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1

Gibbs free energy change of a discrete chemical reaction event

Floyd, Carlos, Papoian, Garegin A., Jarzynski, Christopher

Journal:

The Journal of Chemical Physics

Year:

2020

Language:

english

File:

PDF, 2.12 MB

english, 2020

2

AWSEM-MD: Protein Structure Prediction Using Coarse-Grained Physical Potentials and Bioinformatically Based Local Structure Biasing

Davtyan, Aram, Schafer, Nicholas P., Zheng, Weihua, Clementi, Cecilia, Wolynes, Peter G., Papoian, Garegin A.

Journal:

Journal of Physical Chemistry B

Year:

2012

Language:

english

File:

PDF, 5.14 MB

english, 2012

3

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

Zhuravlev, Pavel I., Papoian, Garegin A.

Journal:

Quarterly Reviews of Biophysics

Year:

2010

Language:

english

File:

PDF, 874 KB

english, 2010

4

Stochastic Ratcheting on a Funneled Energy Landscape Is Necessary for Highly Efficient Contractility of Actomyosin Force Dipoles

Komianos, James E., Papoian, Garegin A.

Journal:

Physical Review X

Year:

2018

Language:

english

File:

PDF, 2.94 MB

english, 2018

5

Generalized perturbational molecular orbital (PMO) theory

Dong-Kyun Seo, Garegin Papoian, Roald Hoffmann

Journal:

International Journal of Quantum Chemistry

Year:

2000

Language:

english

File:

PDF, 230 KB

english, 2000

6

Hypervalenzbindung in einer, zwei und drei Dimensionen: Erweiterung des Zintl-Klemm-Konzepts auf nichtklassische elektronenreiche Netze

Garegin A. Papoian, Roald Hoffmann

Journal:

Angewandte Chemie

Year:

2000

Language:

german

File:

PDF, 1.82 MB

german, 2000

7

Hypervalent Bonding in One, Two, and Three Dimensions: Extending the Zintl–Klemm Concept to Nonclassical Electron-Rich Networks

Garegin A. Papoian, Roald Hoffmann

Journal:

Angewandte Chemie International Edition

Year:

2000

Language:

english

File:

PDF, 1.86 MB

english, 2000

8

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

Garegin A. Papoian, Peter G. Wolynes

Journal:

Year:

2003

Language:

english

File:

PDF, 1.13 MB

english, 2003

9

ChemInform Abstract: Hypervalent Bonding in One, Two, and Three Dimensions: Extending the Zintl—Klemm Concept to Nonclassical Electron-Rich Networks

Garegin A. Papoian, Roald Hoffmann

Journal:

Year:

2000

File:

PDF, 26 KB

2000

10

Building up Complexity from Strips and Sheets: The Electronic Structure of the La12Mn2Sb30Alloy

Garegin Papoian, Roald Hoffmann

Journal:

Journal of Solid State Chemistry

Year:

1998

Language:

english

File:

PDF, 960 KB

english, 1998

11

Free energy calculations of counterion partitioning between DNA and chloride solutions

Alexey Savelyev, Garegin A. Papoian

Journal:

Mendeleev Communications

Year:

2007

Language:

english

File:

PDF, 1.90 MB

english, 2007

12

Evolution of complex probability distributions in enzyme cascades

Yueheng Lan, Garegin A. Papoian

Journal:

Journal of Theoretical Biology

Year:

2007

Language:

english

File:

PDF, 369 KB

english, 2007

13

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

Natsuki Tanaka, Garegin A. Papoian

Journal:

Journal of Theoretical Biology

Year:

2010

Language:

english

File:

PDF, 1.29 MB

english, 2010

14

Tunable Energy Transfer Rates via Control of Primary, Secondary, and Tertiary Structure of a Coiled Coil Peptide Scaffold

Wilger, Dale J., Bettis, Stephanie E., Materese, Christopher K., Minakova, Maria, Papoian, Garegin A., Papanikolas, John M., Waters, Marcey L.

Journal:

Inorganic Chemistry

Year:

2012

Language:

english

File:

PDF, 3.30 MB

english, 2012

15

Functional versus folding landscapes: the same yet different

Pavel I Zhuravlev, Garegin A Papoian

Journal:

Current Opinion in Structural Biology

Year:

2010

Language:

english

File:

PDF, 323 KB

english, 2010

16

Recent successes in coarse-grained modeling of DNA

Davit A. Potoyan, Alexey Savelyev, Garegin A. Papoian

Journal:

Wiley Interdisciplinary Reviews: Computational Molecular Science

Year:

2012

Language:

english

File:

PDF, 709 KB

english, 2012

17

Induced Fit, Folding, and Recognition of the NF-κB-Nuclear Localization Signals by IκBα and IκBβ

Joachim Lätzer, Garegin A. Papoian, Michael C. Prentiss, Elizabeth A. Komives, Peter G. Wolynes

Journal:

Journal of Molecular Biology

Year:

2007

Language:

english

File:

PDF, 1.13 MB

english, 2007

18

Computing free energies of protein conformations from explicit solvent simulations

Pavel I. Zhuravlev, Sangwook Wu, Davit A. Potoyan, Michael Rubinstein, Garegin A. Papoian

Journal:

Year:

2010

Language:

english

File:

PDF, 887 KB

english, 2010

19

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

Vanessa Oklejas, Chenghang Zong, Garegin A. Papoian, Peter G. Wolynes

Journal:

Year:

2010

Language:

english

File:

PDF, 1.00 MB

english, 2010

20

Elimination of fast variables in chemical Langevin equations

Lan, Yueheng, Elston, Timothy C., Papoian, Garegin A.

Journal:

The Journal of Chemical Physics

Year:

2008

Language:

english

File:

PDF, 356 KB

english, 2008

21

Is DNA’s Rigidity Dominated by Electrostatic or Nonelectrostatic Interactions?

Savelyev, Alexey, Materese, Christopher K., Papoian, Garegin A.

Journal:

Journal of the American Chemical Society

Year:

2011

Language:

english

File:

PDF, 1.63 MB

english, 2011

22

Molecular Renormalization Group Coarse-Graining of Polymer Chains: Application to Double-Stranded DNA

Savelyev, Alexey, Papoian, Garegin A.

Journal:

Biophysical Journal

Year:

2009

Language:

english

File:

PDF, 292 KB

english, 2009

23

Mechano-Chemical Feedbacks Regulate Actin Mesh Growth in Lamellipodial Protrusions

Hu, Longhua, Papoian, Garegin A.

Journal:

Biophysical Journal

Year:

2010

Language:

english

File:

PDF, 853 KB

english, 2010

24

Design of Active Transport Must Be Highly Intricate: A Possible Role of Myosin and Ena/VASP for G-Actin Transport in Filopodia

Zhuravlev, Pavel I., Der, Bryan S., Papoian, Garegin A.

Journal:

Biophysical Journal

Year:

2010

Language:

english

File:

PDF, 531 KB

english, 2010

25

Mechano-Chemical Feedbacks Play a Major Role in Regulating Actin Mesh Growth in Lamellipodial Protrusions

Hu, Longhua, Papoian, Garegin A.

Journal:

Biophysical Journal

Year:

2010

Language:

english

File:

PDF, 32 KB

english, 2010

26

The Stochastic Dynamics of Filopodial Growth

Lan, Yueheng, Papoian, Garegin A.

Journal:

Biophysical Journal

Year:

2008

Language:

english

File:

PDF, 857 KB

english, 2008

27

High Resolution Approach to the Native State Ensemble Kinetics and Thermodynamics

Wu, Sangwook, Zhuravlev, Pavel I., Papoian, Garegin A.

Journal:

Biophysical Journal

Year:

2008

Language:

english

File:

PDF, 527 KB

english, 2008

28

Energy Landscape Analysis of Protein Dimers

Yaakov Levy, Garegin A. Papoian, José N. Onuchic, Peter G. Wolynes

Journal:

Israel Journal of Chemistry

Year:

2004

Language:

english

File:

PDF, 2.44 MB

english, 2004

29

Deconstructing the Native State: Energy Landscapes, Function, and Dynamics of Globular Proteins

Zhuravlev, Pavel I., Materese, Christopher Kroboth, Papoian, Garegin A.

Journal:

Journal of Physical Chemistry B

Year:

2009

Language:

english

File:

PDF, 3.83 MB

english, 2009

30

Interfacial Energy Conversion in Ru II Polypyridyl-Derivatized Oligoproline Assemblies on TiO 2

Ma, Da, Bettis, Stephanie E., Hanson, Kenneth, Minakova, Maria, Alibabaei, Leila, Fondrie, William, Ryan, Derek M., Papoian, Garegin A., Meyer, Thomas J., Waters, Marcey L., Papanikolas, John M.

Journal:

Journal of the American Chemical Society

Year:

2013

Language:

english

File:

PDF, 515 KB

english, 2013

31

Multiscale Stochastic Reaction–Diffusion Modeling: Application to Actin Dynamics in Filopodia

Radek Erban, Mark B. Flegg, Garegin A. Papoian

Journal:

Bulletin of Mathematical Biology

Year:

2014

Language:

english

File:

PDF, 905 KB

english, 2014

32

Nonequilibrium Water Transport in a Nonionic Microemulsion System

Minakova, Maria, Savelyev, Alexey, Papoian, Garegin A.

Journal:

Journal of Physical Chemistry B

Year:

2011

Language:

english

File:

PDF, 3.86 MB

english, 2011

33

Molecular Renormalization Group Coarse-Graining of Electrolyte Solutions: Application to Aqueous NaCl and KCl

Savelyev, Alexey, Papoian, Garegin A.

Journal:

Journal of Physical Chemistry B

Year:

2009

Language:

english

File:

PDF, 1.67 MB

english, 2009

34

Stochastic Simulation Study of the Role of Capping and Anti-Capping Proteins in Regulating Actin Network Growth

Hu, Longhua, Papoian, Garegin A.

Journal:

Biophysical Journal

Year:

2011

Language:

english

File:

PDF, 48 KB

english, 2011

35

Energy Landscape Analysis Reveals Residual Order in Histone Tail Dynamics

Potoyan, Davit, Papoian, Garegin

Journal:

Biophysical Journal

Year:

2010

Language:

english

File:

PDF, 37 KB

english, 2010

36

Insight into the Molecular Origins of the Internal Friction in Unfolded Proteins

Echeverria, Ignacia, Makarov, Dmitrii E., Papoian, Garegin

Journal:

Biophysical Journal

Year:

2013

Language:

english

File:

PDF, 40 KB

english, 2013

37

AWSEM-MD: Coarse-Grained Protein Structure Prediction using Physical Potentials and Bioinformatically Based Local Structure Biasing

Davtyan, Aram, Zheng, Weihua, Schafer, Nicholas, Wolynes, Peter, Papoian, Garegin

Journal:

Biophysical Journal

Year:

2012

Language:

english

File:

PDF, 36 KB

english, 2012

38

Capsid Deformations Reveal Complex Mechano-Chemistry

Popov, Konstantin I., Papoian, Garegin A.

Journal:

Biophysical Journal

Year:

2013

Language:

english

File:

PDF, 194 KB

english, 2013

39

Myosin Motor Dynamics in Filopodia

Zhuravlev, Pavel I., Minakova, Maria, Lan, Yueheng, Papoian, Garegin A.

Journal:

Biophysical Journal

Year:

2011

Language:

english

File:

PDF, 36 KB

english, 2011

40

Rigorous Calculation of Free Energy Difference Between Open and Closed States of Adenylate Kinase from Explicit Solvent Molecular Dynamics

Zhuravlev, Pavel I., Potoyan, Davit A., Rubinstein, Michael, Papoian, Garegin A.

Journal:

Biophysical Journal

Year:

2011

Language:

english

File:

PDF, 57 KB

english, 2011

41

Role of Topology, Nonadditivity, and Water-Mediated Interactions in Predicting the Structures of α/β Proteins

Zong, Chenghang, Papoian, Garegin A., Ulander, Johan, Wolynes, Peter G.

Journal:

Journal of the American Chemical Society

Year:

2006

Language:

english

File:

PDF, 798 KB

english, 2006

42

Polyionic Charge Density Plays a Key Role in Differential Recognition of Mobile Ions by Biopolymers

Savelyev, Alexey, Papoian, Garegin A.

Journal:

Journal of Physical Chemistry B

Year:

2008

Language:

english

File:

PDF, 886 KB

english, 2008

43

Role of Water Mediated Interactions in Protein−Protein Recognition Landscapes

Papoian, Garegin A., Ulander, Johan, Wolynes, Peter G.

Journal:

Journal of the American Chemical Society

Year:

2003

Language:

english

File:

PDF, 476 KB

english, 2003

44

Electron-Rich Bonding and the Importance of s,p Mixing as One Moves Across a Period: A Lesson from the LiSn System

Ienco, Andrea, Hoffmann, Roald, Papoian, Garegin

Journal:

Journal of the American Chemical Society

Year:

2001

Language:

english

File:

PDF, 172 KB

english, 2001

45

Counterion Atmosphere and Hydration Patterns near a Nucleosome Core Particle

Materese, Christopher K., Savelyev, Alexey, Papoian, Garegin A.

Journal:

Journal of the American Chemical Society

Year:

2009

Language:

english

File:

PDF, 3.11 MB

english, 2009

46

Molecular Transport Modulates the Adaptive Response of Branched Actin Networks to an External Force

Hu, Longhua, Papoian, Garegin A.

Journal:

Journal of Physical Chemistry B

Year:

2013

Language:

english

File:

PDF, 1.76 MB

english, 2013

47

Computing Free Energy of a Large-Scale Allosteric Transition in Adenylate Kinase Using All Atom Explicit Solvent Simulations

Potoyan, Davit A., Zhuravlev, Pavel I., Papoian, Garegin A.

Journal:

Journal of Physical Chemistry B

Year:

2012

Language:

english

File:

PDF, 3.09 MB

english, 2012

48

A Comparative Theoretical Study of the Hydrogen, Methyl, and Ethyl Chemisorption on the Pt(111) Surface

Papoian, Garegin, Nørskov, Jens K., Hoffmann, Roald

Journal:

Journal of the American Chemical Society

Year:

2000

Language:

english

File:

PDF, 626 KB

english, 2000

49

Electron-Rich Rods as Building Blocks for Sb Strips and Te Sheets

Papoian, Garegin, Hoffmann, Roald

Journal:

Journal of the American Chemical Society

Year:

2001

Language:

english

File:

PDF, 240 KB

english, 2001

50

Energy Landscape Analyses of Disordered Histone Tails Reveal Special Organization of Their Conformational Dynamics

Potoyan, Davit A., Papoian, Garegin A.

Journal:

Journal of the American Chemical Society

Year:

2011

Language:

english

File:

PDF, 3.63 MB

english, 2011