2024 •2023 •2022•2021•2020
2019•2018•2017 •2016•2015•2014•2013•2012•2011 • 2010
2009• 2008•2007• 2006•2005• 2004 •2003•2002•2001•2000
1999• 1998 •1997•1996•1995•1994•1992•1991•1990•1989•1983•1982
2025
………………………………………………….
158 K. Korchagina and S. D. Schwartz,
Targeted TPS shooting using computer vision to generate ensemble of trajectories,
J. Chem. Theor. Comp. (in press) view
enzymes TPS • TPS machine learning
157 K. Korchagina, S. Balasubramani, J. Berreur, E. Gerard, L. Johannissen, A. Green, S. Hay, and S.D. Schwartz,
Directed evolution’s selective use of quantum tunneling in designed enzymes: a combined theoretical and experimental study,
J. Phys. Chem. B 129. 1555-1562 (2025) view
enzymes TPS • enzymes free energy • enzymes evolution • enzymes design
2024
………………………………………………….
156 C. Frost, D. Antoniou, and S.D. Schwartz,
Transition Path Sampling based free energy calculations of evolution’s effect on rates in β-Lactamase:
the contributions of rapid protein dynamics to rate,
J. Phys. Chem. B 128, 11658-11665 (2024) view
enzymes TPS • enzymes lactamase • enzymes free energy
155 K. Ghanta, R. Castillo, J. Tardiff, and S.D. Schwartz,
The transmission of mutation effects in a multiprotein machine: A comprehensive metadynamics study of the cardiac thin filament,
Prot. Sci. 33, e5215 (2024) view
cardiac troponin • cardiac thin filament • cardiac mutations• cardiac drugs • metadynamics • cardiac allosteric effects
154 C. Frost, D. Antoniou, and S.D. Schwartz,
The evolution of the acylation mechanism in β-lactamase and rapid protein dynamics,
ACS Catal. 14 13640-13651 (2024) view
enzymes TPS • enzymes lactamase • enzymes free energy
153 B. Hei, J. Tardiff, and S.D. Schwartz,
Human cardiac β-myosin powerstroke energetics: thin filament, Pi displacement and mutation effects,
Biophys. J. 123, 1-10 (2024) view
cardiac myosin • cardiac thin filament • cardiac mutations• cardiac drugs • metadynamics
152 A. Chakraborti, J. Tardiff, and S.D. Schwartz,
Myosin-catalyzed ATP hydrolysis in the presence of disease-causing mutations: Mavacamten as a way to repair mechanism,
J. Phys. Chem. B 128, 4716-4727 (2024) view
cardiac myosin • cardiac ATP hydrolysis • cardiac drugs • cardiac TPS • metadynamics • free energy
151 S. Balusubramani, K. Korchagina, and S.D. Schwartz,
Transition path sampling study of engineered enzymes that catalyze the Morita–Baylis–Hillman reaction: why Is enzyme design so difficult?,
J. Chem. Inform. Model. 64, 2101-2111 (2024) view
enzymes TPS • enzymes free energy
2023
………………………………………………….
150 D. Antoniou, I. Zoi, and S.D. Schwartz,
Atomistic description of the relationship between protein dynamics and catalysis with transition path sampling,
Methods in Enzymology 685, 319-340, (2023) view
enzymes review
149 S.D. Schwartz,
Protein dynamics and enzyme catalysis,
J. Phys. Chem. B 127, 2649-2660 (2023) view
enzymes review
148 B. Hei, J. Pemberton, and S.D. Schwartz,
Classical molecular dynamics simulation of glyonic liquids: structural insights and relation to conductive properties,
J. Phys. Chem. B 127, 921-931 (2023) view
micelles
147 C. Frost, S. Balasubramani, D. Antoniou, and S.D. Schwartz,
Connecting conformational motions to rapid dynamics in human purine nucleoside phosphorylase,
J. Phys. Chem. B 127, 144-150 (2023) view
enzymes TPS • enzymes PNP • enzymes free energy • enzymes electric field
2022
………………………………………………….
146 A. Chakraborti, J. Tardiff, and S.D. Schwartz,
Insights into the mechanism of the cardiac drug omecamtiv mecarbil – a computational study,
J. Phys. Chem. B 126, 10069-10082 (2022) view
cardiac myosin • cardiac mutations • cardiac drugs • cardiac TPS • metadynamics
145 S.D. Schwartz,
Perspective: Path sampling methods applied to enzymatic catalysis,
J. Comp. Theor. Chem. 18, 6397-6406 (2022) view
enzymes review
144 S. Balasubramani and S.D. Schwartz,
Transition path sampling based calculations of free energies for enzymatic reactions: the case of human methionine adenosyl transferase and plasmodium vivax adenosine deaminase, view
J. Phys. Chem. B 126, 5413-5420 (2022)
enzymes TPS • enzymes free energy • enzymes electric field
143 A. Deranek, A. Baldo, M. Lynn, S.D. Schwartz, and J. Tardiff,
Structure and dynamics of the flexible cardiac troponin T linker domain in a fully reconstituted fhin filament,
Biochemistry 61, 1229-1242 (2022) view
cardiac thin filament • cardiac mutations
142 A. Mason, J. Tardiff, and S.D. Schwartz,
Free-energy surfaces of two cardiac thin filament conformational changes during muscle contraction,
J. Phys. Chem. B 126, 3844-3851 (2022) view
cardiac thin filament • metadynamics
141 J. Schafer, X. Chen, and Schwartz,
Engineered tryptophan synthase balances equilibrium effects and fast dynamic effects,
ACS Catal. 12, 913-922 (2022) view
enzymes TPS • enzymes evolution
140 D. Antoniou and S.D. Schwartz,
Method for identifying common features in reactive trajectories of a transition path sampling ensemble,
J. Comp. Theor. Chem. 18, 3997-4004 (2022) view
enzymes TPS
2021
………………………………………………….
139 A. Mason, M. Lynn, A. Baldo, A. Deranek, J. Tardiff, and S.D. Schwartz,
Computational and biophysical determination of pathogenicity of variants of unknown significance in cardiac thin filament,
J. Clin. Invest. Insight. 6, 154350 (2021) view
cardiac thin filament • cardiac mutations
138 M. Brown, I. Zoi, D. Antoniou, H. Namanja-Magliano, S.D. Schwartz, and V. Schramm,
Inverse heavy enzyme isotope effects in methylthioadenosine nucleosidases, view
Proc. Natl. Acad. Sci. USA 118, e2109118118 (2021)
enzymes TPS • enzymes MTAN
137 A. Chakraborti, A. Baldo, J. Tardiff, and S.D. Schwartz,
Investigation of the recovery stroke and ATP Hydrolysis and changes caused due to the cardiomyopathic point mutations in human cardiac β myosin,
J. Phys. Chem. B 125, 6513-6521 (2021) view
cardiac myosin • cardiac TPS • metadynamics
136 A. Baldo, J. Tardiff, and S.D. Schwartz,
A proposed mechanism for the initial myosin binding event on the cardiac thin filament: a metadynamics study,
J. Phys. Chem. Lett. 12, 3509-3513 (2021) view
cardiac myosin • cardiac thin filament • metadynamics
2020
………………………………………………….
135 A. Baldo, J. Tardiff, and S.D. Schwartz, S. D.,
Mechanochemical function of myosin II: Investigation into the recovery stroke and ATP hydrolysis,
J. Phys. Chem. B 124, 10014-10023 (2020) view
cardiac myosin • cardiac TPS • metadynamics
134 J. Powers, A. Mason, J. Tardiff, S.D. Schwartz, M. Regnier, and F. Moussavi-Harami,
Modulating the tension-time integral of the cardiac twitch prevents dilated cardiomyopathy in murine hearts,
J. Clin. Invest. Insight 5, e142446 (2020) view
cardiac thin filament • cardiac mutations
133 D. Antoniou and S.D. Schwartz,
Role of protein motions in catalysis by formate dehydrogenase,
J. Phys. Chem. B 124, 9483-9489 (2020) view
enzymes TPS • enzymes formate dehydrogenase
132 I. Zoi, D. Antoniou, and S.D. Schwartz,
Linking protein dynamics to enzyme catalysis,
Comprehensive Natural Products III (Chemistry and Biology), vol. 4, pp. 578-587 Elsevier (2020) view
enzymes review
131 X . Chen and S.D. Schwartz,
Multiple reaction pathways in the morphinone reductase-catalyzed hydride transfer reaction,
ACS Omega 5, 23468-23480 (2020) view
enzymes TPS • enzymes morphinone reductase
130 J. Schafer and S.D. Schwartz,
Directed evolution’s influence on rapid density fluctuations illustrates how protein dynamics can become coupled to chemistry,
ACS Catalysis 10, 8476-8484 (2020) view
enzymes TPS • enzymes retroaldolases • enzymes evolution • enzymes density fluctuations
129 C. Luft, E. Munusamy, J. Pemberton, and S.D. Schwartz,
A classical molecular dynamics simulation study of interfacial and bulk solution aggregation properties of dirhamnolipids,
J. Phys. Chem. B 124, 814-827 (2020) view
micelles
2019
………………………………………………….
128 X. Chen and S.D. Schwartz,
Examining the origin of catalytic power of catechol O‑methyltransferase,
ACS Catalysis 9, 9870-9879, (2019) view
enzymes TPS • enzymes catechol-O-methyl • enzymes electric field
127 S. Abdullah, M. Lynn, M. McConnell, A. Baldo, S.D. Schwartz, and J. Tardiff,
FRET-based analysis of the cardiac troponin T linker region reveals the structural basis of the hypertrophic cardiomyopathy-causing Δ160E mutation,
J. Biol. Chem. 294, 13634-13647 (2019) view
cardiac thin filament • cardiac mutations
126 J. Schafer, I. Zoi, D. Antoniou, and S.D. Schwartz,
Optimization of the turnover in artificial enzymes via directed evolution results in the coupling of protein dynamics to chemistry,
J. Am. Chem. Soc. 141, 10431-10439 (2019) view
enzymes TPS • enzymes retroaldolases • enzymes evolution
125 L. Szatkowski, M. Lynn, M. Williams, A. Baldo, J. Tardiff, and S.D. Schwartz,
Proof of principle that molecular modeling followed by a biophysical experiment can develop small molecules that restore function to the cardiac thin filament in the presence of cardiomyopathic mutations, view
ACS Omega 4, 6492-6501 (2019)
cardiac thin filament • cardiac mutations
2018
………………………………………………….
124 R. Harijan, I. Zoi, D. Antoniou, S.D. Schwartz, and V. Schramm,
Inverse enzyme isotope effects in human purine nucleoside phosphorylase with heavy asparagine labels,
Proc. Natl. Acad. Sci. USA 115, 2609-2616 (2018) view
enzymes TPS • enzymes PNP • enzymes design
123 M. Williams, J. Tardiff, and S.D. Schwartz,
The mechanism of cardiac tropomyosin transitions on filamentous actin as revealed by all atom steered molecular dynamics simulations,
J. Phys. Chem. Lett. 9, 3301-3306 (2018) view
cardiac thin filament • cardiac steered MD
122 E. Munusamy, C. Luft, J. Pemberton, and S.D. Schwartz,
Unraveling the differential aggregation of anionic and nonionic monorhamnolipids at air-water and oil-water interfaces: a classical molecular dynamics simulation study,
J. Phys. Chem. B 122, 6403-6416 (2018) view
micelles
121 V. Schramm and S.D. Schwartz,
Promoting vibrations and the function of enzymes. Emerging theoretical and experimental convergence,
Biochemistry 57, 3299-3308 (2018) view
enzymes review
120 X. Chen and S.D. Schwartz,
Directed evolution as a probe of rate promoting vibrations introduced via mutational change,
Biochemistry 57, 3289-3298 (2018) view
enzymes TPS • enzymes Kemp • enzymes evolution
119 C. Luft, E. Munusamy, J. Pemberton, and S.D. Schwartz,
Molecular dynamics simulation of the oil sequestration properties of a nonionic rhamnolipid,
J. Phys. Chem. B 122, 3944-3952 (2018) view
micelles
118 N. Bras, P. Fernandes, M. Ramos, and S.D. Schwartz,
Mechanistic insights on human phosphoglucomutase revealed by transition path sampling and molecular dynamics calculations,
Chem. Eur. J 24, 1978-1987 (2018) view
enzymes TPS
2017
………………………………………………….
117 I. Zoi, D. Antoniou, and S.D. Schwartz,
Electric fields and fast protein dynamics in enzymes,
J. Phys. Chem. Lett. 8, 6165-6170 (2017) view
enzymes TPS • enzymes electric field • enzymes PNP • enzymes LDH • enzymes KSI
116 R. Eismin, E. Munusamy, L. Kegel, D. Hogan, S.D. Schwartz, and J. Pemberton,
Evolution of aggregate structure in solutions of anionic monorhamnolipids: experimental and computational results,
Langmuir 33, 7412-7424 (2017) view
micelles
115 I. Zoi, D. Antoniou, and S.D. Schwartz,
Incorporating fast protein dynamics into enzyme design: a proposed mutant aromatic amine dehydrogenase,
J. Phys. Chem. B 121, 7290-7298 (2017) view
enzymes TPS • enzymes design • enzymes aromatic amine
114 M. McConnell, M. Williams, M. Lynn, B. Schwartz, S.D. Schwartz, and J. Tardiff,
Clinically Divergent Mutation Effects on the Structure and Function of the Human Cardiac Tropomyosin Overlap,
Biochemistry, 56, 3403-3413 (2017) view
cardiac thin filament • cardiac mutations
113 R. Harijan, I. Zoi, D. Antoniou, S.D. Schwartz, and V. Schramm,
Catalytic-site design for inverse heavy-enzyme isotope effects in human PNP,
Proc. Natl. Acad. Sci. USA 114, 6456-6461 (2017) view
enzymes TPS • enzymes design • enzymes PNP
112 E. Munusamy, C. Luft, J. Pemberton, and S.D. Schwartz,
Structural properties of nonionic monorhamnolipid aggregates in water studied by classical molecular dynamics simulations,
J. Phys. Chem. B 121, 5781-5793, (2017) view
micelles
111 M. Varga, M. Dzierlenga, and S.D. Schwartz,
Structurally linked dynamics in lactate dehydrogenases of evolutionarily distinct species,
Biochemistry 56, 2488-2496 (2017) view
enzymes TPS • enzymes LDH
2016
………………………………………………….
110 X. Pan and S.D. Schwartz,
Conformational heterogeneity in the Michaelis complex of LDH: an analysis of vibrational spectroscopy using Markov and hidden Markov models,
J. Phys. Chem. B 120, 6612-6620 (2016) view
enzymes LDH • enzymes substrate binding • enzymes Markov models
109 M. Dzierlenga and S.D. Schwartz,
Targeting a rate-promoting vibration with an allosteric mediator in Lactate Dehydrogenase,
J. Phys. Chem. Lett. 7, 2591-2596 (2016) view
enzymes TPS• enzymes LDH
108 M. Dzierlenga, M. Varga, and S.D. Schwartz,
Path sampling methods for enzymatic quantum particle transfer reactions,
Methods in Enzymology 577, 21-43 (2016) view
enzymes TPS• enzymes YADH
107 M. Varga and S.D. Schwartz,
Enzymatic kinetic isotope effects from first-principles path sampling calculations,
J Chem Theory Comput, 12, 2047-2054 (2016) view
enzymes TPS• enzymes YADH
106 M. Williams, S. Lehman, J. Tardiff, S.D. and Schwartz,
Atomic resolution probe for allostery in the regulatory thin filament,
Proc. Natl. Acad. Sci. USA 113, 3257-3262 (2016) view
cardiac thin filament • cardiac mutations • cardiac steered MD
105 I. Zoi, J. Suarez, D. Antoniou, S. Cameron, V. Schramm, and S.D. Schwartz,
Modulating enzyme catalysis through mutations designed to alter rapid protein dynamics,
J. Am. Chem. Soc. 138, 3403-3409 (2016) view
enzymes TPS• enzymes PNP • enzymes design
104 D. Antoniou and S.D. Schwartz,
Phase space bottlenecks in enzymatic reactions,
J. Phys. Chem. B 120, 433-439 (2016) view
enzymes TPS• enzymes LDH
103 Z. Wang, D. Antoniou, S.D. Schwartz, and V. Schramm,
Hydride transfer in DHFR by transition path sampling, kinetic isotope effects, and heavy enzyme studies,
Biochemistry 55,157-166 (2016) view
enzymes TPS• enzymes DHFR
2015
………………………………………………….
102 X. Pan and S.D. Schwartz,
Free Energy Surface of the Michaelis Complex of Lactate Dehydrogenase: A Network Analysis of Microsecond Simulations,
J. Phys. Chem. B 119, 5430-5436 (2015) view
enzymes LDH• enzymes conformations
101 M. Dzierlenga, D. Antoniou, and S.D. Schwartz,
Another Look at the Mechanisms of Hydride Transfer Enzymes with Quantum and Classical Transition Path Sampling,
J. Phys. Chem. Lett. 6 1177-1181 (2015) view
enzymes TPS• enzymes LDH • enzymes YADH
100 I. Zoi, M. Motley, D. Antoniou, V. Schramm, and S.D. Schwartz,
Enzyme homologues have distinct reaction paths through their transition states,
J. Phys. Chem. B 119, 3662-3668 (2015) view
enzymes TPS• enzymes MTAN • enzymes reaction paths
99 O. v. der Poorten, I. Zoi, S.D. Schwartz, M. Cai, V. Hruby, and S. Ballet,
Azepinone-Containing Tetrapeptide Analogues of Melanotropin Lead to Selective hMC4R Agonists and hMC5R Antagonist,
Medicinal Chemistry Letters 6, 192-197 (2015) view
docking
98 J. Masterson and S.D. Schwartz,
Evolution alters the enzymatic reaction coordinate of dihydrofolate reductase,
J. Phys. Chem. B 119, 989-996 (2015) view
enzymes TPS• enzymes DHFR
2014
………………………………………………….
97 J. Masterson and S.D. Schwartz,
The enzymatic reaction catalyzed by lactate dehydrogenase exhibits one dominant reaction path,
Chem. Phys. 442, 132-136 (2014) view
enzymes TPS• enzymes LDH
2013
………………………………………………….
96 J. Masterson and S.D. Schwartz,
Changes in protein architecture and subpsec protein dynamics impact the reaction catalyzed by LDH,
J. Phys. Chem. A 117, 7107 (2013) view
enzymes TPS• enzymes LDH
95 M. Motley, V. Schramm, and S.D. Schwartz,
Conformational freedom in tight binding enzymatic transition state analogues,
J. Phys. Chem. B 117, 9591 (2013) view
enzymes TPS• enzymes MTAN
94 S. D. Schwartz,
Protein dynamics and the enzymatic reaction coordinate,
Top. Curr. Chem. 337, 189 (2013) view
enzymes review
2012
………………………………………………….
93 M. Dametto, D. Antoniou, and S.D. Schwartz,
Barrier crossing in DHFR does not involve a rate-promoting vibration,
Mol. Phys. 110, 531 (2012) view
enzymes TPS• enzymes DHFR
92 D. Antoniou, X. Ge, V. Schramm, and S.D. Schwartz,
Mass modulation of protein dynamics associated with barrier crossing in PNP,
J. Phys. Chem. Lett. 3, 3538 (2012) view
enzymes TPS• enzymes PNP
91 E. Manning, J. Tardiff, and S.D. Schwartz,
Molecular effects of familial hypertrophic cardiopathy-related mutations in the TNT1 domain of cTnT,
J. Mol. Biol. 421, 54 (2012) view
cardiac troponin • cardiac mutations
2011
………………………………………………….
90 E. Manning, J. Tardiff, and S.D. Schwartz,
A model of Calcium activation of the cardiac thin filament,
Biochemistry 50, 7405 (2011) view
cardiac thin filament
89 D. Gelman and S.D. Schwartz,
Finite temperature application of the corrected propagator method to reactive dynamics in a condensed-phase environment,
J. Chem. Phys. 134, 034109 (2011) view
reaction rates mixed QM/MM
88 D. Antoniou and S.D. Schwartz,
Protein dynamics and enzymatic chemical barrier passage,
J. Phys. Chem. B 115, 15147 (2011) view
enzymes review
87 A. Davarifar, D.Antoniou, and S.D. Schwartz,
The promoting vibration in LDH is a preferred vibrational channel,
JJ. Phys. Chem. B 115, 15439 (2011)
enzymes TPS• enzymes LDH • enzymes density fluctuations
86 D. Antoniou and S.D. Schwartz,
Reply to “Comment on ‘Towards identification of the reaction coordinate directly from the transition state ensemble using the kernel PCA method'”,
J. Phys. Chem. B 115, 12674 (2011) view
85 D. Antoniou and S.D. Schwartz,
Towards identification of the reaction coordinate directly from the transition state ensemble using the kernel PCA method,
J. Phys. Chem. B 115, 2465 (2011) view
enzymes methods• enzymes LDH
2010
………………………………………………….
84 D. Gelman and S.D. Schwartz,
Dissipative dynamics with the corrected propagator method,
Chem. Phys. 370, 62 (2010) view
reaction rates mixed QM/MM
83 S. Quaytman, E. Pineda, and S.D. Schwartz,
On the origin of the chemical barrier and tunneling in enzymes,
J. Phys. Org. Chem. 23, 690 (2010) view
enzymes review
82 E. Pineda, D. Antoniou, and S.D. Schwartz,
Slow conformational motions that favor sub-ps motions important for catalysis,
J. Phys. Chem. B 114, 15985 (2010) view
enzymes TPS• enzymes LDH • enzymes conformational motions
2009
………………………………………………….
81 D. Antoniou and S.D. Schwartz,
Approximate inclusion of quantum effects in TPS,
J. Chem. Phys. 131, 224111 (2009) view
reaction rates methods
80 S. Quaytman and S.D. Schwartz,
Comparison studies of human heart and bacillus stearothermophillus LDH by Transition Path Sampling,
J. Phys. Chem. A 113, 1892 (2009) view
enzymes TPS• enzymes LDH
79 S. D. Schwartz and V. Schramm,
Enzymatic transition states and dynamic motion in barrier crossing,
Nature Chem. Biol. 5, 551 (2009) view
enzymes TPS• enzymes review
78 D. Gelman and S.D. Schwartz,
Modeling vibrational resonance in a linear hydrocarbon chain with a mixed quantum-classical method,
J. Chem. Phys. 130, 134110 (2009) view
reaction rates mixed QM/MM
77 D. Antoniou and S.D. Schwartz,
The stochastic separatrix and the reaction coordinate for complex systems,
J. Chem. Phys. 130, 151103 (2009) view
reaction rates methods
2008
………………………………………………….
76 S. Saen-oon, S. Quaytman, and S.D. Schwartz,
Atomic detail of chemical transformation at the transition state of an enzymatic reaction,
Proc. Natl. Acad. Sci. USA 105, 1654, (2008) view
enzymes TPS • enzymes PNP
75 S. Saen-oon, M. Ghanem, V. Schramm, and S.D. Schwartz,
Remote mutations and active site dynamics correlate with catalytic properties of PNP,
Biophys. J. 94, 4078 (2008) view
enzymes PNP
74 S. Saen-oon, V. Schramm, and S.D. Schwartz,
Transition path sampling study of the reaction catalyzed by Purine Nucleoside Phosphorylase,
Zeit. Phys. Chemie 222, 1359 (2008) view
enzymes TPS • enzymes PNP
73 M. Ghanem, S. Saen-oon, S. Cahill, S.D. Schwartz, and R. Callendar,
Tryptophan-free human PNP reveals catalytic site interactions,
Biochemistry 47, 3202 (2008) view
enzymes PNP
72 D. Gelman and S.D. Schwartz,
Tunneling dynamics with a mixed quantum-classical method: quantum corrected propagator combined with frozen Gaussian wave packets,
J. Chem. Phys. 129, 024504 (2008) view
reaction rates mixed QM/MM
2007
………………………………………………….
71 D. Antoniou, D. Gelman, and S.D. Schwartz,
A new mixed quantum/semiclassical propagation method,
J. Chem. Phys. 126, 184107 (2007) view
reaction rates mixed QM/MM
70 P. Guinto, E. Manning, S.D. Schwartz, and J. Tardiff,
Computational characterization of mutations in cardiac troponin T known to cause familial hypertrophic cardiomyopathy,
J. Theor. Comp. Chem. 6, 413 (2007) view
cardiac troponin • cardiac mutations
69 E. Pineda, R. Callendar, and S.D. Schwartz,
Ligand binding and protein dynamics in lactate dehydrogenase,
Biophys. J. 93, 1474 (2007) view
enzymes LDH • enzymes ligand binding
68 S. Quaytman and S.D. Schwartz,
Reaction coordinate of an enzymatic reaction revealed by transition path sampling,
Proc. Natl. Acad. Sci. USA 104, 12253 (2007) view
enzymes TPS • enzymes LDH
67 S. D. Schwartz,
The quantum Kramers approach to enzymatic hydrogen transfer: protein dynamics as it couples to catalysis,
in Hydrogen-transfer reactions, Eds J. Hynes, J. Klinman, H. Limbach, and R. Schowen, Wiley-VCH, 2007, pp. 1209-1239 view
enzymes review
2006
………………………………………………….
66 D. Antoniou, J. Basner, S. Nunez, and S.D. Schwartz,
Computational and theoretical methods to explore the relation between enzyme dynamics and catalysis,
Chem. Rev. 106, 3170 (2006) view
enzymes review • enzymes LDH • enzymes PNP
65 D. Antoniou, J. Basner, S. Nunez, and S.D. Schwartz,
Effect of enzyme dynamics on catalytic activity,
Adv. Phys. Org. Chem. 41, 317 (2006) view
enzymes review
64 S. Nunez, C. Wing, D. Antoniou, V. Schramm, and S.D. Schwartz,
Insight into catalytically relevant correlated motions in human PNP,
J. Phys. Chem. A, 110, 463 (2006) view
enzymes PNP • enzymes ligand binding
63 E. Pineda and S.D. Schwartz,
Protein dynamics and catalysis: the problems of transition state theory and the subtleties of dynamic control,
Phil. Trans. Roy. Soc. B 361, 1433 (2006) view
enzymes review
62 S. D. Schwartz,
Vibrationally enhanced tunneling and KIE in enzymatic reactions,
in Isotope effects in Chemistry and Biology, Eds A. Kohen and H. Limbach, CRC Press, 2006, pp. 475-498 view
enzymes review
2005
………………………………………………….
61 S. D. Schwartz,
A new semiclassical dynamics from the interaction representation,
J. Theor. Comp. Chem. 4, 1093 (2005) view
reaction rates mixed QM/MM
60 S. D. Schwartz,
Approximate quantum methods for rate computation in complex systems,
in Handbook of materials modeling, S. Yip, Ed. Springer, 2005, pp. 1673-1689. view
reaction rates review
59 B. Eritz-Berger, S. Nunez, S.D. Schwartz, and J. Tardiff,
Changes in the chemical and dynamic properties of cardiac troponin T cause discrete cardiomyopathies in transgenic mice,
Proc. Natl. Acad. Sci. USA 102, 18219 (2005) view
cardiac troponin • cardiac mutations
58 J. Basner and Schwartz, S. D.,
Enzyme dynamics helps catalyze a chemical reaction in atomic detail: a transition path sampling study,
J. Am. Chem. Soc. 127, 3822 (2005) view
enzymes TPS • enzymes LDH
2004
………………………………………………….
57 J. Mincer, S. Nunez, and S.D. Schwartz,
Coupling protein dynamics to reaction center electron density in enzymes: an electronic protein promoting vibration in human PNP,
J. Theor. Comp. Chem. 3, 501 (2004) view
enzymes PNP
56 J. Basner and S.D. Schwartz,
Donor-acceptor distance and protein promoting vibration coupling as a mechanism for kinetic control in isozymes of human LDH,
J. Phys. Chem. B 108, 444 (2004) view
enzymes LDH
55 S. Nunez, D. Antoniou, V. Schramm, and S.D. Schwartz,
Promoting motions in human purine nucleoside phosphorylase: a molecular dynamics and hybrid QM/MM study,
J. Am. Chem. Soc. 126, 15720 (2004) view
enzymes PNP
54 J. Mincer and S.D. Schwartz,
Rate-promoting vibrations and coupled hydrogen-electron transfer reactions in the condensed phase: a model for enzymatic catalysis,
J. Chem. Phys. 120, 7755 (2004) view
reaction rates – promoting motions
53 D. Antoniou, R. Abolfath, and S.D. Schwartz,
Transition path sampling study of classical rate-promoting vibrations,
J. Chem. Phys., 121, 6442 (2004) view
reaction rates – promoting motions • eaction rates TPS
2003
………………………………………………….
52 J. Mincer and S.D> Schwartz,
A computational method to identify residues important in creating a protein promoting-vibration in enzymes,
J. Phys. Chem. B 107, 366 (2003) view
reaction rates – promoting motions
51 D. Antoniou and S.D. Schwartz,
Low-frequency collective motions in proteins,
J. Theor. Comp. Chem. 2, 163 (2003) view
enzymes density fluctuations
50 J. Mincer and S.D. Schwartz,
Protein promoting vibrations in enzyme catalysis: a conserved evolution motif,
J. Proteom. Res. 2, 437 (2003) view
49 S.D. Schwartz,
Response to comment, “Effect of active site mutation Phe 93->Trp in the horse liver alcohol dehydrogenase enzyme on catalysis: a molecular dynamics study”,
J. Phys. Chem. B 107, 12372 (2003) view
48 D. Antoniou and S.D. Schwartz,
The Langevin equation in momentum space,
J. Chem. Phys. 119, 11329 (2003) view
reaction rates
2002
………………………………………………….
47 D. Antoniou, S. Caratzoulas, J. Mincer, and S.D. Schwartz,
Barrier passage and protein dynamics in enzymatically catalyzed reactions,
Eur. J. Biochem. 269, 3103 (2002) view
enzymes review
46 C. Kalyanaraman and S.D. Schwartz,
Effect of active site mutation Phe 93->Trp in the horse liver alcohol dehydrogenase enzyme on catalysis: a molecular dynamics study,
J. Phys. Chem. B 106, 13111 (2002) view
enzymes horse liver ADH
45 S. Caratzoulas, J. Mincer, and S.D. Schwartz,
Identification of a protein promoting vibration in the reaction catalyzed by horse liver alcohol dehydrogenase,
J. Am. Chem. Soc. 124, 3270 (2002) view
enzymes horse liver ADH
2001
………………………………………………….
44 S. Caratzoulas and S.D. Schwartz,
A computational method to discover the existence of promoting vibrations for chemical reactions in condensed phases,
J. Chem. Phys. 114, 2910 (2001) view
reaction rates – promoting motions
43 D. Antoniou and S.D. Schwartz,
Harmonic collective modes in atomic liquids,
J. Chem. Phys. 115, 4670 (2001) view
reaction rates
42 D. Antoniou and S.D. Schwartz,
Internal enzyme motions as a source of catalytic activity: rate promoting vibrations and hydrogen tunneling,
J. Phys. Chem. B, 105, 5553, (2001) view
enzymes – promoting motions • tunneling
41 R. Karmacharya, D.Antoniou, and S.D. Schwartz,
Nonequilibrium solvation and the quantum Kramers problem: proton transfer in aqueous glycine,
J. Phys. Chem. A 105, 2563 (2001) view
reaction rates
2000
………………………………………………….
40 B. Braunheim and S.D. Schwartz,
Neural network methods for identification and optimization of quantum mechanical features needed for bioactivity,
J. Theor. Biol. 26, 27 (2000) view
drug design • neural networks
39 D. Antoniou and S.D. Schwartz,
Proton transfer in condensed phases: Beyond the quantum Kramers paradigm,
in Theoretical Methods in Condensed Phase Chemistry, Kluwer, 2000. view
reaction rates review
38 S. D. Schwartz,
Quantum dynamics in condensed phases via extended modes and exact interaction propagator relations,
J. Chem. Phys. 113, 7437 (2000) view
reaction rates
37 B. Braunheim, C. Bagdassarian, V. Schramm, and S.D. Schwartz,
Quantun neural netowrks can predict binding free energy for enzymatic inhibitors,
Int. J. Quant. Chem. 78, 195 (2000) drug design • neural networks
36 S.D. Schwartz (editor),
Theoretical methods in condensed phase chemistry. Kluwer, 2000 view
1999
………………………………………………….
35 D. Antoniou and S.D. Schwartz,
A molecular dynamics quantum Kramers study of proton transfer in solution,
J. Chem. Phys. 110, 465 (1999) view
reaction rates
34 B. Braunheim and S.D. Schwartz,
Computational methods for transition state and inhibitor recognition,
Methods in Enzymology 308, 398 (1999) view
drug design • neural networks
33 B. Braunheim, R. Miles, V. Schramm, and S.D. Schwartz,
Prediction of inhibitor binding free energies by quantum neural networks: nucleoside analogues binding to trypanosomal nucleoside hydrolase,
Biochemistry 38, 16076 (1999) view
drug design • neural networks
32 R. Karmacharya and S.D. Schwartz,
Quantum proton transfer coupled to a quantum anharmonic mode,
J. Chem. Phys. 110, 7376 (1999) view
reaction rates
31 D. Antoniou and S.D. Schwartz,
Quantum proton transfer with spatially dependent friction: phenol-amine in methyl chloride,
J. Chem. Phys. 110, 7359 (1999) view
reaction rates
30 R. Karmacharya, P. Gross, and S.D. Schwartz,
The effect of coupled nonreactive modes on laser control of quantum wavepacket dynamics,
J. Chem. Phys. 111, 6864 (1999) view
reaction rates
1998
………………………………………………….
29 D. Antoniou and S.D. Schwartz,
Activated chemistry in the presence of a strongly symmetrically coupled vibration,
J. Chem. Phys. 108, 3620 (1998) view
reaction rates • promoting motions
28 P. Gross and S.D. Schwartz,
External field control of condensed phase reactions,
J. Chem. Phys. 109, 4843 (1998) view
reaction rates
27 D. Antoniou and S.D. Schwartz,
Proton transfer in benzoic acid crystals: another look using quantum operator theory,
J. Chem. Phys. 109, 5487 (1998) view
reaction rates • promoting motions
26 D. Antoniou and S.D. Schwartz,
Temperature dependent spectral densities and quantum activated rate theory,
J. Chem. Phys. 109, 2287 (1998) view
reaction rates
1997
………………………………………………….
25 D. Antoniou and S.D. Schwartz,
Large kinetic isotope effects in enzymatic proton transfer and the role of substrate oscillations,
Proc. Natl. Acad. Sci. USA 94, 12360 (1997) view
enzymes reaction rates • promoting motions
24 S. D. Schwartz,
Quantum reactions in a condensed phase: turnover behavior from new adiabatic factorization and corrections,
J. Chem. Phys. 107, 2424 (1997) view
reaction rates
1996
………………………………………………….
23 V. Schramm, B. Horenstein, C. Bagdassarian, S.D. Schwartz, and P. Berti,
Enzymatic transition states and inhibitor design from principles of classical and quantum chemistry,
Int. J. Quant. Chem. 60, 1805 (1996) enymes inhibitor design
22 S. Mitra and S.D. Schwartz,
A mixed momentum-position space representation to study quantum vibrational energy transfer,
J. Chem. Phys. 104, 7539 (1996) view
reaction rates
21 C. Bagdassarian, V. Schramm, and S.D. Schwartz,
Molecular electrostatic potential analysis for enzymatic substrates, competitive inhibitors, and transition state inhibitors,
J. Am. Chem. Soc. 118, 8825 (1996) view
enzymes inhibitor design
20 D. Antoniou and S.D. Schwartz,
Nonadiabatic effects in a method that combines classical and quantum mechanics,
J. Chem. Phys. 104, 3526 (1996) view
reaction rates
19 C. Bagdassarian, B. Braunheim, V. Schramm, and S.D. Schwartz,
Quantitative measures of molecular similarity: methods to analyze transition state analogues for enzymatic reactions,
Int. J. Quant. Chem. 60, 1797 (1996) enzymes TS analogs
18 S. D. Schwartz,
Quantum activated rates: an evolution operator approach,
J. Chem. Phys. 105, 6871 (1996) view
reaction rates
17 S. D. Schwartz,
The interaction representation and non-adiabatic corrections to adiabatic evolution operators II: nonlinear quantum systems,
J. Chem. Phys. 104, 7985 (1996) view
reaction rates
16 S. D. Schwartz,
The interaction representation and non-adiabatic corrections to adiabatic evolution operators,
J. Chem. Phys. 104, 1394 (1996) view
reaction rates
1995
………………………………………………….
15 D. Antoniou and S.D. Schwartz,
Vibrational energy transfer in linear hydrocarbon chains: new quantum results,
J. Chem. Phys. 103, 7277 (1995) view
reaction rates
1994
………………………………………………….
14 S. D. Schwartz,
Accurate quantum mechanics from high order resummed operator expansions,
J. Chem. Phys. 100, 8795 (1994) view
reaction rates
13 S. D. Schwartz,
Vibrational energy transfer from resummed evolution operators,
J. Chem. Phys. 101, 10436 (1994) view
reaction rates
1992
………………………………………………….
12 S. D. Schwartz,
Effective Feynman propagators and Schrodinger equations for processes coupled to many degrees of freedom,
J. Chem. Phys. 96, 5952 (1992) view
reaction rates
11 S. D. Schwartz,
Operator expansions for multidimensional problems: new developments and applications,
J. Chem. Phys. 97, 7377 (1992) view
reaction rates
1991
………………………………………………….
10 S. D. Schwartz,
A density matrix formulation for potential scattering in an oscillating/controlled potential: a model for some biophysical systems,
Chem. Phys. Lett. 185, 16 (1991) view
reaction rates
1990
………………………………………………….
9 G. Ash and S.D. Schwartz,
Network routing evolution,
in Network management and control, Kershenbaum, Malek,, and Wall,, Eds. Plenum, 1990, pp. 357-367. view
network routing
8 S. D. Schwartz,
Stochastic integrals and state-dependent routing,
in Network management and control, Kershenbaum, Malek,, and Wall,, Eds. Plenum, 1990, pp. 415-424. view
network routing
7 G. Ash and S.D. Schwartz,
Traffic control architectures for integrated broadband networks,
Int. J. Digit. Anal. Comm. Systems 3, 167 (1990) view
network routing
1989
………………………………………………….
6 S. D. Schwartz,
Analytic calculations of load balancing performance in dynamic control/state dependent routing networks,
Proceedings IEEE Network Management and Control Workshop, vol. Sep. 1989. pp. 104-115, (1989)
network routing
5 G. Ash, B. Blake, and S.D. Schwartz,
Integrated network routing and design,
12th International Teletraffic Congress, Turin, Italy; M. Bonatti Ed. (North Holland Press). pp. 640-647, 1989. view
network routing
4 S. D. Schwartz,
Propagator expansions for softly coupled potentials: a model for complex reaction dynamics,
J. Chem. Phys. 91, 7621 (1989) view
reaction rates
1983
………………………………………………….
3 W. H. Miller, S.D. Schwartz, and J. Tromp,
Quantum mechanical rate constants for biomolecular reactions,
J. Chem. Phys. 79, 4889 (1983) view
reaction rates
2 S. D. Schwartz and W.H. Miller,
System-bath decomposition of the reaction path Hamiltonian. II. Rotationally inelastic reactive scattering of H + H2 in 3 dimension,
J. Chem. Phys. 79, 3759 (1983) view
reaction rates
1982
………………………………………………….
1 W. H. Miller and S.D. Schwartz,
System-bath decomposition of the reaction path Hamiltonian for polyatomic scattering: quantum perturbative treatment.,
J. Chem. Phys. 77, 2378 (1982) view
reaction rates