Skip to main content


Computational and theoretical biophysics

This section incorporates all aspects of computational and theoretical biophysics including: theory, modeling, simulation and nanotechnology.

  1. Content type: Research article

    Cellular environments are highly crowded with biological macromolecules resulting in frequent non-specific interactions. While the effect of such crowding on protein structure and dynamics has been studied ext...

    Authors: Asli Yildirim, Nathalie Brenner, Robert Sutherland and Michael Feig

    Citation: BMC Biophysics 2018 11:8

    Published on:

  2. Content type: Research Article

    The possibility of validating biological macromolecules with locally disordered domains like RNA against solution properties is helpful to understand their function. In this work, we present a computational sc...

    Authors: Aarón Ayllón Benítez, José Ginés Hernández Cifre, Francisco Guillermo Díaz Baños and José García de la Torre

    Citation: BMC Biophysics 2015 8:11

    Published on:

  3. Content type: Methodology article

    Cells continuously undergo DNA damage from exogenous agents like irradiation or genotoxic chemicals or from endogenous radicals produced by normal cellular metabolic activities. DNA strand breaks are one of th...

    Authors: Michael Junk, Judy Salzwedel, Thilo Sindlinger, Alexander Brkle and Maria Moreno-Villanueva

    Citation: BMC Biophysics 2014 7:9

    Published on:

  4. Content type: Research article

    The complement protein C5a acts by primarily binding and activating the G-protein coupled C5a receptor C5aR (CD88), and is implicated in many inflammatory diseases. The cyclic hexapeptide PMX53 (sequence Ace-P...

    Authors: Phanourios Tamamis, Chris A Kieslich, Gregory V Nikiforovich, Trent M Woodruff, Dimitrios Morikis and Georgios Archontis

    Citation: BMC Biophysics 2014 7:5

    Published on:

  5. Content type: Research article

    Brownian dynamics (BD) simulations can be used to study very large molecular systems, such as models of the intracellular environment, using atomic-detail structures. Such simulations require strategies to con...

    Authors: Paolo Mereghetti, Michael Martinez and Rebecca C Wade

    Citation: BMC Biophysics 2014 7:4

    Published on:

  6. Content type: Research article

    Keratins are important structural proteins found in skin, hair and nails. Keratin Intermediate Filaments are major components of corneocytes, nonviable horny cells of the Stratum Corneum, the outermost layer o...

    Authors: Anna Akinshina, Etienne Jambon-Puillet, Patrick B Warren and Massimo G Noro

    Citation: BMC Biophysics 2013 6:12

    Published on:

  7. Content type: Methodology article

    Biomolecules or other complex macromolecules undergo conformational transitions upon exposure to an external perturbation such as ligand binding or mechanical force. To follow fluctuations in pairwise forces b...

    Authors: Bogdan I Costescu and Frauke Gräter

    Citation: BMC Biophysics 2013 6:5

    Published on:

  8. Content type: Research article

    The V3 loop of the glycoprotein gp120 of HIV-1 plays an important role in viral entry into cells by utilizing as coreceptor CCR5 or CXCR4, and is implicated in the phenotypic tropisms of HIV viruses. It has be...

    Authors: Aliana López de Victoria, Chris A Kieslich, Apostolos K Rizos, Elias Krambovitis and Dimitrios Morikis

    Citation: BMC Biophysics 2012 5:3

    Published on: