Thermodynamical approach
- Fluctuations in Mass-Action Equilibrium of Protein Binding Networks
Koon-Kiu Yan, Dylan Walker, and Sergei Maslov
Phys. Rev. Lett. 101, 268102 (2008)
- Coordinated Chemomechanical Cycles: A Mechanism for Autonomous Molecular Motion
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Phys. Rev. Lett. 101, 238101 (2008)
- Length of Time
Edward H. Feng and Gavin E. Crooks
Phys. Rev. Lett. 101, 090602 (2008)
- Impact of Loop Statistics on the Thermodynamics of RNA Folding
Thomas R. Einert, Paul Näger, Henri Orland, and Roland R. Netz
Phys. Rev. Lett. 101, 048103 (2008)
- Melting of Branched RNA Molecules
Ralf Bundschuh and Robijn Bruinsma
Phys. Rev. Lett. 100, 148101 (2008)
- Reversibility, Heat Dissipation, and the Importance of the Thermal Environment in Stochastic Models of Nonequilibrium Steady States
R. A. Blythe
Phys. Rev. Lett. 100, 010601 (2008)
- Folding proteins by first-passage-times-optimized replica exchange
Walter Nadler, Jan H. Meinke, and Ulrich H. E. Hansmann
Phys. Rev. E 78, 061905 (2008)
- Free-energy landscape of mechanically unfolded model proteins : Extended Jarzinsky versus inherent structure reconstruction
Stefano Luccioli, Alberto Imparato, and Alessandro Torcini
Phys. Rev. E 78, 031907 (2008)
- Domain formation in membranes caused by lipid wetting of protein
Sergey A. Akimov, Vladimir A. J. Frolov, Peter I. Kuzmin, Joshua Zimmerberg, Yuri A. Chizmadzhev, and Fredric S. Cohen
Phys. Rev. E 77, 051901 (2008)
- Maxwell relations for single-DNA experiments: Monitoring protein binding and double-helix torque with force-extension measurements
Houyin Zhang and John F. Marko
Phys. Rev. E 77, 031916 (2008)
- Statistical physics of the melting of inhomogeneous DNA
Sahin Buyukdagli and Marc Joyeux
Phys. Rev. E 77, 031903 (2008)
- Hidden structure in protein energy landscapes
Dengming Ming, Marian Anghel, and Michael E. Wall
Phys. Rev. E 77, 021902 (2008)
- Thermal denaturation of fluctuating finite DNA chains: The role of bending rigidity in bubble nucleation
John Palmeri, Manoel Manghi, and Nicolas Destainville
Phys. Rev. E 77, 011913 (2008)
- Landau theory of crystallization and the capsid structures of small icosahedral viruses
V. L. Lorman and S. B. Rochal
Phys. Rev. B 77, 224109 (2008)
- Nonequilibrium Dynamic Mechanism for Allosteric Effect
Jianhua Xing
Phys. Rev. Lett. 99, 168103 (2007)
- Reconstructing the Free-Energy Landscape of a Mechanically Unfolded Model Protein
Alberto Imparato, Stefano Luccioli, and Alessandro Torcini
Phys. Rev. Lett. 99, 168101 (2007)
- Solvation of Proteins : Linking Thermodynamics to Geometry
Hendrik Hansen-Goos, Roland Roth, Klaus Mecke, and S. Dietrich
Phys. Rev. Lett. 99, 128101 (2007)
- Stretching of Homopolymeric RNA Reveals Single-Stranded Helices and Base-Stacking
Yeonee Seol, Gary M. Skinner, Koen Visscher, Arnaud Buhot, and Avraham Halperin
Phys. Rev. Lett. 98, 158103 (2007)
- Ising-Like Model for Protein Mechanical Unfolding
A. Imparato, A. Pelizzola, and M. Zamparo
Phys. Rev. Lett. 98, 148102 (2007)
- Anharmonicity and Self-Similarity of the Free Energy Landscape of Protein G
F. Pontiggia, G. Colombo, C. Micheletti, and H. Orland
Phys. Rev. Lett. 98, 048102 (2007)
- Theory of conformational transitions of viral shells
Thomas Guérin and Robijn Bruinsma
Phys. Rev. E 76, 061911 (2007)
- Stability domains of actin genes and genomic evolution
E. Carlon, A. Dkhissi, M. Lejard Malki, and R. Blossey
Phys. Rev. E 76, 051916 (2007)
- Theoretical investigation of finite size effects at DNA melting
Sahin Buyukdagli and Marc Joyeux
Phys. Rev. E 76, 021917 (2007)
- Multifractal statistics of the local order parameter at random critical points: Application to wetting transitions with disorder
CÃ
Phys. Rev. E 76, 021114 (2007)
- RNA folding in the presence of counterions
Yevgeni Sh. Mamasakhlisov, Shura Hayryan, V. F. Morozov, and Chin-Kun Hu
Phys. Rev. E 75, 061907 (2007)
- Glass Transition in Biomolecules and the Liquid-Liquid Critical Point of Water
Pradeep Kumar, Z. Yan, L. Xu, M. G. Mazza, S. V. Buldyrev, S.-H. Chen, S. Sastry, and H. E. Stanley
Phys. Rev. Lett. 97, 177802 (2006)
- Polymer Packaging and Ejection in Viral Capsids: Shape Matters
I. Ali, D. Marenduzzo, and J. M. Yeomans
Phys. Rev. Lett. 96, 208102 (2006)
- Bubble statistics and dynamics in double-stranded DNA
B. S. Alexandrov, L. T. Wille, K. Ã
Phys. Rev. E 74, 050901 (2006)
- Statistical mechanics of DNA -mediated colloidal aggregation
Nicholas A. Licata and Alexei V. Tkachenko
Phys. Rev. E 74, 041408 (2006)
- Large-scale oscillation of structure-related DNA sequence features in human chromosome 21
Wentian Li and Pedro Miramontes
Phys. Rev. E 74, 021912 (2006)
- Scaling laws at the phase transition of systems with divergent order parameter and/or internal length: The example of DNA denaturation
Sahin Buyukdagli and Marc Joyeux
Phys. Rev. E 73, 051910 (2006)
- Monte Carlo simulations of polyelectrolytes inside viral capsids
Daniel George Angelescu, Robijn Bruinsma, and Per Linse
Phys. Rev. E 73, 041921 (2006)
- Monte Carlo simulations of polyelectrolytes inside viral capsids
Daniel George Angelescu, Robijn Bruinsma, and Per Linse
Phys. Rev. E 73, 041921 (2006)
- Thermodynamics of DNA Loops with Long-Range Correlated Structural Disorder
C. Vaillant, B. Audit, and A. ArnÃ
Phys. Rev. Lett. 95, 068101 (2005)
- Disorder in DNA -Linked Gold Nanoparticle Assemblies
Nolan C. Harris and Ching-Hwa Kiang
Phys. Rev. Lett. 95, 046101 (2005)
- Exons, Introns, and DNA Thermodynamics
Enrico Carlon, Mehdi Lejard Malki, and Ralf Blossey
Phys. Rev. Lett. 94, 178101 (2005)
- Dynamical model based on finite stacking enthalpies for homogeneous and inhomogeneous DNA thermal denaturation
Marc Joyeux and Sahin Buyukdagli
Phys. Rev. E 72, 051902 (2005)
- Relationship between phase transitions and topological changes in one-dimensional models
L. Angelani, G. Ruocco, and F. Zamponi
Phys. Rev. E 72, 016122 (2005)
- Local cooperativity mechanism in the DNA melting transition
Vassili Ivanov, Dmitri Piontkovski, and Giovanni Zocchi
Phys. Rev. E 71, 041909 (2005)
- Dependence of RNA secondary structure on the energy model
Bernd Burghardt and Alexander K. Hartmann
Phys. Rev. E 71, 021913 (2005)
- Nonlinear Structures and Thermodynamic Instabilities in a One-Dimensional Lattice System
Nikos Theodorakopoulos, Michel Peyrard, and Robert S. MacKay
Phys. Rev. Lett. 93, 258101 (2004)
- Density functional study on the structures and thermodynamic properties of small ions around polyanionic DNA
Ke Wang, Yang-Xin Yu, and Guang-Hua Gao
Phys. Rev. E 70, 011912 (2004)
- Overstretching and force-driven strand separation of double-helix DNA
Simona Cocco, Jie Yan, Jean-Francois LÃ
Phys. Rev. E 70, 011910 (2004)
- Analytical description of finite size effects for RNA secondary structures
Tsunglin Liu and Ralf Bundschuh
Phys. Rev. E 69, 061912 (2004)
- Thermodynamic modeling of donor splice site recognition in pre-mRNA
Jeffrey A. Garland and Daniel P. Aalberts
Phys. Rev. E 69, 041903 (2004)
- Thermal denaturation of a helicoidal DNA model
Maria Barbi, Stefano Lepri, Michel Peyrard, and Nikos Theodorakopoulos
Phys. Rev. E 68, 061909 (2003)
- Long-range interaction and heterogeneity yield a different kind of critical phenomenon
Mark Ya. Azbelâ
Phys. Rev. E 68, 050901 (2003)
- Thermodynamic instabilities in one-dimensional particle lattices: A finite-size scaling approach
Nikos Theodorakopoulos
Phys. Rev. E 68, 026109 (2003)
- Smectic phases of semiflexible manifolds: Constant-pressure ensemble
Lianghui Gao and Leonardo GoluboviÄ
Phys. Rev. E 66, 051918 (2002)
- Coulomb blockage of hybridization in two-dimensional DNA arrays
Arnold Vainrub and B. Montgomery Pettitt
Phys. Rev. E 66, 041905 (2002)
- Single molecule statistics and the polynucleotide unzipping transition
David K. Lubensky and David R. Nelson
Phys. Rev. E 65, 031917 (2002)
- Single molecule statistics and the polynucleotide unzipping transition
David K. Lubensky and David R. Nelson
Phys. Rev. E 65, 031917 (2002)
- Effects of torsional strain on thermal denaturation of DNA
Joseph Rudnick and Robijn Bruinsma
Phys. Rev. E 65, 030902 (2002)
- Equilibrium analysis of the efficiency of an autonomous molecular computer
John A. Rose, Russell J. Deaton, Masami Hagiya, and Akira Suyama
Phys. Rev. E 65, 021910 (2002)
- Thermodynamics of local DNA openings
Tomasz Lipniacki
Phys. Rev. E 64, 051919 (2001)
- Thermodynamics of local DNA openings
Tomasz Lipniacki
Phys. Rev. E 64, 051919 (2001)
- Electrophoresis of DNA and other polyelectrolytes: Physical mechanisms
Jean-Louis Viovy
Rev. Mod. Phys. 72, 813 (2000)
- Structural properties of the sliding columnar phase in layered liquid crystalline systems
L. GoluboviÄ, T. C. Lubensky, and C. S. OâHern
Phys. Rev. E 62, 1069 (2000)
- Negative electrostatic contribution to the bending rigidity of charged membranes and polyelectrolytes screened by multivalent counterions
T. T. Nguyen, I. Rouzina, and B. I. Shklovskii
Phys. Rev. E 60, 7032 (1999)
- Experimental tests of the Peyrard-Bishop model applied to the melting of very short DNA chains
Alessandro Campa and Andrea Giansanti
Phys. Rev. E 58, 3585 (1998)
- Theory of DNA melting based on the Peyrard-Bishop model
Yong-li Zhang, Wei-Mou Zheng, Ji-Xing Liu, and Y. Z. Chen
Phys. Rev. E 56, 7100 (1997)
- Supercoiled and braided DNA under tension
John F. Marko
Phys. Rev. E 55, 1758 (1997)
- Simulating an exploration of RNA conformation space with an appropriate parallel-updating strategy
Ariel Fernández
Phys. Rev. E 48, 3107 (1993)
- Dynamics and thermodynamics of a nonlinear model for DNA denaturation
Thierry Dauxois, Michel Peyrard, and A. R. Bishop
Phys. Rev. E 47, 684 (1993)
- Excluded-volume effects on the stacking of RNA base pairs
Ariel Fernández
Phys. Rev. A 44, R7910 (1991)
- Glassy kinetic barriers between conformational substates in RNA
Ariel Fernández
Phys. Rev. Lett. 64, 2328 (1990)
- Activation-energy landscape for metastable RNA folding
Ariel Fernández and Eugene I. Shakhnovich
Phys. Rev. A 42, 3657 (1990)
- Thermodynamic Fluctuations in a Reacting SystemâMeasurement by Fluorescence Correlation Spectroscopy
Douglas Magde, Elliot Elson, and W. W. Webb
Phys. Rev. Lett. 29, 705 (1972)
- Possibility of Superconductive-Type Enhanced Conductivity in DNA at Room Temperature
J. LADIK, G. BiczÃ, and J. RÃ
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