2007 year
- Structure and interactions of biological helices
Alexei A. Kornyshev, Dominic J. Lee, Sergey Leikin, and Aaron Wynveen
Rev. Mod. Phys. 79, 943 (2007)
- Discrete Breathers in Nonlinear Network Models of Proteins
B. Juanico, Y.-H. Sanejouand, F. Piazza, and P. De Los Rios
Phys. Rev. Lett. 99, 238104 (2007)
- Anomalous Diffusion in Folding Dynamics of Minimalist Protein Landscape
Yasuhiro Matsunaga, Chun-Biu Li, and Tamiki Komatsuzaki
Phys. Rev. Lett. 99, 238103 (2007)
- New Insight into Cataract Formation: Enhanced Stability through Mutual Attraction
A. Stradner, G. Foffi, N. Dorsaz, G. Thurston, and P. Schurtenberger
Phys. Rev. Lett. 99, 198103 (2007)
- Quantifying Intrinsic Specificity: A Potential Complement to Affinity in Drug Screening
Jin Wang, Xiliang Zheng, Yongliang Yang, Dale Drueckhammer, Wei Yang, Gennardy Verkhivker, and Erkang Wang
Phys. Rev. Lett. 99, 198101 (2007)
- Importance of Metastable States in the Free Energy Landscapes of Polypeptide Chains
Stefan Auer, Mark A. Miller, Sergei V. Krivov, Christopher M. Dobson, Martin Karplus, and Michele Vendruscolo
Phys. Rev. Lett. 99, 178104 (2007)
- 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)
- Cross-Linker Unbinding and Self-Similarity in Bundled Cytoskeletal Networks
O. Lieleg and A. R. Bausch
Phys. Rev. Lett. 99, 158105 (2007)
- Curve Encirclement and Protein Structure
Patrick Kessler and Oliver M. O
Phys. Rev. Lett. 99, 158103 (2007)
- Multistability and Clustering in a Population of Synthetic Genetic Oscillators via Phase-Repulsive Cell-to-Cell Communication
Ekkehard Ullner, Alexei Zaikin, Evgenii I. Volkov, and Jordi García-Ojalvo
Phys. Rev. Lett. 99, 148103 (2007)
- Nonequilibrium Statistical Mechanics of Dividing Cell Populations
Naama Brenner and Yair Shokef
Phys. Rev. Lett. 99, 138102 (2007)
- Lattice Dynamics of a Protein Crystal
Lars Meinhold, Franci Merzel, and Jeremy C. Smith
Phys. Rev. Lett. 99, 138101 (2007)
- Solvation of Proteins : Linking Thermodynamics to Geometry
Hendrik Hansen-Goos, Roland Roth, Klaus Mecke, and S. Dietrich
Phys. Rev. Lett. 99, 128101 (2007)
- Interplay between Spinodal Decomposition and Glass Formation in Proteins Exhibiting Short-Range Attractions
Frédéric Cardinaux, Thomas Gibaud, Anna Stradner, and Peter Schurtenberger
Phys. Rev. Lett. 99, 118301 (2007)
- Quantitative Protein Dynamics from Dominant Folding Pathways
M. Sega, P. Faccioli, F. Pederiva, G. Garberoglio, and H. Orland
Phys. Rev. Lett. 99, 118102 (2007)
- Symmetry and Stochastic Gene Regulation
Alexandre F. Ramos and José E. Hornos
Phys. Rev. Lett. 99, 108103 (2007)
Stefano Buzzaccaro, Roberto Rusconi, and Roberto Piazza
Phys. Rev. Lett. 99, 098301 (2007)
- Mechanics of Bundled Semiflexible Polymer Networks
O. Lieleg, M. M. Claessens, C. Heussinger, E. Frey, and A. R. Bausch
Phys. Rev. Lett. 99, 088102 (2007)
- Branching, Capping, and Severing in Dynamic Actin Structures
Ajay Gopinathan, Kun-Chun Lee, J. M. Schwarz, and Andrea J. Liu
Phys. Rev. Lett. 99, 058103 (2007)
- Rate Determining Factors in Protein Model Structures
Pierpaolo Bruscolini, Alessandro Pelizzola, and Marco Zamparo
Phys. Rev. Lett. 99, 038103 (2007)
- Capturing the Interaction Potential of Amyloidogenic Proteins
Nadeem Javid, Karsten Vogtt, Christina Krywka, Metin Tolan, and Roland Winter
Phys. Rev. Lett. 99, 028101 (2007)
- Nonequilibrium-Driven Motion in Actin Networks: Comet Tails and Moving Beads
N. J. Burroughs and D. Marenduzzo
Phys. Rev. Lett. 98, 238302 (2007)
- Determination of Interbilayer and Transbilayer Lipid Transfers by Time-Resolved Small-Angle Neutron Scattering
Minoru Nakano, Masakazu Fukuda, Takayuki Kudo, Hitoshi Endo, and Tetsurou Handa
Phys. Rev. Lett. 98, 238101 (2007)
- Breaking the Diffraction Barrier in Fluorescence Microscopy by Optical Shelving
Stefan Bretschneider, Christian Eggeling, and Stefan W. Hell
Phys. Rev. Lett. 98, 218103 (2007)
- Induced Long-Range Attractive Potentials of Human Serum Albumin by Ligand Binding
Takaaki Sato, Teruyuki Komatsu, Akito Nakagawa, and Eishun Tsuchida
Phys. Rev. Lett. 98, 208101 (2007)
- Subdiffusion and Weak Ergodicity Breaking in the Presence of a Reactive Boundary
Michael A. Lomholt, Irwin M. Zaid, and Ralf Metzler
Phys. Rev. Lett. 98, 200603 (2007)
- Surface Conductivity of Biological Macromolecules Measured by Nanopipette Dielectrophoresis
Richard W. Clarke, Joe D. Piper, Liming Ying, and David Klenerman
Phys. Rev. Lett. 98, 198102 (2007)
- Density-Wave Theory of the Capsid Structure of Small Icosahedral Viruses
V. L. Lorman and S. B. Rochal
Phys. Rev. Lett. 98, 185502 (2007)
- Membrane Waves Driven by Actin and Myosin
R. Shlomovitz and N. S. Gov
Phys. Rev. Lett. 98, 168103 (2007)
- Combined Effect of Pore Radius and Protein Dielectric Coefficient on the Selectivity of a Calcium Channel
Dezső Boda, Mónika Valiskó, Bob Eisenberg, Wolfgang Nonner, Douglas Henderson, and Dirk Gillespie
Phys. Rev. Lett. 98, 168102 (2007)
- Time-Resolved Torsional Relaxation of Spider Draglines by an Optical Technique
O. Emile, A. Le Floch, and F. Vollrath
Phys. Rev. Lett. 98, 167402 (2007)
- Unfolding of Proteins and Long Transient Conformations Detected by Single Nanopore Recording
G. Oukhaled, J. Mathé, A.-L. Biance, L. Bacri, J.-M. Betton, D. Lairez, J. Pelta, and L. Auvray
Phys. Rev. Lett. 98, 158101 (2007)
- Ising-Like Model for Protein Mechanical Unfolding
A. Imparato, A. Pelizzola, and M. Zamparo
Phys. Rev. Lett. 98, 148102 (2007)
- Proton Momentum Distribution in a Protein Hydration Shell
R. Senesi, A. Pietropaolo, A. Bocedi, S. E. Pagnotta, and F. Bruni
Phys. Rev. Lett. 98, 138102 (2007)
- Exploring the Mechanism of Flexible Biomolecular Recognition with Single Molecule Dynamics
Qiang Lu, H. Peter Lu, and Jin Wang
Phys. Rev. Lett. 98, 128105 (2007)
- Conformational Temperature Characterizing the Folding of a Protein
Naoko Nakagawa
Phys. Rev. Lett. 98, 128104 (2007)
- Role of Conformational Entropy in Force-Induced Biopolymer Unfolding
Sanjay Kumar, Iwan Jensen, Jesper L. Jacobsen, and Anthony J. Guttmann
Phys. Rev. Lett. 98, 128101 (2007)
- Probing Anomalous Relaxation by Coherent Multidimensional Optical Spectroscopy
František Šanda and Shaul Mukamel
Phys. Rev. Lett. 98, 080603 (2007)
- Control of Frictional Coupling of Transmembrane Cell Receptors in Model Cell Membranes with Linear Polymer Spacers
Oliver Purrucker, Anton Förtig, Rainer Jordan, Erich Sackmann, and Motomu Tanaka
Phys. Rev. Lett. 98, 078102 (2007)
- Structural Polymorphism of the Actin-Espin System: A Prototypical System of Filaments and Linkers in Stereocilia
Kirstin R. Purdy, James R. Bartles, and Gerard C. Wong
Phys. Rev. Lett. 98, 058105 (2007)
- Two-State Folding, Folding through Intermediates, and Metastability in a Minimalistic Hydrophobic-Polar Model for Proteins
Stefan Schnabel, Michael Bachmann, and Wolfhard Janke
Phys. Rev. Lett. 98, 048103 (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)
- Does Changing the Pulling Direction Give Better Insight into Biomolecules?
Sanjay Kumar and Debaprasad Giri
Phys. Rev. Lett. 98, 048101 (2007)
- Dynamics and optimal number of replicas in parallel tempering simulations
Walter Nadler and Ulrich H. Hansmann
Phys. Rev. E 76, 065701 (2007)
- Theory of conformational transitions of viral shells
Thomas Guérin and Robijn Bruinsma
Phys. Rev. E 76, 061911 (2007)
- Role of electrostatic interactions in the assembly of empty spherical viral capsids
Antonio Šiber and Rudolf Podgornik
Phys. Rev. E 76, 061906 (2007)
- Dynamics of essential collective motions in proteins : Theory
Maria Stepanova
Phys. Rev. E 76, 051918 (2007)
- Stochastic simulations of the repressilator circuit
Adiel Loinger and Ofer Biham
Phys. Rev. E 76, 051917 (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)
- Dynamics of a two-dimensional model of cell tissues with coupled stochastic gene networks
Andre S. Ribeiro
Phys. Rev. E 76, 051915 (2007)
- Alternative hydrogen bond implementations produce opposite effects on collapse cooperativity of lattice homopolypeptide models
Gustavo M. N. Fleury, Marco A. A. Barbosa, and Antônio F. Pereira de Araújo
Phys. Rev. E 76, 051914 (2007)
- How a protein searches for its specific site on DNA: The role of intersegment transfer
Tao Hu and B. I. Shklovskii
Phys. Rev. E 76, 051909 (2007)
- Fragility and mechanosensing in a thermalized cytoskeleton model with forced protein unfolding
Brenton D. Hoffman, Gladys Massiera, and John C. Crocker
Phys. Rev. E 76, 051906 (2007)
- Link and subgraph likelihoods in random undirected networks with fixed and partially fixed degree sequences
Jacob G. Foster, David V. Foster, Peter Grassberger, and Maya Paczuski
Phys. Rev. E 76, 046112 (2007)
- Nanoscale electrical conductivity of the purple membrane monolayer
I. Casuso, L. Fumagalli, J. Samitier, E. Padrós, L. Reggiani, V. Akimov, and G. Gomila
Phys. Rev. E 76, 041919 (2007)
- Analytical phase diagram for colloid-polymer mixtures
Gerard J. Fleer and Remco Tuinier
Phys. Rev. E 76, 041802 (2007)
- Colloids with key-lock interactions: Nonexponential relaxation, aging, and anomalous diffusion
Nicholas A. Licata and Alexei V. Tkachenko
Phys. Rev. E 76, 041405 (2007)
- How the excluded volume architecture influences ion-mediated forces between proteins
V. Dahirel, M. Jardat, J.-F. Dufrêche, and P. Turq
Phys. Rev. E 76, 040902 (2007)
- Simulation via direct computation of partition functions
Cheng Zhang and Jianpeng Ma
Phys. Rev. E 76, 036708 (2007)
- Graph animals, subgraph sampling, and motif search in large networks
Kim Baskerville, Peter Grassberger, and Maya Paczuski
Phys. Rev. E 76, 036107 (2007)
- Steady-state helices of the actin homolog MreB inside bacteria: Dynamics without motors
Jun F. Allard and Andrew D. Rutenberg
Phys. Rev. E 76, 031916 (2007)
- General investigation of elastic thin rods as subject to a terminal twist
Kai Hu
Phys. Rev. E 76, 031910 (2007)
- Microrheological studies reveal semiflexible networks in gels of a ubiquitous cell wall polysaccharide
R. R. Vincent, D. N. Pinder, Y. Hemar, and M. A. K. Williams
Phys. Rev. E 76, 031909 (2007)
- Accuracy and convergence of the Wang-Landau sampling algorithm
Alexander N. Morozov and Sheng Hsien Lin
Phys. Rev. E 76, 026701 (2007)
- Universality in complex networks: Random matrix analysis
Jayendra N. Bandyopadhyay and Sarika Jalan
Phys. Rev. E 76, 026109 (2007)
- Direct measurements of the stabilization of single-stranded DNA under tension by single-stranded binding proteins
K. Hatch, C. Danilowicz, V. Coljee, and M. Prentiss
Phys. Rev. E 76, 021916 (2007)
- Universal power law behaviors in genomic sequences and evolutionary models
Loredana Martignetti and Michele Caselle
Phys. Rev. E 76, 021902 (2007)
- Lattice model for self-assembly with application to the formation of cytoskeletal-like structures
Shannon F. Stewman and Aaron R. Dinner
Phys. Rev. E 76, 016103 (2007)
- Improving an all-atom force field
Sandipan Mohanty and U. H. Hansmann
Phys. Rev. E 76, 012901 (2007)
- Liposome-induced DNA compaction and reentrant condensation investigated by dielectric relaxation spectroscopy and dynamic light scattering techniques
S. Zuzzi, C. Cametti, G. Onori, and S. Sennato
Phys. Rev. E 76, 011925 (2007)
- Simple stochastic model for the evolution of protein lengths
C. Destri and C. Miccio
Phys. Rev. E 76, 011924 (2007)
- Stress fluctuations and motion of cytoskeletal-bound markers
Carina Raupach, Daniel Paranhos Zitterbart, Claudia T. Mierke, Claus Metzner, Frank A. Müller, and Ben Fabry
Phys. Rev. E 76, 011918 (2007)
- Representing perturbed dynamics in biological network models
Gautier Stoll, Jacques Rougemont, and Felix Naef
Phys. Rev. E 76, 011917 (2007)
- Structure optimization and folding mechanisms of off-lattice protein models using statistical temperature molecular dynamics simulation: Statistical temperature annealing
Jaegil Kim, John E. Straub, and Thomas Keyes
Phys. Rev. E 76, 011913 (2007)
- Dynamics of the Davydov-Scott monomer in a thermal bath: Comparison of the full quantum and semiclassical approaches
J. Cuevas, P. A. S. Silva, F. R. Romero, and L. Cruzeiro
Phys. Rev. E 76, 011907 (2007)
- Generalized theory of site-specific DNA-protein interactions
R. Murugan
Phys. Rev. E 76, 011901 (2007)
- Influence of charge and flexibility on smectic phase formation in filamentous virus suspensions
Kirstin R. Purdy and Seth Fraden
Phys. Rev. E 76, 011705 (2007)
- Crystal growth in a three-phase system: Diffusion and liquid-liquid phase separation in lysozyme crystal growth
M. C. R. Heijna, W. J. P. van Enckevort, and E. Vlieg
Phys. Rev. E 76, 011604 (2007)
- Wang-Landau molecular dynamics technique to search for low-energy conformational space of proteins
Takehiro Nagasima, Akira R. Kinjo, Takashi Mitsui, and Ken Nishikawa
Phys. Rev. E 75, 066706 (2007)
- Oscillations in intracellular signaling cascades
K.-H. Chiam and Gunaretnam Rajagopal
Phys. Rev. E 75, 061901 (2007)
- Controllability analysis of networks
Anna Lombardi and Michael Hörnquist
Phys. Rev. E 75, 056110 (2007)
- Clustering coefficients of protein -protein interaction networks
Gerald A. Miller, Yi Y. Shi, Hong Qian, and Karol Bomsztyk
Phys. Rev. E 75, 051910 (2007)
- Construction and application of the weighted amino acid network based on energy
Xiong Jiao, Shan Chang, Chun-hua Li, Wei-zu Chen, and Cun-xin Wang
Phys. Rev. E 75, 051903 (2007)
- Kinetics of viral self-assembly: Role of the single-stranded RNA antenna
Tao Hu and B. I. Shklovskii
Phys. Rev. E 75, 051901 (2007)
- Exploring the assortativity-clustering space of a network
Petter Holme and Jing Zhao
Phys. Rev. E 75, 046111 (2007)
- Diffusion-trapping model of receptor trafficking in dendrites
P. C. Bressloff and B. A. Earnshaw
Phys. Rev. E 75, 041915 (2007)
- Non-Gaussian behavior of elastic incoherent neutron scattering profiles of proteins studied by molecular dynamics simulation
Atsushi Tokuhisa, Yasumasa Joti, Hiroshi Nakagawa, Akio Kitao, and Mikio Kataoka
Phys. Rev. E 75, 041912 (2007)
- Unfolding cross-linkers as rheology regulators in F-actin networks
B. A. DiDonna and Alex J. Levine
Phys. Rev. E 75, 041909 (2007)
- Intracellular transport by single-headed kinesin KIF1A: Effects of single-motor mechanochemistry and steric interactions
Philip Greulich, Ashok Garai, Katsuhiro Nishinari, Andreas Schadschneider, and Debashish Chowdhury
Phys. Rev. E 75, 041905 (2007)
- Continuum theory of a moving membrane
Dan Hu, Pingwen Zhang, and Weinan E
Phys. Rev. E 75, 041605 (2007)
- Effects of hydration water on protein methyl group dynamics in solution
Daniela Russo, Greg L. Hura, and John R. Copley
Phys. Rev. E 75, 040902 (2007)
- Erratum: Effect of supercoiling on formation of protein -mediated DNA loops [Phys. Rev. E 74, 061907 (2006)]
P. K. Purohit and P. C. Nelson
Phys. Rev. E 75, 039903 (2007)
- Measuring peptide mass spectrum correlation using the quantum Grover algorithm
Keng Wah Choo
Phys. Rev. E 75, 031919 (2007)
- Folding behavior of ribosomal protein S6 studied by modified Go̅ -like model
L. Wu, J. Zhang, J. Wang, W. F. Li, and W. Wang
Phys. Rev. E 75, 031914 (2007)
- Solutions of burnt-bridge models for molecular motor transport
Alexander Yu. Morozov, Ekaterina Pronina, Anatoly B. Kolomeisky, and Maxim N. Artyomov
Phys. Rev. E 75, 031910 (2007)
- Wrapping conformations of a polymer on a curved surface
Cheng-Hsiao Lin, Yan-Chr Tsai, and Chin-Kun Hu
Phys. Rev. E 75, 031903 (2007)
- Nonlinear finite-element analysis of nanoindentation of viral capsids
Melissa M. Gibbons and William S. Klug
Phys. Rev. E 75, 031901 (2007)
- Temperature-compensated chemical reactions
Kanaka Rajan and L. F. Abbott
Phys. Rev. E 75, 022902 (2007)
- Cubic equation governing the outer-region dielectric constant of globular proteins
Hwangseo Park and Young Ho Jeon
Phys. Rev. E 75, 021916 (2007)
- Precrystallization clusters of holoferritin and apoferritin at low temperature
S. Boutet and I. K. Robinson
Phys. Rev. E 75, 021913 (2007)
- Stochastic simulations of genetic switch systems
Adiel Loinger, Azi Lipshtat, Nathalie Q. Balaban, and Ofer Biham
Phys. Rev. E 75, 021904 (2007)
- Traffic of interacting ribosomes: Effects of single-machine mechanochemistry on protein synthesis
Aakash Basu and Debashish Chowdhury
Phys. Rev. E 75, 021902 (2007)
- Hexagonal, square, and stripe patterns of the ion channel density in biomembranes
Markus Hilt and Walter Zimmermann
Phys. Rev. E 75, 016202 (2007)
- Fractality in complex networks: Critical and supercritical skeletons
J. S. Kim, K.-I. Goh, G. Salvi, E. Oh, B. Kahng, and D. Kim
Phys. Rev. E 75, 016110 (2007)
- Exploring complex networks through random walks
Luciano da Fontoura Costa and Gonzalo Travieso
Phys. Rev. E 75, 016102 (2007)
- Active elastic network: Cytoskeleton of the red blood cell
Nir S. Gov
Phys. Rev. E 75, 011921 (2007)
- Amino acid hydrophobicity and accessible surface area
M. A. Moret and G. F. Zebende
Phys. Rev. E 75, 011920 (2007)
- Collecting single molecules with conventional optical tweezers
Wolfgang Singer, Timo A. Nieminen, Norman R. Heckenberg, and Halina Rubinsztein-Dunlop
Phys. Rev. E 75, 011916 (2007)
- Equation of state of looped DNA
Igor M. Kulić, Hervé Mohrbach, Rochish Thaokar, and Helmut Schiessel
Phys. Rev. E 75, 011913 (2007)