105; <a href="https://doi.org/10.1063/1.4923367">10.1063/1.4923367</a></li> <li>Barnes, Taylor and Kaminski, Jakub, el al. (2015) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20150422-141500296">Ab initio characterization of the electrochemical stability and solvation properties of condensed-phase ethylene carbonate and dimethyl carbonate mixtures</a>; Abstracts of Papers of the American Chemical Society; Vol. 249; COMP-71</li> <li>Miller, Thomas (2015) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20150407-132132414">New approaches to simulating biological and molecular catalysts</a>; Abstracts of Papers of the American Chemical Society; Vol. 249; PHYS-183</li> <li>Miller, Thomas F. (2015) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20150422-145236274">Wavefunction embedding methods for the study of renewable energy catalysis</a>; Abstracts of Papers of the American Chemical Society; Vol. 249; CATL-11</li> <li>Barnes, Taylor A. and Kaminski, Jakub W., el al. (2015) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20150202-101927300">Ab Initio Characterization of the Electrochemical Stability and Solvation Properties of Condensed-Phase Ethylene Carbonate and Dimethyl Carbonate Mixtures</a>; Journal of Physical Chemistry C; Vol. 119; No. 8; 3865-3880; <a href="https://doi.org/10.1021/jp510882g">10.1021/jp510882g</a></li> <li>Fornace, Mark E. and Lee, Joonho, el al. (2015) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20150202-095906885">Embedded Mean-Field Theory</a>; Journal of Chemical Theory and Computation; Vol. 11; No. 2; 568-580; <a href="https://doi.org/10.1021/ct5011032">10.1021/ct5011032</a></li> <li>Niesen, Michiel J. M. and Miller, Thomas F., III (2015) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20151106-081208446">Coarse-Grained Modeling of Minute-Timescale Co-Translational Membrane Protein Integration via the Sec-Translocon</a>; Biophysical Journal; Vol. 108; No. 2; 501A; <a href="https://doi.org/10.1016/j.bpj.2014.11.2743">10.1016/j.bpj.2014.11.2743</a></li> <li>Wang, Connie Y. and Miller, Thomas F., III (2014) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20140929-091520017">Allosteric response and substrate sensitivity in peptide binding of the signal recognition particle</a>; Journal of Biological Chemistry; Vol. 289; No. 44; 30868-30879; PMCID PMC4215262; <a href="https://doi.org/10.1074/jbc.M114.584912">10.1074/jbc.M114.584912</a></li> <li>Miller, Thomas F. (2014) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20140815-083034164">Accurate and systematically improvable density functional theory embedding for correlated wavefunctions</a></li> <li>Miller, Thomas F. (2014) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20140815-084007652">Multi-scale simulation of electrode interfaces</a></li> <li>Huo, Pengfei and Uyeda, Christopher, el al. (2014) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20140811-133647033">Intra-molecular proton transfer and hydrogen evolution mechanism in cobalt catalysts</a></li> <li>Goodpaster, Jason D. and Barnes, Taylor A., el al. (2014) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20140401-104003729">Accurate and systematically improvable density functional theory embedding for correlated wavefunctions</a>; Journal of Chemical Physics; Vol. 140; No. 18; Art. No. 18A507; <a href="https://doi.org/10.1063/1.4864040">10.1063/1.4864040</a></li> <li>Goodpaster, Jason D. and Barnes, Taylor A., el al. (2014) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20140430-150017261">Accurate and robust wavefunction embedding methodologies</a></li> <li>Menzeleev, Artur R. and Bell, Franziska, el al. (2014) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20140401-101133735">Kinetically constrained ring-polymer molecular dynamics for non-adiabatic chemical reactions</a>; Journal of Chemical Physics; Vol. 140; No. 6; Art. No. 064103; <a href="https://doi.org/10.1063/1.4863919">10.1063/1.4863919</a></li> <li>Webb, Michael A. and Miller, Thomas F., III (2013) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20140113-090540183">Position-Specific and Clumped Stable Isotope Studies: Comparison of the Urey and Path-Integral Approaches for Carbon Dioxide, Nitrous Oxide, Methane, and Propane</a>; Journal of Physical Chemistry A; <a href="https://doi.org/10.1021/jp411134v">10.1021/jp411134v</a></li> <li>Huo, Pengfei and Miller, Thomas F., III, el al. (2013) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20131121-153219343">Communication: Predictive partial linearized path integral simulation of condensed phase electron transfer dynamics</a>; Journal of Chemical Physics; Vol. 139; No. 15; Art. No. 151103; <a href="https://doi.org/10.1063/1.4826163">10.1063/1.4826163</a></li> <li>Miller, Thomas F. (2013) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20131011-110351925">Modeling the dynamics and regulation of Sec-facilitated protein translocation and membrane integration</a></li> <li>Miller, Thomas F. (2013) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20131011-083104186">Quantum dynamics from classical trajectories: New approaches to simulating biological and molecular photocatalysts</a></li> <li>Miller, Thomas F. (2013) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20131011-082934587">Exactly embedded density functional theory for modeling chemical reactions</a></li> <li>Barnes, Taylor A. and Goodpaster, Jason D., el al. (2013) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20130826-111810684">Accurate basis set truncation for wavefunction embedding</a>; Journal of Chemical Physics; Vol. 139; No. 2; Art. No. 024103; <a href="https://doi.org/10.1063/1.4811112">10.1063/1.4811112</a></li> <li>Kretchmer, Joshua S. and Miller, Thomas F., III (2013) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20130603-112629415">Direct simulation of proton-coupled electron transfer across multiple regimes</a>; Journal of Chemical Physics; Vol. 138; No. 13; Art. No. 134109; <a href="https://doi.org/10.1063/1.4797462">10.1063/1.4797462</a></li> <li>Habershon, Scott and Manolopoulos, David E., el al. (2013) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20130827-153007523">Ring-Polymer Molecular Dynamics: Quantum Effects in Chemical Dynamics from Classical Trajectories in an Extended Phase Space</a>; Annual Review of Physical Chemistry; Vol. 64; 387-413; <a href="https://doi.org/10.1146/annurev-physchem-040412-110122">10.1146/annurev-physchem-040412-110122</a></li> <li>Warren, Jeffrey J. and Menzeleev, Artur R., el al. (2013) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20130410-103426798">Long-Range Proton-Coupled Electron-Transfer Reactions of Bis(imidazole) Iron Tetraphenylporphyrins Linked to Benzoates</a>; Journal of Physical Chemistry Letters; Vol. 4; No. 3; 519-523; PMCID PMC3593309; <a href="https://doi.org/10.1021/jz400029w">10.1021/jz400029w</a></li> <li>Mayers, Matthew Z. and Kaminski, Jakub W., el al. (2012) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20130205-103133136">Suppression of Dendrite Formation via Pulse Charging in Rechargeable Lithium Metal Batteries</a>; Journal of Physical Chemistry C; Vol. 116; No. 50; 26214-26221; <a href="https://doi.org/10.1021/jp309321w">10.1021/jp309321w</a></li> <li>Goodpaster, Jason D. and Barnes, Taylor A., el al. (2012) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20130123-093712451">Density functional theory embedding for correlated wavefunctions: Improved methods for open-shell systems and transition metal complexes</a>; Journal of Chemical Physics; Vol. 137; No. 22; Art. No. 224113; <a href="https://doi.org/10.1063/1.4770226">10.1063/1.4770226</a></li> <li>Zhang, Bin and Miller, Thomas F., III (2012) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20121018-141631261">Long-Timescale Dynamics and Regulation of Sec-Facilitated Protein Translocation</a>; Cell Reports; Vol. 2; No. 4; 927-937; PMCID PMC3483636; <a href="https://doi.org/10.1016/j.celrep.2012.08.039">10.1016/j.celrep.2012.08.039</a></li> <li>Zhang, Bin and Miller, Thomas F., III (2012) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20121031-134552173">Direct Simulation of Early-Stage Sec-Facilitated Protein Translocation</a>; Journal of the American Chemical Society; Vol. 134; No. 33; 13700-13707; PMCID PMC3431202; <a href="https://doi.org/10.1021/ja3034526">10.1021/ja3034526</a></li> <li>Manby, Frederick R. and Stella, Martina, el al. (2012) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20121018-135034166">Simple, Exact Density-Functional-Theory Embedding Scheme</a>; Journal of Chemical Theory and Computation; Vol. 8; No. 8; 2564-2568; <a href="https://doi.org/10.1021/ct300544e">10.1021/ct300544e</a></li> <li>Miller, Thomas F. (2012) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20120821-154507047">Direct simulation of electron transfer and proton-coupled electron transfer dynamics in the condensed-phase</a></li> <li>Padilla Araujo, Bernardo Sosa and Miller, Thomas, el al. (2012) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20120824-152508878">In Silico Screening of Computational Enzyme Designs</a>; Protein Science; Vol. 21; No. S1; 132</li> <li>Ananth, Nandini and Miller, Thomas F., III (2012) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20120627-114459530">Flux-correlation approach to characterizing reaction pathways in quantum systems: a study of condensed-phase proton-coupled electron transfer</a>; Molecular Physics; Vol. 110; No. 9-10; 1009-1015; <a href="https://doi.org/10.1080/00268976.2012.686641">10.1080/00268976.2012.686641</a></li> <li>Boekelheide, Nicholas and Salomόn-Ferrer, Romelia, el al. (2011) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20111018-111346185">Dynamics and dissipation in enzyme catalysis</a>; Proceedings of the National Academy of Sciences of the United States of America; Vol. 108; No. 39; 16159-16163; PMCID PMC3182692; <a href="https://doi.org/10.1073/pnas.1106397108">10.1073/pnas.1106397108</a></li> <li>Menzeleev, Artur R. and Ananth, Nandini, el al. (2011) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20110909-122016964">Direct simulation of electron transfer using ring polymer molecular dynamics: Comparison with semiclassical instanton theory and exact quantum methods</a>; Journal of Chemical Physics; Vol. 135; No. 7; Art. No. 074106; <a href="https://doi.org/10.1063/1.3624766">10.1063/1.3624766</a></li> <li>Goodpaster, Jason D. and Barnes, Taylor A., el al. (2011) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20110525-151024690">Embedded density functional theory for covalently bonded and strongly interacting subsystems</a>; Journal of Chemical Physics; Vol. 134; No. 16; Art. No. 164108; <a href="https://doi.org/10.1063/1.3582913">10.1063/1.3582913</a></li> <li>Ananth, Nandini and Miller, Thomas F., III (2010) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20110201-140605973">Exact quantum statistics for electronically nonadiabatic systems using continuous path variables</a>; Journal of Chemical Physics; Vol. 133; No. 23; Art. No. 234103; <a href="https://doi.org/10.1063/1.3511700">10.1063/1.3511700</a></li> <li>Goodpaster, Jason D. and Ananth, Nandini, el al. (2010) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20101011-131128803">Exact nonadditive kinetic potentials for embedded density functional theory</a>; Journal of Chemical Physics; Vol. 133; No. 8; Art. No. 084103; <a href="https://doi.org/10.1063/1.3474575">10.1063/1.3474575</a></li> <li>Adelman, Joshua L. and Chodera, John D., el al. (2010) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20100709-093839488">The Mechanical Properties of PCNA: Implications for the Loading and Function of a DNA Sliding Clamp</a>; Biophysical Journal; Vol. 98; No. 12; 3062-3069; <a href="https://doi.org/10.1016/j.bpj.2010.03.056">10.1016/j.bpj.2010.03.056</a></li> <li>Zhang, Bin and Miller, Thomas F., III (2010) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20100412-111115657">Hydrophobically stabilized open state for the lateral gate of the Sec translocon</a>; Proceedings of the National Academy of Sciences of the United States of America; Vol. 107; No. 12; 5399-5404; PMCID PMC2851780; <a href="https://doi.org/10.1073/pnas.0914752107">10.1073/pnas.0914752107</a></li> <li>Menzeleev, Artur R. and Miller, Thomas F., III (2010) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20100216-110544016">Ring polymer molecular dynamics beyond the linear response regime: Excess electron injection and trapping in liquids</a>; Journal of Chemical Physics; Vol. 132; No. 3; Art. No. 034106; <a href="https://doi.org/10.1063/1.3292576">10.1063/1.3292576</a></li> <li>Miller, Thomas F., III (2008) <a href="https://resolver.caltech.edu/CaltechAUTHORS:MILjcp08">Isomorphic classical molecular dynamics model for an excess electron in a supercritical fluid</a>; Journal of Chemical Physics; Vol. 129; No. 19; Art. No. 194502; <a href="https://doi.org/10.1063/1.3013357">10.1063/1.3013357</a></li> <li>Miller, Thomas F., III and Vanden-Eijnden, Eric, el al. (2007) <a href="https://resolver.caltech.edu/CaltechAUTHORS:MILpnas07">Solvent coarse-graining and the string method applied to the hydrophobic collapse of a hydrated chain</a>; Proceedings of the National Academy of Sciences of the United States of America; Vol. 104; No. 37; 14559-14564; PMCID PMC1955457; <a href="https://doi.org/10.1073/pnas.0705830104">10.1073/pnas.0705830104</a></li> <li>Miller, Thomas F., III and Predescu, Cristian (2007) <a href="https://resolver.caltech.edu/CaltechAUTHORS:MILjcp07">Sampling diffusive transition paths</a>; Journal of Chemical Physics; Vol. 126; No. 14; Art. No. 144102; <a href="https://doi.org/10.1103/10.1063/1.2712444">10.1103/10.1063/1.2712444</a></li> <li>Miller, Thomas F., III and Manolopolous, David E. (2005) <a href="https://resolver.caltech.edu/CaltechAUTHORS:MILjcp05b">Quantum diffusion in liquid water from ring polymer molecular dynamics</a>; Journal of Chemical Physics; Vol. 123; No. 15; Art. No. 154504; <a href="https://doi.org/10.1063/1.2074967">10.1063/1.2074967</a></li> <li>Miller, Thomas F., III and Clary, David C., el al. (2005) <a href="https://resolver.caltech.edu/CaltechAUTHORS:MILjcp05c">Collision-induced conformational changes in glycine</a>; Journal of Chemical Physics; Vol. 122; No. 24; Art. No. 244323; <a href="https://doi.org/10.1063/1.1927527">10.1063/1.1927527</a></li> <li>Miller, Thomas F., III and Clary, David C. (2005) <a href="https://resolver.caltech.edu/CaltechAUTHORS:MILmp05">Torsional anharmonicity in the conformational thermodynamics of flexible molecules</a>; Molecular Physics; Vol. 103; No. 11-12; 1573-1578; <a href="https://doi.org/10.1080/00268970500096145">10.1080/00268970500096145</a></li> <li>Miller, Thomas F., III and Manolopolous, David E. (2005) <a href="https://resolver.caltech.edu/CaltechAUTHORS:MILjcp05d">Quantum diffusion in liquid para-hydrogen from ring-polymer molecular dynamics</a>; Journal of Chemical Physics; Vol. 122; No. 18; Art. No. 184503; <a href="https://doi.org/10.1063/1.1893956">10.1063/1.1893956</a></li> <li>Miller, Thomas F., III and Manolopolous, David E., el al. (2005) <a href="https://resolver.caltech.edu/CaltechAUTHORS:MILjcp05a">Comment on "A centroid molecular dynamics study of liquid para hydrogen and ortho deuterium" [J. Chem. Phys. 121, 6412 (2004)]</a>; Journal of Chemical Physics; Vol. 122; No. 5; Art. No. 057101; <a href="https://doi.org/10.1063/1.1839867">10.1063/1.1839867</a></li> <li>Miller, Thomas F., III and Clary, David C. (2004) <a href="https://resolver.caltech.edu/CaltechAUTHORS:MILpccp04">Quantum free energies of the conformers of glycine on an ab initio potential energy surface</a>; Physical Chemistry Chemical Physics; Vol. 6; No. 10; 2563-2571; <a href="https://doi.org/10.1039/b314644h">10.1039/b314644h</a></li> <li>Nanjia, Shikha and Jasper, Ahren W., el al. (2004) <a href="https://resolver.caltech.edu/CaltechAUTHORS:NANjcp04">Army ants algorithm for rare event sampling of delocalized nonadiabatic transitions by trajectory surface hopping and the estimation of sampling errors by the bootstrap method</a>; Journal of Chemical Physics; Vol. 120; No. 8; 3586-3597; <a href="https://doi.org/10.1063/1.1641019">10.1063/1.1641019</a></li> <li>Miller, Thomas F., III and Clary, David C. (2003) <a href="https://resolver.caltech.edu/CaltechAUTHORS:MILjcp03">Torsional path integral Monte Carlo method for calculating the absolute quantum free energy of large molecules</a>; Journal of Chemical Physics; Vol. 119; No. 1; 68-76; <a href="https://doi.org/10.1063/1.1568727">10.1063/1.1568727</a></li> <li>Miller, T. F., III and Eleftheriou, M., el al. (2002) <a href="https://resolver.caltech.edu/CaltechAUTHORS:MILjcp02b">Symplectic quaternion scheme for biophysical molecular dynamics</a>; Journal of Chemical Physics; Vol. 116; No. 20; 8649-8659; <a href="https://doi.org/10.1063/1.1473654">10.1063/1.1473654</a></li> <li>Miller, Thomas F., III and Clary, David C. (2002) <a href="https://resolver.caltech.edu/CaltechAUTHORS:MILjcp02a">Torsional path integral Monte Carlo method for the quantum simulation of large molecules</a>; Journal of Chemical Physics; Vol. 116; No. 19; 8262-8269; <a href="https://doi.org/10.1063/1.1467342">10.1063/1.1467342</a></li> <li>Miller, J. Scott and Poliakoff, E. D., el al. (2001) <a href="https://resolver.caltech.edu/CaltechAUTHORS:MILjcp01">Excitation of the symmetry forbidden bending mode in molecular photoionization</a>; Journal of Chemical Physics; Vol. 114; No. 10; 4496-4504; <a href="https://doi.org/10.1063/1.1349090">10.1063/1.1349090</a></li> <li>Miller, Thomas F., III and Hall, Michael B. (1999) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20130301-152550052">Structural and bonding trends in platinum-carbon clusters</a>; Journal of the American Chemical Society; Vol. 121; No. 32; 7389-7396; <a href="https://doi.org/10.1021/ja990854n">10.1021/ja990854n</a></li> <li>Miller, Thomas F., III and Strout, Douglas L., el al. (1998) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20130301-153738878">Linear Semibridging Carbonyls. 6. Structure and Bonding in the Dimers of 17-Electron Tantalum Hexacarbonyl and Tetracarbonyl Diphosphine</a>; Organometallics; Vol. 17; No. 19; 4164-4168; <a href="https://doi.org/10.1021/om980144a">10.1021/om980144a</a></li> <li>Strout, Douglas L. and Miller, Thomas F., III, el al. (1998) <a href="https://resolver.caltech.edu/CaltechAUTHORS:20130301-153144543">Structure and Stability of Palladium−Carbon Cations</a>; Journal of Physical Chemistry A; Vol. 102; No. 31; 6307-6310; <a href="https://doi.org/10.1021/jp980640c">10.1021/jp980640c</a></li> </ul>