Miller, Thomas F.

• Qiao, Zhuoran; 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
• Qiao, Zhuoran; 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; 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; 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; Nie, Weili; et el. (2022) Dynamic-Backbone Protein-Ligand Structure Prediction with Multiscale Generative Diffusion Models; 10.48550/arXiv.2209.15171
• Cheng, Lixue; 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.; 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; 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; 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.; 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; 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; 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; 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; 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; Shoshani, Manar M.; et el. (2022) Mechanistic studies of P,O-chelated nickel complexes targeting functional polyolefin synthesis
• Carmody, Patrick J.; 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.; 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.; 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; 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; Tao, Xuecheng; et el. (2021) Nuclear Quantum Effects in Scattering of H and D from Graphene; 10.48550/arXiv.2007.03372
• Rawlings, Dakota; 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; 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; 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; 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.; 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; 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.; 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; 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; 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; 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; 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.; 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; 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; 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.; 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
• Ferguson, Andrew L.; 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.; 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
• Mead, Griffin; 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; 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; 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.; 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.; 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.; 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; 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; 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.; 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; 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.; Miller, Thomas F., III; et el. (2020) entos: A Quantum Molecular Simulation Package; 10.26434/chemrxiv.7762646.v2
• Eldridge, Daniel L.; 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; 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.; 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.; 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; 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.; 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.; 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.; 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; 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
• Geiger, Franz; Miller, Thomas F.; et el. (2019) Nanolayers from earth-abundant elements for renewable energy applications
• Yao, Yunxi; 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.; 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; 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; 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; 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
• Lee, Sebastian James Rice; Ding, Feizhi; et el. (2019) Analytical nuclear gradients for projection-based wavefunction-in-DFT embedding
• Welborn, Matthew; Manby, Frederick R.; et el. (2019) Balancing the description of subsystems in wavefunction-in-DFT and DFT-in-lower embedding
• Miller, Thomas F. (2019) DFT-based embedding theories: Wavefunction-embedding, dynamics, excited states, and applications
• Miller, Thomas F. (2019) Electron transfer in the solid-electrolyte interphase
• Welborn, Matthew; Cheng, Lixue; et el. (2019) Transferability in machine-learning for electronic structure via the molecular orbital basis
• 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.; 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.; 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; 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; 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 F. (2018) DFT-based embedding theories: Wavefunction-embedding, dynamics, excited states, and applications
• Miller, Thomas (2018) Including nuclear quantum effects in mixed-quantum classical non-adiabatic dynamics
• Miller, Thomas (2018) Understanding and improving membrane protein expression in cells
• Webb, Michael A.; 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.; 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; 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; 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; 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
• Ding, Feizhi; 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
• Niesen, Michiel J. M. and Miller, Thomas (2018) Forces on nascent polypeptides during membrane insertion and translocation via the Sec translocon
• Fu, Yu-Hsien Hwang; 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.; 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.; 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; 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.; 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; 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; 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; 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.; 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.; 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.; 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.; 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; 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; 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; 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; 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.; 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.; 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.; 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.; 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
• Webb, Michael; Savoie, Brett; et el. (2016) Chemically specific dynamic bond percolation model for computational screening of polymer electrolytes
• Van Lehn, Reid; Zhang, Bin; et el. (2016) Determinants of membrane protein integration mediated by the Sec translocon
• Wang, Connie and Miller, Thomas (2016) Modeling of lithium deposition and dissolution during battery cycling
• Welsch, Ralph; Althorpe, Stuart; et el. (2016) Non-equilibrium ring-polymer molecular dynamics
• 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
• Niesen, Michiel J. M.; Marshall, Stephen S.; et el. (2016) Sequence-level prediction and control of the production of a membrane protein
• Webb, Michael A.; Savoie, Brett M.; et el. (2016) Systematic computational and experimental investigation of lithium-ion transport mechanisms in polymer electrolytes
• Niesen, Michiel J. M.; 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.; 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; 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; 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.; 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.; 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; 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
• Webb, Michael A.; Savoie, Brett M.; et el. (2015) Design of next-generation polymer electrolytes: A site network model for ion transport from mechanistic insight
• Lee, Joonho; Miyamoto, Kaito; et el. (2015) Embedded mean-field theory: Toward a large-scale ab-initio molecular dynamics
• 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
• Miller, Thomas F. (2015) New approaches to simulating biological and molecular catalysts
• Webb, Michael A.; 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.; 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
• Barnes, Taylor; 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
• Miller, Thomas (2015) New approaches to simulating biological and molecular catalysts; Abstracts of Papers of the American Chemical Society; Vol. 249; PHYS-183
• 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
• Barnes, Taylor A.; 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.; 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
• Miller, Thomas F. (2014) Accurate and systematically improvable density functional theory embedding for correlated wavefunctions
• Huo, Pengfei; 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
• Goodpaster, Jason D.; 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.; Barnes, Taylor A.; et el. (2014) Accurate and robust wavefunction embedding methodologies
• Menzeleev, Artur R.; 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; 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) Exactly embedded density functional theory for modeling chemical reactions
• 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
• Barnes, Taylor A.; 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; 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.; 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.; 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.; 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.; 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; 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; 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.; 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.; 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.; 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.; 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; 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; 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; 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; 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; 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; 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; 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.; 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