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	51. 26 Accesses	Research article On the electrostatic component of protein-protein binding free energy Kemper Talley, Carmen Ng, Michael Shoppell, Petras Kundrotas, Emil Alexov PMC Biophysics 2008, 1:2 (5 November 2008) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary This paper presents a comprehensive statistical analysis of the sensitivity of the electrostatic component of binding free energy (DDGel) with respect with different force fields (Charmm, Amber, and OPLS), different values of the internal dielectric constant, and different presentations of molecular surface (different values of the probe radius).
	52. 21 Accesses	Research article Using default constraints of the spindle assembly checkpoint to estimate the associated chemical rates Khanh Dao Duc, David Holcman BMC Biophysics 2012, 5:1 (19 January 2012) Abstract \| Full text \| PDF \| PubMed
	53. 19 Accesses	Research article Inverse tuning of metal binding affinity and protein stability by altering charged coordination residues in designed calcium binding proteins Anna Maniccia, Wei Yang, Julian A Johnson, Shunyi Li, Harianto Tjong, Huan-Xiang Zhou, Lev A Shaket, Jenny J Yang PMC Biophysics 2009, 2:11 (21 December 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary We report a systematic investigation of the role of local charge number and type of coordination residues in Ca2+ binding and protein stability, and observe a striking tradeoff between Ca2+/Ln3+ affinity and protein stability when the net charge of the coordination residues is varied.
	54. 17 Accesses	Research article ATR-FTIR spectroscopy detects alterations induced by organotin(IV) carboxylates in MCF-7 cells at sub-cytotoxic/-genotoxic concentrations Muhammad S Ahmad, Bushra Mirza, Mukhtiar Hussain, Muhammad Hanif, Saqib Ali, Michael J Walsh, Francis L Martin PMC Biophysics 2008, 1:3 (5 November 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The environmental impact of metal complexes such as organotin(IV) compounds is of increasing concern. This work shows that IR spectra, derived following ATR-FTIR spectroscopy, from organotin-treated MCF-7 cells exhibit molecular alterations following low-dose exposures. This approach highlights the potential applicability of mid-IR spectroscopy to signature toxic effects at sub-lethal concentrations following typical environmental exposures to environmental contaminants.
	55. 17 Accesses	Research article Label-free electrical quantification of the dielectrophoretic response of DNA Anja Henning, Jörg Henkel, Frank F Bier, Ralph Hölzel PMC Biophysics 2008, 1:4 (5 November 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A purely electrical sensing scheme is presented that determines the concentration of macromolecules in solution, in good agreement with dielectrophotoretic studies. The method has been applied to the characterisation of the dielectrophoretic response of DNA without the need for any chemical modifications. Extension of the method down to the single molecule level appears feasible.
	56. 17 Accesses	Research article Assembly dynamics of PML nuclear bodies in living cells Peter Brand, Thorsten Lenser, Peter Hemmerich PMC Biophysics 2010, 3:3 (5 March 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Promyelocytic leukemia nuclear bodies (PML NBs) are involved in the regulation of apoptosis, antiviral responses, the DNA damage response and chromatin structure, but their precise biochemical function in these nuclear pathways is unknown. In this study we determined PML NB assembly dynamics by live cell imaging, combined with mathematical modeling.
	57. 17 Accesses	Research article Geometric constrains for detecting short actin filaments by cryogenic electron tomography Mikhail Kudryashev, Simone Lepper, Wolfgang Baumeister, Marek Cyrklaff, Friedrich Frischknecht PMC Biophysics 2010, 3:6 (5 March 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary Polymerization of actin into filaments can push membranes forming extensions like filopodia or lamellipodia, which are important during processes such as cell motility and phagocytosis. Here, we investigated Plasmodium sporozoites, the motile forms of the malaria parasite that are transmitted by the mosquito, using cryogenic electron tomography.
	58. 17 Accesses	Research article Self-organizing actin waves that simulate phagocytic cup structures Günther Gerisch PMC Biophysics 2010, 3:7 (18 March 2010) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary This report deals with actin waves that are spontaneously generated on the planar, substrate-attached surface of Dictyostelium cells.
	59. 17 Accesses	Research article Probing the folding of mini-protein Beta3s by two-dimensional infrared spectroscopy; simulation study Christopher NJ Marai, Shaul Mukamel, Jin Wang PMC Biophysics 2010, 3:8 (19 March 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary In this study Beta3s was folded by molecular dynamics (MD) simulation and intermediate conformational ensembles were identified. In addition to exploring the folding mechanism the work presented here can be applied in combination with experiment to refine and validate current molecular dynamics force fields.
	60. 16 Accesses	Research article Two-color STED microscopy reveals different degrees of colocalization between hexokinase-I and the three human VDAC isoforms Daniel Neumann, Johanna Bückers, Lars Kastrup, Stefan W Hell, Stefan Jakobs PMC Biophysics 2010, 3:4 (5 March 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The voltage-dependent anion channel (VDAC, also known as mitochondrial porin) is the major transport channel mediating the transport of metabolites, including ATP, across the mitochondrial outer membrane. In this study we show that whereas hVDAC1 and hVDAC2 are localized predominantly within the same distinct domains in the outer membrane, hVDAC3 is mostly uniformly distributed over the surface of the mitochondrion.
	61. 15 Accesses	Research article Simple modeling of FtsZ polymers on flat and curved surfaces: correlation with experimental in vitro observations Alfonso Paez, Pablo Mateos-Gil, Ines Hörger, Jesús Mingorance, Germán Rivas, Miguel Vicente, Marisela Vélez, Pedro Tarazona PMC Biophysics 2009, 2:8 (22 October 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary FtsZ is a GTPase that assembles at midcell into a dynamic ring that constricts the membrane to induce cell division in the majority of bacteria and some organelles. Based on data derived from the measurement of the in vitro polymerization of E coli FtsZ cell division protein, we have formulated a model in which the fine balance between curvature, flexibility and lateral interactions accounts for structural and dynamic properties of the FtsZ polymers observed with AFM.
	62. 15 Accesses	Research article Kinetics of diffusion-controlled enzymatic reactions with charged substrates Benzhuo Lu, J Andrew McCammon PMC Biophysics 2010, 3:1 (18 January 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary We show in this work that through numerical solution of the Poisson-Nernst-Planck equations, diffusion-reaction processes can be studied at a variety of conditions including realistically concentrated solutions, high ionic strength, and certainly with non-equilibrium charge distributions.
	63. 14 Accesses	Research article Resolution of complex fluorescence spectra of lipids and nicotinic acetylcholine receptor by multivariate analysis reveals protein-mediated effects on the receptor's immediate lipid microenvironment Jorge J Wenz, Francisco J Barrantes PMC Biophysics 2008, 1:6 (18 December 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Resolution of complex fluorescence spectra of lipids and nicotinic acetylcholine receptor by multivariate analysis reveals protein-mediated effects on the receptor's immediate microenvironment, rigidifying the surrounding lipid and preferring dioleoylphosphatidic acid over dioleoylphosphatidylcholine.
	64. 12 Accesses	Research article An effective all-atom potential for proteins Anders Irbäck, Simon Mitternacht, Sandipan Mohanty PMC Biophysics 2009, 2:2 (8 April 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary We describe and test an implicit solvent all-atom potential for simulations of protein folding and aggregation. The potential is developed through studies of structural and thermodynamic properties of 17 peptides with diverse secondary structure.
	65. 11 Accesses	Research article Zwanzig-Mori projection operators and EEG dynamics: deriving a simple equation of motion David Hsu, Murielle Hsu PMC Biophysics 2009, 2:6 (13 July 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary This work shows that EEG dynamics obeys a generalized Langevin equation, pointing out that the parameters of this equation represent macroscopic properties, and identifies two variational principles that allow these parameters to be extracted from experimental data.
	66. 10 Accesses	Mini-review The multiple faces of self-assembled lipidic systems Guillaume Tresset PMC Biophysics 2009, 2:3 (17 April 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary From the plasma membrane of archaebacteria to gene delivery, self-assembled lipidic systems have left their mark in cell biology and nanobiotechnology; however, the underlying physics is yet to be fully unraveled.
	67. 10 Accesses	Research article Two-dimensional nanosecond electric field mapping based on cell electropermeabilization Meng-Tse Chen, Chunqi Jiang, P Thomas Vernier, Yu-Hsuan Wu, Martin A Gundersen PMC Biophysics 2009, 2:9 (11 November 2009) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary This paper details a live-cell method for measuring a nanosecond pulsed electric field distribution, providing an operationally meaningful calibration for electrode designs for biological applications and permitting visualization of the relative sensitivities of different cell types to nanoelectropulse stimulation.
	68. 10 Accesses	Research article Live cell flattening — traditional and novel approaches Christian Westendorf, Albert J Bae, Christoph Erlenkamper, Edouard Galland, Carl Franck, Eberhard Bodenschatz, Carsten Beta PMC Biophysics 2010, 3:9 (19 April 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Eukaryotic cell flattening is valuable for improving microscopic observations, ranging from bright field (BF) to total internal reflection fluorescence (TIRF) microscopy. Here, we review the well known agar overlayer protocol and the oil overlay method. In addition, we present more elaborate microfluidics-based techniques that provide us with a greater level of control.
	69. 9 Accesses	Research article The influence of membrane physical properties on microvesicle release in human erythrocytes Laurie J Gonzalez, Elizabeth Gibbons, Rachel W Bailey, Jeremy Fairbourn, Thaothanh Nguyen, Samantha K Smith, Katrina B Best, Jennifer Nelson, Allan M Judd, John D Bell PMC Biophysics 2009, 2:7 (24 August 2009) Abstract \| Full text \| PDF \| PubMed \| 1 comment \| Editor’s summary Exposure of human erythrocytes to elevated intracellular calcium causes fragments of the cell membrane to be shed as microvesicles. This study tested the hypothesis that microvesicle release depends on microscopic membrane physical properties such as lipid order, fluidity, and composition.
	70. 9 Accesses	Problem Tubulohelical membrane arrays: From the initial observation to the elucidation of nanophysical properties and cellular function Siegfried Reipert, Józefa Wesierska-Gadek, Sebastian Wienerroither PMC Biophysics 2010, 3:13 (28 June 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Lipids undergo self-assembly to form ordered nonlamellar, nanoperiodic arrays both in vitro and in vivo. As a starting point for functional studies of these structures we found a connection between tubulohelical membrane arrays and primary cilia.
	71. 8 Accesses	Research article Robustness, dissipations and coherence of the oscillation of circadian clock: potential landscape and flux perspectives Jin Wang, Li Xu, Erkang Wang PMC Biophysics 2008, 1:7 (30 December 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary We have uncovered the underlying potential energy landscape of a simple cyanobacteria biochemical network, and the corresponding flux which is the driving force for the oscillation of the circadian clock. Our approach is quite general and can be applied to other oscillatory cellular networks.
	72. 8 Accesses	Research article Structural and functional implications of p53 missense cancer mutations Yuhong Tan, Ray Luo PMC Biophysics 2009, 2:5 (26 June 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary In this study, the stabilities of all core domain missense mutations are predicted and are used to infer their likely inactivation mechanisms. Our correlation analysis shows that loss of protein-protein contacts may be an alternative cause for p53 inactivation.
	73. 7 Accesses	Research article Stochastic reconstruction of protein structures from effective connectivity profiles Katrin Wolff, Michele Vendruscolo, Markus Porto PMC Biophysics 2008, 1:5 (26 November 2008) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A stochastic approach for reconstructing the native structures of proteins is discussed, which uses knowledge of the "effective connectivity" - a one-dimensional structural profile constructed as a linear combination of the eigenvectors of the contact map of the target structure. It is suggested that the protocol presented here could be combined effectively with current methods for predicting native structures.
	74. 7 Accesses	Research article Amplitude distribution of stochastic oscillations in biochemical networks due to intrinsic noise Moritz Lang, Steffen Waldherr, Frank Allgöwer PMC Biophysics 2009, 2:10 (17 November 2009) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Intrinsic noise is a common phenomenon in biochemical reaction networks and may affect the occurence and amplitude of sustained oscillations in the states of the network. We present a new method to compute the amplitude distribution of the oscillations without the need for long-term stochastic simulations.
	75. 7 Accesses	Research article Nanoscopy of the cellular response to hypoxia by means of fluorescence resonance energy transfer (FRET) and new FRET software Christoph Wotzlaw, Silke Gneuss, Rebecca Konietzny, Joachim Fandrey PMC Biophysics 2010, 3:5 (5 March 2010) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Fluorescence resonance energy transfer (FRET) was established to determine the assembly of the Hypoxia-Inducible-Factor-1 complex and to study the interaction of the alpha-subunit of HIF-1 with O2-sensing hydroxylase. New software was developed to improve the quality and reliability of FRET measurements.