2004 year
- Joining and Scission in the Self-Assembly of Nanotubes from DNA Tiles
Axel Ekani-Nkodo, Ashish Kumar, and Deborah Kuchnir Fygenson
Phys. Rev. Lett. 93, 268301 (2004)
- Finite Size Effects on Thermal Denaturation of Globular Proteins
M. S. Li, D. K. Klimov, and D. Thirumalai
Phys. Rev. Lett. 93, 268107 (2004)
- Membrane Undulations Driven by Force Fluctuations of Active Proteins
N. Gov
Phys. Rev. Lett. 93, 268104 (2004)
- Model of RecA-Mediated Homologous Recognition
Kevin D. Dorfman, Renaud Fulconis, Marie Dutreix, and Jean-Louis Viovy
Phys. Rev. Lett. 93, 268102 (2004)
- Dendritic Branching and Homogenization of Actin Networks Mediated by Arp2/3 Complex
Y. Tseng and D. Wirtz
Phys. Rev. Lett. 93, 258104 (2004)
- High-Fidelity DNA Sensing by Protein Binding Fluctuations
Tsvi Tlusty, Roy Bar-Ziv, and Albert Libchaber
Phys. Rev. Lett. 93, 258103 (2004)
- Stepwise Elastic Behavior in a Model Elastomer
D. M. Bhawe, C. Cohen, and F. A. Escobedo
Phys. Rev. Lett. 93, 257804 (2004)
- Brownian Dynamics in Fourier Space: Membrane Simulations over Long Length and Time Scales
L. C.-L. Lin and F. L. H. Brown
Phys. Rev. Lett. 93, 256001 (2004)
- Spatial Distribution of Competing Ions around DNA in Solution
K. Andresen, R. Das, H. Y. Park, H. Smith, L. W. Kwok, J. S. Lamb, E. J. Kirkland, D. Herschlag, K. D. Finkelstein, and L. Pollack
Phys. Rev. Lett. 93, 248103 (2004)
- Reversible Temperature and Pressure Denaturation of a Protein Fragment: A Replica Exchange Molecular Dynamics Simulation Study
D. Paschek and A. E. García
Phys. Rev. Lett. 93, 238105 (2004)
- Electronic Structure of Regular Bacterial Surface Layers
D. V. Vyalikh, S. Danzenbächer, M. Mertig, A. Kirchner, W. Pompe, Y. S. Dedkov, and S. L. Molodtsov
Phys. Rev. Lett. 93, 238103 (2004)
- Fluctuation-Driven Molecular Transport Through an Asymmetric Membrane Channel
I. Kosztin and K. Schulten
Phys. Rev. Lett. 93, 238102 (2004)
- Lattice Tube Model of Proteins
J. R. Banavar, M. Cieplak, and A. Maritan
Phys. Rev. Lett. 93, 238101 (2004)
- Dielectric Modulation of Biological Water
F. Despa, A. Fernández, and R. S. Berry
Phys. Rev. Lett. 93, 228104 (2004)
- Pattern Formation within Escherichia coli: Diffusion, Membrane Attachment, and Self-Interaction of MinD Molecules
R. V. Kulkarni, K. C. Huang, M. Kloster, and N. S. Wingreen
Phys. Rev. Lett. 93, 228103 (2004)
- Hidden Dynamics of Vesicle Adhesion Induced by Specific Stickers
D. Cuvelier and P. Nassoy
Phys. Rev. Lett. 93, 228101 (2004)
- Protein Folding Rates Correlate with Heterogeneity of Folding Mechanism
B. Öztop, M. R. Ejtehadi, and S. S. Plotkin
Phys. Rev. Lett. 93, 208105 (2004)
- Ordered Self-Assembled Monolayers of Peptide Nucleic Acids with DNA Recognition Capability
C. Briones, E. Mateo-Marti, C. Gómez-Navarro, V. Parro, E. Román, and J. A. Martín-Gago
Phys. Rev. Lett. 93, 208103 (2004)
- Synchrotron X-ray Diffraction Study of Microtubules Buckling and Bundling under Osmotic Stress: A Probe of Interprotofilament Interactions
D. J. Needleman, M. A. Ojeda-Lopez, U. Raviv, K. Ewert, J. B. Jones, H. P. Miller, L. Wilson, and C. R. Safinya
Phys. Rev. Lett. 93, 198104 (2004)
- Clustered Bottlenecks in mRNA Translation and Protein Synthesis
Tom Chou and Greg Lakatos
Phys. Rev. Lett. 93, 198101 (2004)
- Clustered Bottlenecks in mRNA Translation and Protein Synthesis
T. Chou and G. Lakatos
Phys. Rev. Lett. 93, 198101 (2004)
- Generalized Langevin Equation with Fractional Gaussian Noise: Subdiffusion within a Single Protein Molecule
S. C. Kou and X. S. Xie
Phys. Rev. Lett. 93, 180603 (2004)
- Enhancement of Association Rates by Nonspecific Binding to DNA and Cell Membranes
Huan-Xiang Zhou and Attila Szabo
Phys. Rev. Lett. 93, 178101 (2004)
- Breakdown of Classical Nucleation Theory near Isostructural Phase Transitions
A. Cacciuto, S. Auer, and D. Frenkel
Phys. Rev. Lett. 93, 166105 (2004)
- Long Time Molecular Dynamics for Enhanced Conformational Sampling in Biomolecular Systems
P. Minary, M. E. Tuckerman, and G. J. Martyna
Phys. Rev. Lett. 93, 150201 (2004)
- Kinetic Pinning and Biological Antifreezes
L. M. Sander and A. V. Tkachenko
Phys. Rev. Lett. 93, 128102 (2004)
- Elastic Properties of a Single-Stranded Charged Homopolymeric Ribonucleotide
Yeonee Seol, Gary M. Skinner, and Koen Visscher
Phys. Rev. Lett. 93, 118102 (2004)
- Dynamic Phase Transitions in Cell Spreading
H.-G. Döbereiner, B. Dubin-Thaler, G. Giannone, H. S. Xenias, and M. P. Sheetz
Phys. Rev. Lett. 93, 108105 (2004)
- Low Frequency Rhythms in Human DNA Sequences: A Key to the Organization of Gene Location and Orientation?
S. Nicolay, F. Argoul, M. Touchon, Y. d'Aubenton-Carafa, C. Thermes, and A. Arneodo
Phys. Rev. Lett. 93, 108101 (2004)
- Coarse-Grained Model Of Entropic Allostery
Rhoda J. Hawkins and Tom C. B. McLeish
Phys. Rev. Lett. 93, 098104 (2004)
- Coarse-Grained Model Of Entropic Allostery
R. J. Hawkins and T. C. B. McLeish
Phys. Rev. Lett. 93, 098104 (2004)
- Measurement of the Phase Diagram of DNA Unzipping in the Temperature-Force Plane
C. Danilowicz, Y. Kafri, R. S. Conroy, V. W. Coljee, J. Weeks, and M. Prentiss
Phys. Rev. Lett. 93, 078101 (2004)
- Direct Determination of Vibrational Density of States Change on Ligand Binding to a Protein
E. Balog, T. Becker, M. Oettl, R. Lechner, R. Daniel, J. Finney, and J. C. Smith
Phys. Rev. Lett. 93, 028103 (2004)
- Skin Layer at the Actin-Gel Surface: Quenched Protein Membranes form Flat, Crumpled, and Tubular Morphologies
L. S. Hirst and C. R. Safinya
Phys. Rev. Lett. 93, 018101 (2004)
- DNA Spools under Tension
I. M. Kulic and H. Schiessel
Phys. Rev. Lett. 92, 228101 (2004)
- DNA Spools under Tension
I. M. Kulic and H. Schiessel
Phys. Rev. Lett. 92, 228101 (2004)
- Reconstruction of Protein Structures from a Vectorial Representation
M. Porto, U. Bastolla, H. E. Roman, and M. Vendruscolo
Phys. Rev. Lett. 92, 218101 (2004)
- Continuous Melting of Compact Polymers
Jesper Lykke Jacobsen and Jané Kondev
Phys. Rev. Lett. 92, 210601 (2004)
- Single Molecule Diffraction
J. C. H. Spence and R. B. Doak
Phys. Rev. Lett. 92, 198102 (2004)
- Water Induced Effects on the Thermal Response of a Protein
S. Melchionna, G. Briganti, P. Londei, and P. Cammarano
Phys. Rev. Lett. 92, 158101 (2004)
- Folding and Unfolding of an Elastinlike Oligopeptide: "Inverse Temperature Transition," Reentrance, and Hydrogen-Bond Dynamics
E. Schreiner, C. Nicolini, B. Ludolph, R. Ravindra, N. Otte, A. Kohlmeyer, R. Rousseau, R. Winter, and D. Marx
Phys. Rev. Lett. 92, 148101 (2004)
- Crystallization of a Globular Protein in Lipid Cubic Phase
S. Tanaka, S. U. Egelhaaf, and W. C. K. Poon
Phys. Rev. Lett. 92, 128102 (2004)
- Simulation and Analysis of in vitro DNA Evolution
Morten Kloster and Chao Tang
Phys. Rev. Lett. 92, 038101 (2004)
- Simulation and Analysis of in vitro DNA Evolution
M. Kloster and C. Tang
Phys. Rev. Lett. 92, 038101 (2004)
- Specular neutron reflectivity and the structure of artificial protein maquettes vectorially oriented at interfaces
J. Strzalka, B. R. Gibney, S. Satija, and J. K. Blasie
Phys. Rev. E 70, 061905 (2004)
- Isotropic-cholesteric phase transition of filamentous virus suspensions as a function of rod length and charge
K. R. Purdy and S. Fraden
Phys. Rev. E 70, 061703 (2004)
- Interaction of proteins with spherical polyelectrolyte brushes in solution as studied by small-angle x-ray scattering
S. Rosenfeldt, A. Wittemann, M. Ballauff, E. Breininger, J. Bolze, and N. Dingenouts
Phys. Rev. E 70, 061403 (2004)
- Memoryless control of boundary concentrations of diffusing particles
A. Singer, Z. Schuss, B. Nadler, and R. S. Eisenberg
Phys. Rev. E 70, 061106 (2004)
- Relaxation to native conformation of a bond-fluctuating protein chain with hydrophobic and polar nodes
J. Bjursell and R. B. Pandey
Phys. Rev. E 70, 052904 (2004)
- Designing specificity of protein-substrate interactions
I. Coluzza and D. Frenkel
Phys. Rev. E 70, 051917 (2004)
- Saturation of conductance in single ion channels: The blocking effect of the near reaction field
B. Nadler, Z. Schuss, U. Hollerbach, and R. S. Eisenberg
Phys. Rev. E 70, 051912 (2004)
- Sequence-related human proteins cluster by degree of evolutionary conservation
R. Mrowka, A. Patzak, H. Herzel, and D. Holste
Phys. Rev. E 70, 051908 (2004)
- Efficient expansion, folding, and unfolding of proteins
E. D. Nelson and N. V. Grishin
Phys. Rev. E 70, 051906 (2004)
- Self-assembly of polyhedral shells: A molecular dynamics study
D. C. Rapaport
Phys. Rev. E 70, 051905 (2004)
- Model for the dynamics of a water cluster in an x-ray free electron laser beam
M. Bergh, N. Tîmneanu, and D. van der Spoel
Phys. Rev. E 70, 051904 (2004)
- Structure-function relationship of biological gels revealed by multiple-particle tracking and differential interference contrast microscopy: The case of human lamin networks
P. Panorchan, D. Wirtz, and Y. Tseng
Phys. Rev. E 70, 041906 (2004)
- Unified perspective on proteins: A physics approach
J. R. Banavar, T. X. Hoang, A. Maritan, F. Seno, and A. Trovato
Phys. Rev. E 70, 041905 (2004)
- Base-sequence-dependent sliding of proteins on DNA
M. Barbi, C. Place, V. Popkov, and M. Salerno
Phys. Rev. E 70, 041901 (2004)
- Base-sequence-dependent sliding of proteins on DNA
M. Barbi, C. Place, V. Popkov, and M. Salerno
Phys. Rev. E 70, 041901 (2004)
- Base-sequence-dependent sliding of proteins on DNA
M. Barbi, C. Place, V. Popkov, and M. Salerno
Phys. Rev. E 70, 041901 (2004)
- Bubble generation in a twisted and bent DNA-like model
P. V. Larsen, P. L. Christiansen, O. Bang, J. F. R. Archilla, and Yu. B. Gaididei
Phys. Rev. E 70, 036609 (2004)
- Stabilization of surface-immobilized enzymes using grafted polymers
Y. Moskovitz and S. Srebnik
Phys. Rev. E 70, 032902 (2004)
- Solitons in alpha -helical proteins
L. Brizhik, A. Eremko, B. Piette, and W. Zakrzewski
Phys. Rev. E 70, 031914 (2004)
- Self-organized pattern formation in motor-microtubule mixtures
S. Sankararaman, G. I. Menon, and P. B. Sunil Kumar
Phys. Rev. E 70, 031905 (2004)
- Teaching computers to fold proteins
O. Winther and A. Krogh
Phys. Rev. E 70, 030903 (2004)
- Multiphoton switching dynamics of single green fluorescent proteins
G. Chirico, F. Cannone, A. Diaspro, S. Bologna, V. Pellegrini, R. Nifosì, and F. Beltram
Phys. Rev. E 70, 030901 (2004)
- Picometer-scale dynamical observations of individual membrane proteins: The case of bacteriorhodopsin
Y. Okumura, T. Oka, M. Kataoka, Y. Taniguchi, and Y. C. Sasaki
Phys. Rev. E 70, 021917 (2004)
- Exact solution of a linear molecular motor model driven by two-step fluctuations and subjectto protein friction
H. C. Fogedby, R. Metzler, and A. Svane
Phys. Rev. E 70, 021905 (2004)
- Mean-field approaches to the totally asymmetric exclusion process with quenched disorder and large particles
L. B. Shaw, J. P. Sethna, and K. H. Lee
Phys. Rev. E 70, 021901 (2004)
- Unwrapping of DNA-protein complexes under external stretching
Takahiro Sakaue and Hartmut Löwen
Phys. Rev. E 70, 021801 (2004)
- Unwrapping of DNA-protein complexes under external stretching
T. Sakaue and H. Löwen
Phys. Rev. E 70, 021801 (2004)
- Convective instability in protein crystal growth
D. Lima and A. De Wit
Phys. Rev. E 70, 021603 (2004)
- Simulations of a small protein in a specifically designed generalized ensemble
U. H. E. Hansmann
Phys. Rev. E 70, 012902 (2004)
- Stretching of homopolymers and contact order
M. Cieplak, T. X. Hoang, and M. O. Robbins
Phys. Rev. E 70, 011917 (2004)
- Nucleosome interactions in chromatin: Fiber stiffening and hairpin formation
Boris Mergell, Ralf Everaers, and Helmut Schiessel
Phys. Rev. E 70, 011915 (2004)
- Dynamics of gene regulatory networks with cell division cycle
Luonan Chen, Ruiqi Wang, Tetsuya J. Kobayashi, and Kazuyuki Aihara
Phys. Rev. E 70, 011909 (2004)
- Near-field-magnetic-tweezer manipulation of single DNA molecules
Jie Yan, Dunja Skoko, and John F. Marko
Phys. Rev. E 70, 011905 (2004)
- Refolding of lysozyme by quasistatic and direct dilution reaction paths: A first-order-like state transition
C.-C. Chang, X.-C. Yeh, H.-T. Lee, P.-Y. Lin, and L.-S. Kan
Phys. Rev. E 70, 011904 (2004)
- Diffusion of actin filaments within a thin layer between two walls
G. Li and J. X. Tang
Phys. Rev. E 69, 061921 (2004)
- Effect of chain connectivity on the structure of Lennard-Jones liquid and its implicationon statistical potentials for protein folding
W. C. Lu, C. Z. Wang, and K. M. Ho
Phys. Rev. E 69, 061920 (2004)
- Diffusion in correlated random potentials, with applications to DNA
Michael Slutsky, Mehran Kardar, and Leonid A. Mirny
Phys. Rev. E 69, 061903 (2004)
- Diffusion in correlated random potentials, with applications to DNA
M. Slutsky, M. Kardar, and L. A. Mirny
Phys. Rev. E 69, 061903 (2004)
- Liquid-liquid phase transitions for soft-core attractive potentials
A. Skibinsky, S. V. Buldyrev, G. Franzese, G. Malescio, and H. E. Stanley
Phys. Rev. E 69, 061206 (2004)
- Analytical study of the effect of recombination on evolution via DNA shuffling
Weiqun Peng, Herbert Levine, Terence Hwa, and David A. Kessler
Phys. Rev. E 69, 051911 (2004)
- Analytical study of the effect of recombination on evolution via DNA shuffling
W. Peng, H. Levine, T. Hwa, and D. A. Kessler
Phys. Rev. E 69, 051911 (2004)
- Dynamics of the minimally frustrated helices determine the hierarchical folding of small helical proteins
M. Compiani, E. Capriotti, and R. Casadio
Phys. Rev. E 69, 051905 (2004)
- Elastic deformations of grafted layers with surface stress
A. Nicolas and S. A. Safran
Phys. Rev. E 69, 051902 (2004)
- Relaxation channels of two-vibron bound states in alpha -helix proteins
V. Pouthier and C. Falvo
Phys. Rev. E 69, 041906 (2004)
- Transcription rate of RNA polymerase under rotary torque
H. Kiryu
Phys. Rev. E 69, 041902 (2004)
- Structural stability study of protein monolayers in air
P. P. Pompa, A. Biasco, R. Cingolani, R. Rinaldi, M. Ph. Verbeet, and G. W. Canters
Phys. Rev. E 69, 032901 (2004)
- Self-similar processes and flicker noise from a fluctuating nanopore in a lipid membrane
M. Kotulska, S. Koronkiewicz, and S. Kalinowski
Phys. Rev. E 69, 031920 (2004)
- Numerical path integration technique for the calculation of transport properties of proteins
E.-H. Kang, M. L. Mansfield, and J. F. Douglas
Phys. Rev. E 69, 031918 (2004)
- Atomic force microscopy contact, tapping, and jumping modes for imaging biological samples in liquids
F. Moreno-Herrero, J. Colchero, J. Gómez-Herrero, and A. M. Baró
Phys. Rev. E 69, 031915 (2004)
- Cooperativity and contact order in protein folding
M. Cieplak
Phys. Rev. E 69, 031907 (2004)
- Energy funneling in a bent chain of Morse oscillators with long-range coupling
P. V. Larsen, P. L. Christiansen, O. Bang, J. F. R. Archilla, and Yu. B. Gaididei
Phys. Rev. E 69, 026603 (2004)
- Model study of protein unfolding by interfaces
S. D. Chakarova and A. E. Carlsson
Phys. Rev. E 69, 021907 (2004)
- Simulation of the kinetics of a sphere attached to a fluctuating polymer: Implications for target search by DNA-binding proteins
J. Chakrabarti and S. Roy
Phys. Rev. E 69, 021904 (2004)
- Simulation of the kinetics of a sphere attached to a fluctuating polymer: Implications for target search by DNA-binding proteins
J. Chakrabarti and S. Roy
Phys. Rev. E 69, 021904 (2004)
- Mechanism of protein binding to spherical polyelectrolyte brushes studied in situ using two-photon excitation fluorescence fluctuation spectroscopy
C. Czeslik, R. Jansen, M. Ballauff, A. Wittemann, C. A. Royer, E. Gratton, and T. Hazlett
Phys. Rev. E 69, 021401 (2004)
- Motor protein with nonequilibrium potential: Its thermodynamics and efficiency
H. Qian
Phys. Rev. E 69, 012901 (2004)
- Stretching of proteins in the entropic limit
M. Cieplak, T. X. Hoang, and M. O. Robbins
Phys. Rev. E 69, 011912 (2004)
- DNA-protein interactions under random jump conditions
R. Murugan
Phys. Rev. E 69, 011911 (2004)
- DNA-protein interactions under random jump conditions
R. Murugan
Phys. Rev. E 69, 011911 (2004)
- Sequence variability of proteins evolutionarily constrained by solution-thermodynamic function
F. N. Braun
Phys. Rev. E 69, 011903 (2004)
- Spectral response of crystalline acetanilide and N -methylacetamide: Vibrational self-trapping in hydrogen-bonded crystals
J. Edler and P. Hamm
Phys. Rev. B 69, 214301 (2004)
- Numerical atomic basis orbitals from H to Kr
T. Ozaki and H. Kino
Phys. Rev. B 69, 195113 (2004)