Miller, Thomas F.
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
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
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
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
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
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
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 B; Vol. 124; No. 44; 9767-9772; 10.1021/acs.jpcb.0c09206
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
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
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
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
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
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
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
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 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
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
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
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
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
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
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 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
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
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
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
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
