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Empirical Maps For The Calculation of Amide I Vibrational Spectra of Proteins From Classical Molecular Dynamics Simulations

The journal of physical chemistry. B, 2014-07, Vol.118 (28), p.7848-7855

2014

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Sequence Determines the Switch in the Fibril Forming Regions in the Low-Complexity FUS Protein and Its Variants

The journal of physical chemistry letters, 2021-09, Vol.12 (37), p.9026-9032

2021

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Specific Binding of Cholesterol to C99 Domain of Amyloid Precursor Protein Depends Critically on Charge State of Protein

The journal of physical chemistry letters, 2016-09, Vol.7 (18), p.3535-3541

2016

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Order parameter free enhanced sampling of the vapor-liquid transition using the generalized replica exchange method

The Journal of chemical physics, 2013-03, Vol.138 (10), p.104119-104119

2013

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Exploring the Solid–Liquid Phase Change of an Adapted Dzugutov Model Using Generalized Replica Exchange Method

The journal of physical chemistry. B, 2012-07, Vol.116 (29), p.8654-8661

2012

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Investigating the solid-liquid phase transition of water nanofilms using the generalized replica exchange method

The Journal of chemical physics, 2014-11, Vol.141 (18), p.18C525-18C525

2014

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Mode-Specific Vibrational Energy Relaxation of Amide I′ and II′ Modes in N-Methylacetamide/Water Clusters: Intra- and Intermolecular Energy Transfer Mechanisms

The journal of physical chemistry. A, Molecules, spectroscopy, kinetics, environment, & general theory, 2009-04, Vol.113 (13), p.3051-3060

2009

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Molecular Dynamics Study on the Solvent Dependent Heme Cooling Following Ligand Photolysis in Carbonmonoxy Myoglobin

The journal of physical chemistry. B, 2007-03, Vol.111 (12), p.3243-3250

2007

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Replica exchange statistical temperature Monte Carlo

The Journal of chemical physics, 2009-03, Vol.130 (12), p.124112-124112-10

2009

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Vibrational Energy Relaxation of Isotopically Labeled Amide I Modes in Cytochrome c: Theoretical Investigation of Vibrational Energy Relaxation Rates and Pathways

The journal of physical chemistry. B, 2007-10, Vol.111 (41), p.12017-12023

2007

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Time-dependent perturbation theory for vibrational energy relaxation and dephasing in peptides and proteins

The Journal of chemical physics, 2006-04, Vol.124 (14), p.144910-144910

2006

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Direct evidence for mode-specific vibrational energy relaxation from quantum time-dependent perturbation theory. I. Five-coordinate ferrous iron porphyrin model

The Journal of chemical physics, 2009-01, Vol.130 (2), p.025102-025102

2009

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Directed Energy “Funneling" Mechanism for Heme Cooling Following Ligand Photolysis or Direct Excitation in Solvated Carbonmonoxy Myoglobin

The journal of physical chemistry. B, 2001-07, Vol.105 (29), p.7057-7063

2001

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Simulating Vibrational Energy Flow in Proteins: Relaxation Rate and Mechanism for Heme Cooling in Cytochrome c

The journal of physical chemistry. B, 2003-11, Vol.107 (44), p.12339-12345

2003

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Vibrational Energy Relaxation of “Tailored” Hemes in Myoglobin Following Ligand Photolysis Supports Energy Funneling Mechanism of Heme “Cooling”

The journal of physical chemistry. B, 2003-09, Vol.107 (38), p.10634-10639

2003

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Vibrational energy flow across heme–cytochrome c and cytochrome c–water interfaces

Theoretical chemistry accounts, 2014-07, Vol.133 (7), Article 1504

2014

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Quantum dynamics of N-methylacetamide studied by the vibrational configuration interaction method

Chemical physics letters, 2007-07, Vol.443 (1), p.6-11

2007

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Direct evidence for mode-specific vibrational energy relaxation from quantum time-dependent perturbation theory. III. The ν4 and ν7 modes of nonplanar nickel porphyrin models

The Journal of chemical physics, 2009-06, Vol.130 (21)

2009

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Direct evidence for mode-specific vibrational energy relaxation from quantum time-dependent perturbation theory. II. The ν4 and ν7 modes of iron-protoporphyrin IX and iron porphine

The Journal of chemical physics, 2009-03, Vol.130 (9)

2009

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Time scales and pathways for kinetic energy relaxation in solvated proteins: Application to carbonmonoxy myoglobin

The Journal of chemical physics, 2000-11, Vol.113 (17), p.7702-7711

2000

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Quantum and classical vibrational relaxation dynamics of N-methylacetamide on ab initio potential energy surfaces

International journal of quantum chemistry, 2009, Vol.109 (10), p.2047-2057

2009

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On Monte Carlo and molecular dynamics methods inspired by Tsallis statistics: Methodology, optimization, and application to atomic clusters

The Journal of chemical physics, 1997-12, Vol.107 (21), p.9117-9124

1997

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Molecular dynamics study of the photodissociation of carbon monoxide from myoglobin: Ligand dynamics in the first 10 ps

Chemical physics, 1991-12, Vol.158 (2), p.221-248

1991

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Approximate solution of the classical Liouville equation using Gaussian phase packet dynamics : application to enhanced equilibrium averaging and global optimization

The Journal of chemical physics, 1993-09, Vol.99 (5), p.4024-4035

1993

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Molecular dynamics study of an isomerizing diatomic in a Lennard-Jones fluid

The Journal of chemical physics, 1988-10, Vol.89 (8), p.4833-4847

1988

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Empirical Maps For The Calculation of Amide I Vibrational Spectra of Proteins From Classical Molecular Dynamics Simulations

Sequence Determines the Switch in the Fibril Forming Regions in the Low-Complexity FUS Protein and Its Variants

Specific Binding of Cholesterol to C99 Domain of Amyloid Precursor Protein Depends Critically on Charge State of Protein

Order parameter free enhanced sampling of the vapor-liquid transition using the generalized replica exchange method

Exploring the Solid–Liquid Phase Change of an Adapted Dzugutov Model Using Generalized Replica Exchange Method

Investigating the solid-liquid phase transition of water nanofilms using the generalized replica exchange method

Mode-Specific Vibrational Energy Relaxation of Amide I′ and II′ Modes in N-Methylacetamide/Water Clusters: Intra- and Intermolecular Energy Transfer Mechanisms

Molecular Dynamics Study on the Solvent Dependent Heme Cooling Following Ligand Photolysis in Carbonmonoxy Myoglobin

Replica exchange statistical temperature Monte Carlo

Vibrational Energy Relaxation of Isotopically Labeled Amide I Modes in Cytochrome c: Theoretical Investigation of Vibrational Energy Relaxation Rates and Pathways

Time-dependent perturbation theory for vibrational energy relaxation and dephasing in peptides and proteins

Direct evidence for mode-specific vibrational energy relaxation from quantum time-dependent perturbation theory. I. Five-coordinate ferrous iron porphyrin model

Directed Energy “Funneling" Mechanism for Heme Cooling Following Ligand Photolysis or Direct Excitation in Solvated Carbonmonoxy Myoglobin

Simulating Vibrational Energy Flow in Proteins: Relaxation Rate and Mechanism for Heme Cooling in Cytochrome c

Vibrational Energy Relaxation of “Tailored” Hemes in Myoglobin Following Ligand Photolysis Supports Energy Funneling Mechanism of Heme “Cooling”

Vibrational energy flow across heme–cytochrome c and cytochrome c–water interfaces

Quantum dynamics of N-methylacetamide studied by the vibrational configuration interaction method

Direct evidence for mode-specific vibrational energy relaxation from quantum time-dependent perturbation theory. III. The ν4 and ν7 modes of nonplanar nickel porphyrin models

Direct evidence for mode-specific vibrational energy relaxation from quantum time-dependent perturbation theory. II. The ν4 and ν7 modes of iron-protoporphyrin IX and iron porphine

Time scales and pathways for kinetic energy relaxation in solvated proteins: Application to carbonmonoxy myoglobin

Quantum and classical vibrational relaxation dynamics of N-methylacetamide on ab initio potential energy surfaces

On Monte Carlo and molecular dynamics methods inspired by Tsallis statistics: Methodology, optimization, and application to atomic clusters

Molecular dynamics study of the photodissociation of carbon monoxide from myoglobin: Ligand dynamics in the first 10 ps

Approximate solution of the classical Liouville equation using Gaussian phase packet dynamics : application to enhanced equilibrium averaging and global optimization

Molecular dynamics study of an isomerizing diatomic in a Lennard-Jones fluid

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