Thomas F. Miller - Publications

Affiliations: 
California Institute of Technology, Pasadena, CA 
Area:
Theory and simulation of chemical, biochemical, and soft matter systems
Website:
http://millergroup.caltech.edu/Miller_Group/Tom_Miller.html

79 high-probability publications. We are testing a new system for linking publications to authors. You can help! If you notice any inaccuracies, please sign in and mark papers as correct or incorrect matches. If you identify any major omissions or other inaccuracies in the publication list, please let us know.

Year Citation  Score
2019 Rosa-Raíces JL, Zhang B, Miller TF. Path-accelerated stochastic molecular dynamics: Parallel-in-time integration using path integrals. The Journal of Chemical Physics. 151: 164120. PMID 31675892 DOI: 10.1063/1.5125455  1
2019 Cheng L, Kovachki NB, Welborn M, Miller TF. Regression-clustering for Improved Accuracy and Training Cost with Molecular-Orbital-Based Machine Learning. Journal of Chemical Theory and Computation. PMID 31638804 DOI: 10.1021/acs.jctc.9b00884  1
2019 Korol R, Bou-Rabee N, Miller TF. Cayley modification for strongly stable path-integral and ring-polymer molecular dynamics. The Journal of Chemical Physics. 151: 124103. PMID 31575166 DOI: 10.1063/1.5120282  0.52
2019 Jiang H, Kammler M, Ding F, Dorenkamp Y, Manby FR, Wodtke AM, Miller TF, Kandratsenka A, Bünermann O. Imaging covalent bond formation by H atom scattering from graphene. Science (New York, N.Y.). 364: 379-382. PMID 31023921 DOI: 10.1126/science.aaw6378  1
2019 Lee SJR, Welborn M, Manby FR, Miller TF. Projection-Based Wavefunction-in-DFT Embedding. Accounts of Chemical Research. PMID 30969117 DOI: 10.1021/acs.accounts.8b00672  1
2019 Cheng L, Welborn M, Christensen AS, Miller TF. A universal density matrix functional from molecular orbital-based machine learning: Transferability across organic molecules. The Journal of Chemical Physics. 150: 131103. PMID 30954042 DOI: 10.1063/1.5088393  1
2018 Davis VK, Bates CM, Omichi K, Savoie BM, Momčilović N, Xu Q, Wolf WJ, Webb MA, Billings KJ, Chou NH, Alayoglu S, McKenney RK, Darolles IM, Nair NG, Hightower A, ... ... Miller TF, et al. Room-temperature cycling of metal fluoride electrodes: Liquid electrolytes for high-energy fluoride ion cells. Science (New York, N.Y.). 362: 1144-1148. PMID 30523107 DOI: 10.1126/science.aat7070  0.36
2018 Niesen MJM, Müller-Lucks A, Hedman R, von Heijne G, Miller TF. Forces on Nascent Polypeptides during Membrane Insertion and Translocation via the Sec Translocon. Biophysical Journal. PMID 30366631 DOI: 10.1016/j.bpj.2018.10.002  1
2018 Welborn M, Manby FR, Miller TF. Even-handed subsystem selection in projection-based embedding. The Journal of Chemical Physics. 149: 144101. PMID 30316266 DOI: 10.1063/1.5050533  1
2018 Welborn M, Cheng L, Miller TF. Transferability in Machine Learning for Electronic Structure via the Molecular Orbital Basis. Journal of Chemical Theory and Computation. PMID 30040892 DOI: 10.1021/acs.jctc.8b00636  1
2018 Kretchmer JS, Boekelheide N, Warren JJ, Winkler JR, Gray HB, Miller TF. 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. PMID 29844178 DOI: 10.1073/pnas.1805719115  1
2018 Chapovetsky A, Welborn M, Luna JM, Haiges R, Miller TF, Marinescu SC. Pendant Hydrogen-Bond Donors in Cobalt Catalysts Independently Enhance CO Reduction. Acs Central Science. 4: 397-404. PMID 29632886 DOI: 10.1021/acscentsci.7b00607  1
2017 Miller TF, Wang ZG, Coates GW, Balsara NP. Designing Polymer Electrolytes for Safe and High Capacity Rechargeable Lithium Batteries. Accounts of Chemical Research. 50: 590-593. PMID 28945396 DOI: 10.1021/acs.accounts.6b00568  0.36
2017 Niesen MJM, Marshall SS, Miller TF, Clemons WM. Improving membrane protein expression by optimizing integration efficiency. The Journal of Biological Chemistry. PMID 28918393 DOI: 10.1074/jbc.M117.813469  1
2017 Ding F, Tsuchiya T, Manby FR, Miller TF. Linear-response time-dependent embedded mean-field theory. Journal of Chemical Theory and Computation. PMID 28783359 DOI: 10.1021/acs.jctc.7b00666  1
2017 Niesen MJ, Wang CY, Van Lehn RC, Miller TF. Structurally detailed coarse-grained model for Sec-facilitated co-translational protein translocation and membrane integration. Plos Computational Biology. 13: e1005427. PMID 28328943 DOI: 10.1371/journal.pcbi.1005427  0.44
2017 Pennifold RC, Bennie SJ, Miller TF, Manby FR. Correcting density-driven errors in projection-based embedding. The Journal of Chemical Physics. 146: 084113. PMID 28249446 DOI: 10.1063/1.4974929  1
2017 Ding F, Manby FR, Miller TF. Embedded mean-field theory with block-orthogonalized partitioning. Journal of Chemical Theory and Computation. PMID 28245122 DOI: 10.1021/acs.jctc.6b01065  1
2017 Savoie BM, Webb MA, Miller TF. Enhancing Cation Diffusion and Suppressing Anion Diffusion via Lewis-Acidic Polymer Electrolytes. The Journal of Physical Chemistry Letters. PMID 28075599 DOI: 10.1021/acs.jpclett.6b02662  0.36
2016 Angulo G, Astumian RD, Beniwal V, Bolhuis PG, Dellago C, Ellis J, Ensing B, Glowacki DR, Hammes-Schiffer S, Kästner J, Lelièvre T, Makri N, Manolopoulos D, Menzl G, Miller TF, et al. New methods: general discussion. Faraday Discussions. PMID 27929586 DOI: 10.1039/C6FD90075E  0.64
2016 Miyamoto K, Miller TF, Manby FR. Fock-matrix corrections in density-functional theory, and use in embedded mean-field theory. Journal of Chemical Theory and Computation. PMID 27749063 DOI: 10.1021/acs.jctc.6b00685  1
2016 Welsch R, Driscoll E, Dawlaty JM, Miller TF. Molecular Seesaw: How Increased Hydrogen Bonding Can Hinder Excited-state Proton Transfer. The Journal of Physical Chemistry Letters. PMID 27556887 DOI: 10.1021/acs.jpclett.6b01391  1
2016 Marshall SS, Niesen MJ, Müller A, Tiemann K, Saladi SM, Galimidi RP, Zhang B, Clemons WM, Miller TF. A Link between Integral Membrane Protein Expression and Simulated Integration Efficiency. Cell Reports. PMID 27524616 DOI: 10.1016/j.celrep.2016.07.042  1
2016 Finneran IA, Welsch R, Allodi MA, Miller TF, Blake GA. Coherent two-dimensional terahertz-terahertz-Raman spectroscopy. Proceedings of the National Academy of Sciences of the United States of America. PMID 27274067 DOI: 10.1073/pnas.1605631113  1
2015 Webb MA, Jung Y, Pesko DM, Savoie BM, Yamamoto U, Coates GW, Balsara NP, Wang ZG, Miller TF. Systematic Computational and Experimental Investigation of Lithium-Ion Transport Mechanisms in Polyester-Based Polymer Electrolytes. Acs Central Science. 1: 198-205. PMID 27162971 DOI: 10.1021/acscentsci.5b00195  0.36
2015 Fornace ME, Lee J, Miyamoto K, Manby FR, Miller TF. Embedded Mean-Field Theory. Journal of Chemical Theory and Computation. 11: 568-580. PMID 26580914 DOI: 10.1021/ct5011032  1
2015 Fornace ME, Lee J, Miyamoto K, Manby FR, Miller TF. Correction to Embedded Mean-Field Theory. Journal of Chemical Theory and Computation. 11: 3968. PMID 26574476 DOI: 10.1021/acs.jctc.5b00630  1
2015 Kretchmer JS, Miller TF. Tipping the Balance between Concerted versus Sequential Proton-Coupled Electron Transfer. Inorganic Chemistry. PMID 26440812 DOI: 10.1021/acs.inorgchem.5b01821  1
2015 Van Lehn RC, Zhang B, Miller TF. Regulation of multispanning membrane protein topology via post-translational annealing. Elife. 4. PMID 26408961 DOI: 10.7554/eLife.08697  1
2015 Kowalczyk P, Terzyk AP, Gauden PA, Furmaniak S, Kaneko K, Miller TF. Nuclear Quantum Effects in the Layering and Diffusion of Hydrogen Isotopes in Carbon Nanotubes. The Journal of Physical Chemistry Letters. 3367-3372. PMID 26270239 DOI: 10.1021/acs.jpclett.5b01545  1
2015 Bennie SJ, Stella M, Miller TF, Manby FR. Accelerating wavefunction in density-functional-theory embedding by truncating the active basis set. The Journal of Chemical Physics. 143: 024105. PMID 26178088 DOI: 10.1063/1.4923367  1
2015 Huo P, Miller Iii TF. Electronic coherence and the kinetics of inter-complex energy transfer in light-harvesting systems. Physical Chemistry Chemical Physics : Pccp. PMID 26073739 DOI: 10.1039/c5cp02517f  1
2015 Barnes TA, Kaminski JW, Borodin O, Miller TF. Ab initio characterization of the electrochemical stability and solvation properties of condensed-phase ethylene carbonate and dimethyl carbonate mixtures Journal of Physical Chemistry C. 119: 3865-3880. DOI: 10.1021/jp510882g  1
2015 Fornace ME, Lee J, Miyamoto K, Manby FR, Miller TF. Embedded mean-field theory Journal of Chemical Theory and Computation. 11: 568-580. DOI: 10.1021/ct5011032  1
2015 Webb MA, Savoie BM, Wang ZG, Miller TF. Chemically Specific Dynamic Bond Percolation Model for Ion Transport in Polymer Electrolytes Macromolecules. 48: 7346-7358. DOI: 10.1021/acs.macromol.5b01437  1
2014 Wang CY, Miller TF. Allosteric response and substrate sensitivity in peptide binding of the signal recognition particle. The Journal of Biological Chemistry. 289: 30868-79. PMID 25237192 DOI: 10.1074/jbc.M114.584912  1
2014 Goodpaster JD, Barnes TA, Manby FR, Miller TF. Accurate and systematically improvable density functional theory embedding for correlated wavefunctions. The Journal of Chemical Physics. 140: 18A507. PMID 24832315 DOI: 10.1063/1.4864040  1
2014 Menzeleev AR, Bell F, Miller TF. Kinetically constrained ring-polymer molecular dynamics for non-adiabatic chemical reactions. The Journal of Chemical Physics. 140: 064103. PMID 24527896 DOI: 10.1063/1.4863919  1
2014 Webb MA, Miller TF. Position-specific and clumped stable isotope studies: comparison of the Urey and path-integral approaches for carbon dioxide, nitrous oxide, methane, and propane. The Journal of Physical Chemistry. A. 118: 467-74. PMID 24372450 DOI: 10.1021/jp411134v  1
2013 Huo P, Miller TF, Coker DF. Communication: Predictive partial linearized path integral simulation of condensed phase electron transfer dynamics. The Journal of Chemical Physics. 139: 151103. PMID 24160492 DOI: 10.1063/1.4826163  1
2013 Barnes TA, Goodpaster JD, Manby FR, Miller TF. Accurate basis set truncation for wavefunction embedding. The Journal of Chemical Physics. 139: 024103. PMID 23862925 DOI: 10.1063/1.4811112  1
2013 Kretchmer JS, Miller TF. Direct simulation of proton-coupled electron transfer across multiple regimes. The Journal of Chemical Physics. 138: 134109. PMID 23574210 DOI: 10.1063/1.4797462  1
2013 Warren JJ, Menzeleev AR, Kretchmer JS, Miller TF, Gray HB, Mayer JM. Long Range Proton-Coupled Electron Transfer Reactions of Bis(imidazole) Iron Tetraphenylporphyrins Linked to Benzoates. The Journal of Physical Chemistry Letters. 4: 519-523. PMID 23493584 DOI: 10.1021/jz400029w  1
2013 Habershon S, Manolopoulos DE, Markland TE, Miller TF. Ring-polymer molecular dynamics: quantum effects in chemical dynamics from classical trajectories in an extended phase space. Annual Review of Physical Chemistry. 64: 387-413. PMID 23298242 DOI: 10.1146/annurev-physchem-040412-110122  1
2012 Goodpaster JD, Barnes TA, Manby FR, Miller TF. Density functional theory embedding for correlated wavefunctions: improved methods for open-shell systems and transition metal complexes. The Journal of Chemical Physics. 137: 224113. PMID 23248993 DOI: 10.1063/1.4770226  1
2012 Zhang B, Miller TF. Long-timescale dynamics and regulation of Sec-facilitated protein translocation. Cell Reports. 2: 927-37. PMID 23084746 DOI: 10.1016/j.celrep.2012.08.039  1
2012 Manby FR, Stella M, Goodpaster JD, Miller TF. A Simple, Exact Density-Functional-Theory Embedding Scheme. Journal of Chemical Theory and Computation. 8: 2564-2568. PMID 22904692 DOI: 10.1021/ct300544e  1
2012 Zhang B, Miller TF. Direct simulation of early-stage Sec-facilitated protein translocation. Journal of the American Chemical Society. 134: 13700-7. PMID 22852862 DOI: 10.1021/ja3034526  1
2012 Ananth N, Miller TF. Flux-correlation approach to characterizing reaction pathways in quantum systems: A study of condensed-phase proton-coupled electron transfer Molecular Physics. 110: 1009-1015. DOI: 10.1080/00268976.2012.686641  1
2012 Mayers MZ, Kaminski JW, Miller TF. Suppression of dendrite formation via pulse charging in rechargeable lithium metal batteries Journal of Physical Chemistry C. 116: 26214-26221. DOI: 10.1021/jp309321w  1
2011 Boekelheide N, Salomón-Ferrer R, Miller TF. Dynamics and dissipation in enzyme catalysis. Proceedings of the National Academy of Sciences of the United States of America. 108: 16159-63. PMID 21930950 DOI: 10.1073/pnas.1106397108  1
2011 Menzeleev AR, Ananth N, Miller TF. Direct simulation of electron transfer using ring polymer molecular dynamics: comparison with semiclassical instanton theory and exact quantum methods. The Journal of Chemical Physics. 135: 074106. PMID 21861555 DOI: 10.1063/1.3624766  1
2011 Goodpaster JD, Barnes TA, Miller TF. Embedded density functional theory for covalently bonded and strongly interacting subsystems. The Journal of Chemical Physics. 134: 164108. PMID 21528951 DOI: 10.1063/1.3582913  1
2010 Ananth N, Miller TF. Exact quantum statistics for electronically nonadiabatic systems using continuous path variables. The Journal of Chemical Physics. 133: 234103. PMID 21186854 DOI: 10.1063/1.3511700  1
2010 Goodpaster JD, Ananth N, Manby FR, Miller TF. Exact nonadditive kinetic potentials for embedded density functional theory. The Journal of Chemical Physics. 133: 084103. PMID 20815556 DOI: 10.1063/1.3474575  1
2010 Adelman JL, Chodera JD, Kuo IF, Miller TF, Barsky D. The mechanical properties of PCNA: implications for the loading and function of a DNA sliding clamp. Biophysical Journal. 98: 3062-9. PMID 20550919 DOI: 10.1016/j.bpj.2010.03.056  1
2010 Zhang B, Miller TF. 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. 107: 5399-404. PMID 20203009 DOI: 10.1073/pnas.0914752107  1
2010 Menzeleev AR, Miller TF. Ring polymer molecular dynamics beyond the linear response regime: Excess electron injection and trapping in liquids. The Journal of Chemical Physics. 132: 034106. PMID 20095727 DOI: 10.1063/1.3292576  1
2008 Miller TF. Isomorphic classical molecular dynamics model for an excess electron in a supercritical fluid. The Journal of Chemical Physics. 129: 194502. PMID 19026061 DOI: 10.1063/1.3013357  1
2008 Rufino RJ, Miller TF, Gandhi FS. Morphing hull concepts for unmanned underwater vehicles Oceans 2008. DOI: 10.1109/OCEANS.2008.5151979  0.04
2007 Miller TF, Vanden-Eijnden E, Chandler D. 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. 104: 14559-64. PMID 17726097 DOI: 10.1073/pnas.0705830104  1
2007 Miller TF, Predescu C. Sampling diffusive transition paths. The Journal of Chemical Physics. 126: 144102. PMID 17444696 DOI: 10.1063/1.2712444  1
2006 Miller TF, Clary DC. Quantum simulation of a hydrated noradrenaline analog with the torsional path integral method. The Journal of Physical Chemistry. A. 110: 731-40. PMID 16405347 DOI: 10.1021/jp055108l  1
2006 Braams BJ, Miller TF, Manolopoulos DE. Sum rule constraints on Kubo-transformed correlation functions Chemical Physics Letters. 418: 179-184. DOI: 10.1016/j.cplett.2005.10.127  1
2005 Miller TF, Manolopoulos DE. Quantum diffusion in liquid water from ring polymer molecular dynamics. The Journal of Chemical Physics. 123: 154504. PMID 16252959 DOI: 10.1063/1.2074967  1
2005 Miller TF, Clary DC, Meijer AJ. Collision-induced conformational changes in glycine. The Journal of Chemical Physics. 122: 244323. PMID 16035773 DOI: 10.1063/1.1927527  1
2005 Miller TF, Manolopoulos DE. Quantum diffusion in liquid para-hydrogen from ring-polymer molecular dynamics. The Journal of Chemical Physics. 122: 184503. PMID 15918725 DOI: 10.1063/1.1893956  1
2005 Miller TF, Manolopoulos DE, Madden PA, Konieczny M, Oberhofer H. Comment on "A centroid molecular dynamics study of liquid para hydrogen and ortho deuterium" [J. Chem. Phys. 121, 6412 (2004)]. The Journal of Chemical Physics. 122: 57101; author reply . PMID 15740356 DOI: 10.1063/1.1839867  1
2005 Miller TF, Clary DC. Torsional anharmonicity in the conformational thermodynamics of flexible molecules Molecular Physics. 103: 1573-1578. DOI: 10.1080/00268970500096145  1
2004 Nangia S, Jasper AW, Miller TF, Truhlar DG. 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. The Journal of Chemical Physics. 120: 3586-97. PMID 15268520 DOI: 10.1063/1.1641019  1
2004 Miller TF, Clary DC. Quantum free energies of the conformers of glycine on an ab initio potential energy surface Physical Chemistry Chemical Physics. 6: 2563-2571. DOI: 10.1039/b314644h  1
2004 Miller TF, Clary DC. Predicting conformations of biomolecules: Application to a noradrenaline analogue Journal of Physical Chemistry B. 108: 2484-2488.  1
2003 Miller TF, Clary DC. Torsional path integral Monte Carlo method for calculating the absolute quantum free energy of large molecules Journal of Chemical Physics. 119: 68-76. DOI: 10.1063/1.1568727  1
2002 Miller TF, Eleftheriou M, Pattnaik P, Ndirango A, Newns D, Martyna GJ. Symplectic quaternion scheme for biophysical molecular dynamics Journal of Chemical Physics. 116: 8649-8659. DOI: 10.1063/1.1473654  1
2002 Miller TF, Clary DC. Torsional path integral Monte Carlo method for the quantum simulation of large molecules Journal of Chemical Physics. 116: 8262-8269. DOI: 10.1063/1.1467342  1
2001 Miller JS, Poliakoff ED, Miller TF, Natalense APP, Lucchese RR. Excitation of the symmetry forbidden bending mode in molecular photoionization Journal of Chemical Physics. 114: 4496-4504. DOI: 10.1063/1.1349090  1
1999 Miller TF, Hall MB. Structural and bonding trends in platinum-carbon clusters Journal of the American Chemical Society. 121: 7389-7396. DOI: 10.1021/ja990854n  1
1998 Miller TF, Strout DL, Hall MB. Linear semibridging carbonyls. 6. Structure and bonding in the dimers of 17-electron tantalum hexacarbonyl and tetracarbonyl diphosphine Organometallics. 17: 4161-4168.  1
1998 Strout DL, Miller TF, Hall MB. Structure and stability of palladium-carbon cations Journal of Physical Chemistry A. 102: 6307-6310.  1
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