Welcome to the homepage of Oded Farago

Professor at:

Biomedical Engineering Department
Ben Gurion University, Be'er Sheva 84105, Israel
Phone: +972-8-6479830; Fax: +972-8-6479628
email:ofarago@bgu.ac.il





News

  • 2019: M. Sc., Ph. D, and postdoctoral positions are available to work in my group. For details, contact me via email.
  • 08/2014: Yotam's work on the cover of EPJE (click here)

    Research:

    My research combines analytical and computational methods of statistical mechanics to understand the physical principles behind the functioning of complex biological and biomedical systems.

    Click here for a more detailed description of my current research ...

    ... and here for some research highlights from the past

    My Group

  • Matan Sivan, M.Sc. (2017 - 2019)
    Thesis: Diffusion in Periodic Systems.

  • Nadiv Dharan, M.Sc. (2010 - 2012) ; Ph.D. (2013 - 2017)
    M.Sc. Thesis: Duty ratio of cooperative molecular motors.
    Ph.D. Thesis: Condensation of adhesion domains in biological and bio-mimetic membranes.

  • Shaked Regev, M.Sc. (2015 - 2017)
    Thesis: Diffusion in Inhomogeneous Systems.

  • Yotam Y. Avital, Ph.D. (2010 - 2015)
    Thesis: Instability phenomena in lipid bilayers and lipid-DNA complexes.

  • Noam Weil, M.Sc. (2009 - 2011)
    Thesis: Entropy driven aggregation of adhesion sites of supported membranes.

  • Barak Gur, M.Sc. (2008 - 2010)
    Thesis: Cooperative dynamics of motor proteins on elastic cytoskeletal filaments.

  • Daniel Gordon, M.Sc. (2007 - 2009)
    Thesis: Large scale self-organization in simulated actin/myosin systems.

    Brief Bio

  • 2001-2005 Materials Research Laboratory, UC Santa Barbara, USA.
    Post-doc in Phil Pincus group.

  • 1996-2001 Tel Aviv University, Israel, Ph.D. in Physics,
    Thesis: Elasticity of Entropy-Dominated Systems. Supervisor: Prof. Yacov Kantor
    2001 Ph.D. in Physics with distinction. Gzipped PS file of Ph.D. thesis

  • 1993-1996 Tel Aviv University, Israel, Masters degree in Physics,
    Thesis: Directed Chaotic Motion. Supervisor: Prof. Yacov Kantor
    1997 M.Sc. in Physics Summa Cum Laude. Gzipped PS file of Masters thesis

  • 1988-1991 Tel Aviv University, Israel Undergraduate studies in Physics and Mathematics.
    1992 B.Sc. in Physics and Mathematics Magna Cum Laude.

    Publications (click on title for the PDF file)

    1. O. Farago and Y. Kantor
      Directed chaotic motion in a periodic potential
      Physica A 249, 151 (1998)

    2. O. Farago and Y. Kantor
      Pseudo-boundaries in discontinuous 2-dimensional maps
      J. Phys. A 31, 445 (1998)

    3. O. Farago and Y. Kantor
      Fluctuation formalism for elastic constants in hard-spheres-and-tethers systems
      Phys. Rev. E 61, 2478 (2000)

    4. O. Farago and Y. Kantor
      Entropic elasticity of two-dimensional self-avoiding percolation systems
      Phys. Rev. Lett. 85, 2533 (2000)

    5. O. Farago and Y. Kantor
      Elasticity of Gaussian and nearly Gaussian phantom networks
      Phys. Rev. E 62, 6094 (2000)

    6. O. Farago and Y. Kantor
      The elastic behavior of entropic ``fisherman's net''
      Eur. Phys. J. E 3, 253 (2000)

    7. O. Farago and Y. Kantor
      Entropic elasticity of phantom percolation networks
      Europhys. Lett. 52, 413 (2000)

    8. O. Farago and Y. Kantor
      Entropic elasticity at the sol-gel transition
      Europhys. Lett. 57, 458 (2002)

    9. O. Farago and P. Pincus
      Solute effects on the helix-coil transition
      Eur. Phys. J. E 7, 393 (2002)

    10. O. Farago, Y. Kantor, and M. Kardar
      Pulling knotted polymers
      Europhys. Lett. 60, 53 (2002)

    11. O. Farago
      ``Water-free'' computer model for fluid bilayer membranes
      J. Chem. Phys. 119, 596 (2003)

    12. O. Farago and P. Pincus
      The effect of thermal fluctuations on Schulman area elasticity
      Eur. Phys. J. E 11, 399 (2003)

    13. O. Farago and P. Pincus
      Statistical mechanics of bilayer membrane with a fixed projected area
      J. Chem. Phys. 120, 2934 (2004)

    14. O. Farago and C. D. Santangelo
      Pore formation in fluctuating membranes
      J. Chem. Phys. 122, 044901 (2005).

    15. O. Farago, N. Gronbech-Jensen, and P. Pincus
      Meso-scale computer modeling of lipid-DNA complexes for gene therapy
      Phys. Rev. Lett. 96, 018102 (2006).

    16. O. Farago and N. Gronbech-Jensen
      Computational and analytical modeling of cationic lipid-DNA complexes
      Biophys. J. 92, 3228 (2007).

    17. C. D. Santangelo and O. Farago
      Membrane fluctuations around inclusions
      J. Computer-Aided Mater. Des. 14, 103 (2007).

    18. O. Farago
      Mode excitation Monte Carlo simulations of mesoscopically large membranes
      J. Chem Phys. 128, 184105 (2008).

    19. O. Farago, K. Ewert, A. Ahmad, H. M. Evans, N. Gronbech-Jensen, and C. R. Safinya
      Transitions between distinct compaction regimes in complexes of multivalent cationic lipids and DNA
      Biophys. J. 95, 836 (2008).

    20. O. Farago
      Membrane fluctuations near a plane rigid surface
      Phys. Rev. E 78, 051919 (2008).

    21. O. Farago and N. Gronbech-Jensen
      Simulation of self-assembly of cationic lipids and DNA into structured complexes
      J. Am. Chem. Soc. 131, 2875 (2009).

    22. B. Gilboa, D. Gillo, O. Farago and A. Bernheim-Groswasser
      Bidirectional cooperative motion of myosin-II motors on actin tracks with randomly alternating polarities
      Soft Matter 5, 2223 (2009).

    23. D. Gillo, B. Gur, A. Bernheim-Groswasser and O. Farago
      Cooperative molecular motors moving back and forth
      Phys. Rev. E 80, 021929 (2009).

    24. O. Farago
      Fluctuation-induced attraction between adhesion sites of supported membranes
      Phys. Rev. E 81, 050902(R) (2010).

    25. B. Gur and O. Farago
      Biased transport of elastic cytoskeletal filaments with alternating polarities by molecular motors
      Phys. Rev. Lett. 104, 238101 (2010).

    26. N. Weil and O. Farago
      Entropy driven aggregation of adhesion sites of supported membranes
      Eur. Phys. J. E 33, 81 (2010).

    27. O. Farago and A. Bernheim-Groswasser
      Crosstalk between non-processive myosin motors mediated by the actin filament elasticity (Review)
      Soft Matter 7, 3066 (2011).

    28. O. Farago and N. Gronbech-Jensen
      Molecular simulation analysis of structural variations in lipoplexes
      Soft Matter 7, 4302 (2011).

    29. O. Farago
      Statistical thermodynamics of adhesion points in supported membranes (Book Chapter)
      Chapter 5 in Advances in Planar Lipid Bilayers and Liposomes, Vol. 14 (Ed. A. Iglič), pp.129-155 (2011).

    30. N. Weil and O. Farago
      Entropic attraction of adhesion bonds toward cell boundaries
      Phys. Rev. E 84, 051907 (2011).

    31. O. Farago
      Mechanical surface tension governs membrane thermal fluctuations
      Phys. Rev. E 84, 051914 (2011).

    32. N. Dharan and O. Farago
      Duty ratio of cooperative molecular motors
      Phys. Rev. E 85, 021904 (2012).

    33. D. Gordon, A. Bernheim-Groswasser, C. Keasar and O. Farago
      Hierarchical self-organization of cytoskeletal active networks
      Phys. Biol. 9, 026005 (2012).

    34. N. Dharan and O. Farago
      Muscle contraction and the elasticity-mediated crosstalk effect
      Phys. Rev. E 87, 052714 (2013).

    35. N. Gronbech-Jensen and O. Farago
      A simple and effective Verlet-type algorithm for simulating Langevin dynamics
      Mol. Phys. 111, 983 (2013).

    36. N. Gronbech-Jensen, N. R. Hayre and O. Farago
      Application of the G-JF discrete-time thermostat for fast and accurate molecular simulations
      Comput. Phys. Commun. 185, 524 (2014).

    37. O. Farago and N. Gronbech-Jensen
      Langevin dynamics in inhomogeneous media: Re-examining the Ito-Stratonovich dilemma
      Phys. Rev. E 89, 013301 (2014).

    38. N. Dharan and O. Farago
      Coarse-grained molecular simulations of membrane adhesion domains
      J. Chem. Phys. 141, 024903 (2014).

    39. O. Farago and N. Gronbech-Jensen
      Fluctuation-dissipation relation for systems with spatially varying friction
      J. Stat. Phys. 156, 1093 (2014).

    40. Y. Y. Avital, N. Gronbech-Jensen, and O. Farago
      Elasticity and mechanical instability of charged lipid bilayers in ionic solutions
      Eur. Phys. J. E 37, 69 (2014).

    41. N. Gronbech-Jensen and O. Farago
      Constant pressure and temperature discrete-time Langevin molecular dynamics
      J. Chem. Phys. 141, 194108 (2014).

    42. Y. Y. Avital and O. Farago
      Small membranes under negative surface tension
      J. Chem. Phys. 142, 124902 (2015).

    43. N. Dharan and O. Farago
      Formation of adhesion domains in stressed and confined membranes
      Soft Matter 11, 3780 (2015).

    44. Y. Y. Avital, N. Gronbech-Jensen, and O. Farago
      The thermodynamics of endosomal escape and DNA release from lipoplexes
      Phys. Chem. Chem. Phys. 18, 2591 (2016).

    45. O. Farago and N. Gronbech-Jensen
      On the connection between dissipative particle dynamics and the Ito-Stratonovich dilemma
      J. Chem. Phys. 144, 084102 (2016).

    46. S. Regev, N. Gronbech-Jensen, and O. Farago
      Isothermal Langevin dynamics in systems with power-law spatially dependent friction
      Phys Rev. E 94, 012116 (2016).

    47. N. Dharan and O. Farago
      Formation of semi-dilute adhesion domains driven by weak elasticity-mediated interactions
      Soft Matter 12, 6649 (2016).

    48. E. Arad, O. Farago, and N. Gronbech-Jensen
      The G-JF thermostat for accurate configurational sampling in soft-matter simulations
      Isr. J. Chem. 56, 629 (2016).

    49. N. Dharan and O. Farago
      Interplay between membrane elasticity and active cytoskeleton forces regulates the aggregation dynamics of the immunological synapse
      Soft Matter 13, 6938 (2017).

    50. O. Farago
      Noise-induced drift in two-dimensional anisotropic systems
      Phys. Rev. E 96, 042141 (2017).

    51. S. Regev and O. Farago
      Application of underdamped Langevin dynamics simulations for the study of diffusion from a drug-eluting stent
      Physica A 507, 231 (2018).

    52. M. Sivan and O. Farago
      Probability distribution of Brownian motion in periodic potentials
      Phys. Rev. E 98, 052117 (2018).

    53. M. Sivan and O. Farago
      Non-steady-state diffusion in two-dimensional periodic channels
      Phys. Rev. E 99, 022141 (2019).

    54. O. Farago
      Different measures for characterizing the motion of molecules along a temperature gradient
      Phys. Rev. E 99, 062108 (2019).

    55. O. Farago
      Langevin thermostat for robust configurational and kinetic sampling
      Physica A 534, 122210 (2019).

    56. O. Farago
      A simple statistical-mechanical interpretation of Onsager reciprocal relations and Derjaguin theory of thermo-osmosis
      Eur. Phys. J. E 42, 136 (2019).