Miller, Thomas F.
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- Jacobson, Daniel and Miller, Thomas F., III (2022) Compact-to-Dendritic Transition in the Reactive Deposition of Brownian Particles; 10.48550/arXiv.2204.01173
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- 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
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- 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
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- 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
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- 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
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- Geiger, Franz and Miller, Thomas F., et el. (2019) Nanolayers from earth-abundant elements for renewable energy applications
- Geiger, Franz and Miller, Thomas F. (2019) Energy transduction via metal nanofilms
- Geiger, Franz and Miller, Thomas F., et el. (2019) Energy conversion using inorganic nanolayers made from a single element
- 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
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- 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
- Miller, Thomas F. (2019) Dynamics of Co-Translational Membrane Integration; Biophysical Journal; Vol. 116; No. 3; 11a; 10.1016/j.bpj.2018.11.096
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- 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
- Miller, Thomas F. (2018) DFT-based embedding theories: Wavefunction-embedding, dynamics, excited states, and applications
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- Kretchmer, Joshua and Miller, Thomas (2017) Direct simulation of non-adiabatic dynamics in large-scale enzymatic systems
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- 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
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- 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
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- Wang, Connie and Miller, Thomas (2016) Modeling of lithium deposition and dissolution during battery cycling
- Niesen, Michiel J. M. and Marshall, Stephen S., et el. (2016) Sequence-level prediction and control of the production of a membrane protein
- 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
- Van Lehn, Reid and Zhang, Bin, et el. (2016) Determinants of membrane protein integration mediated by the Sec translocon
- Webb, Michael and Savoie, Brett, et el. (2016) Chemically specific dynamic bond percolation model for computational screening of polymer electrolytes
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- 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
- 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 Savoie, Brett M., et el. (2015) Design of next-generation polymer electrolytes: A site network model for ion transport from mechanistic insight
- 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
- 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
- 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 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 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) Quantum dynamics from classical trajectories: New approaches to simulating biological and molecular photocatalysts
- Miller, Thomas F. (2013) Modeling the dynamics and regulation of Sec-facilitated protein translocation and membrane integration
- 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
- Padilla Araujo, Bernardo Sosa and Miller, Thomas, et el. (2012) In Silico Screening of Computational Enzyme Designs; Protein Science; Vol. 21; No. S1; 132
- Miller, Thomas F. (2012) Direct simulation of electron transfer and proton-coupled electron transfer dynamics in the condensed-phase
- 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