Biophysical Journal -- BioFAST (by date view)

Biophysical Journal BioFAST:
Chronological list of articles [View by section]

In order to make new research readily available to readers throughout the world, Biophysical Journal (BJ) will prepublish, in manuscript format, all accepted papers within one week of acceptance and make them available at no cost to readers. These papers have undergone full scientific review but no editing, such as copyediting, typesetting, and proofreading. These papers will appear later in final, edited format in the print version of BJ and in BJ Online.

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3 July 2008

Karina Tveen Jensen, giovanni Strambini, Margherita Gonnelli, Jaap Broos, and J Baz Jackson: MUTATIONS IN TRANSHYDROGENASE CHANGE THE FLUORESCENCE EMISSION STATE OF TRP-72 FROM 1La to 1Lb
Biophys. J. BioFAST: July 3, 2008. doi:10.1529/biophysj.108.134650 [Abstract] [Accepted Manuscript]

Deepak Sharma, Gang Feng, Dingyue Khor, Georgi Genchev, Hui Lu, and Hongbin Li: Stabilization provided by neighboring strands is critical for the mechanical stability of proteins
Biophys. J. BioFAST: July 3, 2008. doi:10.1529/biophysj.108.134072 [Abstract] [Accepted Manuscript]

Stefan Legewie, Dennis Dienst, Annegret Wilde, Hanspeter Herzel, and Ilka Axmann: Small RNAs Establish Delays and Temporal Thresholds in Gene Expression
Biophys. J. BioFAST: July 3, 2008. doi:10.1529/biophysj.108.133819 [Abstract] [Accepted Manuscript]

Mark S Dillingham, Katherine L Tibbles, Jackie L Hunter, Jason C Bell, Stephen C. Kowalczykowski, and Martin R. Webb: A fluorescent single-stranded DNA binding protein as a probe for sensitive, real time assays of helicase activity
Biophys. J. BioFAST: July 3, 2008. doi:10.1529/biophysj.108.133512 [Abstract] [Accepted Manuscript]

Fa-Qing Zhao, Raul Padron, and Roger Craig: Blebbistatin Stabilizes the Helical Order of Myosin Filaments by Promoting the Switch 2 Closed State
Biophys. J. BioFAST: July 3, 2008. doi:10.1529/biophysj.108.137067 [Abstract] [Accepted Manuscript]

Jong-chin Lin, Daniel L Cox, and Rajiv R Singh: Theoretical Study of DNA Damage Recognition via Electron Transfer from the [4Fe-4S] Complex of MutY
Biophys. J. BioFAST: July 3, 2008. doi:10.1529/biophysj.108.132183 [Abstract] [Accepted Manuscript]

Cristina S. Pereira and Philippe H. Hunenberger: The effect of trehalose on a phospholipid membrane under mechanical stress
Biophys. J. BioFAST: July 3, 2008. doi:10.1529/biophysj.108.131656 [Abstract] [Accepted Manuscript]

Michael I Smith, James S Sharp, and Clive J Roberts: Insulin fibril nucleation: the role of prefibrillar aggregates
Biophys. J. BioFAST: July 3, 2008. doi:10.1529/biophysj.108.131482 [Abstract] [Accepted Manuscript]

Jeremy L. England and Vijay S. Pande: Potential for modulation of the hydrophobic effect inside chaperonins
Biophys. J. BioFAST: July 3, 2008. doi:10.1529/biophysj.108.131037 [Abstract] [Accepted Manuscript]

Chad E Miller, David D Busath, Bradley Strongin, and Jaroslaw Majewski: Integration of Ganglioside GT_1b Receptor into DPPE and DPPC Phospholipid Monolayers: An X-ray Reflectivity and Grazing Incidence Diffraction Study
Biophys. J. BioFAST: July 3, 2008. doi:10.1529/biophysj.107.128538 [Abstract] [Accepted Manuscript]

Xin Fang, William E. Bentley, and Evanghelos Zafiriou: Stochastic Modeling of Gene Positive Autoregulation Networks Involving Signal Molecules
Biophys. J. BioFAST: July 3, 2008. doi:10.1529/biophysj.107.127175 [Abstract] [Accepted Manuscript]

Simon Schweizer and Jennifer Reed: Effect of variation of the strength of the aromatic interactions of tryptophan on the cooperative structural refolding behavior of a peptide from HIV 1
Biophys. J. BioFAST: July 3, 2008. doi:10.1529/biophysj.107.126375 [Abstract] [Accepted Manuscript]

Jingxian Liu and Jianxing Song: NMR Evidence for Forming Highly-Populated Helical Conformations in the Partially-Folded hNck2 SH3 Domain
Biophys. J. BioFAST: July 3, 2008. doi:10.1529/biophysj.107.125641 [Abstract] [Accepted Manuscript]

Chaouqi Misbah, Vitkova Victoria, Mader Maud-Alix, Polack Beno\^it Polack, and Podgorski Thomas: Micro-macro link in rheology of erythrocyte and vesicle suspensions
Biophys. J. BioFAST: July 3, 2008. doi:10.1529/biophysj.108.138826 [Abstract] [Accepted Manuscript]

Olga Cañadas, Ingnacio García-Verdugo, Kevin M.W. Keough, and Cristina Casals: SP-A permeabilizes lipopolysaccharide membranes by forming protein aggregates that extract lipids from the membrane
Biophys. J. BioFAST: July 3, 2008. doi:10.1529/biophysj.108.137323 [Abstract] [Accepted Manuscript]

Philippe Robert, Kheya Sengupta, Pierre-Henri Puech, Pierre Bongrand, and Laurent Limozin: Tuning the formation and rupture of single ligand-receptor bonds by hyaluronan-induced repulsion
Biophys. J. BioFAST: July 3, 2008. doi:10.1529/biophysj.108.135947 [Abstract] [Accepted Manuscript]

Dusan Lazar and Jiri Jablonsky: Response to Kinetic Models of Photosystem II should incorporate a Role for QB-nonreducing Reaction Centers
Biophys. J. BioFAST: July 3, 2008. doi:10.1529/biophysj.108.135566 [Abstract] [Accepted Manuscript]

Wim J Vredenberg: Kinetic Models of Photosystem II should incorporate a Role for QB-nonreducing Reaction Centers
Biophys. J. BioFAST: July 3, 2008. doi:10.1529/biophysj.108.135426 [Abstract] [Accepted Manuscript]

Piotras Cimmperman, Lina Baranauskiene, Simona Jachimoviciute, Jelena Jachno, Jolanta Torresan, Vilma Michailoviene, Jurgita Matuliene, Jolanta Sereikaite, Vladas Bumelis, and Daumantas Matulis: A Quantitative Model of Thermal Stabilization and Destabilization of Proteins by Ligands
Biophys. J. BioFAST: July 3, 2008. doi:10.1529/biophysj.108.134973 [Abstract] [Accepted Manuscript]

Victor A Streltsov, Stephen J. J. Titmuss, V. Chandana Epa, Kevin J. Barnham, Colin L. Masters, and Jose N. Varghese: The structure of the Amyloid ${beta}$ -peptide high affinity Copper II binding site in Alzheimer's Disease
Biophys. J. BioFAST: July 3, 2008. doi:10.1529/biophysj.108.134429 [Abstract] [Accepted Manuscript]

Ilka B. Bischofs, Franziska Klein, Dirk Lehnert, Martin Bastmeyer, and Ulrich S. Schwarz: Filamentous Network Mechanics and Active Contractility Determine Cell and Tissue Shape
Biophys. J. BioFAST: July 3, 2008. doi:10.1529/biophysj.108.134296 [Abstract] [Accepted Manuscript]

27 June 2008

Florian Milde, Michael Bergdorf, and Petros Koumoutsakos: A Hybrid Model for 3D Simulations of Sprouting Angiogenesis
Biophys. J. BioFAST: June 27, 2008. doi:10.1529/biophysj.107.124511 [Abstract] [Accepted Manuscript]

Jane H. Sheeba, Aneta Stefanovska, and Peter V.E. McClintock: Neuronal synchrony during anaesthesia - A thalamocortical model
Biophys. J. BioFAST: June 27, 2008. doi:10.1529/biophysj.108.134635 [Abstract] [Accepted Manuscript]

Björn Neu, Rosalinda Wenby, and Herbert J Meiselman: Effects of dextran molecular weight on red blood cell aggregation
Biophys. J. BioFAST: June 27, 2008. doi:10.1529/biophysj.108.130328 [Abstract] [Accepted Manuscript]

Sandra N Pinto, Liana C Silva, Rodrigo F. M. de Almeida, and Manuel Jose Prieto: Membrane domain formation, interdigitation and morphological alterations induced by the very long chain asymmetric C24:1 ceramide
Biophys. J. BioFAST: June 27, 2008. doi:10.1529/biophysj.108.129858 [Abstract] [Accepted Manuscript] [Supplement]

Thomas Craighead Edrington, Michael Paul Bennett, and Arlene D Albert: Calorimetric Studies of Bovine Rod Outer Segment Disk Membranes Support a Monomeric Unit for Both Rhodopsin and Opsin
Biophys. J. BioFAST: June 27, 2008. doi:10.1529/biophysj.108.128868 [Abstract] [Accepted Manuscript]

Xiefan Lin and Brian P. Helmke: Micropatterned Structural Control Suppresses Mechanotaxis of Endothelial Cells
Biophys. J. BioFAST: June 27, 2008. doi:10.1529/biophysj.107.127761 [Abstract] [Accepted Manuscript]

Jeffrey G. Jacot, Andrew D. McCulloch, and Jeffrey H. Omens: Substrate Stiffness Affects the Functional Maturation of Neonatal Rat Ventricular Myocytes
Biophys. J. BioFAST: June 27, 2008. doi:10.1529/biophysj.107.124545 [Abstract] [Accepted Manuscript]

Kate M. Nairn, Russell E. Lyons, Roger J. Mulder, Stephen T. Mudie, David J. Cookson, Emmanuelle Lesieur, Misook Kim, Deborah Lau, Fiona H. Scholes, and Christopher M. Elvin: A synthetic resilin is largely unstructured
Biophys. J. BioFAST: June 27, 2008. doi:10.1529/biophysj.107.119107 [Abstract] [Accepted Manuscript]

Xingding Zhou, Tien-Chye Tan, Suresh Valiyaveettil, Mei-Lin Go, R. Manjunatha Kini, Adrian Velazquez-Campoy, and Jayaraman Sivaraman: Structural Characterization of Myotoxic Ecarpholin S from Echis carinatus Venom
Biophys. J. BioFAST: June 27, 2008. doi:10.1529/biophysj.107.117747 [Abstract] [Accepted Manuscript]

Bruno Zappone, Philipp Thurner, Jonathan Adams, Georg E. Fantner, and Paul K. Hansma: Effect of Ca²⁺ ions on the adhesion and mechanical properties of adsorbed layers of human Osteopontin
Biophys. J. BioFAST: June 27, 2008. doi:10.1529/biophysj.108.135889 [Abstract] [Accepted Manuscript]

Carlos Mattea, Johan Qvist, and Bertil Halle: Dynamics at the Protein-Water Interface from ¹⁷O Spin Relaxation in Deeply Supercooled Solutions
Biophys. J. BioFAST: June 27, 2008. doi:10.1529/biophysj.108.135194 [Abstract] [Accepted Manuscript]

Elizabeth J. Denning and Thomas B. Woolf: Double Bilayers and Transmembrane Gradients: A Molecular Dynamics Study of a Highly Charged Peptide
Biophys. J. BioFAST: June 27, 2008. doi:10.1529/biophysj.108.134049 [Abstract] [Accepted Manuscript]

Qi Xu, Miyeon Kim, David Ho, Pawel Lachowicz, Gail Fanucci, and David Cafiso: Membrane Hydrocarbon Thickness Modulates the Dynamics of a Membrane Transport Protein
Biophys. J. BioFAST: June 27, 2008. doi:10.1529/biophysj.108.133629 [Abstract] [Accepted Manuscript]

Dianwen Zhang, Hannes Lans, Aufried Lenferink, Wim Vermeulen, and Cees Otto: Quantitative Fluorescence Correlation Spectroscopy reveals a 1000-fold increase in lifetime of protein functionality
Biophys. J. BioFAST: June 27, 2008. doi:10.1529/biophysj.108.133215 [Abstract] [Accepted Manuscript]

Julio Kovacs, Mark Yeager, and Ruben Abagyan: Damped-Dynamics Flexible Fitting
Biophys. J. BioFAST: June 27, 2008. doi:10.1529/biophysj.108.132357 [Abstract] [Accepted Manuscript]

Michèle Koenigsberger, Roger Sauser, Dominique Seppey, Jean-Louis Bény, and Jean-Jacques Meister: Calcium dynamics and vasomotion in arteries subject to isometric, isobaric, and isotonic conditions
Biophys. J. BioFAST: June 27, 2008. doi:10.1529/biophysj.108.131136 [Abstract] [Accepted Manuscript]

20 June 2008

Gianina Panaghie, Kerry Purtell, Kwok-Keung Tai, and Geoffrey W. Abbott: Voltage-dependent C-type inactivation in a constitutively open K⁺ channel
Biophys. J. BioFAST: June 20, 2008. doi:10.1529/biophysj.108.133678 [Abstract] [Accepted Manuscript]

Yoichi Katsumoto, Yoshihito Hayashi, Ikuya Oshige, Shinji Omori, Noriyuki Kishii, Akio Yasuda, and Koji Asami: Dielectric Cytometry with Three-Dimensional Cellular Modeling
Biophys. J. BioFAST: June 20, 2008. doi:10.1529/biophysj.108.132019 [Abstract] [Accepted Manuscript]

Vasilica Nache, Jana Kusch, Christoph Biskup, Eckhard Schulz, Thomas Zimmer, Volker Hagen, and Klaus Benndorf: Thermodynamics of activation gating in olfactory-type cyclic nucleotide-gated (CNGA2) channels
Biophys. J. BioFAST: June 20, 2008. doi:10.1529/biophysj.108.129718 [Abstract] [Accepted Manuscript]

Mark A. Hallen, Jianghai Ho, Christine D. Yankel, and Sharyn A. Endow: Fluorescence Recovery Kinetic Analysis of ${gamma}$ -Tubulin Binding to the Mitotic Spindle
Biophys. J. BioFAST: June 20, 2008. doi:10.1529/biophysj.108.134593 [Abstract] [Accepted Manuscript] [Supplement]

Peter Jonsson, Magnus P Jonsson, Jonas O Tegenfeldt, and Fredrik Hook: A method improving the accuracy of fluorescence recovery after photobleaching analysis
Biophys. J. BioFAST: June 20, 2008. doi:10.1529/biophysj.108.134874 [Abstract] [Accepted Manuscript]

Joshua S Weitz, Yuriy Mileyko, Richard I Joh, and Eberhard O Voit: Collective decision making in bacterial viruses
Biophys. J. BioFAST: June 20, 2008. doi:10.1529/biophysj.108.133694 [Abstract] [Accepted Manuscript]

Mathias Grote, Enrica Bordignon, Yevhen Polyhach, Gunnar Jeschke, Heinz-Jürgen Steinhoff, and Erwin Schneider: A comparative EPR study of the nucleotide-binding domains' catalytic cycle in the assembled maltose ABC-importer
Biophys. J. BioFAST: June 20, 2008. doi:10.1529/biophysj.108.132456 [Abstract] [Accepted Manuscript]

Hao Wang, Jason de Joannis, Yong Jiang, Jeffrey C. Gaulding, Birgit Albrecht, Fuchang Yin, Kunal Khanna, and James T. Kindt: Bilayer edge and curvature effects on partitioning of lipids by tail length: atomistic simulations
Biophys. J. BioFAST: June 20, 2008. doi:10.1529/biophysj.108.131409 [Abstract] [Accepted Manuscript] [Supplement]

Andras Szabo, Elod Mehes, Edina Kosa, and Andras Czirok: Multicellular sprouting in vitro
Biophys. J. BioFAST: June 20, 2008. doi:10.1529/biophysj.108.129668 [Abstract] [Accepted Manuscript] [Supplement]

Richard James Law, Keith Munson, George Sachs, and Felice Chu Lightstone: An Ion Gating Mechanism of the Gastric H,K-ATPase Based on Molecular Dynamics Simulations
Biophys. J. BioFAST: June 20, 2008. doi:10.1529/biophysj.107.128025 [Abstract] [Accepted Manuscript]

Joanna I. Sulkowska and Marek Cieplak: Selection of optimal variants of Go-like models of proteins through studies of stretching
Biophys. J. BioFAST: June 20, 2008. doi:10.1529/biophysj.107.127233 [Abstract] [Accepted Manuscript]

13 June 2008

Gintaras Valincius, Frank Heinrich, Rima Budvytyte, David J. Vanderah, Duncan J. McGillivray, Yuri Sokolov, James E. Hall, and Mathias Lösche: Soluble amyloid ${beta}$ oligomers affect dielectric membrane properties by bilayer insertion and domain formation: Implications for cell toxicity
Biophys. J. BioFAST: June 13, 2008. doi:10.1529/biophysj.108.130997 [Abstract] [Accepted Manuscript] [Supplement]

Willy Supatto, Scott E Fraser, and Julien Vermot: An All-Optical Approach for Probing Microscopic Flows in Living Embryos
Biophys. J. BioFAST: June 13, 2008. doi:10.1529/biophysj.108.137786 [Abstract] [Accepted Manuscript] [Supplement]

Aprotim Mazumder, T Roopa, Aakash Basu, L Mahadevan, and G.V. Shivashankar: Dynamics of chromatin decondensation reveals the structural integrity of a mechanically prestressed nucleus
Biophys. J. BioFAST: June 13, 2008. doi:10.1529/biophysj.108.132274 [Abstract] [Accepted Manuscript] [Supplement]

Fang Jie, Tomoyo Sakata, Gerard Marriott, and Kuni H. Iwasa: Probing conformational changes of prestin with thiol-reactive optical switches
Biophys. J. BioFAST: June 13, 2008. doi:10.1529/biophysj.108.132878 [Abstract] [Accepted Manuscript]

Courtney L. Lopreore, Thomas M. Bartol, Jay S. Coggan, Daniel X. Keller, Gina E. Sosinsky, Mark H. Ellisman, and Terrence J. Sejnowski: Computational modeling of 3D electrodiffusion in biological systems: Application to the node of Ranvier
Biophys. J. BioFAST: June 13, 2008. doi:10.1529/biophysj.108.132167 [Abstract] [Accepted Manuscript]

P. Muthu, Nils Calander, Ignacy Gryczynski, Zygmunt Gryczynski, John M Talent, Tatiana Shtoyko, Irina Akopova, and Julian Borejdo: Monolayers of Silver Nanoparticles Decrease Photobleaching: Application to Muscle Myofibrils
Biophys. J. BioFAST: June 13, 2008. doi:10.1529/biophysj.108.130799 [Abstract] [Accepted Manuscript]

R. E. Lee DeVille and Eric Vanden-Eijnden: Regular gaits and optimal velocities for motor proteins
Biophys. J. BioFAST: June 13, 2008. doi:10.1529/biophysj.108.130674 [Abstract] [Accepted Manuscript]

Hiroshi Nakagawa, Yasumasa Joti, Akio Kitao, and Mikio Kataoka: Hydration affects both harmonic and anharmonic nature of protein dynamics
Biophys. J. BioFAST: June 13, 2008. doi:10.1529/biophysj.107.128546 [Abstract] [Accepted Manuscript]

6 June 2008

Gorazd Pucihar, Tadej Kotnik, Damijan Miklavic, and Justin Teissie: Kinetics of transmembrane transport of small molecules into electropermeabilized cells
Biophys. J. BioFAST: June 6, 2008. doi:10.1529/biophysj.108.135541 [Abstract] [Accepted Manuscript]

Dragomir N. Ganchev, Nathan J. Cobb, Krystyna Surewicz, and Witold K. Surewicz: Nanomechanical Properties of Human Prion Protein Amyloid as Probed by Force Spectroscopy
Biophys. J. BioFAST: June 6, 2008. doi:10.1529/biophysj.108.133108 [Abstract] [Accepted Manuscript]

Sergi Padilla-Parra, Nicolas Audugé, Maite Coppey-Moisan, and Marc Tramier: Quantitative FRET analysis by fast acquisition time domain FLIM at high spatial resolution in living cells
Biophys. J. BioFAST: June 6, 2008. doi:10.1529/biophysj.108.131276 [Abstract] [Accepted Manuscript]

Lai-Hua Xie, Daisuke Sato, Alan Garfinkel, Zhilin Qu, and James N. Weiss: Intracellular Ca Alternans: Coordinated Regulation by Sarcoplasmic Reticulum Release, Uptake and Leak
Biophys. J. BioFAST: June 6, 2008. doi:10.1529/biophysj.108.130955 [Abstract] [Accepted Manuscript]

Yi Y. Zuo, Seyed M. Tadayyon, Eleonora Keating, Lin Zhao, Ruud Veldhuizen, Nils O. Petersen, Matthias Walter Amrein, and Fred Possmayer: Atomic force microscopy studies of functional and dysfunctional pulmonary surfactant films. II. Albumin-inhibited pulmonary surfactant films and the effect of SP-A
Biophys. J. BioFAST: June 6, 2008. doi:10.1529/biophysj.108.130732 [Abstract] [Accepted Manuscript]

Jason E Shoemaker and Francis J Doyle III: Identifying Fragilities in Biochemical Networks: Robust Performance Analysis of Fas Signaling-Induced Apoptosis
Biophys. J. BioFAST: June 6, 2008. doi:10.1529/biophysj.107.123398 [Abstract] [Accepted Manuscript]

Natalia A Koubassova, Sergey Y Bershitsky, Michael A Ferenczi, and Andrey K Tsaturyan: Direct Modeling of X-Ray Diffraction Pattern from Contracting Skeletal Muscle
Biophys. J. BioFAST: June 6, 2008. doi:10.1529/biophysj.107.120832 [Abstract] [Accepted Manuscript]

30 May 2008

Genevieve Dupont, Aurelie Abou-Lovergne, and Laurent Combettes: Stochastic aspects of oscillatory Ca²⁺ dynamics in hepatocytes
Biophys. J. BioFAST: May 30, 2008. doi:10.1529/biophysj.108.133777 [Abstract] [Accepted Manuscript]

M. Hamsa Priya, Jindal K. Shah, Dilip Asthagiri, and Michael E. Paulaitis: Distinguishing Thermodynamic and Kinetic Views of the Preferential Hydration of Protein Surfaces
Biophys. J. BioFAST: May 30, 2008. doi:10.1529/biophysj.108.133553 [Abstract] [Accepted Manuscript]

Gregg Lois, Jerzy Blawzdziewicz, and Corey S O'Hern: Reliable protein folding on complex energy landscapes: the free energy reaction path
Biophys. J. BioFAST: May 30, 2008. doi:10.1529/biophysj.108.133132 [Abstract] [Accepted Manuscript] [Supplement]

Danielle Chandler, Jen Hsin, Christopher B. Harrison, James Gumbart, and Klaus Schulten: Intrinsic Curvature Properties of Photosynthetic Proteins in Chromatophores
Biophys. J. BioFAST: May 30, 2008. doi:10.1529/biophysj.108.132852 [Abstract] [Accepted Manuscript] [Supplement]

Anton Arkhipov, Ying Yin, and Klaus Schulten: Four-scale description of membrane sculpting by BAR domains
Biophys. J. BioFAST: May 30, 2008. doi:10.1529/biophysj.108.132563 [Abstract] [Accepted Manuscript] [Supplement]

Allison N Dickey and Roland Faller: Examining the Contributions of Lipid Shape and Headgroup Charge on Bilayer Behavior
Biophys. J. BioFAST: May 30, 2008. doi:10.1529/biophysj.107.128074 [Abstract] [Accepted Manuscript]

Ben Corry and Dylan Jayatilaka: Simulation of structure, orientation and energy transfer between AlexaFluor molecules attached to MscL
Biophys. J. BioFAST: May 30, 2008. doi:10.1529/biophysj.107.126243 [Abstract] [Accepted Manuscript]

Simon Jungbauer, Huajian Gao, Joachim P. Spatz, and Ralf Kemkemer: Two Characteristic Regimes in Frequency Dependent Dynamic Reorientation of Fibroblasts on Cyclically Stretched Substrates
Biophys. J. BioFAST: May 30, 2008. doi:10.1529/biophysj.107.128611 [Abstract] [Accepted Manuscript] [Supplement]

Francesco Miceli, Maria Virginia Soldovieri, Ciria Carolina Hernandez, Mark Steven Shapiro, Lucio Annunziato, and Maurizio Taglialatela: GATING CONSEQUENCES OF CHARGE NEUTRALIZATION OF ARGININE RESIDUES IN THE S₄ DOMAIN OF K_v7.2, AN EPILEPSY-LINKED K⁺ CHANNEL SUBUNIT
Biophys. J. BioFAST: May 30, 2008. doi:10.1529/biophysj.107.128371 [Abstract] [Accepted Manuscript]

Sébastien Buchoux, Joséphine Lai-Ke-Him, Marie Garnier, Pascale Tsan, Françoise Besson, Alain Brisson, and Erick J. Dufourc: SURFACTIN-TRIGGERED SMALL VESICLE FORMATION OF NEGATIVELY CHARGED MEMBRANES. A NOVEL MEMBRANE-LYSIS MECHANISM
Biophys. J. BioFAST: May 30, 2008. doi:10.1529/biophysj.107.128322 [Abstract] [Accepted Manuscript]

Dirk Gillespie and Dezso Boda: The anomalous mole fraction effect in calcium channels: A measure of preferential selectivity
Biophys. J. BioFAST: May 30, 2008. doi:10.1529/biophysj.107.127977 [Abstract] [Accepted Manuscript]

Harianto Tjong and Huan-Xiang Zhou: Prediction of Protein Solubility from Calculation of Transfer Free Energy
Biophys. J. BioFAST: May 30, 2008. doi:10.1529/biophysj.107.127746 [Abstract] [Accepted Manuscript]

Yi-der Chen, Shaokun Wang, and Arthur Sherman: Identifying the targets of the amplifying pathway for insulin secretion in pancreatic beta cells by kinetic modeling of granule exocytosis
Biophys. J. BioFAST: May 30, 2008. doi:10.1529/biophysj.107.124990 [Abstract] [Accepted Manuscript]

Jianwen Wendy Gu, Werner Hemmert, Dennis M Freeman, and Alexander J Aranyosi: Frequency-Dependent Shear Impedance Of The Tectorial Membrane
Biophys. J. BioFAST: May 30, 2008. doi:10.1529/biophysj.107.124727 [Abstract] [Accepted Manuscript] [Supplement]

Norbert Kucerka, Jason D. Perlmutter, Jianjun Pan, Stephanie Tristram-Nagle, John Katsaras, and Jonathan N. Sachs: The effect of cholesterol on short- and long-chain monounsaturated lipid bilayers as determined by molecular dynamics simulations and x-ray scattering
Biophys. J. BioFAST: May 30, 2008. doi:10.1529/biophysj.107.122465 [Abstract] [Accepted Manuscript] [Supplement]

Urszula Golebiewska and Suzanne Scarlata: G ${alpha}$ q Binds Two Effectors Separately in Cells: Evidence for Pre-determined Signaling Pathways
Biophys. J. BioFAST: May 30, 2008. doi:10.1529/biophysj.108.129353 [Abstract] [Accepted Manuscript]

Yeshitila Gebremichael, Jhih-Wei Chu, and Gregory A. Voth: Intrinsic Bending and Structural Rearrangement of Tubulin Dimer: Molecular Dynamics Simulations and Coarse-grained Analysis
Biophys. J. BioFAST: May 30, 2008. doi:10.1529/biophysj.108.129072 [Abstract] [Accepted Manuscript] [Supplement]

Nipa A. Mody and Michael R. King: Platelet Adhesive Dynamics II. High Shear-Induced Transient Aggregation via GPIb ${alpha}$ -vWF-GPIb ${alpha}$ Bridging
Biophys. J. BioFAST: May 30, 2008. doi:10.1529/biophysj.107.128520 [Abstract] [Accepted Manuscript]

Nipa A. Mody and Michael R. King: Platelet Adhesive Dynamics I. Characterization of Platelet Hydrodynamic Collisions and Wall Effects
Biophys. J. BioFAST: May 30, 2008. doi:10.1529/biophysj.107.127670 [Abstract] [Accepted Manuscript]

Irene Iscla, Robin Wray, and Paul Blount: On the Structure of the N-terminal of the MscL Channel: Helical Bundle or Membrane Interface
Biophys. J. BioFAST: May 30, 2008. doi:10.1529/biophysj.107.127423 [Abstract] [Accepted Manuscript] [Supplement]

Clark A Miller and Daniel A Beard: The Effects of Reversibility and Noise on Stochastic Phosphorylation Cycles and Cascades
Biophys. J. BioFAST: May 30, 2008. doi:10.1529/biophysj.107.126185 [Abstract] [Accepted Manuscript]

Sergei P Balashov, Eleonora S Imasheva, Jennifer M. Wang, and Janos K Lanyi: Excitation energy-transfer and the relative orientation of retinal and carotenoid in xanthorhodopsin
Biophys. J. BioFAST: May 30, 2008. doi:10.1529/biophysj.108.132175 [Abstract] [Accepted Manuscript]

Karen Sabatini, Juha-Pekka Mattila, and Paavo K. Kinnunen: Interfacial Behavior of Cholesterol, Ergosterol, and Lanosterol in Mixtures with DPPC and DMPC
Biophys. J. BioFAST: May 30, 2008. doi:10.1529/biophysj.108.132076 [Abstract] [Accepted Manuscript]

William J. Galush, Jeffrey A. Nye, and Jay T. Groves: Quantitative fluorescence microscopy using supported lipid bilayer standards
Biophys. J. BioFAST: May 30, 2008. doi:10.1529/biophysj.108.131540 [Abstract] [Accepted Manuscript] [Supplement]

Atsushi Matsumoto, Tetsuji Kamata, Junichi Takagi, Kenji Iwasaki, and Kei Yura: Key interactions in integrin ectodomain responsible for global conformational change detected by elastic network normal mode analysis
Biophys. J. BioFAST: May 30, 2008. doi:10.1529/biophysj.108.131045 [Abstract] [Accepted Manuscript]

Guillem Portella, Jochen S. Hub, Martin S. Vesper, and Bert L. de Groot: "Not only enthalpy: large entropy contribution to ion permeation barriers in single-file channels"
Biophys. J. BioFAST: May 30, 2008. doi:10.1529/biophysj.108.130609 [Abstract] [Accepted Manuscript]

Mark Stuart Miller, Panagiotis Lekkas, Joan M Braddock, Gerrie P Farman, Bryan A Ballif, Thomas C Irving, David W Maughan, and Jim O Vigoreaux: Aging enhances indirect flight muscle fiber performance yet decreases flight ability in Drosophila
Biophys. J. BioFAST: May 30, 2008. doi:10.1529/biophysj.108.130005 [Abstract] [Accepted Manuscript]

Daniel Sánchez, Nick Johnson, Chao Li, Pavel Novak, Johannes Rheinlaender, Yanjun Zhang, Uma Anand, Praveen Anand, Julia Gorelik, Gregory Frolenkov, Christopher Benham, Max Lab, Victor Ostanin, Tilman E Schäffer, David Klenerman, and Yuri Korchev: Non-contact measurement of the local mechanical properties of living cells using pressure applied via a pipette
Biophys. J. BioFAST: May 30, 2008. doi:10.1529/biophysj.108.129551 [Abstract] [Accepted Manuscript] [Supplement]

Yen Sun, Chang-Chun Lee, Wei-Chin Hung, Fang-Yu Chen, Ming-Tao Lee, and Huey W. Huang: The bound states of amphipathic drugs in lipid bilayers: study of curcumin
Biophys. J. BioFAST: May 30, 2008. doi:10.1529/biophysj.108.133736 [Abstract] [Accepted Manuscript]

Zhijian Huang and Emad Tajkhorshid: Dynamics of the Extracellular Gate and Ion-Substrate Coupling in the Glutamate Transporter
Biophys. J. BioFAST: May 30, 2008. doi:10.1529/biophysj.108.133421 [Abstract] [Accepted Manuscript]

Heiko Enderling, Nelson R Alexander, Emily S Clark, Kevin Branch, Lourdes Estrada, Cornelia Crooke, Jerome Jourquin, Nichole A Lobdell, Muhammad H Zaman, Scott A Guelcher, Alexander Robertson Allan Anderson, and Alissa M Weaver: Dependence of invadopodia function on collagen fiber spacing and crosslinking: computational modeling and experimental evidence
Biophys. J. BioFAST: May 30, 2008. doi:10.1529/biophysj.108.133199 [Abstract] [Accepted Manuscript] [Supplement]

Felix Campelo, Harvey T McMahon, and Michael M Kozlov: The hydrophobic insertion mechanism of membrane curvature generation by proteins
Biophys. J. BioFAST: May 30, 2008. doi:10.1529/biophysj.108.133173 [Abstract] [Accepted Manuscript]

Anatoly M. Ruvinsky and Ilya A. Vakser: Chasing Funnels on Protein-Protein Energy Landscapes at Different Resolutions
Biophys. J. BioFAST: May 30, 2008. doi:10.1529/biophysj.108.132977 [Abstract] [Accepted Manuscript]

Xin Xu, Carolina Pulido-Carrasco, Pedro Jose de Pablo, Julio Gomez-Herrero, and Arvind Raman: Unmasking Imaging Forces on Soft Biological Samples in Liquids When Using Dynamic Atomic Force Microscopy: Case Study on Viral Capsids
Biophys. J. BioFAST: May 30, 2008. doi:10.1529/biophysj.108.132829 [Abstract] [Accepted Manuscript]

Kelvin J Liu and Tza-Huei Wang: Cylindrical Illumination Confocal Spectroscopy Rectifying the Limitations of Confocal Single Molecule Spectroscopy through 1-D Beam Shaping
Biophys. J. BioFAST: May 30, 2008. doi:10.1529/biophysj.108.132472 [Abstract] [Accepted Manuscript] [Supplement]

23 May 2008

Kohei Eguchi, Mitsumasa Yoda, Tomoki P Terada, and Masaki Sasai: Mechanism of robust circadian oscillation of KaiC phosphorylation in vitro
Biophys. J. BioFAST: May 23, 2008. doi:10.1529/biophysj.107.127555 [Abstract] [Accepted Manuscript] [Supplement]

Vasili Hauryliuk, Sebastian Hansson, and Måns Ehrenberg: Co-factor dependent conformational switching of GTPases
Biophys. J. BioFAST: May 23, 2008. doi:10.1529/biophysj.107.127290 [Abstract] [Accepted Manuscript]

Simone Furini, Carmen Domene, Michele Rossi, Marco Tartagni, and Silvio Cavalcanti: Model-based prediction of the ${alpha}$ -Hemolysin structure in the hexameric state
Biophys. J. BioFAST: May 23, 2008. doi:10.1529/biophysj.107.127019 [Abstract] [Accepted Manuscript]

Kévin CARVALHO, Laurence RAMOS, Christian ROY, and Catherine PICART: Giant unilamellar vesicles containing phosphatidylinositol(4,5)bisphosphate : characterization and functionality
Biophys. J. BioFAST: May 23, 2008. doi:10.1529/biophysj.107.126912 [Abstract] [Accepted Manuscript]

Matt Ferguson, Kondury Prasad, Hacene Boukari, Dan Sackett, Susan Krueger, Eileen Lafer, and Ralph Nossal: Clathrin Triskelia Show Evidence of Molecular Flexibility
Biophys. J. BioFAST: May 23, 2008. doi:10.1529/biophysj.107.126342 [Abstract] [Accepted Manuscript] [Supplement]

Emily Miraldi, Peter J. Thomas, and Laura Romberg: Allosteric Models for Cooperative Polymerization of Linear Polymers
Biophys. J. BioFAST: May 23, 2008. doi:10.1529/biophysj.107.126219 [Abstract] [Accepted Manuscript] [Supplement]

Luigi Catacuzzeno, Bernard Fioretti, and Fabio Franciolini: MODELLING STUDY OF THE EFFECTS OF MEMBRANE SURFACE CHARGE ON CALCIUM MICRODOMAINS AND NEUROTRANSMITTER RELEASE
Biophys. J. BioFAST: May 23, 2008. doi:10.1529/biophysj.107.124909 [Abstract] [Accepted Manuscript] [Supplement]

Suliana Manley, Margaret Ruth Horton, Szymon Leszczynski, and Alice Petry Gast: Sorting of streptavidin protein coats on phase-separating model membranes
Biophys. J. BioFAST: May 23, 2008. doi:10.1529/biophysj.107.124024 [Abstract] [Accepted Manuscript]

Hiroaki Chiba, Natalie Schneider, Satoshi Matsuoka, and Akinori Noma: A simulation study on the activation of cardiac CaMKII ${delta}$ -isoform and its regulation by phosphatases
Biophys. J. BioFAST: May 23, 2008. doi:10.1529/biophysj.107.118505 [Abstract] [Accepted Manuscript]

Shelly Tzlil, Diana Murray, and Avinoam Ben-Shaul: The "Electrostatic-Switch" Mechanism: Monte Carlo Study of MARCKS-Membrane Interaction
Biophys. J. BioFAST: May 23, 2008. doi:10.1529/biophysj.108.132522 [Abstract] [Accepted Manuscript]

Enrico Di Stasio, Stefano Lancellotti, Flora Peyvandi, Roberta Palla, Pier Mannuccio Mannucci, and Raimondo De Cristofaro: MECHANISTIC STUDIES ON ADAMTS-13 CATALYSIS
Biophys. J. BioFAST: May 23, 2008. doi:10.1529/biophysj.108.131532 [Abstract] [Accepted Manuscript] [Supplement]

Sara I Börjesson, Sven Hammarström, and Fredrik Elinder: Lipoelectric modification of ion channel voltage gating by polyunsaturated fatty acids
Biophys. J. BioFAST: May 23, 2008. doi:10.1529/biophysj.108.130757 [Abstract] [Accepted Manuscript]

Igor Novak, Boris Slepchenko, and Alexander Mogilner: Quantitative analysis of G-actin transport in motile cells
Biophys. J. BioFAST: May 23, 2008. doi:10.1529/biophysj.108.130096 [Abstract] [Accepted Manuscript]

Yechun Xu, Jacques Philippe Colletier, Martin Weik, Hualiang Jiang, John Moult, Israel Silman, and Joel L Sussman: Flexibility of Aromatic Residues in the Active-Site Gorge of Acetylcholinesterase: X-ray vs MD
Biophys. J. BioFAST: May 23, 2008. doi:10.1529/biophysj.108.129601 [Abstract] [Accepted Manuscript]

Michael I. Monine and Jason M. Haugh: Signal Transduction at Point-blank Range: Analysis of a Spatial Coupling Mechanism for Pathway Crosstalk
Biophys. J. BioFAST: May 23, 2008. doi:10.1529/biophysj.108.128892 [Abstract] [Accepted Manuscript] [Supplement]

Anna Tourovskaia, Nianzhen Li, and Albert Folch: Localized acetylcholine receptor clustering dynamics in response to microfluidic focal stimulation with agrin
Biophys. J. BioFAST: May 23, 2008. doi:10.1529/biophysj.107.128173 [Abstract] [Accepted Manuscript] [Supplement]

Gernot Guigas and Matthias Weiss: Influence of hydrophobic mismatching on membrane protein diffusion
Biophys. J. BioFAST: May 23, 2008. doi:10.1529/biophysj.108.136069 [Abstract] [Accepted Manuscript]

Fei Ma, Yukihiro Kimura, Xiao-Hui Zhao, Yi-Shi Wu, Peng Wang, Li-Min Fu, Zheng-Yu Wang, and Jian-Ping Zhang: Excitation Dynamics of Two Spectral Forms of the core complexes from Photosynthetic Bacterium Thermochromatium tepidum
Biophys. J. BioFAST: May 23, 2008. doi:10.1529/biophysj.108.133835 [Abstract] [Accepted Manuscript]

Yelena A. Arnautova and Harold A. Scheraga: Use of decoys to optimize an all-atom force field including hydration
Biophys. J. BioFAST: May 23, 2008. doi:10.1529/biophysj.108.133587 [Abstract] [Accepted Manuscript]

Azucena Gonzalez-Horta, David Andreu, Michael R. Morrow, and Jesus Perez-Gil: Effects of palmitoylation on dynamics and phospholipid-bilayer-perturbing properties of the N-terminal segment of pulmonary surfactant protein SP-C, as revealed by ²H-NMR
Biophys. J. BioFAST: May 23, 2008. doi:10.1529/biophysj.108.132845 [Abstract] [Accepted Manuscript]

Norbert Kucerka, John F Nagle, Jonathan N Sachs, Scott Feller, Jeremy Pencer, Andrew J Jackson, and John Katsaras: Lipid bilayer structure determined by the simultaneous analysis of neutron and x-ray scattering data
Biophys. J. BioFAST: May 23, 2008. doi:10.1529/biophysj.108.132662 [Abstract] [Accepted Manuscript] [Supplement]

Vahid Rezania, Olga Azarenko, Mary Ann Jordan, Hannes Bolterauer, Richard F Ludueña, J. Torin Huzil, and Jack A. Tuszynski: Microtubule Assembly of Isotypically Purified Tubulin and Its Mixtures
Biophys. J. BioFAST: May 23, 2008. doi:10.1529/biophysj.108.132233 [Abstract] [Accepted Manuscript]

Takako Takeda and Dmitri Klimov: Temperature induced dissociation of A ${beta}$ monomers from amyloid fibril
Biophys. J. BioFAST: May 23, 2008. doi:10.1529/biophysj.108.131698 [Abstract] [Accepted Manuscript]

16 May 2008

Phil Prior and Bradley J Roth: Calculation of Optical Signal using 3-D Bidomain/Diffusion Model Reveals Distortion of the Transmembrane Potential
Biophys. J. BioFAST: May 16, 2008. doi:10.1529/biophysj.107.127852 [Abstract] [Accepted Manuscript]

Maureen L. Upton, Christopher L. Gilchrist, Farshid Guilak, and Lori A. Setton: Transfer of macro-scale tissue strain to micro-scale cell regions in the deformed meniscus
Biophys. J. BioFAST: May 16, 2008. doi:10.1529/biophysj.107.126938 [Abstract] [Accepted Manuscript]

George S. B. Williams, Marco A Huertas, Eric A Sobie, M. Saleet Jafri, and Gregory D. Smith: Moment Closure for Local Control Models of Calcium-Induced Calcium Release in Cardiac Myocytes
Biophys. J. BioFAST: May 16, 2008. doi:10.1529/biophysj.107.125948 [Abstract] [Accepted Manuscript]

Frédérick Jean-Marie de Meyer, Maddalena Venturoli, and Berend Smit: Molecular simulations of lipid mediated protein-protein interactions
Biophys. J. BioFAST: May 16, 2008. doi:10.1529/biophysj.107.124164 [Abstract] [Accepted Manuscript]

Giuseppe Nicosia and Giovanni Stracquadanio: Generalized Pattern Search Algorithm for Peptide Structure Prediction
Biophys. J. BioFAST: May 16, 2008. doi:10.1529/biophysj.107.124016 [Abstract] [Accepted Manuscript]

Jianrong Wu and Keith M. Berland: Propagators and time-dependent diffusion coefficients for anomalous diffusion
Biophys. J. BioFAST: May 16, 2008. doi:10.1529/biophysj.107.121608 [Abstract] [Accepted Manuscript]

Ingrid E. Chesnick, Jeffrey T. Mason, Anthony A. Giuseppetti, Naomi Eidelman, and Kimberlee Potter: Magnetic Resonance Microscopy of Collagen Mineralization
Biophys. J. BioFAST: May 16, 2008. doi:10.1529/biophysj.107.120923 [Abstract] [Accepted Manuscript]

Ellen Krasik, Kelly E. Caputo, and Daniel A. Hammer: Adhesive Dynamics Simulation of Neutrophil Arrest with Stochastic Activation
Biophys. J. BioFAST: May 16, 2008. doi:10.1529/biophysj.107.119677 [Abstract] [Accepted Manuscript]

Agusti Emperador, Oliver Carrillo, Manuel Rueda, and Modesto Orozco: EXPLORING THE SUITABILITY OF COARSE-GRAINED TECHNIQUES FOR THE REPRESENTATION OF PROTEIN DYNAMICS
Biophys. J. BioFAST: May 16, 2008. doi:10.1529/biophysj.107.119115 [Abstract] [Accepted Manuscript] [Supplement]

Eleonora Savio-Galimberti, Joy Frank, Masashi Inoue, Joshua I. Goldhaber, Mark B. Cannell, John H. Bridge, and Frank B. Sachse: Novel features of the rabbit transverse tubular system revealed by quantitative analysis of three-dimensional reconstructions from confocal images
Biophys. J. BioFAST: May 16, 2008. doi:10.1529/biophysj.108.130617 [Abstract] [Accepted Manuscript] [Supplement]

Christopher B. Wolf and Mohammad R. K. Mofrad: On the Octagonal Structure of the Nuclear Pore Complex: Insights from Coarse-Grained Models
Biophys. J. BioFAST: May 16, 2008. doi:10.1529/biophysj.108.130336 [Abstract] [Accepted Manuscript]

Sherry-Ann Brown, Frank Morgan, James Watras, and Leslie M. Loew: Analysis of Phosphatidylinositol-4,5-bisphosphate Signaling in Cerebellar Purkinje Spines
Biophys. J. BioFAST: May 16, 2008. doi:10.1529/biophysj.108.130195 [Abstract] [Accepted Manuscript] [Supplement]

Seung Yup Lee and Jeffrey Skolnick: Benchmarking of TASSER_2.0: An improved protein structure prediction algorithm with more accurate predicted contact restraints
Biophys. J. BioFAST: May 16, 2008. doi:10.1529/biophysj.108.129759 [Abstract] [Accepted Manuscript] [Supplement]

Stephanie R Taylor, Francis J Doyle III, and Linda R Petzold: Oscillator Model Reduction Preserving the Phase Response: Application to the Circadian Clock
Biophys. J. BioFAST: May 16, 2008. doi:10.1529/biophysj.107.128678 [Abstract] [Accepted Manuscript] [Supplement]

Nurit Even-Tzur, Yoel Kloog, Michael Wolf, and David Elad: Mucus Secretion and Cytoskeletal Modifications in Cultured Nasal Epithelial Cells Exposed to Wall Shear Stresses
Biophys. J. BioFAST: May 16, 2008. doi:10.1529/biophysj.107.127142 [Abstract] [Accepted Manuscript]

Ágnes Szabó, Gábor Horváth, János Szöllosi, and Peter Nagy: Quantitative characterization of the large-scale association of ErbB1 and ErbB2 by flow cytometric homo-FRET measurements
Biophys. J. BioFAST: May 16, 2008. doi:10.1529/biophysj.108.133371 [Abstract] [Accepted Manuscript]

Nickolay Zhadin, Miriam Gulotta, and Robert Callender: Probing the Role of Dynamics in Hydride Transfer Catalyzed by Lactate Dehydrogenase
Biophys. J. BioFAST: May 16, 2008. doi:10.1529/biophysj.108.132464 [Abstract] [Accepted Manuscript] [Supplement]

Mattia Falconi, Francesco Oteri, Tommaso Eliseo, Daniel O. Cicero, and Alessandro Desideri: MD Simulations of Papillomavirus DNA-E2 Protein Complexes Hints at a Protein Structural Code for DNA Deformation
Biophys. J. BioFAST: May 16, 2008. doi:10.1529/biophysj.108.130849 [Abstract] [Accepted Manuscript] [Supplement]

Manami Nishizawa and Kazuhisa Nishizawa: Molecular Dynamics Simulation of Kv channel Voltage Sensor Helix in a Lipid Membrane with Applied Electric Field
Biophys. J. BioFAST: May 16, 2008. doi:10.1529/biophysj.108.130658 [Abstract] [Accepted Manuscript] [Supplement]

9 May 2008

Santhosh Palani and Casim A. Sarkar: Positive Receptor Feedback during Lineage Commitment Can Generate Ultrasensitivity to Ligand and Confer Robustness to a Bistable Switch
Biophys. J. BioFAST: May 9, 2008. doi:10.1529/biophysj.107.120600 [Abstract] [Accepted Manuscript] [Supplement]

Chze-Ling Wee, Kia Balali-Mood, David Gavaghan, and Mark S.P. Sansom: The Interaction of Phospholipase A2 with a Phospholipid Bilayer: Coarse-Grained Molecular Dynamics Simulations
Biophys. J. BioFAST: May 9, 2008. doi:10.1529/biophysj.107.123190 [Abstract] [Accepted Manuscript]

Philip D Blood, Richard D. Swenson, and Gregory A. Voth: Factors Influencing Local Membrane Curvature Induction by N-BAR Domains as Revealed by Molecular Dynamics Simulations
Biophys. J. BioFAST: May 9, 2008. doi:10.1529/biophysj.107.121160 [Abstract] [Accepted Manuscript] [Supplement]

Charles Wolgemuth: Collective swimming and the dynamics of bacterial turbulence
Biophys. J. BioFAST: May 9, 2008. doi:10.1529/biophysj.107.118257