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List of works by Garegin A Papoian

A variational approach to the stochastic aspects of cellular signal transduction

scientific article published in September 2006

AWSEM-IDP: A Coarse-Grained Force Field for Intrinsically Disordered Proteins

scientific article published on 09 August 2018

AWSEM-MD: protein structure prediction using coarse-grained physical potentials and bioinformatically based local structure biasing

scientific article

AWSEM-Suite: a protein structure prediction server based on template-guided, coevolutionary-enhanced optimized folding landscapes

scientific article published on 08 May 2020

Capsid deformations reveal complex mechano-chemistry

scientific article published on November 2013

Chemically accurate coarse graining of double-stranded DNA.

scientific article

Computing free energies of protein conformations from explicit solvent simulations.

scientific article published on 20 May 2010

Computing free energy of a large-scale allosteric transition in adenylate kinase using all atom explicit solvent simulations.

scientific article

Concerted dihedral rotations give rise to internal friction in unfolded proteins

scientific article published on 04 June 2014

Counterion atmosphere and hydration patterns near a nucleosome core particle

scientific article published on 01 October 2009

DNA exit ramps are revealed in the binding landscapes obtained from simulations in helical coordinates

scientific article published on 12 February 2015

Deconstructing the native state: energy landscapes, function, and dynamics of globular proteins

scientific article published on July 2009

Electron-rich rods as building blocks for Sb strips and Te sheets

scientific article published in July 2001

Elimination of fast variables in chemical Langevin equations

scientific article published on December 2008

Energy landscape analyses of disordered histone tails reveal special organization of their conformational dynamics

scientific article published on 25 April 2011

Evolution of complex probability distributions in enzyme cascades

scientific article published on 12 June 2007

Exploring the Free Energy Landscape of Nucleosomes

scientific article published on 14 June 2016

Gibbs free energy change of a discrete chemical reaction event

scientific article published on 01 February 2020

Hierarchical organization of eglin c native state dynamics is shaped by competing direct and water-mediated interactions.

scholarly article

High resolution approach to the native state ensemble kinetics and thermodynamics

scientific article

How does the antagonism between capping and anti-capping proteins affect actin network dynamics?

scientific article

Induced fit, folding, and recognition of the NF-kappaB-nuclear localization signals by IkappaBalpha and IkappaBbeta.

scientific article

Inter-DNA electrostatics from explicit solvent molecular dynamics simulations

scientific article published on 25 April 2007

Interfacial energy conversion in Ru(II) polypyridyl-derivatized oligoproline assemblies on TiO2.

scientific article published on 26 March 2013

Internal modifications in the CENP-A nucleosome modulate centromeric dynamics.

scientific article

Intrinsic elasticity of nucleosomes is encoded by histone variants and calibrated by their binding partners

scientific article published on 11 November 2019

Is DNA's rigidity dominated by electrostatic or nonelectrostatic interactions?

scientific article published on 11 November 2011

Low-dimensional manifold of actin polymerization dynamics

scientific article published on 18 December 2017

MEDYAN: Mechanochemical Simulations of Contraction and Polarity Alignment in Actomyosin Networks

scientific article (publication date: April 2016)

Mechano-chemical feedbacks regulate actin mesh growth in lamellipodial protrusions.

scientific article

Molecular noise of capping protein binding induces macroscopic instability in filopodial dynamics.

scholarly article

Molecular renormalization group coarse-graining of electrolyte solutions: application to aqueous NaCl and KCl.

scientific article published in June 2009

Molecular renormalization group coarse-graining of polymer chains: application to double-stranded DNA.

scientific article published on May 2009

Molecular transport modulates the adaptive response of branched actin networks to an external force

scientific article published on 5 September 2013

Multiscale stochastic reaction-diffusion modeling: application to actin dynamics in filopodia

scientific article published on 3 May 2013

Nonequilibrium water transport in a nonionic microemulsion system.

scientific article published on 29 April 2011

On Stretching, Bending, Shearing, and Twisting of Actin Filaments I: Variational Models

scientific article published on 27 July 2022

Polyionic charge density plays a key role in differential recognition of mobile ions by biopolymers

scientific article published on 3 July 2008

Predictive energy landscapes for protein-protein association

scientific article

Promiscuous Histone Mis-Assembly Is Actively Prevented by Chaperones

scientific article published on 25 July 2016

Protein fluxes along the filopodium as a framework for understanding the growth-retraction dynamics: the interplay between diffusion and active transport

scientific article published on September 2011

Protein functional landscapes, dynamics, allostery: a tortuous path towards a universal theoretical framework.

scientific article published on August 2010

Protein structure prediction: do hydrogen bonding and water-mediated interactions suffice?

scientific article

Proteins with weakly funneled energy landscapes challenge the classical structure-function paradigm

scholarly article

Quantifying dissipation in actomyosin networks

scientific article published on 19 April 2019

Regulation of the H4 tail binding and folding landscapes via Lys-16 acetylation.

scientific article

Remarkable structural transformations of actin bundles are driven by their initial polarity, motor activity, crosslinking, and filament treadmilling

scientific article published on 09 July 2019

Reverse-engineering of biochemical reaction networks from spatio-temporal correlations of fluorescence fluctuations

scientific article published on 18 February 2010

Role of topology, nonadditivity, and water-mediated interactions in predicting the structures of alpha/beta proteins.

scientific article

Role of water mediated interactions in protein-protein recognition landscapes

scientific article

Shearing of the CENP-A dimerization interface mediates plasticity in the octameric centromeric nucleosome.

scientific article

Simulated actin reorganization mediated by motor proteins

scientific article published on 07 April 2022

Steric Effects Induce Geometric Remodeling of Actin Bundles in Filopodia ⬇️

scientific article published on May 2016

Stochastic Resonance in Protein Folding Dynamics

scientific article

Stochastic resonant signaling in enzyme cascades

scientific article published in June 2007

Tensile force-induced cytoskeletal remodeling: Mechanics before chemistry

scientific article published on 10 June 2020

The Acetylation Landscape of the H4 Histone Tail: Disentangling the Interplay between the Specific and Cumulative Effects.

scientific article published on 8 May 2015

The interplay between discrete noise and nonlinear chemical kinetics in a signal amplification cascade

scientific article published in October 2006

The physics and bioinformatics of binding and folding-an energy landscape perspective

scientific article published in March 2003

Theoretical and computational validation of the Kuhn barrier friction mechanism in unfolded proteins

scientific article

Theory of active transport in filopodia and stereocilia.

scientific article

Tunable energy transfer rates via control of primary, secondary, and tertiary structure of a coiled coil peptide scaffold

scientific article published on 8 June 2012

Water in protein structure prediction

scientific article

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