Publications

  1. Yuanzhong Zhang, Sara Anbir, Joseph McTiernan, Siyu Li, Michael Worcester, Pratyasha Mishra, Michael E Colvin, Ajay Gopinathan, Umar Mohideen, Roya Zandi, Thomas E Kuhlman, "Synthesis, insertion, and characterization of SARS-CoV-2 membrane protein within lipid bilayers", Sci. Adv. 10, eadm7030 (2024).
  2. Kalouna Kra, Siyu Li, Laetitia Gargowitsch, Jéril Degrouard, Javier Pérez, Roya Zandi, Stéphane Bressanelli, Guillaume Tresset. "Energetics and Kinetic Assembly Pathways of Hepatitis B Virus Capsids in the Presence of Antivirals", ACS nano 17, 13, 12723 (2023).
  3. A. Clark, A. Safdari, S. Zoroob, R. Zandi, P. van der Schoot, “Relaxational dynamics of the T-number conversion of virus capsids”, J. Chem. Phys. 159, 084904 (2023).
  4. A Ramezani, S Britton, R Zandi, M Alber, A Nematbakhsh, W Chen. "A multiscale chemical-mechanical model predicts impact of morphogen spreading on tissue growth", NPJ Systems Biology and Applications 9.1 16 (2023).
  5. Siyu Li and Roya Zandi. "Biophysical Modeling of SARS-CoV-2 Assembly: Genome Condensation and Budding", Viruses 14.10 2089 (2022).
  6. Ata Akatay, Tianyao Wu, Umidahan Djakbarova, Cristopher Thompson, Emanuele Cocucci, Roya Zandi, Joseph Rudnick and Comert Kural. "Endocytosis at Extremes: Formation and Internalization of Giant Clathrin-coated Pits Under Elevated Membrane Tension", Frontier in Molecular Bioscience 9 959737 (2022).
  7. Yinan Dong, Roya Zandi and Alex Travesset, “Exact Solution for Elastic Networks on Curved Surfaces”, Physical Review Letters 129 088001 (2022).
  8. Suzanne B. P. E. Timmermans, Alireza Ramezani, Toni Montalvo, Mark Nguyen, Paul van der Schoot, Jan C. M. van Hest, and Roya Zandi, "The Dynamics of Viruslike Capsid Assembly and Disassembly", JACS 144 12608−12612 (2022).
  9. Sanaz Panahandeh, Siyu Li, Bogdan Dragnea, and Roya Zandi, "Virus assembly pathways inside a host cell", ACS Nano 16, 317 (2022).
  10. Laurent Marichal, Laetitia Gargowitsch, Rafael Leite Rubim, Christina Sizun, Kalouna Kra, Stephane Bressanelli, Yinan Dong Y, Sanaz Panahandeh, Roya Zandi, Guillaume Tresset, "Relationships between RNA topology and nucleocapsid structure in a model icosahedral virus", Biophys J. 120, 3925 (2021).
  11. M. Comas-Garcia, E. I. Rubio-Hernandez, I. Lara-Hernandez, M. Colunga-Saucedo, C. G. Castillo, A. Monsivais-Urenda, R. Zandi, "Basic virology aspects of SARS-CoV-2", Biomedical Innovations to Combat COVID-19: 1-30 (2021).
  12. Mohammadamin Safdari, Roya Zandi, Paul van der Schoot, "Effect of Electric Fields on the Director Field and Shape of Nematic Tactoids", Physical Review E, 103, 062703 (2021).
  13. Cheng Zeng, Liam Scott, Andrey Malyutin, Roya Zandi, Paul Van der Schoot, and Bogdan Dragnea, "Virus Mechanics under Molecular Crowding", J. Phys. Chem. B 125, 1790–1798 (2021).
  14. N. M. Willy, Joshua P. Ferguson, Salih Silahli, Cemal Cakez, Farah Hasan, C. Chang, Alex Travesset, Siyu Li, Roya Zandi, Dong Li, Eric Betzig, Emanuele Cocucci, Comert Kural, "Endocytic Clathrin Coats Develop Curvature at Early Stages of Their Formation", Developmental Cell, 56, 3146-3159 (2021).
  15. Yinan Dong, Siyu Li, Roya Zandi, "Effect of the charge distribution of virus coat proteins on the length of packaged RNAs", Review E, 102, 062423 (2020).
  16. Kevin Tsai, Samuel Britton, Ali Nematbakhsh, Roya Zandi, Weitao Chen, Mark Alber, "Role of combined cell membrane and wall mechanical properties regulated by polarity signals in cell budding", Physical Biology 17, 065011 (2020).
  17. Sanaz Panahandeh, Siyu Li, Laurent Marichal, Rafael Leite Rubim, Guillaume Tresset and Roya Zandi, "How a virus circumvents energy barriers to form symmetric shells", American Chemical Society Nano, 14, 3, 3170-3180 (2020).
  18. Roya Zandi, Bogdan Dragnea, Alex Travesset, Rudolf Podgornik, "On virus growth and form", Physics Reports, 847, 1-102 (2020).
  19. Shaolong Chen, Jun Xu, Mingyue Liu, A. L. N. Rao, Roya Zandi, Sarjeet S. Gill, Umar Mohideen , "Investigation of HIV-1 Gag binding with RNAs and lipids using Atomic Force Microscopy", PLoS One, 15(2): e0228036 (2020).
  20. Siyu Li, Roya Zandi, Alex Travesset and Gregory M. Grason, "Ground States of Crystalline Caps: Generalized Jellium on Curved Space", Physical Review Letters, 123 (2019).
  21. Roya Zandi, "Geometric frustrated assemblies, commentary for the Journal Club for Condensed Matter Physics", Journal Club for Condensed Matter Physics (2019) .
  22. Siyu Li, Roya Zandi and Alex Travesset, "Elasticity in Curved Topographies: Exact Theories and Linear Approximations", Phys. Rev. E, 99, 063005 (2019).
  23. Sanaz Panahandeh, Siyu Li, Roya Zandi, "The equilibrium structure of self-assembled protein nano-cages", Nanoscale, 10, 22802 (2018).
  24. Siyu Li, Polly Roy, Alex Travesset, and Roya Zandi, "Why large icosahedral viruses need scaffolding proteins", Proceedings of the National Academy of Sciences 115, 10971 (2018).
  25. Mingyue Liu, Jun Xu, Roya Zandi, Umar Mohideen, "Measurement of entropic force from polymers attached to a pyramidal tip", J. Phys.: Condens. Matter (2018).
  26. Bart van der Holst, Willem K. Kegel, Roya Zandi and Paul van der Schoot, "The Different Faces of Mass Action in Virus Assembly", Journal of Biological Physics 44, 163-179 (2018).
  27. Siyu Li, Henri Orland and Roya Zandi, "Self consistent field theory of virus assembly", J. Phys.: Condens. Matter, 30,144002(2018).
  28. Siyu Li, Gonca Erdemci-Tandogan, Paul van der Schoot and Roya Zandi, "The effect of RNA stiffness on the self-assembly of virus particles", J. Phys.: Condens. Matter, 30, 044002 (2017).
  29. Gonca Erdemci-Tandogan, Henri Orland, and Roya Zandi, "RNA Base Pairing Determines the Conformations of RNA Inside Spherical Viruses", Phys. Rev. Lett. 119, 188102 (2017).
  30. Siyu Li, Gonca Erdemci-Tandogan, Jef Wagner, Paul van der Schoot, and Roya Zandi, "Impact of a nonuniform charge distribution on virus assembly", Phys. Rev. E 96, 022401 (2017).
  31. Cheng Zeng, Mercedes Hernando-Pérez, and Bogdan Dragnea, Xiang Ma, Paul van der Schoot, Roya Zandi, "Contact Mechanics of a Small Icosahedral Virus", Phys. Rev. Lett. 119, 038102 (2017).
  32. 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 7, 13689 (2016).
  33. 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)
  34. 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)
  35. 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)
  36. 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)
  37. Michael Hagan and Roya Zandi, "Recent advances in coarse-grained modeling of virus assembly," Curr. Opin. Virol. 18, 36-43 (2016).
  38. Jef Wagner, Gonca Erdemci and Roya Zandi, "Adsorption of annealed branched polymers on curved surfaces," J. Phys.: Condens. Matter 27, 495101 (2015)
  39. Jef Wagner and Roya Zandi, "The Robust Assembly of Small Symmetric Nanoshells," Biophys. J. 109, 956 (2015)
  40. 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).
  41. 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).
  42. 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).
  43. Jef Wagner and Roya Zandi, "Calculating Casimir interactions for periodic surface-relief gratings using the C method," Phys. Rev. A 90, 012516 (2014).
  44. 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).
  45. D. Ando, R. Zandi, Y. W. Kim, M. Colvin, M. Rexach, and A. Gopinathan, "Nuclear Pore Complex Protein Sequences Determine Overall Copolymer Brush Structure and Function", Biophys. J. 106, 1997 (2014).
  46. 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).
  47. 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).
  48. E. Noruzifar, J. Wagner, and R. Zandi, "Scattering Approach for Fluctuation-Induced Interactions at Fluid Interfaces", Phys. Rev. E 88, 042314 (2013).
  49. 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).
  50. 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).
  51. Ehsan Noruzifar, Pablo Rodriguez, Thorsten Emig, and Roya Zandi, "Material dependence of the wire-particle Casimir interaction", Phys. Rev. A 87, 042504 (2013).
  52. 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).
  53. 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).
  54. 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).
  55. 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).
  56. 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).
  57. Lincoln Chayes, Joseph Rudnick, Aviva Shackell and Roya Zandi, "On the Thinning of Films (I)", Physica A 391, 2353 (2012).
  58. 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).
  59. Ehsan Noruzifar, Thorsten Emig and Roya Zandi, "Universality versus material dependence of fluctuation forces between metallic wires," Phys. Rev. A 84, 042501 (2011).
  60. 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)
  61. 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).
  62. Antonio Siber, Roya Zandi and Rudolf Podgornik, "Thermodynamics of nano-spheres encapsulated in virus capsids", Phys. Rev. E 81, 051919 (2010).
  63. Antoni Luque, Roya Zandi and David Reguera, "Optimal architectures of elongated viruses", PNAS 107, 5323-8 (2010).
  64. Roya Zandi and Paul van der Schoot, "Size Regulation of ss RNA Viruses", Biophys. J. 96, 9-20 (2009).
  65. Artem Levandovsky and Roya Zandi, "Nonequilibirum assembly, retroviruses and conical shape," Phys. Rev. Lett. 102, 198102 (2009)
  66. 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).
  67. 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).
  68. Paul van der Schoot and Roya Zandi, "Kinetic Theory of Virus Capsid Assembly", Phys. Biol. 4, 296-304 (2007
  69. 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)
  70. Roya Zandi, David Reguera and Howard Reiss, "Nucleation Rates in a New Phenomenological Model", J. Phys. Chem. B. 110, 22251 (2006).
  71. Roya Zandi, Paul van der Schoot, David Reguera, Willem Kegel and Howard Reiss, "Classical Nucleation Theory of Virus Capsids", Biophys. J. 90, 1938 (2006).
  72. Roya Zandi and David Reguera, "Mechanical properties of viral capsids", Phys. Rev. E 72, 021917 (2005).
  73. Roya Zandi, David Reguera, Robijn Bruinsma, William Gelbart and Joseph Rudnick, "Assembly and disassembly of viral capsids", Journal of theoretical medicine 2, 69 (2005).
  74. Michael Slutsky, Roya Zandi, Yacov Kantor and Mehran Kardar, "Apex exponents for polymer-probe interactions", Phys. Rev. Lett. 94, 198303 (2005).
  75. 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).
  76. Roya Zandi, Joseph Rudnick and Mehran Kardar, "Casimir forces, surface fluctuations and thinning of superfluid films", Phys. Rev. Lett. 93, 155302 (2004).
  77. Roya Zandi, Ramin Golestanian, and Joseph Rudnick, "Electromechanical stiffening of rods and tubes", Applied Physics Letters 84, 5467 (2004).
  78. R. Bruinsma, W. Gelbart, D. Reguera, J. Rudnick, and R. Zandi, "Viral self-assembly as a thermodynamic process", Phys. Rev. Lett., 90, 248101 (2003).
  79. Roya Zandi, Yacov Kantor and Mehran Kardar, "Entropic competition between knots and slip-links, " ARI, Bull. ITU, 53 ,6 (2003).
  80. 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).
  81. Roya Zandi, Joseph Rudnick and Ramin Golestanian, "Anomalous bending of a Polyelectrolyte", Physical Review E 67, 061805 (2003).
  82. Roya Zandi, Joseph Rudnick and Ramin Golestanian "Probing Polyelectrolyte elasticity using radial distribution function", Physical Review E 67, 021803 (2003).
  83. Roya Zandi, Joseph Rudnick and Ramin Golestanian "Radial distribution of Polyelectrolytes", European Physical Journal E 9, 41 (2002).
  84. Roya Zandi, Joseph Rudnick, "Constraints, histones, and the 30-nm spiral", Physical Review E 64 , 51918 (2001).