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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