2005 year
- Picosecond-Time-Scale Fluctuations of Proteins in Glassy Matrices: The Role of Viscosity
E. Cornicchi, G. Onori, and A. Paciaroni
Phys. Rev. Lett. 95, 158104 (2005)
- Coarse-Graining Protein Energetics in Sequence Variables
F. Zhou, G. Grigoryan, S. R. Lustig, A. E. Keating, G. Ceder, and D. Morgan
Phys. Rev. Lett. 95, 148103 (2005)
- Conductance of Ion Channels and Nanopores with Charged Walls: A Toy Model
J. Zhang, A. Kamenev, and B. I. Shklovskii
Phys. Rev. Lett. 95, 148101 (2005)
- Efficient Sampling of Protein Structures by Model Hopping
W. Kwak and U. H. E. Hansmann
Phys. Rev. Lett. 95, 138102 (2005)
- Symmetry-Breaking Motility
A. Lee, H. Y. Lee, and M. Kardar
Phys. Rev. Lett. 95, 138101 (2005)
- Trapping Single Molecules by Dielectrophoresis
R. Hölzel, N. Calander, Z. Chiragwandi, M. Willander, and F. F. Bier
Phys. Rev. Lett. 95, 128102 (2005)
- Effective Long-Range Attraction between Protein Molecules in Solutions Studied by Small Angle Neutron Scattering
Y. Liu, E. Fratini, P. Baglioni, W.-R. Chen, and S.-H. Chen
Phys. Rev. Lett. 95, 118102 (2005)
- Structure and Stability of Self-Assembled Actin-Lysozyme Complexes in Salty Water
L. K. Sanders, C. Guáqueta, T. E. Angelini, J.-W. Lee, S. C. Slimmer, E. Luijten, and G. C. L. Wong
Phys. Rev. Lett. 95, 108302 (2005)
- Form of Growing Strings
D. Marenduzzo, T. X. Hoang, F. Seno, M. Vendruscolo, and A. Maritan
Phys. Rev. Lett. 95, 098103 (2005)
- Infinite Average Lifetime of an Unstable Bright State in the Green Fluorescent Protein
P. Didier, L. Guidoni, and F. Bardou
Phys. Rev. Lett. 95, 090602 (2005)
- Model for Codon Position Bias in RNA Editing
T. Liu and R. Bundschuh
Phys. Rev. Lett. 95, 088101 (2005)
- Viscoelastic Phase Separation of Protein Solutions
H. Tanaka and Y. Nishikawa
Phys. Rev. Lett. 95, 078103 (2005)
- Electrostatically Driven Spatial Patterns in Lipid Membrane Composition
R. Parthasarathy, P. A. Cripe, and J. T. Groves
Phys. Rev. Lett. 95, 048101 (2005)
- Discontinuous Unbinding Transitions of Filament Bundles
J. Kierfeld, T. Kühne, and R. Lipowsky
Phys. Rev. Lett. 95, 038102 (2005)
- Onsets of Anharmonicity in Protein Dynamics
J. H. Roh, V. N. Novikov, R. B. Gregory, J. E. Curtis, Z. Chowdhuri, and A. P. Sokolov
Phys. Rev. Lett. 95, 038101 (2005)
- Coupling of Two Motor Proteins: A New Motor Can Move Faster
E. B. Stukalin, H. Phillips, III, and A. B. Kolomeisky
Phys. Rev. Lett. 94, 238101 (2005)
- Langevin Trajectories between Fixed Concentrations
B. Nadler, Z. Schuss, and A. Singer
Phys. Rev. Lett. 94, 218101 (2005)
- How White Noise Generates Power-Law Switching in Bacterial Flagellar Motors
Y. Tu and G. Grinstein
Phys. Rev. Lett. 94, 208101 (2005)
- Observation of a Power-Law Memory Kernel for Fluctuations within a Single Protein Molecule
W. Min, G. Luo, B. J. Cherayil, S. C. Kou, and X. S. Xie
Phys. Rev. Lett. 94, 198302 (2005)
- Miscibility Gap in the Microbial Fitness Landscape
F. N. Braun, S. Paulsen, R. P. Sear, and P. B. Warren
Phys. Rev. Lett. 94, 178105 (2005)
- Exons, Introns, and DNA Thermodynamics
E. Carlon, M. L. Malki, and R. Blossey
Phys. Rev. Lett. 94, 178101 (2005)
- Quantum Mechanical Free Energy Barrier for an Enzymatic Reaction
T. H. Rod and U. Ryde
Phys. Rev. Lett. 94, 138302 (2005)
- Picosecond Thermometer in the Amide I Band of Myoglobin
R. H. Austin, A. Xie, L. van der Meer, B. Redlich, P.-A. Lindgård, H. Frauenfelder, and D. Fu
Phys. Rev. Lett. 94, 128101 (2005)
- Mechanics of Binding of a Single Integration-Host-Factor Protein to DNA
S. Dixit, M. Singh-Zocchi, J. Hanne, and G. Zocchi
Phys. Rev. Lett. 94, 118101 (2005)
- Filament Depolymerization by Motor Molecules
G. A. Klein, K. Kruse, G. Cuniberti, and F. Jülicher
Phys. Rev. Lett. 94, 108102 (2005)
- Optical Rheology of Biological Cells
F. Wottawah, S. Schinkinger, B. Lincoln, R. Ananthakrishnan, M. Romeyke, J. Guck, and J. Käs
Phys. Rev. Lett. 94, 098103 (2005)
- Passive or Active Fluctuations in Membranes Containing Proteins
P. Girard, J. Prost, and P. Bassereau
Phys. Rev. Lett. 94, 088102 (2005)
- Protein Structural Change Upon Ligand Binding: Linear Response Theory
M. Ikeguchi, J. Ueno, M. Sato, and A. Kidera
Phys. Rev. Lett. 94, 078102 (2005)
- Artificial Allosteric Control of Maltose Binding Protein
B. Choi, G. Zocchi, S. Canale, Y. Wu, S. Chan, and L. J. Perry
Phys. Rev. Lett. 94, 038103 (2005)
- Icosahedral Packing of RNA Viral Genomes
J. Rudnick and R. Bruinsma
Phys. Rev. Lett. 94, 038101 (2005)
- Hierarchical Chain Model of Spider Capture Silk Elasticity
H. Zhou and Y. Zhang
Phys. Rev. Lett. 94, 028104 (2005)
- Nonequilibrium Thermodynamics and Nonlinear Kinetics in a Cellular Signaling Switch
H. Qian and T. C. Reluga
Phys. Rev. Lett. 94, 028101 (2005)
- Replica-Exchange Monte Carlo Scheme for Bayesian Data Analysis
M. Habeck, M. Nilges, and W. Rieping
Phys. Rev. Lett. 94, 018105 (2005)
- In Silico Folding of a Three Helix Protein and Characterization of Its Free-Energy Landscape in an All-Atom Force Field
T. Herges and W. Wenzel
Phys. Rev. Lett. 94, 018101 (2005)
- Apparent persistence length renormalization of bent DNA
I. M. Kulic, H. Mohrbach, V. Lobaskin, R. Thaokar, and H. Schiessel
Phys. Rev. E 72, 041905 (2005)
- Fluctuations and instability of a biological membrane induced by interaction with macromolecules
F. Divet, G. Danker, and C. Misbah
Phys. Rev. E 72, 041901 (2005)
- Sampling properties of random graphs: The degree distribution
M. P. H. Stumpf and C. Wiuf
Phys. Rev. E 72, 036118 (2005)
- Effects of hydrophobic mismatch and spontaneous curvature on ion channel gating with a hinge
K.-J.-B. Lee
Phys. Rev. E 72, 031917 (2005)
- Core genetic module: The mixed feedback loop
P. François and V. Hakim
Phys. Rev. E 72, 031908 (2005)
- Micromechanical mass sensors for biomolecular detection in a physiological environment
T. Braun, V. Barwich, M. K. Ghatkesar, A. H. Bredekamp, C. Gerber, M. Hegner, and H. P. Lang
Phys. Rev. E 72, 031907 (2005)
- Modeling DNA unzipping in the presence of bound proteins
F. Habib and R. Bundschuh
Phys. Rev. E 72, 031906 (2005)
- Coupled dynamics of DNA breathing and of proteins that selectively bind to single-stranded DNA
T. Ambjörnsson and R. Metzler
Phys. Rev. E 72, 030901 (2005)
- Geometric and physical considerations for realistic protein models
I. A. Hubner and E. I. Shakhnovich
Phys. Rev. E 72, 022901 (2005)
- Direct stochastic simulation of Ca2+ motion in Xenopus eggs
Y.-B. Yi, H. Wang, A. M. Sastry, and C. M. Lastoskie
Phys. Rev. E 72, 021913 (2005)
- Fast method for estimating the energy distribution of globular states of proteins
H.-B. Cao, C.-Z. Wang, and K.-M. Ho
Phys. Rev. E 72, 021907 (2005)
- Medium effects on the selection of sequences folding into stable proteins in a simple model
Y.-Q. Li, Y.-Y. Ji, J.-W. Mao, and X.-W. Tang
Phys. Rev. E 72, 021904 (2005)
- Growth algorithm for finding low energy configurations of simple lattice proteins
W. Huang, Z. Lü, and H. Shi
Phys. Rev. E 72, 016704 (2005)
- Nonlinear software sensor for monitoring genetic regulation processes with noise and modeling errors
V. Ibarra-Junquera, L. A. Torres, H. C. Rosu, G. Argüello, and J. Collado-Vides
Phys. Rev. E 72, 011919 (2005)
- Structure optimization by conformational space annealing in an off-lattice protein model
S.-Y. Kim, S. B. Lee, and J. Lee
Phys. Rev. E 72, 011916 (2005)
- Perceptron learning of pairwise contact energies for proteins incorporating the amino acid environment
M. Heo, S. Kim, E.-J. Moon, M. Cheon, K. Chung, and I. Chang
Phys. Rev. E 72, 011906 (2005)
- Tunable generic model for fluid bilayer membranes
I. R. Cooke, K. Kremer, and M. Deserno
Phys. Rev. E 72, 011506 (2005)
- Electrostatics and the assembly of an RNA virus
P. van der Schoot and R. Bruinsma
Phys. Rev. E 71, 061928 (2005)
- Dynamic hysteresis in a one-dimensional Ising model: Application to allosteric proteins
I. Graham and T. A. J. Duke
Phys. Rev. E 71, 061923 (2005)
- Analytical derivation of thermodynamic characteristics of lipid bilayer from a flexible string model
S. I. Mukhin and S. Baoukina
Phys. Rev. E 71, 061918 (2005)
- Temperature dependence and counter effect of the correlations of folding rate with chain length and with native topology
H. K. Nakamura and M. Takano
Phys. Rev. E 71, 061913 (2005)
- Duplication-divergence model of protein interaction network
I. Ispolatov, P. L. Krapivsky, and A. Yuryev
Phys. Rev. E 71, 061911 (2005)
- Kinetics of the polymer collapse transition: The role of hydrodynamics
N. Kikuchi, J. F. Ryder, C. M. Pooley, and J. M. Yeomans
Phys. Rev. E 71, 061804 (2005)
- Subgraph centrality in complex networks
E. Estrada and J. A. Rodríguez-Velázquez
Phys. Rev. E 71, 056103 (2005)
- Hydrodynamic stability of helical growth at low Reynolds number
A. Balter and J. X. Tang
Phys. Rev. E 71, 051912 (2005)
- Effects of kinks on DNA elasticity
Yu. O. Popov and A. V. Tkachenko
Phys. Rev. E 71, 051905 (2005)
- Nonexponential relaxation and hierarchically constrained dynamics in a protein
E. Abrahams
Phys. Rev. E 71, 051901 (2005)
- Stochastic modeling of protein motions within cell membranes
S. Khan, A. M. Reynolds, I. E. G. Morrison, and R. J. Cherry
Phys. Rev. E 71, 041915 (2005)
- Spatial distribution of protein molecules adsorbed at a polyelectrolyte multilayer
G. Jackler, C. Czeslik, R. Steitz, and C. A. Royer
Phys. Rev. E 71, 041912 (2005)
- Spectral analysis of protein-protein interactions in Drosophila melanogaster
C. Kamp and K. Christensen
Phys. Rev. E 71, 041911 (2005)
- Nonlinear elasticity of an alpha -helical polypeptide
B. Chakrabarti and A. J. Levine
Phys. Rev. E 71, 031905 (2005)
- Discrete layers of interacting growing protein seeds: Convective and morphological stages of evolution
M. Lappa
Phys. Rev. E 71, 031904 (2005)
- Understanding mechanochemical coupling in kinesins using first-passage-time processes
A. B. Kolomeisky, E. B. Stukalin, and A. A. Popov
Phys. Rev. E 71, 031902 (2005)
- Understanding mechanochemical coupling in kinesins using first-passage-time processes
A. B. Kolomeisky, E. B. Stukalin, and A. A. Popov
Phys. Rev. E 71, 031902 (2005)
- Characterization of degree frequency distribution in protein interaction networks
S. A. Romano and M. C. Eguia
Phys. Rev. E 71, 031901 (2005)
- Exact solution of a one-dimensional model of strained epitaxy on a periodically modulated substrate
V. I. Tokar and H. Dreyssé
Phys. Rev. E 71, 031604 (2005)
- Glassy behavior of a percolative water-protein system
S. E. Pagnotta, R. Gargana, F. Bruni, and A. Bocedi
Phys. Rev. E 71, 031506 (2005)
- Numerical study of a binary Yukawa model in regimes characteristic of globular proteins in solutions
A. Giacometti, D. Gazzillo, G. Pastore, and T. K. Das
Phys. Rev. E 71, 031108 (2005)
- Analytical tools for solitons and periodic waves corresponding to phonons on Lennard-Jones lattices in helical proteins
F. d’Ovidio, H. G. Bohr, and P.-A. Lindgård
Phys. Rev. E 71, 026606 (2005)
- Brownian simulations and unidirectional flux in diffusion
A. Singer and Z. Schuss
Phys. Rev. E 71, 026115 (2005)
- Formation of loops in DNA under tension
S. Sankararaman and J. F. Marko
Phys. Rev. E 71, 021911 (2005)
- Theoretical studies of the kinetics of mechanical unfolding of cross-linked polymer chains and their implications for single-molecule pulling experiments
K. Eom, D. E. Makarov, and G. J. Rodin
Phys. Rev. E 71, 021904 (2005)
- Coarse-graining and self-dissimilarity of complex networks
S. Itzkovitz, R. Levitt, N. Kashtan, R. Milo, M. Itzkovitz, and U. Alon
Phys. Rev. E 71, 016127 (2005)
- Spectral analysis and the dynamic response of complex networks
M. A. M. de Aguiar and Y. Bar-Yam
Phys. Rev. E 71, 016106 (2005)
- Self-similarity and protein chains
M. A. Moret, J. G. V. Miranda, E. Nogueira, Jr., M. C. Santana, and G. F. Zebende
Phys. Rev. E 71, 012901 (2005)
- Theoretical analysis of opening-up vesicles with single and two holes
T. Umeda, Y. Suezaki, K. Takiguchi, and H. Hotani
Phys. Rev. E 71, 011913 (2005)
- Mass fractal dimension and the compactness of proteins
M. B. Enright and D. M. Leitner
Phys. Rev. E 71, 011912 (2005)
- Opening of nucleic-acid double strands by helicases: Active versus passive opening
M. D. Betterton and F. Jülicher
Phys. Rev. E 71, 011904 (2005)
- Molecular dynamics simulations of the indentation of a crystalline surface by an atomic force microscope tip
R. Ferrando, M. Andrei, A. Relini, R. Rolandi, and A. Gliozzi
Phys. Rev. B 72, 045412 (2005)
- Magnetic resonance force microscopy of nuclear spins: Detection and manipulation of statistical polarization
H. J. Mamin, R. Budakian, B. W. Chui, and D. Rugar
Phys. Rev. B 72, 024413 (2005)