2003 year
- Colloquium: Geometrical approach to protein folding: a tube picture
J. R. Banavar and A. Maritan
Rev. Mod. Phys. 75, 23 (2003)
- Competition between Diffusion and Fragmentation: An Important Evolutionary Process of Nature
J. Ferkinghoff-Borg, M. H. Jensen, J. Mathiesen, P. Olesen, and K. Sneppen
Phys. Rev. Lett. 91, 266103 (2003)
- A Motor that Makes Its Own Track: Helicase Unwinding of DNA
M. D. Betterton and Frank Jülicher
Phys. Rev. Lett. 91, 258103 (2003)
- A Motor that Makes Its Own Track: Helicase Unwinding of DNA
M. D. Betterton and F. Jülicher
Phys. Rev. Lett. 91, 258103 (2003)
- Effective Interactions Cannot Replace Solvent Effects in a Lattice Model of Proteins
G. Salvi and P. De Los Rios
Phys. Rev. Lett. 91, 258102 (2003)
- Principal Components of the Protein Dynamical Transition
A. L. Tournier and J. C. Smith
Phys. Rev. Lett. 91, 208106 (2003)
- Multicanonical Chain-Growth Algorithm
M. Bachmann and W. Janke
Phys. Rev. Lett. 91, 208105 (2003)
- Structure and Dynamics of Annexin 12 Bound to a Planar Lipid Bilayer
T. Risse, W. L. Hubbell, J. M. Isas, and H. T. Haigler
Phys. Rev. Lett. 91, 188101 (2003)
- Reproducible Protein Folding with the Stochastic Tunneling Method
A. Schug, T. Herges, and W. Wenzel
Phys. Rev. Lett. 91, 158102 (2003)
- Processive Motor Protein as an Overdamped Brownian Stepper
M. Bier
Phys. Rev. Lett. 91, 148104 (2003)
- Chromatin Dynamics: Nucleosomes go Mobile through Twist Defects
I. M. Kulic and H. Schiessel
Phys. Rev. Lett. 91, 148103 (2003)
- Structure of Actin Cross-Linked with alpha -Actinin: A Network of Bundles
O. Pelletier, E. Pokidysheva, L. S. Hirst, N. Bouxsein, Y. Li, and C. R. Safinya
Phys. Rev. Lett. 91, 148102 (2003)
- Preferential Attachment in the Protein Network Evolution
E. Eisenberg and E. Y. Levanon
Phys. Rev. Lett. 91, 138701 (2003)
- Possible Mechanism for Cold Denaturation of Proteins at High Pressure
M. I. Marqués, J. M. Borreguero, H. E. Stanley, and N. V. Dokholyan
Phys. Rev. Lett. 91, 138103 (2003)
- Adiabatic Pumping Mechanism for Ion Motive ATPases
R. D. Astumian
Phys. Rev. Lett. 91, 118102 (2003)
- Deformation of Cross-Linked Semiflexible Polymer Networks
D. A. Head, A. J. Levine, and F. C. MacKintosh
Phys. Rev. Lett. 91, 108102 (2003)
- Deformation and Collapse of Microtubules on the Nanometer Scale
P. J. de Pablo, I. A. T. Schaap, F. C. MacKintosh, and C. F. Schmidt
Phys. Rev. Lett. 91, 098101 (2003)
- Sequence Space Localization in the Immune System Response to Vaccination and Disease
M. W. Deem and H. Y. Lee
Phys. Rev. Lett. 91, 068101 (2003)
- Publisher's Note: Dynamic Force Spectroscopy of Protein-DNA Interactions by Unzipping DNA [Phys. Rev. Lett. 91, 028103 (2001)]
S. J. Koch and M. D. Wang
Phys. Rev. Lett. 91, 049903 (2003)
- Particle Dispersion on Rapidly Folding Random Heteropolymers
D. Brockmann and T. Geisel
Phys. Rev. Lett. 91, 048303 (2003)
- Particle Dispersion on Rapidly Folding Random Heteropolymers
D. Brockmann and T. Geisel
Phys. Rev. Lett. 91, 048303 (2003)
- Stochastic Annealing
R. C. Ball, T. M. A. Fink, and N. E. Bowler
Phys. Rev. Lett. 91, 030201 (2003)
- Dynamic Force Spectroscopy of Protein-DNA Interactions by Unzipping DNA
Steven J. Koch and Michelle D. Wang
Phys. Rev. Lett. 91, 028103 (2003)
- Dynamic Force Spectroscopy of Protein-DNA Interactions by Unzipping DNA
S. J. Koch and M. D. Wang
Phys. Rev. Lett. 91, 028103 (2003)
- Lamellar Phase of Stacked Two-Dimensional Rafts of Actin Filaments
G. C. L. Wong, A. Lin, J. X. Tang, Y. Li, P. A. Janmey, and C. R. Safinya
Phys. Rev. Lett. 91, 018103 (2003)
- Adherence of Packing Defects in Soluble Proteins
A. Fernández and L. R. Scott
Phys. Rev. Lett. 91, 018102 (2003)
- Origins of Chevron Rollovers in Non-Two-State Protein Folding Kinetics
H. Kaya and H. S. Chan
Phys. Rev. Lett. 90, 258104 (2003)
- Time-Dependent Density-Functional Approach for Biological Chromophores: The Case of the Green Fluorescent Protein
M. A. L. Marques, X. López, D. Varsano, A. Castro, and A. Rubio
Phys. Rev. Lett. 90, 258101 (2003)
- Viral Self-Assembly as a Thermodynamic Process
R. F. Bruinsma, W. M. Gelbart, D. Reguera, J. Rudnick, and R. Zandi
Phys. Rev. Lett. 90, 248101 (2003)
- Unzipping Kinetics of Double-Stranded DNA in a Nanopore
Alexis F. Sauer-Budge, Jacqueline A. Nyamwanda, David K. Lubensky, and Daniel Branton
Phys. Rev. Lett. 90, 238101 (2003)
- Unzipping Kinetics of Double-Stranded DNA in a Nanopore
A. F. Sauer-Budge, J. A. Nyamwanda, D. K. Lubensky, and D. Branton
Phys. Rev. Lett. 90, 238101 (2003)
- Shearing or Compressing a Soft Glass in 2D: Time-Concentration Superposition
P. Cicuta, E. J. Stancik, and G. G. Fuller
Phys. Rev. Lett. 90, 236101 (2003)
- Structural Determinant of Protein Designability
J. L. England and E. I. Shakhnovich
Phys. Rev. Lett. 90, 218101 (2003)
- Liquid-Liquid Phase Separation of a Surfactant-Solubilized Membrane Protein
R. Piazza, M. Pierno, E. Vignati, G. Venturoli, F. Francia, A. Mallardi, and G. Palazzo
Phys. Rev. Lett. 90, 208101 (2003)
- Fast Chain Contraction during Protein Folding: "Foldability" and Collapse Dynamics
L. Qiu, C. Zachariah, and S. J. Hagen
Phys. Rev. Lett. 90, 168103 (2003)
- Twisted Protein Aggregates and Disease: The Stability of Sickle Hemoglobin Fibers
M. S. Turner, R. W. Briehl, F. A. Ferrone, and R. Josephs
Phys. Rev. Lett. 90, 128103 (2003)
- Pattern Formation inside Bacteria: Fluctuations due to the Low Copy Number of Proteins
M. Howard and A. D. Rutenberg
Phys. Rev. Lett. 90, 128102 (2003)
- Vibrationally Resolved Photoabsorption Spectroscopy of Red Fluorescent Protein Chromophore Anions
S. Boyé, H. Krogh, I. B. Nielsen, S. B. Nielsen, S. U. Pedersen, U. V. Pedersen, L. H. Andersen, A. F. Bell, X. He, and P. J. Tonge
Phys. Rev. Lett. 90, 118103 (2003)
- Dynamics of Competitive Evolution on a Smooth Landscape
Weiqun Peng, Ulrich Gerland, Terence Hwa, and Herbert Levine
Phys. Rev. Lett. 90, 088103 (2003)
- Dynamics of Competitive Evolution on a Smooth Landscape
W. Peng, U. Gerland, T. Hwa, and H. Levine
Phys. Rev. Lett. 90, 088103 (2003)
- Colloid-Polymer Mixtures in the Protein Limit
P. G. Bolhuis, E. J. Meijer, and A. A. Louis
Phys. Rev. Lett. 90, 068304 (2003)
- Elastic Response of Single DNA Molecules Exhibits a Reentrant Collapsing Transition
Yoshihiro Murayama, Yoshihiko Sakamaki, and Masaki Sano
Phys. Rev. Lett. 90, 018102 (2003)
- Some asymptotic properties of duplication graphs
A. Raval
Phys. Rev. E 68, 066119 (2003)
- Two-electron transfer reactions in proteins: Bridge-mediated and proton-assisted processes
E. G. Petrov, V. I. Teslenko, and V. May
Phys. Rev. E 68, 061916 (2003)
- Modeling the concentration-dependent permeation modes of the KcsA potassium ion channel
P. H. Nelson
Phys. Rev. E 68, 061908 (2003)
- Motion of a rotatory molecular motor and the chemical reaction rate
H. Miki, M. Sato, and M. Kohmoto
Phys. Rev. E 68, 061906 (2003)
- Network rigidity at finite temperature: Relationships between thermodynamic stability, the nonadditivity of entropy, and cooperativity in molecular systems
D. J. Jacobs, S. Dallakyan, G. G. Wood, and A. Heckathorne
Phys. Rev. E 68, 061109 (2003)
- Virus shapes and buckling transitions in spherical shells
J. Lidmar, L. Mirny, and D. R. Nelson
Phys. Rev. E 68, 051910 (2003)
- Statistical mechanics of RNA folding: A lattice approach
P. Leoni and C. Vanderzande
Phys. Rev. E 68, 051904 (2003)
- Time scale and other invariants of integrative mechanical behavior in living cells
B. Fabry, G. N. Maksym, J. P. Butler, M. Glogauer, D. Navajas, N. A. Taback, E. J. Millet, and J. J. Fredberg
Phys. Rev. E 68, 041914 (2003)
- Helix versus sheet formation in a small peptide
Y. Peng and U. H. E. Hansmann
Phys. Rev. E 68, 041911 (2003)
- Statistical mechanics of RNA folding: Importance of alphabet size
Ranjan Mukhopadhyay, Eldon Emberly, Chao Tang, and Ned S. Wingreen
Phys. Rev. E 68, 041904 (2003)
- Publisher's Note: Effects of DNA-distorting proteins on DNA elastic response [Phys. Rev. E 68, 011905 (2003)]
J. Yan and J. F. Marko
Phys. Rev. E 68, 039901 (2003)
- Structure optimization in an off-lattice protein model
H.-P. Hsu, V. Mehra, and P. Grassberger
Phys. Rev. E 68, 037703 (2003)
- Dynamics of DNA in vitro evolution with Mnt-repressor: Simulations and analysis
Yufeng Yang, Hongli Wang, and Qi Ouyang
Phys. Rev. E 68, 031903 (2003)
- Structure, dynamics, and energetics of water at the surface of a small globular protein: A molecular dynamics simulation
S. G. Dastidar and C. Mukhopadhyay
Phys. Rev. E 68, 021921 (2003)
- Multifractal and correlation analyses of protein sequences from complete genomes
Zu-Guo Yu, Vo Anh, and Ka-Sing Lau
Phys. Rev. E 68, 021913 (2003)
- Multifractal and correlation analyses of protein sequences from complete genomes
Z.-G. Yu, V. Anh, and K.-S. Lau
Phys. Rev. E 68, 021913 (2003)
- Totally asymmetric exclusion process with extended objects: A model for protein synthesis
L. B. Shaw, R. K. P. Zia, and K. H. Lee
Phys. Rev. E 68, 021910 (2003)
- Two-vibron bound states in alpha -helix proteins: The interplay between the intramolecular anharmonicity and the strong vibron
V. Pouthier
Phys. Rev. E 68, 021909 (2003)
- Dielectric boundary force and its crucial role in gramicidin
B. Nadler, U. Hollerbach, and R. S. Eisenberg
Phys. Rev. E 68, 021905 (2003)
- Intrinsic fluorescence spectroscopy of glutamate dehydrogenase: Integrated behavior and deconvolution analysis
P. P. Pompa, R. Cingolani, and R. Rinaldi
Phys. Rev. E 68, 011907 (2003)
- Effects of DNA-distorting proteins on DNA elastic response
Jie Yan and John F. Marko
Phys. Rev. E 68, 011905 (2003)
- Effects of DNA-distorting proteins on DNA elastic response
J. Yan and J. F. Marko
Phys. Rev. E 68, 011905 (2003)
- Thermodynamic instability in supersaturated lysozyme solutions: Effect of salt and role of concentration fluctuations
M. Manno, C. Xiao, D. Bulone, V. Martorana, and P. L. San Biagio
Phys. Rev. E 68, 011904 (2003)
- Effective pair potentials between protein amino acids
P. Pliego-Pastrana and M. D. Carbajal-Tinoco
Phys. Rev. E 68, 011903 (2003)
- Guided simulated annealing method for optimization problems
C. I. Chou, R. S. Han, S. P. Li, and T.-K. Lee
Phys. Rev. E 67, 066704 (2003)
- Repeats and correlations in human DNA sequences
Dirk Holste, Ivo Grosse, Stephan Beirer, Patrick Schieg, and Hanspeter Herzel
Phys. Rev. E 67, 061913 (2003)
- Repeats and correlations in human DNA sequences
D. Holste, I. Grosse, S. Beirer, P. Schieg, and H. Herzel
Phys. Rev. E 67, 061913 (2003)
- Conformational rigidity in a lattice model of proteins
O. Collet
Phys. Rev. E 67, 061912 (2003)
- Protein crystals and charged surfaces: Interactions and heterogeneous nucleation
R. P. Sear
Phys. Rev. E 67, 061907 (2003)
- Folding behaviors of lattice model proteins with three kinds of contact potentials
M. Qin, J. Wang, Y. Tang, and W. Wang
Phys. Rev. E 67, 061905 (2003)
- Quasiequilibrium unfolding thermodynamics of a small protein studied by molecular dynamics simulation with an explicit water model
J. Wang, Z. Zhang, H. Liu, and Y. Shi
Phys. Rev. E 67, 061903 (2003)
- Distance, dissimilarity index, and network community structure
H. Zhou
Phys. Rev. E 67, 061901 (2003)
- Competition between crystallization and gelation: A local description
N. M. Dixit and C. F. Zukoski
Phys. Rev. E 67, 061501 (2003)
- Distances and classification of amino acids for different protein secondary structures
X. Liu, L.-m. Zhang, S. Guan, and W.-M. Zheng
Phys. Rev. E 67, 051927 (2003)
- Simulation of protonic fluctuations in hydrated protein powders
G. Careri and E. Milotti
Phys. Rev. E 67, 051923 (2003)
- Relevance of structural segregation and chain compaction for the thermodynamics of folding of a hydrophobic protein model
M. A. A. Barbosa and A. F. Pereira de Araújo
Phys. Rev. E 67, 051919 (2003)
- Transverse fluctuations of single DNA molecules attached at both extremities to a surface
A. Crut, D. Lasne, J.-F. Allemand, M. Dahan, and P. Desbiolles
Phys. Rev. E 67, 051910 (2003)
- Transverse fluctuations of single DNA molecules attached at both extremities to a surface
A. Crut, D. Lasne, J.-F. Allemand, M. Dahan, and P. Desbiolles
Phys. Rev. E 67, 051910 (2003)
- Role of bulk and of interface contacts in the behavior of lattice model dimeric proteins
G. Tiana, D. Provasi, and R. A. Broglia
Phys. Rev. E 67, 051909 (2003)
- Nonmonotonic variation with salt concentration of the second virial coefficient in protein solutions
E. Allahyarov, H. Löwen, J. P. Hansen, and A. A. Louis
Phys. Rev. E 67, 051404 (2003)
- Molecular dynamics simulation of compression-induced solid-to-solid phase transitions in colloidal monolayers
J. Sun and T. Stirner
Phys. Rev. E 67, 051107 (2003)
- Preferential adsorption of hydrophobic-polar model proteins on patterned surfaces
N.-K. Lee and T. A. Vilgis
Phys. Rev. E 67, 050901 (2003)
- Universal behavior of localization of residue fluctuations in globular proteins
Y. Wu, X. Yuan, X. Gao, H. Fang, and J. Zi
Phys. Rev. E 67, 041909 (2003)
- Interactions between proteins bound to biomembranes
A. R. Evans, M. S. Turner, and P. Sens
Phys. Rev. E 67, 041907 (2003)
- Diffusion dynamics, moments, and distribution of first-passage time on the protein-folding energy landscape, with applications to single molecules
C.-L. Lee, C.-T. Lin, G. Stell, and J. Wang
Phys. Rev. E 67, 041905 (2003)
- Optical characterization of glutamate dehydrogenase monolayers chemisorbed on SiO2
P. P. Pompa, L. Blasi, L. Longo, R. Cingolani, G. Ciccarella, G. Vasapollo, R. Rinaldi, A. Rizzello, C. Storelli, and M. Maffia
Phys. Rev. E 67, 041902 (2003)
- Continuous isotropic-nematic liquid crystalline transition of F-actin solutions
J. Viamontes and J. X. Tang
Phys. Rev. E 67, 040701 (2003)
- Unfolding proteins in an external field: Can we always observe the intermediate states?
A. S. Lemak, J. R. Lepock, and J. Z. Y. Chen
Phys. Rev. E 67, 031910 (2003)
- Steric constraints as folding coadjuvant
M. E. P. Tarragó, L. F. O. Rocha, R. A. daSilva, and A. Caliri
Phys. Rev. E 67, 031901 (2003)
- Charged colloids and proteins at an air-water interface: The effect of dielectric substrates on interaction and phase behavior
E. C. Mbamala and H. H. von Grünberg
Phys. Rev. E 67, 031608 (2003)
- Dissipating step bunches during crystallization under transport control
H. Lin, S.-T. Yau, and P. G. Vekilov
Phys. Rev. E 67, 031606 (2003)
- Electromagnetic optimization of light-harvesting proteins
P. Etchegoin and R. C. Maher
Phys. Rev. E 67, 022902 (2003)
- Energy resolution and dynamical heterogeneity effects on elastic incoherent neutron scattering from molecular systems
T. Becker and J. C. Smith
Phys. Rev. E 67, 021904 (2003)
- Compact phases of polymers with hydrogen bonding
A. Trovato, J. Ferkinghoff-Borg, and M. H. Jensen
Phys. Rev. E 67, 021805 (2003)
- Glass transition in an off-lattice protein model studied by molecular dynamics simulations
A. Baumketner, J.-E. Shea, and Y. Hiwatari
Phys. Rev. E 67, 011912 (2003)
- Protein-induced morphological transitions in KCl crystal growth
B. Szabó and T. Vicsek
Phys. Rev. E 67, 011908 (2003)
- Phase diagrams of hard spheres with algebraic attractive interactions
P. J. Camp
Phys. Rev. E 67, 011503 (2003)
- Clustering under short-range finite interactions
M. Tirado-Miranda, A. Schmitt, J. Callejas-Fernández, and A. Fernández-Barbero
Phys. Rev. E 67, 011402 (2003)