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Journal Articles

Simulated annealing with adaptive cooling rates

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Mariia Karabin, Steven J. Stuart
Journal: The Journal of Chemical Physics
J. Chem. Phys. 153, 114103 (2020)
https://doi.org/10.1063/5.0018725
Published: September 2020
View article titled, Simulated annealing with adaptive cooling rates
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Journal Articles

Application of advanced sampling and analysis methods to predict the structure of adsorbed protein on a material surface

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Tigran M. Abramyan, David L. Hyde-Volpe, Steven J. Stuart, Robert A. Latour
Journal: Biointerphases
Biointerphases 12, 02D409 (2017)
https://doi.org/10.1116/1.4983274
Published: May 2017
View article titled, Application of advanced sampling and analysis methods to predict the structure of adsorbed protein on a material surface
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Includes: Supplementary data
Journal Articles

TIGER2 with solvent energy averaging (TIGER2A): An accelerated sampling method for large molecular systems with explicit representation of solvent

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Xianfeng Li, James A. Snyder, Steven J. Stuart, Robert A. Latour
Journal: The Journal of Chemical Physics
J. Chem. Phys. 143, 144105 (2015)
https://doi.org/10.1063/1.4932341
Published: October 2015
View article titled, TIGER2 with solvent energy averaging (TIGER2A): An accelerated sampling method for large molecular systems with explicit representation of solvent
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Journal Articles

Parameterization of an interfacial force field for accurate representation of peptide adsorption free energy on high-density polyethylene

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Tigran M. Abramyan, James A. Snyder, Jeremy A. Yancey, Aby A. Thyparambil, Yang Wei, Steven J. Stuart, Robert A. Latour
Journal: Biointerphases
Biointerphases 10, 021002 (2015)
https://doi.org/10.1116/1.4916361
Published: March 2015
View article titled, Parameterization of an interfacial force field for accurate representation of peptide adsorption free energy on high-density polyethylene
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Includes: Supplementary data
Journal Articles

Development of a Tuned Interfacial Force Field Parameter Set for the Simulation of Protein Adsorption to Silica Glass

Open Access
James A. Snyder, Tigran Abramyan, Jeremy A. Yancey, Aby A. Thyparambil, Yang Wei, Steven J. Stuart, Robert A. Latour
Journal: Biointerphases
Biointerphases 7, 56 (2012)
https://doi.org/10.1007/s13758-012-0056-4
Published: September 2012
View article titled, Development of a Tuned Interfacial Force Field Parameter Set for the Simulation of Protein Adsorption to Silica Glass
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Journal Articles

Modified reactive empirical bond-order potential for heterogeneous bonding environments

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Jaewoong Hur (허재웅), Steven J. Stuart
Journal: The Journal of Chemical Physics
J. Chem. Phys. 137, 054102 (2012)
https://doi.org/10.1063/1.4738879
Published: August 2012
View article titled, Modified reactive empirical bond-order potential for heterogeneous bonding environments
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Includes: Supplementary data
Journal Articles

Bond-order potentials with split-charge equilibration: Application to C-, H-, and O-containing systems

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M. Todd Knippenberg, Paul T. Mikulski, Kathleen E. Ryan, Steven J. Stuart, Guangtu Gao, Judith A. Harrison
Journal: The Journal of Chemical Physics
J. Chem. Phys. 136, 164701 (2012)
https://doi.org/10.1063/1.4704800
Published: April 2012
View article titled, Bond-order potentials with split-charge equilibration: Application to C-, H-, and O-containing systems
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Journal Articles

Comparison Between Empirical Protein Force Fields for the Simulation of the Adsorption Behavior of Structured LK Peptides on Functionalized Surfaces

Open Access
Galen Collier, Nadeem A. Vellore, Jeremy A. Yancey, Steven J. Stuart, Robert A. Latour
Journal: Biointerphases
Biointerphases 7, 24 (2012)
https://doi.org/10.1007/s13758-012-0024-z
Published: March 2012
View article titled, Comparison Between Empirical Protein Force Fields for the Simulation of the Adsorption Behavior of Structured LK Peptides on Functionalized Surfaces
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Includes: Supplementary data
Journal Articles

Development of molecular simulation methods to accurately represent protein-surface interactions: The effect of pressure and its determination for a system with constrained atoms

Open Access
Jeremy A. Yancey, Nadeem A. Vellore, Galen Collier, Steven J. Stuart, Robert A. Latour
Journal: Biointerphases
Biointerphases 5, 85–95 (2010)
https://doi.org/10.1116/1.3493470
Published: October 2010
View article titled, Development of molecular simulation methods to accurately represent protein-surface interactions: The effect of pressure and its determination for a system with constrained atoms
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Journal Articles

Development of molecular simulation methods to accurately represent protein-surface interactions: Method assessment for the calculation of electrostatic effects

Open Access
Galen Collier, Nadeem A. Vellore, Robert A. Latour, Steven J. Stuart
Journal: Biointerphases
Biointerphases 4, 57–64 (2009)
https://doi.org/10.1116/1.3266417
Published: January 2010
View article titled, Development of molecular simulation methods to accurately represent protein-surface interactions: Method assessment for the calculation of electrostatic effects
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Journal Articles

TIGER2: An improved algorithm for temperature intervals with global exchange of replicas

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Xianfeng Li, Robert A. Latour, Steven J. Stuart
Journal: The Journal of Chemical Physics
J. Chem. Phys. 130, 174106 (2009)
https://doi.org/10.1063/1.3129342
Published: May 2009
View article titled, TIGER2: An improved algorithm for temperature intervals with global exchange of replicas
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Includes: Supplementary data
Journal Articles

Calculation of adsorption free energy for solute-surface interactions using biased replica-exchange molecular dynamics

Open Access
Feng Wang, Steven J. Stuart, Robert A. Latour
Journal: Biointerphases
Biointerphases 3, 9–18 (2008)
https://doi.org/10.1116/1.2840054
Published: February 2008
View article titled, Calculation of adsorption free energy for solute-surface interactions using biased replica-exchange molecular dynamics
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Journal Articles

An improved replica-exchange sampling method: Temperature intervals with global energy reassignment

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Xianfeng Li, Christopher P. O’Brien, Galen Collier, Nadeem A. Vellore, Feng Wang, Robert A. Latour, David A. Bruce, Steven J. Stuart
Journal: The Journal of Chemical Physics
J. Chem. Phys. 127, 164116 (2007)
https://doi.org/10.1063/1.2780152
Published: October 2007
View article titled, An improved replica-exchange sampling method: Temperature intervals with global energy reassignment
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Journal Articles

Parallel replica dynamics with a heterogeneous distribution of barriers: Application to n-hexadecane pyrolysis

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Oyeon Kum, Brad M. Dickson, Steven J. Stuart, Blas P. Uberuaga, Arthur F. Voter
Journal: The Journal of Chemical Physics
J. Chem. Phys. 121, 9808–9819 (2004)
https://doi.org/10.1063/1.1807823
Published: November 2004
View article titled, Parallel replica dynamics with a heterogeneous distribution of barriers: Application to n-hexadecane pyrolysis
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Journal Articles

Molecular dynamics investigation on liquid–liquid phase change in carbon with empirical bond-order potentials

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Oyeon Kum, Francis H. Ree, Steven J. Stuart, Christine J. Wu
Journal: The Journal of Chemical Physics
J. Chem. Phys. 119, 6053–6056 (2003)
https://doi.org/10.1063/1.1601216
Published: September 2003
View article titled, Molecular dynamics investigation on liquid–liquid phase change in carbon with empirical bond-order potentials
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Journal Articles

A reactive potential for hydrocarbons with intermolecular interactions

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Steven J. Stuart, Alan B. Tutein, Judith A. Harrison
Journal: The Journal of Chemical Physics
J. Chem. Phys. 112, 6472–6486 (2000)
https://doi.org/10.1063/1.481208
Published: April 2000
View article titled, A reactive potential for hydrocarbons with intermolecular interactions
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Journal Articles

Molecular dynamics with multiple time scales: The selection of efficient reference system propagators

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Steven J. Stuart, Ruhong Zhou, B. J. Berne
Journal: The Journal of Chemical Physics
J. Chem. Phys. 105, 1426–1436 (1996)
https://doi.org/10.1063/1.472005
Published: July 1996
View article titled, Molecular dynamics with multiple time scales: The selection of efficient reference system propagators
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Journal Articles

Molecular dynamics for nonequilibrium systems in which there are a small number of very hot particles in a cold bath: Reference system propagator methods

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Ruhong Zhou, Steven J. Stuart, B. J. Berne
Journal: The Journal of Chemical Physics
J. Chem. Phys. 105, 235–239 (1996)
https://doi.org/10.1063/1.471868
Published: July 1996
View article titled, Molecular dynamics for nonequilibrium systems in which there are a small number of very hot particles in a cold bath: Reference system propagator methods
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Journal Articles

Dynamical fluctuating charge force fields: Application to liquid water

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Steven W. Rick, Steven J. Stuart, B. J. Berne
Journal: The Journal of Chemical Physics
J. Chem. Phys. 101, 6141–6156 (1994)
https://doi.org/10.1063/1.468398
Published: October 1994
View article titled, Dynamical fluctuating charge force fields: Application to liquid water
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