Miller, Thomas F.

Combined from CaltechAUTHORS

• Qiao, Zhuoran and Nie, Weili, et el. (2024) State-specific protein–ligand complex structure prediction with a multiscale deep generative model; Nature Machine Intelligence; 10.1038/s42256-024-00792-z
• Mai, Huanghao and Zimmer, Matthew H., et el. (2023) Exploring PROTAC Cooperativity with Coarse-Grained Alchemical Methods; Journal of Physical Chemistry B; Vol. 127; No. 2; 446-455; PMCID PMC9869335; 10.1021/acs.jpcb.2c05795
• Dommer, Abigail and Casalino, Lorenzo, et el. (2023) #COVIDisAirborne: AI-enabled multiscale computational microscopy of delta SARS-CoV-2 in a respiratory aerosol; International Journal of High Performance Computing Applications; Vol. 37; No. 1; 28-44; PMCID PMC9527558; 10.1177/10943420221128233
• Qiao, Zhuoran and Nie, Weili, et el. (2022) Dynamic-Backbone Protein-Ligand Structure Prediction with Multiscale Generative Diffusion Models; 10.48550/arXiv.2209.15171
• Cheng, Lixue and Sun, Jiace, et el. (2022) Molecular-orbital-based machine learning for open-shell and multi-reference systems with kernel addition Gaussian process regression; Journal of Chemical Physics; Vol. 157; No. 15; Art. No. 154105; 10.1063/5.0110886
• Lawniczak, James J. and Zhang, Xinglong, et el. (2022) Solution-Phase Conformational/Vibrational Anharmonicity in Comonomer Incorporation Polyolefin Catalysis; Journal of Physical Chemistry A; Vol. 126; No. 39; 6858-6869; 10.1021/acs.jpca.2c04038
• Sun, Jiace and Cheng, Lixue, et el. (2022) Molecular dipole moment learning via rotationally equivariant derivative kernels in molecular-orbital-based machine learning; Journal of Chemical Physics; Vol. 157; No. 10; Art. No. 104109; 10.1063/5.0101280
• Cheng, Lixue and Sun, Jiace, et el. (2022) Accurate Molecular-Orbital-Based Machine Learning Energies via Unsupervised Clustering of Chemical Space; Journal of Chemical Theory and Computation; Vol. 18; No. 8; 4826-4835; 10.1021/acs.jctc.2c00396
• Shoshani, Manar M. and Xiong, Shuoyan, et el. (2022) Phosphine-Phenoxide Nickel Catalysts for Ethylene/Acrylate Copolymerization: Olefin Coordination and Complex Isomerization Studies Relevant to the Mechanism of Catalysis; Organometallics; Vol. 41; No. 15; 2119-2131; 10.1021/acs.organomet.2c00241
• Qiao, Zhuoran and Christensen, Anders S., et el. (2022) Informing geometric deep learning with electronic interactions to accelerate quantum chemistry; Proceedings of the National Academy of Sciences; Vol. 119; No. 31; Art. No. e2205221119; PMCID PMC9351474; 10.1073/pnas.2205221119
• Sun, Jiace and Cheng, Lixue, et el. (2022) Molecular Dipole Moment Learning via Rotationally Equivariant Gaussian Process Regression with Derivatives in Molecular-orbital-based Machine Learning; 10.22002/D1.1177
• Lu, Fenris and Cheng, Lixue, et el. (2022) Fast Near Ab Initio Potential Energy Surfaces Using Machine Learning; Journal of Physical Chemistry A; Vol. 126; No. 25; 4013-4024; 10.1021/acs.jpca.2c02243
• Jacobson, Daniel and Miller, Thomas F., III (2022) Compact-to-Dendritic Transition in the Reactive Deposition of Brownian Particles; 10.48550/arXiv.2204.01173
• Begušić, Tomislav and Tao, Xuecheng, et el. (2022) Equilibrium–nonequilibrium ring-polymer molecular dynamics for nonlinear spectroscopy; Journal of Chemical Physics; Vol. 156; No. 13; Art. No. 131102; 10.1063/5.0087156
• Xiong, Shuoyan and Shoshani, Manar M., et el. (2022) Mechanistic studies of P,O-chelated nickel complexes targeting functional polyolefin synthesis
• Carmody, Patrick J. and Zimmer, Matthew H., et el. (2021) Coordination of -1 programmed ribosomal frameshifting by transcript and nascent chain features revealed by deep mutational scanning; Nucleic Acids Research; Vol. 49; No. 22; 12943-12954; PMCID PMC8682741; 10.1093/nar/gkab1172
• Turner, Andrew C. and Korol, Roman, et el. (2021) Experimental and theoretical determinations of hydrogen isotopic equilibrium in the system CH₄-H₂-H₂O from 3 to 200°C; Geochimica et Cosmochimica Acta; Vol. 314; 223-269; 10.1016/j.gca.2021.04.026
• Christensen, Anders S. and Sirumalla, Sai Krishna, et el. (2021) OrbNet Denali: A machine learning potential for biological and organic chemistry with semi-empirical cost and DFT accuracy; Journal of Chemical Physics; Vol. 155; No. 20; Art. No. 204103; 10.1063/5.0061990
• Dommer, Abigail and Casalino, Lorenzo, et el. (2021) #COVIDisAirborne: AI-Enabled Multiscale Computational Microscopy of Delta SARS-CoV-2 in a Respiratory Aerosol; PMCID PMC8609898; 10.1101/2021.11.12.468428
• Jiang, Hongyan and Tao, Xuecheng, et el. (2021) Nuclear Quantum Effects in Scattering of H and D from Graphene; 10.48550/arXiv.2007.03372
• Rawlings, Dakota and Lee, Dongwook, et el. (2021) Li⁺ and Oxidant Addition To Control Ionic and Electronic Conduction in Ionic Liquid-Functionalized Conjugated Polymers; Chemistry of Materials; Vol. 33; No. 16; 6464-6474; 10.1021/acs.chemmater.1c01811
• Ma, Emily and Kim, Jeongmin, et el. (2021) Stern and Diffuse Layer Interactions during Ionic Strength Cycling; Journal of Physical Chemistry C; Vol. 125; No. 32; 18002-18014; 10.1021/acs.jpcc.1c04836
• Li, Bo and Zhang, Xinglong, et el. (2021) Electronic Structure of Superoxidized Radical Cationic Dodecaborate-Based Clusters; Journal of Physical Chemistry A; Vol. 125; No. 28; 6141-6150; 10.1021/acs.jpca.1c03927
• Ma, Emily and Ohno, Paul E., et el. (2021) A New Imaginary Term in the Second-Order Nonlinear Susceptibility from Charged Interfaces; Journal of Physical Chemistry Letters; Vol. 12; No. 24; 5649-5659; 10.1021/acs.jpclett.1c01103
• Zimmer, Matthew H. and Niesen, Michiel J. M., et el. (2021) Force transduction creates long-ranged coupling in ribosomes stalled by arrest peptides; Biophysical Journal; Vol. 120; No. 12; 2425-2435; 10.1016/j.bpj.2021.03.041
• Xiong, Shuoyan and Shoshani, Manar M., et el. (2021) Efficient Copolymerization of Acrylate and Ethylene with Neutral P, O-Chelated Nickel Catalysts: Mechanistic Investigations of Monomer Insertion and Chelate Formation; Journal of the American Chemical Society; Vol. 143; No. 17; 6516-6527; 10.1021/jacs.1c00566
• Magdău, Ioan-Bogdan and Miller, Thomas F., III (2021) Machine Learning Solvation Environments in Conductive Polymers: Application to ProDOT-2Hex with Solvent Swelling; Macromolecules; Vol. 54; No. 7; 3377-3387; 10.1021/acs.macromol.0c02132
• Lee, Sebastian J. R. and Husch, Tamara, et el. (2021) Analytical gradients for molecular-orbital-based machine learning; Journal of Chemical Physics; Vol. 154; No. 12; Art. No. 124120; 10.1063/5.0040782
• Kim, Jeongmin and Savoie, Brett M., et el. (2021) Interfacial Electron Transfer and Ion Solvation in the Solid Electrolyte Interphase; Journal of Physical Chemistry C; Vol. 125; No. 8; 4614-4622; 10.1021/acs.jpcc.0c11194
• Jiang, Hongyan and Tao, Xuecheng, et el. (2021) Small Nuclear Quantum Effects in Scattering of H and D from Graphene; Journal of Physical Chemistry Letters; Vol. 12; No. 7; 1991-1996; 10.1021/acs.jpclett.0c02933
• Husch, Tamara and Sun, Jiace, et el. (2021) Improved accuracy and transferability of molecular-orbital-based machine learning: Organics, transition-metal complexes, non-covalent interactions, and transition states; Journal of Chemical Physics; Vol. 154; No. 6; Art. No. 064108; 10.1063/5.0032362
• Nicolaus, Felix and Metola, Ane, et el. (2021) Residue-by-residue analysis of cotranslational membrane protein integration in vivo; eLife; Vol. 10; Art. No. e64302; 10.7554/eLife.64302
• Rosa-Raíces, Jorge L. and Sun, Jiace, et el. (2021) A generalized class of strongly stable and dimension-free T-RPMD integrators; Journal of Chemical Physics; Vol. 154; No. 2; Art. No. 024106; PMCID PMC7796824; 10.1063/5.0036954
• Qiao, Zhuoran and Ding, Feizhi, et el. (2020) Multi-task learning for electronic structure to predict and explore molecular potential energy surfaces; 10.48550/arXiv.2011.02680
• Das, Pratyusha and Zayat, Billal, et el. (2020) Dihexyl-Substituted Poly(3,4-Propylenedioxythiophene) as a Dual Ionic and Electronic Conductive Cathode Binder for Lithium-Ion Batteries; Chemistry of Materials; Vol. 32; No. 21; 9176-9189; 10.1021/acs.chemmater.0c02601
• Ferguson, Andrew L. and Hachmann, Johannes, et el. (2020) The Journal of Physical Chemistry A/B/C Virtual Special Issue on Machine Learning in Physical Chemistry; Journal of Physical Chemistry C; Vol. 124; No. 44; 24033-24038; 10.1021/acs.jpcc.0c09208
• Ferguson, Andrew L. and Hachmann, Johannes, et el. (2020) The Journal of Physical Chemistry A/B/C Virtual Special Issue on Machine Learning in Physical Chemistry; Journal of Physical Chemistry A; Vol. 124; No. 44; 9113-9118; 10.1021/acs.jpca.0c09205
• Ferguson, Andrew L. and Hachmann, Johannes, et el. (2020) The Journal of Physical Chemistry A/B/C Virtual Special Issue on Machine Learning in Physical Chemistry; Journal of Physical Chemistry B; Vol. 124; No. 44; 9767-9772; 10.1021/acs.jpcb.0c09206
• Mead, Griffin and Lin, Haw-Wei, et el. (2020) Sum-Frequency Signals in 2D-Terahertz-Terahertz-Raman Spectroscopy; Journal of Physical Chemistry B; Vol. 124; No. 40; 8904-8908; 10.1021/acs.jpcb.0c07935
• Qiao, Zhuoran and Welborn, Matthew, et el. (2020) OrbNet: Deep learning for quantum chemistry using symmetry-adapted atomic-orbital features; Journal of Chemical Physics; Vol. 153; No. 12; Art. No. 124111; 10.1063/5.0021955
• Chapovetsky, Alon and Liu, Jeffrey J., et el. (2020) Electronically Modified Cobalt Aminopyridine Complexes Reveal an Orthogonal Axis for Catalytic Optimization for CO₂ Reduction; Inorganic Chemistry; Vol. 59; No. 18; 13709-13718; 10.1021/acs.inorgchem.0c02086
• Stauber, Julia M. and Schwan, Josef, et el. (2020) A Super-Oxidized Radical Cationic Icosahedral Boron Cluster; Journal of the American Chemical Society; Vol. 142; No. 30; 12948-12953; 10.1021/jacs.0c06159
• Chen, Leanne D. and Lawniczak, James J., et el. (2020) Embedded Mean-Field Theory for Solution-Phase Transition-Metal Polyolefin Catalysis; Journal of Chemical Theory and Computation; Vol. 16; No. 7; 4226-4237; 10.1021/acs.jctc.0c00169
• Harrington, Haley R. and Zimmer, Matthew H., et el. (2020) Cotranslational Folding Stimulates Programmed Ribosomal Frameshifting in the Alphavirus Structural Polyprotein; Journal of Biological Chemistry; Vol. 295; No. 20; 6798-6808; PMCID PMC7242702; 10.1074/jbc.RA120.012706
• Werner, Hans-Joachim and Knowles, Peter J., et el. (2020) Molpro quantum chemistry package; Journal of Chemical Physics; Vol. 152; No. 14; Art. No. 144107; 10.1063/5.0005081
• Tao, Xuecheng and Shushkov, Philip, et el. (2020) Microcanonical rates from ring-polymer molecular dynamics: Direct-shooting, stationary-phase, and maximum-entropy approaches; Journal of Chemical Physics; Vol. 152; No. 12; Art. No. 124117; 10.1063/1.5144307
• Niesen, Michiel J. M. and Zimmerman, Michael H., et el. (2020) Dynamics of Co-translational Membrane Protein Integration and Translocation via the Sec Translocon; Journal of the American Chemical Society; Vol. 142; No. 12; 5449-5460; 10.1021/jacs.9b07820
• Korol, Roman and Rosa-Raíces, Jorge L., et el. (2020) Dimension-free path-integral molecular dynamics without preconditioning; Journal of Chemical Physics; Vol. 152; No. 10; Art. No. 104102; 10.1063/1.5134810
• Manby, Frederick R. and Miller, Thomas F., III, et el. (2020) entos: A Quantum Molecular Simulation Package; 10.26434/chemrxiv.7762646.v2
• Eldridge, Daniel L. and Korol, Roman, et el. (2019) Comparison of Experimental vs Theoretical Abundances of ¹³CH₃D and ¹²CH₂D₂ for Isotopically Equilibrated Systems from 1 to 500 °C; ACS Earth and Space Chemistry; Vol. 3; No. 12; 2747-2764; 10.1021/acsearthspacechem.9b00244
• Cheng, Lixue and Kovachki, Nikola B., et el. (2019) Regression-clustering for Improved Accuracy and Training Cost with Molecular-Orbital-Based Machine Learning; Journal of Chemical Theory and Computation; Vol. 15; No. 12; 6668-6677; 10.1021/acs.jctc.9b00884
• Davis, Victoria K. and Munoz, Stephen, et el. (2019) Fluoride-ion solvation in non-aqueous electrolyte solutions; Materials Chemistry Frontiers; Vol. 3; No. 12; 2721-2727; 10.1039/c9qm00512a
• Rosa-Raíces, Jorge L. and Zhang, Bin, et el. (2019) Path-accelerated stochastic molecular dynamics: Parallel-in-time integration using path integrals; Journal of Chemical Physics; Vol. 151; No. 16; Art. No. 164120; 10.1063/1.5125455
• Shushkov, Philip and Miller, Thomas F., III (2019) Real-time density-matrix coupled-cluster approach for closed and open systems at finite temperature; Journal of Chemical Physics; Vol. 151; No. 13; Art. No. 134107; 10.1063/1.5121749
• Korol, Roman and Bou-Rabee, Nawaf, et el. (2019) Cayley modification for strongly stable path-integral and ring-polymer molecular dynamics; Journal of Chemical Physics; Vol. 151; No. 12; Art. No. 124103; 10.1063/1.5120282
• Magdău, Ioan B. and Mead, Griffin J., et el. (2019) Interpretation of the THz-THz-Raman Spectrum of Bromoform; Journal of Physical Chemistry A; Vol. 123; No. 33; 7278-7287; 10.1021/acs.jpca.9b05165
• Lee, Sebastian J. R. and Ding, Feizhi, et el. (2019) Analytical Gradients for Projection-Based Wavefunction-in-DFT Embedding; Journal of Chemical Physics; Vol. 151; No. 6; Art. No. 064112; 10.1063/1.5109882
• Boamah, Mavis D. and Lozier, Emilie H., et el. (2019) Energy Conversion via Metal Nanolayers; Proceedings of the National Academy of Sciences of the United States of America; Vol. 116; No. 33; 16210-16215; PMCID PMC6697787; 10.1073/pnas.1906601116
• Geiger, Franz and Miller, Thomas F., et el. (2019) Nanolayers from earth-abundant elements for renewable energy applications
• Geiger, Franz and Miller, Thomas F., et el. (2019) Energy conversion using inorganic nanolayers made from a single element
• Geiger, Franz and Miller, Thomas F. (2019) Energy transduction via metal nanofilms
• Yao, Yunxi and Shushkov, Philip, et el. (2019) Direct dioxygen evolution in collisions of carbon dioxide with surfaces; Nature Communications; Vol. 10; Art. No. 2294; PMCID PMC6534623; 10.1038/s41467-019-10342-6
• Lee, Sebastian J. R. and Welborn, Matthew, et el. (2019) Projection-Based Wavefunction-in-DFT Embedding; Accounts of Chemical Research; Vol. 52; No. 5; 1359-1368; 10.1021/acs.accounts.8b00672
• Jiang, Hongyan and Kammler, Marvin, et el. (2019) Imaging covalent bond formation by H atom scattering from graphene; Science; Vol. 364; No. 6438; 379-382; 10.1126/science.aaw6378
• Cheng, Lixue and Welborn, Matthew, et el. (2019) A universal density matrix functional from molecular orbital-based machine learning: Transferability across organic molecules; Journal of Chemical Physics; Vol. 150; No. 13; Art. No. 131103; 10.1063/1.5088393
• Tao, Xuecheng and Shushkov, Philip, et el. (2019) A Simple Flux-Side Formulation of State-Resolved Thermal Reaction Rates for Ring-Polymer Surface Hopping; Journal of Physical Chemistry A; Vol. 123; No. 13; 3013-3020; 10.1021/acs.jpca.9b00877
• Welborn, Matthew and Manby, Frederick R., et el. (2019) Balancing the description of subsystems in wavefunction-in-DFT and DFT-in-lower embedding
• Welborn, Matthew and Cheng, Lixue, et el. (2019) Transferability in machine-learning for electronic structure via the molecular orbital basis
• Miller, Thomas F. (2019) DFT-based embedding theories: Wavefunction-embedding, dynamics, excited states, and applications
• Lee, Sebastian James Rice and Ding, Feizhi, et el. (2019) Analytical nuclear gradients for projection-based wavefunction-in-DFT embedding
• Miller, Thomas F. (2019) Electron transfer in the solid-electrolyte interphase
• Miller, Thomas F. (2019) Dynamics of Co-Translational Membrane Integration; Biophysical Journal; Vol. 116; No. 3; 11a; 10.1016/j.bpj.2018.11.096
• Davis, Victoria K. and Bates, Christopher M., et el. (2018) Room-temperature cycling of metal fluoride electrodes: Liquid electrolytes for high-energy fluoride ion cells; Science; Vol. 362; No. 6419; 1144-1148; 10.1126/science.aat7070
• Niesen, Michiel J. M. and Müller-Lucks, Annika, et el. (2018) Forces on nascent polypeptides during membrane insertion and translocation via the Sec translocon; Biophysical Journal; Vol. 115; No. 10; 1885-1894; PMCID PMC6303271; 10.1016/j.bpj.2018.10.002
• Welborn, Matthew and Manby, Frederick R., et el. (2018) Even-handed subsystem selection in projection-based embedding; Journal of Chemical Physics; Vol. 149; No. 14; Art. No. 144101; 10.1063/1.5050533
• Welborn, Matthew and Cheng, Lixue, et el. (2018) Transferability in Machine Learning for Electronic Structure via the Molecular Orbital Basis; Journal of Chemical Theory and Computation; Vol. 14; No. 9; 4772-4779; 10.1021/acs.jctc.8b00636
• Miller, Thomas (2018) Including nuclear quantum effects in mixed-quantum classical non-adiabatic dynamics
• Miller, Thomas F. (2018) DFT-based embedding theories: Wavefunction-embedding, dynamics, excited states, and applications
• Miller, Thomas (2018) Understanding and improving membrane protein expression in cells
• Webb, Michael A. and Yamamoto, Umi, et el. (2018) Globally Suppressed Dynamics in Ion-Doped Polymers; ACS Macro Letters; Vol. 7; No. 6; 734-738; 10.1021/acsmacrolett.8b00237
• Kretchmer, Joshua S. and Boekelheide, Nicholas, et el. (2018) Fluctuating hydrogen-bond networks govern anomalous electron transfer kinetics in a blue copper protein; Proceedings of the National Academy of Sciences of the United States of America; Vol. 115; No. 24; 6129-6134; PMCID PMC6004490; 10.1073/pnas.1805719115
• Zheng, Qi and Pesko, Danielle M., et el. (2018) Optimizing Ion Transport in Polyether-Based Electrolytes for Lithium Batteries; Macromolecules; Vol. 51; No. 8; 2847-2858; 10.1021/acs.macromol.7b02706
• Chapovetsky, Alon and Welborn, Matthew, et el. (2018) Pendant Hydrogen-Bond Donors in Cobalt Catalysts Independently Enhance CO₂ Reduction; ACS Central Science; Vol. 4; No. 3; 397-404; PMCID PMC5879468; 10.1021/acscentsci.7b00607
• Tao, Xuecheng and Shushkov, Philip, et el. (2018) Path-integral isomorphic Hamiltonian for including nuclear quantum effects in non-adiabatic dynamics; Journal of Chemical Physics; Vol. 148; No. 10; Art. No. 102327; 10.1063/1.5005544
• Niesen, Michiel J. M. and Miller, Thomas (2018) Forces on nascent polypeptides during membrane insertion and translocation via the Sec translocon
• Ding, Feizhi and Manby, Frederick, et el. (2018) Embedded mean-field theory for high-efficiency electronic structure
• Welborn, Matthew and Miller, Thomas F. (2018) Even-handed active space selection in projection-based wavefunction-in-DFT embedding
• Fu, Yu-Hsien Hwang and Huang, William Y. C., et el. (2018) Two-Step Membrane Binding by the Bacterial SRP Receptor Enables Efficient and Accurate Co-Translational Protein Targeting; Biophysical Journal; Vol. 114; No. 3; 209A; 10.1016/j.bpj.2017.11.1170
• Niesen, Michiel J. M. and Marshall, Stephen S., et el. (2017) Improving membrane protein expression by optimizing integration efficiency; Journal of Biological Chemistry; Vol. 292; No. 47; 19537-19545; PMCID PMC5702688; 10.1074/jbc.M117.813469
• Finneran, Ian A. and Welsch, Ralph, et el. (2017) 2D THz-THz-Raman Photon-Echo Spectroscopy of Molecular Vibrations in Liquid Bromoform; Journal of Physical Chemistry Letters; Vol. 8; No. 18; 4640-4644; 10.1021/acs.jpclett.7b02106
• Ding, Feizhi and Tsuchiya, Takashi, et el. (2017) Linear-response time-dependent embedded mean-field theory; Journal of Chemical Theory and Computation; Vol. 13; No. 9; 4216-4227; 10.1021/acs.jctc.7b00666
• Lee, Sebastian J. R. and Miyamoto, Kaito, et el. (2017) Density-based errors in mixed-basis mean-field electronic structure, with implications for embedding and QM/MM methods; Chemical Physics Letters; Vol. 683; 375-382; 10.1016/j.cplett.2017.04.059
• Kretchmer, Joshua and Miller, Thomas (2017) Direct simulation of non-adiabatic dynamics in large-scale enzymatic systems
• Fu, Yu-Hsien Hwang and Huang, William Y. C., et el. (2017) Two-step membrane binding by the bacterial SRP receptor enable efficient and accurate Co-translational protein targeting; eLife; Vol. 6; Art. No. e25885; PMCID PMC5533587; 10.7554/eLife.25885
• Ding, Feizhi and Manby, Frederick R., et el. (2017) Embedded Mean-Field Theory with Block-Orthogonalized Partitioning; Journal of Chemical Theory and Computation; Vol. 13; No. 4; 1605-1615; 10.1021/acs.jctc.6b01065
• Miller, Thomas F., III and Wang, Zhen-Gang, et el. (2017) Designing Polymer Electrolytes for Safe and High Capacity Rechargeable Lithium Batteries; Accounts of Chemical Research; Vol. 50; No. 3; 590-593; 10.1021/acs.accounts.6b00568
• Niesen, Michiel J. M. and Wang, Connie Y., et el. (2017) Structurally detailed coarse-grained model for Sec-facilitated co-translational protein translocation and membrane integration; PLOS Computational Biology; Vol. 13; No. 3; Art. No. e1005427; PMCID PMC5381951; 10.1371/journal.pcbi.1005427
• Pennifold, Robert C. R. and Bennie, Simon J., et el. (2017) Correcting density-driven errors in projection-based embedding; Journal of Chemical Physics; Vol. 146; No. 8; Art. No. 084113; 10.1063/1.4974929
• Savoie, Brett M. and Webb, Michael A., et el. (2017) Enhancing Cation Diffusion and Suppressing Anion Diffusion via Lewis-Acidic Polymer Electrolytes; Journal of Physical Chemistry Letters; Vol. 8; No. 3; 641-646; 10.1021/acs.jpclett.6b02662
• Webb, Michael A. and Wang, Yimin, et el. (2017) Equilibrium Clumped-Isotope Effects in Doubly Substituted Isotopologues of Ethane; Geochimica et Cosmochimica Acta; Vol. 197; 14-26; 10.1016/j.gca.2016.10.001
• Miyamoto, Kaito and Miller, Thomas F., III, et el. (2016) Fock-Matrix Corrections in Density Functional Theory and Use in Embedded Mean-Field Theory; Journal of Chemical Theory and Computation; Vol. 12; No. 12; 5811-5822; 10.1021/acs.jctc.6b00685
• Kretchmer, Joshua S. and Miller, Thomas F., III (2016) Kinetically-constrained ring-polymer molecular dynamics for non-adiabatic chemistries involving solvent and donor–acceptor dynamical effects; Faraday Discussions; Vol. 195; 191-214; 10.1039/C6FD00143B
• Welsch, Ralph and Song, Kai, et el. (2016) Non-equilibrium dynamics from RPMD and CMD; Journal of Chemical Physics; Vol. 145; No. 20; Art. No. 204118; 10.1063/1.4967958
• Welsch, Ralph and Driscoll, Eric, et el. (2016) Molecular Seesaw: How Increased Hydrogen Bonding Can Hinder Excited-State Proton Transfer; Journal of Physical Chemistry Letters; Vol. 7; No. 18; 3616-3620; 10.1021/acs.jpclett.6b01391
• Huo, Pengfei and Uyeda, Christopher, et el. (2016) Breaking the Correlation between Energy Costs and Kinetic Barriers in Hydrogen Evolution via a Cobalt Pyridine-Diimine-Dioxime Catalyst; ACS Catalysis; Vol. 6; No. 9; 6114-6123; 10.1021/acscatal.6b01387
• Marshall, Stephen S. and Niesen, Michiel J. M., et el. (2016) A Link between Integral Membrane Protein Expression and Simulated Integration Efficiency; Cell Reports; Vol. 16; No. 8; 2169-2177; PMCID PMC5001948; 10.1016/j.celrep.2016.07.042
• Pesko, Danielle M. and Webb, Michael A., et el. (2016) Universal Relationship between Conductivity and Solvation-Site Connectivity in Ether-Based Polymer Electrolytes; Macromolecules; Vol. 49; No. 14; 5244-5255; 10.1021/acs.macromol.6b00851
• Finneran, Ian A. and Welsch, Ralph, et el. (2016) Coherent two-dimensional terahertz-terahertz-Raman spectroscopy; Proceedings of the National Academy of Sciences of the United States of America; Vol. 113; No. 25; 6857-6861; PMCID PMC4922159; 10.1073/pnas.1605631113
• Pesko, Danielle M. and Jung, Yukyung, et el. (2016) Effect of monomer structure on ionic conductivity in a systematic set of polyester electrolytes; Solid State Ionics; Vol. 289; 118-124; 10.1016/j.ssi.2016.02.020
• Niesen, Michiel J. M. and Marshall, Stephen S., et el. (2016) Sequence-level prediction and control of the production of a membrane protein
• Van Lehn, Reid and Zhang, Bin, et el. (2016) Determinants of membrane protein integration mediated by the Sec translocon
• Webb, Michael and Miller, Thomas (2016) Path-integral methods for clumped and position-specific isotope studies
• Savoie, Brett M. and Miller, Thomas F. (2016) Scalable models of ion transport for electrolyte materials discovery
• Wang, Connie and Miller, Thomas (2016) Modeling of lithium deposition and dissolution during battery cycling
• Welsch, Ralph and Althorpe, Stuart, et el. (2016) Non-equilibrium ring-polymer molecular dynamics
• Webb, Michael A. and Savoie, Brett M., et el. (2016) Systematic computational and experimental investigation of lithium-ion transport mechanisms in polymer electrolytes
• Webb, Michael and Savoie, Brett, et el. (2016) Chemically specific dynamic bond percolation model for computational screening of polymer electrolytes
• Niesen, Michiel J. M. and Wang, Connie Y., et el. (2016) Coarse-Grained Modeling of Membrane Protein Integration via the Sec Translocon; Biophysical Journal; Vol. 110; No. 3; 56A; 10.1016/j.bpj.2015.11.371
• Van Lehn, Reid C. and Zhang, Bin, et el. (2016) Determinants of Multispanning Membrane Protein Integration Mediated by the Sec Translocon; Biophysical Journal; Vol. 110; No. 3; 56A-57A; 10.1016/j.bpj.2015.11.372
• Wang, Connie and Wang, Shuai, et el. (2016) Inversion of Signal Sequence Topology during Membrane Integration; Biophysical Journal; Vol. 110; No. 3; 226A-227A; 10.1016/j.bpj.2015.11.1252
• Miller, Thomas (2016) Regulation of Sec-Facilitated Protein Translocation and Membrane Integration; Biophysical Journal; Vol. 110; No. 3; 3A; 10.1016/j.bpj.2015.11.062
• Forte, Lila and Wang, Connie Y., et el. (2016) Statistical Mechanical Framework for Predicting Cellular Responses from Single-Cell Data; Biophysical Journal; Vol. 110; No. 3; 350A; 10.1016/j.bpj.2015.11.1883
• Kretchmer, Joshua S. and Miller, Thomas F., III (2016) Tipping the Balance between Concerted versus Sequential Proton-Coupled Electron Transfer; Inorganic Chemistry; Vol. 55; No. 3; 1022-1031; 10.1021/acs.inorgchem.5b01821
• Huo, Pengfei and Miller, Thomas F., III (2015) Electronic coherence and the kinetics of inter-complex energy transfer in light-harvesting systems; Physical Chemistry Chemical Physics; Vol. 17; No. 46; 30914-30924; 10.1039/c5cp02517f
• Webb, Michael A. and Savoie, Brett M., et el. (2015) Chemically Specific Dynamic Bond Percolation Model for Ion Transport in Polymer Electrolytes; Macromolecules; Vol. 48; No. 19; 7346-7358; 10.1021/acs.macromol.5b01437
• Van Lehn, Reid C. and Zhang, Bin, et el. (2015) Regulation of multispanning membrane protein topology via post-translational annealing; eLife; Vol. 4; Art. No. e08697; PMCID PMC4635508; 10.7554/eLife.08697
• Kowalczyk, Piotr and Terzyk, Artur P., et el. (2015) Nuclear Quantum Effects in the Layering and Diffusion of Hydrogen Isotopes in Carbon Nanotubes; Journal of Physical Chemistry Letters; Vol. 6; No. 17; 3367-3372; 10.1021/acs.jpclett.5b01545
• Savoie, Brett M. and Miller, Thomas F. (2015) Loosening the grip of polymer electrolytes: How the asymmetry of ion diffusion in conventional polyethers reveals a new design paradigm
• Webb, Michael A. and Savoie, Brett M., et el. (2015) Design of next-generation polymer electrolytes: A site network model for ion transport from mechanistic insight
• Miller, Thomas F. (2015) New approaches to simulating biological and molecular catalysts
• Lee, Joonho and Miyamoto, Kaito, et el. (2015) Embedded mean-field theory: Toward a large-scale ab-initio molecular dynamics
• Webb, Michael A. and Jung, Yukyung, et el. (2015) Systematic Computational and Experimental Investigation of Lithium-Ion Transport Mechanisms in Polyester-Based Polymer Electrolytes; ACS Central Science; Vol. 1; No. 4; 198-205; PMCID PMC4827473; 10.1021/acscentsci.5b00195
• Bennie, Simon J. and Stella, Martina, et el. (2015) Accelerating wavefunction in density-functional-theory embedding by truncating the active basis set; Journal of Chemical Physics; Vol. 143; No. 2; Art. No. 024105; 10.1063/1.4923367
• Miller, Thomas F. (2015) Wavefunction embedding methods for the study of renewable energy catalysis; Abstracts of Papers of the American Chemical Society; Vol. 249; CATL-11
• Miller, Thomas (2015) New approaches to simulating biological and molecular catalysts; Abstracts of Papers of the American Chemical Society; Vol. 249; PHYS-183
• Barnes, Taylor and Kaminski, Jakub, et el. (2015) Ab initio characterization of the electrochemical stability and solvation properties of condensed-phase ethylene carbonate and dimethyl carbonate mixtures; Abstracts of Papers of the American Chemical Society; Vol. 249; COMP-71
• Barnes, Taylor A. and Kaminski, Jakub W., et el. (2015) Ab Initio Characterization of the Electrochemical Stability and Solvation Properties of Condensed-Phase Ethylene Carbonate and Dimethyl Carbonate Mixtures; Journal of Physical Chemistry C; Vol. 119; No. 8; 3865-3880; 10.1021/jp510882g
• Fornace, Mark E. and Lee, Joonho, et el. (2015) Embedded Mean-Field Theory; Journal of Chemical Theory and Computation; Vol. 11; No. 2; 568-580; 10.1021/ct5011032
• Niesen, Michiel J. M. and Miller, Thomas F., III (2015) Coarse-Grained Modeling of Minute-Timescale Co-Translational Membrane Protein Integration via the Sec-Translocon; Biophysical Journal; Vol. 108; No. 2; 501A; 10.1016/j.bpj.2014.11.2743
• Wang, Connie Y. and Miller, Thomas F., III (2014) Allosteric response and substrate sensitivity in peptide binding of the signal recognition particle; Journal of Biological Chemistry; Vol. 289; No. 44; 30868-30879; PMCID PMC4215262; 10.1074/jbc.M114.584912
• Huo, Pengfei and Uyeda, Christopher, et el. (2014) Intra-molecular proton transfer and hydrogen evolution mechanism in cobalt catalysts
• Miller, Thomas F. (2014) Multi-scale simulation of electrode interfaces
• Miller, Thomas F. (2014) Accurate and systematically improvable density functional theory embedding for correlated wavefunctions
• Goodpaster, Jason D. and Barnes, Taylor A., et el. (2014) Accurate and systematically improvable density functional theory embedding for correlated wavefunctions; Journal of Chemical Physics; Vol. 140; No. 18; Art. No. 18A507; 10.1063/1.4864040
• Goodpaster, Jason D. and Barnes, Taylor A., et el. (2014) Accurate and robust wavefunction embedding methodologies
• Menzeleev, Artur R. and Bell, Franziska, et el. (2014) Kinetically constrained ring-polymer molecular dynamics for non-adiabatic chemical reactions; Journal of Chemical Physics; Vol. 140; No. 6; Art. No. 064103; 10.1063/1.4863919
• Webb, Michael A. and Miller, Thomas F., III (2013) Position-Specific and Clumped Stable Isotope Studies: Comparison of the Urey and Path-Integral Approaches for Carbon Dioxide, Nitrous Oxide, Methane, and Propane; Journal of Physical Chemistry A; 10.1021/jp411134v
• Huo, Pengfei and Miller, Thomas F., III, et el. (2013) Communication: Predictive partial linearized path integral simulation of condensed phase electron transfer dynamics; Journal of Chemical Physics; Vol. 139; No. 15; Art. No. 151103; 10.1063/1.4826163
• Miller, Thomas F. (2013) Modeling the dynamics and regulation of Sec-facilitated protein translocation and membrane integration
• Miller, Thomas F. (2013) Quantum dynamics from classical trajectories: New approaches to simulating biological and molecular photocatalysts
• Miller, Thomas F. (2013) Exactly embedded density functional theory for modeling chemical reactions
• Barnes, Taylor A. and Goodpaster, Jason D., et el. (2013) Accurate basis set truncation for wavefunction embedding; Journal of Chemical Physics; Vol. 139; No. 2; Art. No. 024103; 10.1063/1.4811112
• Kretchmer, Joshua S. and Miller, Thomas F., III (2013) Direct simulation of proton-coupled electron transfer across multiple regimes; Journal of Chemical Physics; Vol. 138; No. 13; Art. No. 134109; 10.1063/1.4797462
• Habershon, Scott and Manolopoulos, David E., et el. (2013) Ring-Polymer Molecular Dynamics: Quantum Effects in Chemical Dynamics from Classical Trajectories in an Extended Phase Space; Annual Review of Physical Chemistry; Vol. 64; 387-413; 10.1146/annurev-physchem-040412-110122
• Warren, Jeffrey J. and Menzeleev, Artur R., et el. (2013) Long-Range Proton-Coupled Electron-Transfer Reactions of Bis(imidazole) Iron Tetraphenylporphyrins Linked to Benzoates; Journal of Physical Chemistry Letters; Vol. 4; No. 3; 519-523; PMCID PMC3593309; 10.1021/jz400029w
• Mayers, Matthew Z. and Kaminski, Jakub W., et el. (2012) Suppression of Dendrite Formation via Pulse Charging in Rechargeable Lithium Metal Batteries; Journal of Physical Chemistry C; Vol. 116; No. 50; 26214-26221; 10.1021/jp309321w
• Goodpaster, Jason D. and Barnes, Taylor A., et el. (2012) Density functional theory embedding for correlated wavefunctions: Improved methods for open-shell systems and transition metal complexes; Journal of Chemical Physics; Vol. 137; No. 22; Art. No. 224113; 10.1063/1.4770226
• Zhang, Bin and Miller, Thomas F., III (2012) Long-Timescale Dynamics and Regulation of Sec-Facilitated Protein Translocation; Cell Reports; Vol. 2; No. 4; 927-937; PMCID PMC3483636; 10.1016/j.celrep.2012.08.039
• Zhang, Bin and Miller, Thomas F., III (2012) Direct Simulation of Early-Stage Sec-Facilitated Protein Translocation; Journal of the American Chemical Society; Vol. 134; No. 33; 13700-13707; PMCID PMC3431202; 10.1021/ja3034526
• Manby, Frederick R. and Stella, Martina, et el. (2012) Simple, Exact Density-Functional-Theory Embedding Scheme; Journal of Chemical Theory and Computation; Vol. 8; No. 8; 2564-2568; 10.1021/ct300544e
• Miller, Thomas F. (2012) Direct simulation of electron transfer and proton-coupled electron transfer dynamics in the condensed-phase
• Padilla Araujo, Bernardo Sosa and Miller, Thomas, et el. (2012) In Silico Screening of Computational Enzyme Designs; Protein Science; Vol. 21; No. S1; 132
• Ananth, Nandini and Miller, Thomas F., III (2012) Flux-correlation approach to characterizing reaction pathways in quantum systems: a study of condensed-phase proton-coupled electron transfer; Molecular Physics; Vol. 110; No. 9-10; 1009-1015; 10.1080/00268976.2012.686641
• Boekelheide, Nicholas and Salomόn-Ferrer, Romelia, et el. (2011) Dynamics and dissipation in enzyme catalysis; Proceedings of the National Academy of Sciences of the United States of America; Vol. 108; No. 39; 16159-16163; PMCID PMC3182692; 10.1073/pnas.1106397108
• Menzeleev, Artur R. and Ananth, Nandini, et el. (2011) Direct simulation of electron transfer using ring polymer molecular dynamics: Comparison with semiclassical instanton theory and exact quantum methods; Journal of Chemical Physics; Vol. 135; No. 7; Art. No. 074106; 10.1063/1.3624766
• Goodpaster, Jason D. and Barnes, Taylor A., et el. (2011) Embedded density functional theory for covalently bonded and strongly interacting subsystems; Journal of Chemical Physics; Vol. 134; No. 16; Art. No. 164108; 10.1063/1.3582913
• Ananth, Nandini and Miller, Thomas F., III (2010) Exact quantum statistics for electronically nonadiabatic systems using continuous path variables; Journal of Chemical Physics; Vol. 133; No. 23; Art. No. 234103; 10.1063/1.3511700
• Goodpaster, Jason D. and Ananth, Nandini, et el. (2010) Exact nonadditive kinetic potentials for embedded density functional theory; Journal of Chemical Physics; Vol. 133; No. 8; Art. No. 084103; 10.1063/1.3474575
• Adelman, Joshua L. and Chodera, John D., et el. (2010) The Mechanical Properties of PCNA: Implications for the Loading and Function of a DNA Sliding Clamp; Biophysical Journal; Vol. 98; No. 12; 3062-3069; 10.1016/j.bpj.2010.03.056
• Zhang, Bin and Miller, Thomas F., III (2010) Hydrophobically stabilized open state for the lateral gate of the Sec translocon; Proceedings of the National Academy of Sciences of the United States of America; Vol. 107; No. 12; 5399-5404; PMCID PMC2851780; 10.1073/pnas.0914752107
• Menzeleev, Artur R. and Miller, Thomas F., III (2010) Ring polymer molecular dynamics beyond the linear response regime: Excess electron injection and trapping in liquids; Journal of Chemical Physics; Vol. 132; No. 3; Art. No. 034106; 10.1063/1.3292576
• Miller, Thomas F., III (2008) Isomorphic classical molecular dynamics model for an excess electron in a supercritical fluid; Journal of Chemical Physics; Vol. 129; No. 19; Art. No. 194502; 10.1063/1.3013357
• Miller, Thomas F., III and Vanden-Eijnden, Eric, et el. (2007) Solvent coarse-graining and the string method applied to the hydrophobic collapse of a hydrated chain; Proceedings of the National Academy of Sciences of the United States of America; Vol. 104; No. 37; 14559-14564; PMCID PMC1955457; 10.1073/pnas.0705830104
• Miller, Thomas F., III and Predescu, Cristian (2007) Sampling diffusive transition paths; Journal of Chemical Physics; Vol. 126; No. 14; Art. No. 144102; 10.1103/10.1063/1.2712444
• Miller, Thomas F., III and Manolopolous, David E. (2005) Quantum diffusion in liquid water from ring polymer molecular dynamics; Journal of Chemical Physics; Vol. 123; No. 15; Art. No. 154504; 10.1063/1.2074967
• Miller, Thomas F., III and Clary, David C., et el. (2005) Collision-induced conformational changes in glycine; Journal of Chemical Physics; Vol. 122; No. 24; Art. No. 244323; 10.1063/1.1927527
• Miller, Thomas F., III and Clary, David C. (2005) Torsional anharmonicity in the conformational thermodynamics of flexible molecules; Molecular Physics; Vol. 103; No. 11-12; 1573-1578; 10.1080/00268970500096145
• Miller, Thomas F., III and Manolopolous, David E. (2005) Quantum diffusion in liquid para-hydrogen from ring-polymer molecular dynamics; Journal of Chemical Physics; Vol. 122; No. 18; Art. No. 184503; 10.1063/1.1893956
• Miller, Thomas F., III and Manolopolous, David E., et el. (2005) Comment on "A centroid molecular dynamics study of liquid para hydrogen and ortho deuterium" [J. Chem. Phys. 121, 6412 (2004)]; Journal of Chemical Physics; Vol. 122; No. 5; Art. No. 057101; 10.1063/1.1839867
• Miller, Thomas F., III and Clary, David C. (2004) Quantum free energies of the conformers of glycine on an ab initio potential energy surface; Physical Chemistry Chemical Physics; Vol. 6; No. 10; 2563-2571; 10.1039/b314644h
• Nanjia, Shikha and Jasper, Ahren W., et el. (2004) 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; Journal of Chemical Physics; Vol. 120; No. 8; 3586-3597; 10.1063/1.1641019
• Miller, Thomas F., III and Clary, David C. (2003) Torsional path integral Monte Carlo method for calculating the absolute quantum free energy of large molecules; Journal of Chemical Physics; Vol. 119; No. 1; 68-76; 10.1063/1.1568727
• Miller, T. F., III and Eleftheriou, M., et el. (2002) Symplectic quaternion scheme for biophysical molecular dynamics; Journal of Chemical Physics; Vol. 116; No. 20; 8649-8659; 10.1063/1.1473654
• Miller, Thomas F., III and Clary, David C. (2002) Torsional path integral Monte Carlo method for the quantum simulation of large molecules; Journal of Chemical Physics; Vol. 116; No. 19; 8262-8269; 10.1063/1.1467342
• Miller, J. Scott and Poliakoff, E. D., et el. (2001) Excitation of the symmetry forbidden bending mode in molecular photoionization; Journal of Chemical Physics; Vol. 114; No. 10; 4496-4504; 10.1063/1.1349090
• Miller, Thomas F., III and Hall, Michael B. (1999) Structural and bonding trends in platinum-carbon clusters; Journal of the American Chemical Society; Vol. 121; No. 32; 7389-7396; 10.1021/ja990854n
• Miller, Thomas F., III and Strout, Douglas L., et el. (1998) Linear Semibridging Carbonyls. 6. Structure and Bonding in the Dimers of 17-Electron Tantalum Hexacarbonyl and Tetracarbonyl Diphosphine; Organometallics; Vol. 17; No. 19; 4164-4168; 10.1021/om980144a
• Strout, Douglas L. and Miller, Thomas F., III, et el. (1998) Structure and Stability of Palladium−Carbon Cations; Journal of Physical Chemistry A; Vol. 102; No. 31; 6307-6310; 10.1021/jp980640c