UCR

Department of Physics & Astronomy



Roya Zandi


Roya Zandi

Roya Zandi

Professor

Office:
Physics 3026

Telephone: 951-827-2096
Email: roya.zandi@ucr.edu
Fax: 951-827-4529

Research Interests:

  • Theoretical Condensed Matter Physics & Biophysics

Education:

Ph.D. 2001, University of California, Los Angeles

Current Research:

My research interest lies in the fields of statistical mechanics and condensed matter physics. A principal area of current research is the statistical mechanics of virus assembly, both equilibrium and nonequilibrium aspects. I am, in particular, interested in the influences of electrostatic and entropic mechanisms on the stability of viral structure and on the dynamics of the self-assembly process. Other current projects include the statistical mechanics of both neutral and charged polymers, the dynamics of the passage of polymers through membrane pores, knot theory and Casimir forces in superfluid films.

Awards:

NSF CAREER Award (2007)

Publications:

  1. J. Ning, G. Erdemci-Tandogan, E. L. Yufenyuy, J. Wagner, B. A. Himes, G. Zhao, C. Aiken, R. Zandi and P. Zhang, “In vitro Protease Cleavage and Computer Simulations Reveal the HIV-1 Capsid Maturation Pathway”, Nature Communications, in press (2016). 

  2. G. Erdemci-Tandogan, J. Wagner, P. van der Schoot, R. Podgornik, and R. Zandi, “Effects of RNA branching on the electrostatic stabilization of viruses”, Phys. Rev. E 94, 022408, (2016) (Editors’ Suggestion)

  3. S. Paquay, Halim Kusumaatmaja, D. Wales, R. Zandi, and P. van der Schoot, “Energetically favoured defects in dense packings of particles on spherical surfaces”, Soft Matter 12, 5708, (2016)

  4. G. Erdemci-Tandogan, J. Wagner, P. van der Schoot and R. Zandi, “Role of genome in the formation of conical retroviral shells”, J. Phys. Chem. B 120, 6298, (2016) 

  5. V. Sivanandam, D. Mathews, R. Garmann, G. Erdemci-Tandogan, R. Zandi and A.L.N. Rao, “Functional analysis of the N-terminal basic motif of a eukaryotic satellite RNA virus capsid protein in replication and packaging”, Scientific Reports 6, 26328, (2016) 

  6.  Michael Hagan and Roya Zandi, "Recent advances in coarse-grained modeling of virus assembly," Curr. Opin. Virol. 18, 36-43 (2016).

  7. Jef Wagner, Gonca Erdemci and Roya Zandi, “Adsorption of annealed branched polymers on curved surfaces,” J. Phys.: Condens. Matter 27, 495101  (2015)

  8. Jef Wagner and Roya Zandi, “The Robust Assembly of Small Symmetric Nanoshells,” Biophys. J. 109, 956 (2015)

  9. R. Kusters, H.-K Lin, R. Zandi, I. Tsvetkova, B. Dragnea, P. van der Schoot, “Role of Charge Regulation and Size Polydispersity in Nanoparticle Encapsulation by Viral Coat Proteins,” Journal of Physical Chemistry B 119 (5), 1869-1880 (2015).

  10. P. Rodriguez-Lopez, T. Emig, E. Noruzifar, R. Zandi, “Effect of Curvature and Confinement on the Casimir-Polder Interaction,” Phys. Rev. A 91, 012516 (2015).

  11. Dong Gui, Sharad Gupta, Jun Xu,  Roya Zandi, Sarjeet Gill, I-Chueh Huang, A.L.N. Rao, and Umar Mohideen, “A novel minimal in vitro system for analyzing HIV-1 Gag mediated budding”, Journal of Biological Physics 41, 135-149 (2014).

  12. Jef Wagner and Roya Zandi, “Calculating Casimir interactions for periodic surface-relief gratings using the C method,” Phys. Rev. A 88, 042314 (2014).
  13. A. Banishev, J. Wagner, T. Emig, R. Zandi, and U. Mohideen, ”Experiemtnal and theoretical investigation of the angular dependence of the Casimir force between sinusoidally corrugated surfaces,” Phys. Rev. B 89, 235436 (2014).
  14. D. Ando, R. Zandi, Y. W. Kim, M. Colvin, M. Rexach, and A. Gopinathan, “Individual nucleoporin amino acid sequences determine the overall diblock copolymer brush structure of the nuclear pore complex,” Biophys. J. 106, 1997 (2014).
  15. G. Erdemci-Tandogan, J. Wagner, P. van der Schoot, R. Podgornik, and R. Zandi “RNA topology remolds electrostatic stabilization of viruses”, Phys. Rev. E 89, 032707 (2014).
  16. S. Gupta, D. Gui, R. Zandi, S. Gill, U. Mohideen. “Fluorescence Interference Contrast Based Approach to Study Real Time Interaction of Melittin with Plasma Membranes,” Proceedings of SPIE 8947, 894723 (2014).

  17. E. Noruzifar, J. Wagner, and R. Zandi, “Scattering Approach for Fluctuation-Induced Interactions at Fluid Interfaces”, Phys. Rev. E 88, 042314 (2013).
  18. A. Banishev, J. Wagner, T. Emig, R. Zandi, and U. Mohideen,” Demonstration of angle-dependent Casimir force between corrugations” ”, Phys. Rev. Lett. 110, 250403 (2013).
  19. Paul van der Schoot and Roya Zandi, “Impact of the Topology of Viral RNAs on their Encapsulation by Virus Coat Proteins”, Journal of Biological Physics 39, 289 (2013).
  20. Ehsan Noruzifar, Pablo Rodriguez, Thorsten Emig, and Roya Zandi, “Material dependence of the wire-particle Casimir interaction”, Phys. Rev. A 87, 042504 (2013).
  21. Ehsan Noruzifar, Jef Wagner and Roya Zandi, “Three-body fluctuation-induced interaction at fluid interfaces: A strong deviation from the pairwise summation”, Phys. Rev. E 87, 020301(R) (2013).
  22. Hsiang-Ku Lin, Paul van der Schoot and Roya Zandi, “Impact of Charge Variation on the Encapsulation of Nanoparticles by Virus Coat Proteins”, Physical Biology 9, 066004 (2012).
  23. Z. Yu, M. J. Dobro, A. Levandovsky, Cindy M. Danielson, V. Sandrin, J. Shi, C. Aiken, R. Zandi, T. J. Hope, G. J. Jensen ,“Unclosed HIV-1 Capsids Suggest a Curled Sheet Model of Assembly”, JMB 425, 112-23 (2013).
  24. Ehsan Noruzifar, Thorsten Emig, Umar Mohideen and Roya Zandi, “Collective charge fluctuations and Casimir interactions for quasi one-dimensional metals”, Phys. Rev. B 86, 115449 (2012).
  25. A. Banishev, C. C. Chang, Roya Zandi and Umar Mohideen, “Modulation and cancellation of the Casimir force by using radiation pressure”, Applied Physics Letters 100, 033112 (2012).
  26. Lincoln Chayes, Joseph Rudnick, Aviva Shackell and Roya Zandi, “On the Thinning of Films (I)”, Physica A 391, 2353 (2012).
  27. Hsiang-Ku Lin, Roya Zandi, Umar Mohideen and Leonid Pryadko, “Fluctuation-induced forces between inclusions in a fluid membrane under tension “, Phys. Rev. Lett. 107, 228104 (2011).
  28. Ehsan Noruzifar, Thorsten Emig and Roya Zandi, “Universality versus material dependence of fluctuation forces between metallic wires,” Phys. Rev. A 84, 042501 (2011).
  29. Joseph Rudnick, Roya Zandi, Aviva Shackell and Doug Abraham, “Boundary conditions and the critical Casimir force on an Ising model film: Exact results in one and two dimensions”, Phys. Rev. E 82, 041118 (2010) 
  30. R. Zandi, Thorsten Emig, and Umar Mohideen, “Quantum and thermal Casimir interaction between a sphere and a plate: Comparison of Drude and Plasma models”, Phys. Rev. B 81, 195423 (2010)
  31. Antonio Siber, Roya Zandi and Rudolf Podgornik, “Thermodynamics of nano-spheres encapsulated in virus capsids”, Phys. Rev. E 81, 051919 (2010).
  32. Antoni Luque, Roya Zandi and David Reguera, “Optimal architectures of elongated viruses”, PNAS 107, 5323-8 (2010).
  33. Roya Zandi and Paul van der Schoot, “Size Regulation of ss RNA Viruses”, Biophys. J. 96, 9-20 (2009)
  34. Artem Levandovsky and Roya Zandi, “Nonequilibirum assembly, retroviruses and conical shape,” Phys. Rev. Lett. 102, 198102 (2009)
  35. Hsiang-Ku Lin, Leonid Pryadko and Roya Zandi, “Effect of particle straining, attachment and detachment in deep bed filtration”, Phys. Rev. E 79, 046321 (2009).
  36. Yufang Hu, Roya Zandi, Adriana Anavitarte, Charles M. Knobler, and William M. Gelbart, “Packaging of a Polymer by a Viral Capsid: The Interplay Between Polymer Length and Capsid Size”, Biophys. J. 94, 1428-1436 (2008).
  37. Paul van der Schoot and Roya Zandi, “Kinetic Theory of Virus Capsid Assembly”, Phys. Biol. 4, 296-304 (2007 
  38. Roya Zandi, Aviva Shackell, Joseph Rudnick, Mehran Kardar and Lincoln Chayes, “Thinning of superfluid films below the critical point”, Phys. Rev. E 76, 030601(R) (2007)
  39. Roya Zandi, David Reguera and Howard Reiss, “Nucleation Rates in a New Phenomenological Model”, J. Phys. Chem. B. 110, 22251 (2006).
  40. Roya Zandi, Paul van der Schoot, David Reguera, Willem Kegel and Howard Reiss, “Classical Nucleation Theory of Virus Capsids”, Biophys. J. 90, 1938 (2006).
  41. Roya Zandi and David Reguera, “Mechanical properties of viral capsids”, Phys. Rev. E 72, 021917 (2005).
  42. Roya Zandi, David Reguera, Robijn Bruinsma, William Gelbart and Joseph Rudnick, “Assembly and disassembly of viral capsids”, Journal of theoretical medicine 2, 69 (2005).
  43. Michael Slutsky, Roya Zandi, Yacov Kantor and Mehran Kardar, “Apex exponents for polymer--probe interactions”, Phys. Rev. Lett. 94, 198303 (2005).
  44. Roya Zandi, David Reguera, Robijn Bruinsma, William Gelbart and Joseph Rudnick, “Origin of icosaheral symmetry in viruses”, Proceedings of the National Academy of Sciences (PNAS) USA, 101, 15556 (2004).  Featured in, “Search and Discovery”, Physics Today (December 2004); Natural History Magazine (Feb. 2005); Science News (Sept. 2005); Math in the Media (Oct. 2005); and the cover of the (PNAS), with an accompanying commentary by Professor Adam Zlotnick (“Viruses and the physics of soft condensed matter,” PNAS 2004).
  45. Roya Zandi, Joseph Rudnick and Mehran Kardar, “Casimir forces, surface fluctuations and thinning of superfluid films”, Phys. Rev. Lett. 93, 155302 (2004).
  46. Roya Zandi, Ramin Golestanian, and Joseph Rudnick, “Electromechanical stiffening of rods and tubes”, Applied Physics Letters 84, 5467 (2004).
  47. R. Bruinsma, W. Gelbart, D. Reguera, J. Rudnick, and R. Zandi, “Viral self-assembly as a thermodynamic process”, Phys. Rev. Lett., 90, 248101 (2003).
  48. Roya Zandi, Yacov Kantor and Mehran Kardar, “Entropic competition between knots and slip-links, ” ARI, Bull. ITU, 53 ,6 (2003).
  49. Roya Zandi, David Reguera, Joseph Rudnick and William M. Gelbart, “What drives the translocation of stiff chains?”, Proceedings of the National Academy of Sciences USA, 100, 8649 (2003).
  50. Roya Zandi, Joseph Rudnick and Ramin Golestanian, “Anomalous bending of a Polyelectrolyte”, Physical Review E 67, 061805 (2003).
  51. Roya Zandi, Joseph Rudnick and Ramin Golestanian “Probing Polyelectrolyte elasticity using radial distribution function”, Physical Review E 67, 021803 (2003).
  52. Roya Zandi, Joseph Rudnick and Ramin Golestanian “Radial distribution of Polyelectrolytes”, European Physical Journal E 9, 41 (2002).
  53. Roya Zandi, Joseph Rudnick, “Constraints, histones, and the 30-nm spiral”, Physical Review E 64 , 51918 (2001).

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