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	1. 248 Accesses	Methodology article Improving accuracy of cell and chromophore concentration measurements using optical density John A Myers, Brandon S Curtis, Wayne R Curtis BMC Biophysics 2013, 6:4 (22 April 2013) Abstract \| Provisional PDF
	2. 233 Accesses	Research article A biophysical model for transcription factories Ana Z Canals-Hamann, Ricardo das Neves, Joyce E Reittie, Carlos Iñiguez, Shamit Soneji, Tariq Enver, Veronica J Buckle, Francisco J Iborra BMC Biophysics 2013, 6:2 (9 February 2013) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Chromatin can act as a multi-block copolymer with active-inactive monomers that spontaneously self-organize to form microdomains, demonstrating that geometrical constraints alone can potentially yield an organized transcription factory.
	3. 161 Accesses	Research article Stochastic dynamics of virus capsid formation: direct versus hierarchical self-assembly Johanna E Baschek, Heinrich C R Klein, Ulrich S Schwarz BMC Biophysics 2012, 5:22 (17 December 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Computational modeling of the way that viruses are able to self-assemble their protein capsid coats suggests that for complex viruses with more stable bonds, a piecemeal hierarchical assembly process is most likely.
	4. 156 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.
	5. 127 Accesses	Research article Molecular dynamics simulations on aqueous two-phase systems - Single PEG-molecules in solution Stefan A Oelmeier, Florian Dismer, Jürgen Hubbuch BMC Biophysics 2012, 5:14 (8 August 2012) Abstract \| Full text \| PDF \| PubMed
	6. 123 Accesses	Review Diffusion in crowded biological environments: applications of Brownian dynamics Maciej Długosz, Joanna Trylska BMC Biophysics 2011, 4:3 (2 March 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Maciej Dlugosz and Joanna Trylska review recent developments in particle-based Brownian dynamics algorithms and their application to model diffusive transport in crowded systems, which are proving useful in improving our understanding of metabolism, transport and signaling.
	7. 120 Accesses	Editorial Diffusion and association processes in biological systems: theory, computation and experiment Paolo Mereghetti, Daria Kokh, J Andrew McCammon, Rebecca C Wade BMC Biophysics 2011, 4:2 (2 March 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Rebecca Wade and colleagues provide a snapshot of research from a thematic series of articles on biological diffusion and Brownian dynamics simulations, which highlights a vibrant research field with growing synergy between experimental and computational studies.
	8. 121 Accesses	Research article Molecular dynamics and mutational analysis of the catalytic and translocation cycle of RNA polymerase Maria L Kireeva, Kristopher Opron, Steve A Seibold, Céline Domecq, Robert I Cukier, Benoit Coulombe, Mikhail Kashlev, Zachary F Burton BMC Biophysics 2012, 5:11 (7 June 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The catalytic confirmation of the RNA polymerase ternary elongation complex (TEC) has a closed trigger loop with a relatively dehydrated active site, in contrast to the inactive open confirmation of the trigger loop which supports translocation.
	9. 120 Accesses	Research article Pulling chromatin apart: Unstacking or Unwrapping? Jean Marc Victor, Jordanka Zlatanova, Maria Barbi, Julien Mozziconacci BMC Biophysics 2012, 5:21 (27 November 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A zig-zag model of chromatin fiber morphology is able to quantitatively explain the mechanical properties of chromatin under external stress, and provides an alternative explanation to the widespread solenoid model interpretation.
	10. 112 Accesses	Correspondence Can dietary fibre help provide safer food products for sufferers of gluten intolerance? A well-established biophysical probe may help towards providing an answer M Kök, Richard Gillis, Shirley Ang, David Lafond, Arthur S Tatham, Gary Adams, Stephen E Harding BMC Biophysics 2012, 5:10 (17 May 2012) Abstract \| Full text \| PDF \| PubMed \| 1 comment \| Editor’s summary Stephen Harding and colleagues speculate on the role that the ultracentrifuge assay procedure could play in detecting non-toxic biopolymers capable of sequestering ingested gluten peptides, with the eventual aim of reducing gluten intolerance symptoms.
	11. 105 Accesses	Software DelPhi: a comprehensive suite for DelPhi software and associated resources Lin Li, Chuan Li, Subhra Sarkar, Jie Zhang, Shawn Witham, Zhe Zhang, Lin Wang, Nicholas Smith, Marharyta Petukh, Emil Alexov BMC Biophysics 2012, 5:9 (14 May 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| Editor’s summary The DelPhi package is a comprehensive and user-friendly suite of tools for modelling electrostatic potentials in macromolecules using the Poisson-Boltzmann Equation, and is now enriched with additional features for greater usability.
	12. 104 Accesses	Research article Hierarchical super-structure identified by polarized light microscopy, electron microscopy and nanoindentation: Implications for the limits of biological control over the growth mode of abalone sea shells Andreas S Schneider, Birgit Heiland, Nicolas J Peter, Christina Guth, Eduard Arzt, Ingrid M Weiss BMC Biophysics 2012, 5:19 (12 September 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The hierarchical super-structure of abalone mollusc shells can be revealed by conventional light microscopy methods, opening the potential to study shell growth mechanisms in vivo at high resolution.
	13. 94 Accesses	Review Hierarchies in eukaryotic genome organization: Insights from polymer theory and simulations Balaji VS Iyer, Martin Kenward, Gaurav Arya BMC Biophysics 2011, 4:8 (15 April 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Gaurav Arya and colleagues review results from state-of-the-art microscopy and chromosome conformation capture techniques that are being used to understand the three dimensional structure of the genome and the physical principles governing its folding.
	14. 89 Accesses	Methodology article Detection and differentiation of bacterial spores in a mineral matrix by Fourier transform infrared spectroscopy (FTIR) and chemometrical data treatment Andrea Brandes Ammann, Helmut Brandl BMC Biophysics 2011, 4:14 (14 July 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Fourier transform infrared spectroscopy (FTIR) combined with chemometrical data treatment enables differentiation of Bacillus spores down to the species level in pure culture and in the presence of clay mineral matrix such as bentonite.
	15. 86 Accesses	Research article Wavelet-based protocols for ion channel electrophysiology Armin Kargol BMC Biophysics 2013, 6:3 (14 March 2013) Abstract \| Full text \| PDF \| ePUB \| PubMed
	16. 81 Accesses	Research article Diffusion of hydrophobin proteins in solution and interactions with a graphite surface Paolo Mereghetti, Rebecca C Wade BMC Biophysics 2011, 4:9 (21 April 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Hydrophobins, the most powerful surface-active proteins known, exist in solution as a mixture of monomers in equilibrium with different types of oligomers but in contact with a graphite layer they form tetramers and accumulate close to the hydrophobic surface.
	17. 77 Accesses	Research article Protein dynamics at Eph receptor-ligand interfaces as revealed by crystallography, NMR and MD simulations Haina Qin, Liangzhong Lim, Jianxing Song BMC Biophysics 2012, 5:2 (25 January 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central \| F1000 Biology \| Editor’s summary Structural determination of the EphA4 ligand binding domain provides the first experimental and computational evidence that intrinsic dynamics are most likely to be responsible for the observed high conformational diversity that mediates binding affinity and specificity.
	18. 74 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.
	19. 75 Accesses	Research article Many-particle Brownian and Langevin Dynamics Simulations with the Brownmove package Tihamér Geyer BMC Biophysics 2011, 4:7 (13 April 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A new "brownmove" simulation package designed for coarse-grained many-particle simulations of biologically relevant diffusion and transport processes combines Brownian and Langevin Dynamics propagation with fast hydrodynamics, a flexible protein model and interfaces for "open" simulation settings.
	20. 71 Accesses	Research article An upper limit for macromolecular crowding effects Andrew C Miklos, Conggang Li, Courtney D Sorrell, L Andrew Lyon, Gary J Pielak BMC Biophysics 2011, 4:13 (31 May 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Synthetic microgels that interact weakly with proteins do not strongly influence protein dynamics or stability because these large microgels constitute an upper size limit on crowding effects.
	21. 72 Accesses	Research article Introduction of non-linear elasticity models for characterization of shape and deformation statistics: application to contractility assessment of isolated adult cardiocytes Carlos Bazan, Trevor Hawkins, David Torres-Barba, Peter Blomgren, Paul Paolini BMC Biophysics 2011, 4:17 (22 August 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A novel image analysis approach to assess cardiocyte contractility successfully captures the full extent of contractile behavior by incorporating biomechanical properties, energy conservation principles and information content measures.
	22. 71 Accesses	Methodology article Time-resolved force distribution analysis Bogdan I Costescu, Frauke Gräter BMC Biophysics 2013, 6:5 (1 May 2013) Abstract \| Provisional PDF
	23. 69 Accesses	Research article Flexibility of EF-hand motifs: structural and thermodynamic studies of Calcium Binding Protein-1 from Entamoeba histolytica with Pb²⁺, Ba²⁺, and Sr²⁺ Shivesh Kumar, Ejaz Ahmad, Sanjeev Kumar, Rizwan Khan, Samudrala Gourinath BMC Biophysics 2012, 5:15 (20 August 2012) Abstract \| Full text \| PDF \| PubMed
	24. 66 Accesses	Research article Clustering of HIV-1 Subtypes Based on gp120 V3 Loop electrostatic properties Aliana López de Victoria, Chris A Kieslich, Apostolos K Rizos, Elias Krambovitis, Dimitrios Morikis BMC Biophysics 2012, 5:3 (7 February 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The spatial distributions of electrostatic potentials and charges in the V3 loop of HIV-1 protein gp120 may be responsible for both long- and short-range interactions with co-receptors, ultimately affecting viral entry into cells
	25. 64 Accesses	Research article Lipid recognition propensities of amino acids in membrane proteins from atomic resolution data Mizuki Morita, AVSK Katta, Shandar Ahmad, Takaharu Mori, Yuji Sugita, Kenji Mizuguchi BMC Biophysics 2011, 4:21 (14 December 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Tightly-bound lipid molecules and lipids in the annular shell interact with membrane proteins in a similar manner, largely explained by general lipophilicity, that suggests a common pattern of lipid tail-amino acid interactions
	26. 62 Accesses	Research article Two-photon time-lapse microscopy of BODIPY-cholesterol reveals anomalous sterol diffusion in chinese hamster ovary cells Frederik W Lund, Michael A Lomholt, Lukasz M Solanko, Robert Bittman, Daniel Wüstner BMC Biophysics 2012, 5:20 (18 October 2012) Abstract \| Full text \| PDF \| PubMed
	27. 61 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).
	28. 62 Accesses	Research article Intrinsic thermodynamics of ethoxzolamide inhibitor binding to human carbonic anhydrase XIII Lina Baranauskienė, Daumantas Matulis BMC Biophysics 2012, 5:12 (7 June 2012) Abstract \| Full text \| PDF \| PubMed
	29. 62 Accesses	Commentary Intracellular chemical gradients: morphing principle in bacteria Robert G Endres BMC Biophysics 2012, 5:18 (7 September 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Robert Endres discusses a new study in BMC Biophysics that supports the emerging view that intracellular chemical gradients can exist in bacterial cells, and how these may limit in vitro analyses.
	30. 61 Accesses	Research article Differences in adhesion and protrusion properties correlate with differences in migration speed under EGF stimulation Yue Hou, Sarah Hedberg, Ian C Schneider BMC Biophysics 2012, 5:8 (11 May 2012) Abstract \| Full text \| PDF \| PubMed
	31. 60 Accesses	Research article Fluorescence anisotropy of diphenylhexatriene and its cationic Trimethylamino derivative in liquid dipalmitoylphosphatidylcholine liposomes: opposing responses to isoflurane Steven C Nelson, Steven K Neeley, Eric D Melonakos, John D Bell, David D Busath BMC Biophysics 2012, 5:5 (24 March 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Steady-state anisotropy of two fluorescent probes at different depths in a lipid bilayer reveals a decrease in anisotropy with increasing isoflurane anesthetic concentration, reflecting changes in the lateral pressure profile of the membrane.
	32. 60 Accesses	Research article Arbitrary protein−protein docking targets biologically relevant interfaces Juliette Martin, Richard Lavery BMC Biophysics 2012, 5:7 (6 May 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Docking of target proteins against an arbitrary set of partners generally leads to non-random localization of interaction interfaces as the false complexes favor residues from true interaction sites, allowing prediction of biologically relevant protein interfaces
	33. 58 Accesses	Research article Sensing the Heat Stress by Mammalian Cells Jordan Cates, Garrett C Graham, Natalie Omattage, Elizabeth Pavesich, Ian Setliff, Jack Shaw, Caitlin Smith, Ovidiu Lipan BMC Biophysics 2011, 4:16 (11 August 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A new system-level mathematical approach is proposed to model the heat-shock response network in mammalian cells and the key heat-shock transcription factor-1 (HSF) which is transiently activated by elevated temperatures.
	34. 58 Accesses	Research article Brownian dynamics simulation of analytical ultracentrifugation experiments AI Díez, A Ortega, J Garcia de la Tore BMC Biophysics 2011, 4:6 (2 March 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Using Brownian dynamics to simulate the trajectories of the particles could lead to improved and efficient predictions of time-dependent concentration profiles during analytical ultracentrifugation experiments.
	35. 57 Accesses	Research article Effects of spermine NONOate and ATP on the thermal stability of hemoglobin Rasha Bassam, Juergen Hescheler, Ayseguel Temiz-Artmann, Gerhard M Artmann, Ilya Digel BMC Biophysics 2012, 5:16 (28 August 2012) Abstract \| Full text \| PDF \| PubMed
	36. 57 Accesses	Software APM_GUI: analyzing particle movement on the cell membrane and determining confinement Silvia A Menchón, Mauricio G Martín, Carlos G Dotti BMC Biophysics 2012, 5:4 (20 February 2012) Abstract \| Full text \| PDF \| PubMed
	37. 55 Accesses	Research article Spindles and active vortices in a model of confined filament-motor mixtures David A Head, WJ Briels, Gerhard Gompper BMC Biophysics 2011, 4:18 (16 November 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A discrete filament-motor protein model of subcellular microtubule self-assembly in fission yeast spontaneously generates a number of steady states, including spindles, nematics, and asters, highlighting potential mechanisms for self-organisation in filaments
	38. 55 Accesses	Research article Effects of spermine NONOate and ATP on protein aggregation: light scattering evidences Rasha Bassam, Ilya Digel, Juergen Hescheler, Ayseguel Temiz Artmann, Gerhard M Artmann BMC Biophysics 2013, 6:1 (4 January 2013) Abstract \| Full text \| PDF \| PubMed
	39. 54 Accesses	Methodology article A Bayesian method for inferring quantitative information from FRET data Catherine A Lichten, Peter S Swain BMC Biophysics 2011, 4:10 (9 May 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary A new Bayesian algorithm is available for extracting quantitative information on molecular interactions from FRET (Forster resonance energy transfer) data which yields both an estimate of the dissociation constant and the uncertainty associated with that estimate.
	40. 53 Accesses	Research article Mechanism of PhosphoThreonine/Serine Recognition and Specificity for Modular Domains from All-atom Molecular Dynamics Yu-ming M Huang, Chia-en A Chang BMC Biophysics 2011, 4:12 (25 May 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Mechanism of phosphothreonine/serine recognition and specificity is elucidated for three well-known phosphopeptide-binding domains important for signal transduction: BRCT repeats, WW domain and forkhead-associated domain (FHA) with the use of molecular dynamics simulations.
	41. 53 Accesses	Research article Membrane microdomains emergence through non-homogeneous diffusion Hédi A Soula, Antoine Coulon, Guillaume Beslon BMC Biophysics 2012, 5:6 (30 April 2012) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Non-homogeneous diffusion in cell membranes leads to the formation of protein/ lipid enriched microdomains in a model of membrane dynamics, with domains of high viscosity tending to gather a statistically larger proportion of diffusive particles
	42. 52 Accesses	Research article Physical constraints on the establishment of intracellular spatial gradients in bacteria Carolina Tropini, Naveed Rabbani, Kerwyn Huang BMC Biophysics 2012, 5:17 (29 August 2012) Abstract \| Full text \| PDF \| PubMed \| Cited on BioMed Central
	43. 51 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.
	44. 47 Accesses	Research article Thermotropic phase behavior and headgroup interactions of the nonbilayer lipids phosphatidylethanolamine and monogalactosyldiacylglycerol in the dry state Antoaneta V Popova, Dirk K Hincha BMC Biophysics 2011, 4:11 (10 May 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary The thermotropic phase behavior and molecular interactions of the two biologically important non-bilayer lipids, egg phosphatidylethanolamine (EPE) and monogalactosyldiacylglycerol (MGDG) have been comprehensively characterized by Fourier-transform Infrared spectroscopy and Differential Scanning Calorimetry.
	45. 45 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.
	46. 45 Accesses	Research article Characterizing low affinity epibatidine binding to α4β2 nicotinic acetylcholine receptors with ligand depletion and nonspecific binding Alexandra M Person, Gregg B Wells BMC Biophysics 2011, 4:19 (23 November 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Manipulation of maximum ligand and receptor concentrations and intentionally increasing ligand depletion are potentially helpful approaches to study low affinity binding of epibatidine to an independent binding site of alpha4beta2 nicotinic acetylcholine receptor.
	47. 44 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.
	48. 41 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.
	49. 42 Accesses	Research article Probabilistic modeling and analysis of the effects of extra-cellular matrix density on the sizes, shapes, and locations of integrin clusters in adherent cells Erik S Welf, Ulhas P Naik, Babatunde A Ogunnaike BMC Biophysics 2011, 4:15 (9 August 2011) Abstract \| Full text \| PDF \| PubMed \| Editor’s summary Cells can sense the availability of extracellular matrix binding sites and in response they regulate the sizes, shapes, and locations of integrin clusters that mediate cell adhesion to surrounding tissues.
	50. 42 Accesses	Research article A minimal ligand binding pocket within a network of correlated mutations identified by multiple sequence and structural analysis of G protein coupled receptors Subhodeep Moitra, Kalyan C Tirupula, Judith Klein-Seetharaman, Christopher Langmead BMC Biophysics 2012, 5:13 (29 June 2012) Abstract \| Full text \| PDF \| PubMed