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		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.
		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
		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.
		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.
		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
		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.
		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.
		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
		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
		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
		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
		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
		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
		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.
		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.
		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.
		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
		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
		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
		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.
		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
		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
		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.
		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
		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

	All
		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.
		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
		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.
		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.
		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
		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.
		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.
		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
		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
		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
		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
		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
		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
		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.
		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.
		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.
		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
		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
		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
		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.
		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
		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
		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.
		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
		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