RZ
Roya Zandi
cond-mat.softphysics.bio-phcond-mat.stat-mechq-bio.BMbiophysicsVirus AssemblyModels, BiologicalModels, ChemicalModels, MolecularBromovirus
On Valency
published · living versionsW_4v5myjyz·v2 · currentpublished
Effects of RNA branching on the electrostatic stabilization of viruses
with Gonca Erdemci-Tandogan, Jef Wagner, Paul van der Schoot, Rudolf Podgornik
2 versions
W_dey9f63q·v1published
W_xfgrv59f·v1published
W_5d28gwjs·v1published
Preprints & journals
106 papers in the corpus · 2001–2026Mechanisms of viral budding through cellular membranes.42678214 · Zhang, Shuyang, Li, Siyu, Coronado-Ipiña, Miguel Angel et al.2026 · 0 citationsThe Journal of chemical physics. 2026;165(9)
ToolGate: An Executable Acceptance Pipeline for Tool-Dependent Scientific Benchmark Construction2609.02067v1 · Ke Zhang, Yankang Liu, Roya Zandi et al.2026 · 0 citationsarXivon Valency
Highly Conserved Core Residues Define Old-World Alphaviruses and Trace Early Evolutionary Divergence.42507035 · Piña-Ruiz, Wendy Carolina, Jaime-Rocha, Luis Rubén, Castorena-Robles, Andrea et al.2026 · 0 citationsJournal of molecular evolution. 2026;94(4):668-685
Study of wrap mode impact on Pseudomonas aeruginosa motion in the chemotactic field of fungi.42477330 · Hansen, Austin, Ramezani, Alireza, A Pelletier, Dale et al.2026 · 0 citationsNPJ systems biology and applications. 2026;12(1)
SARS-CoV-2 membrane protein conformations induce distinct membrane curvatures.42465366 · McTiernan, Joseph, Zandi, Roya, Colvin, Michael E et al.2026 · 0 citationsbioRxiv : the preprint server for biology. 2026
Multiple Protein-Protein Interactions Drive the Assembly and Budding of the Chikungunya Virion.42267519 · Coronado-Ipiña, Miguel Angel, Zhang, Shuyang, Li, Siyu et al.2026 · 2 citationsACS infectious diseases. 2026;12(7):2383-2395
Effects of rim fluctuations in classical nucleation theory of virus capsids.42223104 · Clark, Alexander Bryan, van der Schoot, Paul, Orland, Henri et al.2026 · 0 citationsThe Journal of chemical physics. 2026;164(21)
Clustering of SARS-CoV-2 membrane proteins in lipid bilayer membranes.42044155 · McTiernan, Joseph, Zhang, Yuanzhong, Li, Siyu et al.2026 · 2 citationsPLoS computational biology. 2026;22(4):e1014229
Learning Parameterized Nonlinear Elasticity on Curved Surfaces2604.12170v1 · Yankang Liu, Ke Zhang, Maziar Raissi et al.2026 · 0 citationsarXiv
Encapsulation of fragmented cargo by virus coat proteins.41603455 · van der Schoot, Paul, Zandi, Roya, Amjad, Ayesha et al.2026 · 1 citationThe Journal of chemical physics. 2026;164(4)
Thermodynamic stability and kinetic control of capsid morphologies in hepatitis B virus.41489153 · Yang, Kevin, Gonzalez, Juana Martin, Ramezani, Alireza et al.2026 · 3 citationsThe Journal of chemical physics. 2026;164(1)
An Assembly-Line Mechanism for In Vitro Encapsulation of Fragmented Cargo in Virus-Like Particles.41460313 · Amjad, Ayesha, Tsvetkova, Irina B, Lowry, Lena G et al.2026 · 3 citationsACS nano. 2026;20(7):5438-5451
From disorder to icosahedral symmetry: How conformation-switching subunits enable RNA virus assembly.40991695 · Li, Siyu, Tresset, Guillaume, Zandi, Roya2025 · 17 citationsScience advances. 2025;11(39):eady7241
Impact of the RNA binding domain localization of the protein shell on virus particle stability.41116478 · Safdari, Mohammadamin, Li, Siyu, Panahandeh, Sanaz et al.2025 · 1 citationPhysical review. E. 2025;112(3-1):034402
Competitive binding and geometric changes allow fast, complete translocation of intact HIV-1 capsids through the nuclear pore complex10.1101/2025.08.11.669633v1 · Mishra, B., Zandi, R., Gopinathan, A.2025 · 0 citationsbioRxiv
Dynamics and Regulation of mRNA Cap Recognition by Human eIF4F.40667164 · Hong, Hea Jin, Guevara, Matthew G, Li, Siyu et al.2025 · 0 citationsbioRxiv : the preprint server for biology. 2025
Human Stress Response Specificity through Bioresonance Selectivity.40161696 · Worcester, Michael, Nejad, Shayan, O'Donnell, Devin et al.2025 · 0 citationsbioRxiv : the preprint server for biology. 2025
General solution for elastic networks on arbitrary curved surfaces in the absence of rotational symmetry.39972832 · Liu, Yankang, Li, Siyu, Zandi, Roya et al.2025 · 1 citationPhysical review. E. 2025;111(1-2):015423
Glass-like Relaxation Dynamics during the Disorder-to-Order Transition of Viral Nucleocapsids.39356145 · Tresset, Guillaume, Li, Siyu, Gargowitsch, Laetitia et al.2024 · 2 citationsThe journal of physical chemistry letters. 2024;15(40):10210-10218
Switchable Conformation in Protein Subunits: Unveiling Assembly Dynamics of Icosahedral Viruses2409.00226v1 · Siyu Li, Guillaume Tresset, Roya Zandi2024 · 2 citationsarXiv
Overview of the 2023 Physical Virology Gordon Research Conference-Viruses at Multiple Levels of Complexity.38932189 · Hagan, Michael F, Zandi, Roya, Uetrecht, Charlotte2024 · 0 citationsViruses. 2024;16(6)
Dynamics of elongation of nematic tactoids in an electric field.38907476 · Safdari, Mohammadamin, Zandi, Roya, van der Schoot, Paul2024 · 0 citationsPhysical review. E. 2024;109(5-1):054706
Study of Impacts of Two Types of Cellular Aging on the Yeast Bud Morphogenesis.38464259 · Tsai, Kevin, Zhou, Zhen, Yang, Jiadong et al.2026 · 5 citationsbioRxiv : the preprint server for biology. 2024
Synthesis, insertion, and characterization of SARS-CoV-2 membrane protein within lipid bilayers.38416838 · Zhang, Yuanzhong, Anbir, Sara, McTiernan, Joseph et al.2024 · 26 citationsScience advances. 2024;10(9):eadm7030
Relaxational dynamics of the T-number conversion of virus capsids.37610017 · Clark, Alexander Bryan, Safdari, Mohammadamin, Zoorob, Selim et al.2023 · 2 citationsThe Journal of chemical physics. 2023;159(8)
Energetics and Kinetic Assembly Pathways of Hepatitis B Virus Capsids in the Presence of Antivirals.37342963 · Kra, Kalouna, Li, Siyu, Gargowitsch, Laetitia et al.2023 · 23 citationsACS nano. 2023;17(13):12723-12733
A multiscale chemical-mechanical model predicts impact of morphogen spreading on tissue growth.37210381 · Ramezani, Alireza, Britton, Samuel, Zandi, Roya et al.2023 · 7 citationsNPJ systems biology and applications. 2023;9(1):16
Endocytosis at extremes: Formation and internalization of giant clathrin-coated pits under elevated membrane tension.36213118 · Akatay, Ahmet Ata, Wu, Tianyao, Djakbarova, Umidahan et al.2023 · 23 citationsFrontiers in molecular biosciences. 2022;9:959737
Biophysical Modeling of SARS-CoV-2 Assembly: Genome Condensation and Budding.36298645 · Li, Siyu, Zandi, Roya2022 · 35 citationsViruses. 2022;14(10)
Exact Solution for Elastic Networks on Curved Surfaces.36053686 · Dong, Yinan, Zandi, Roya, Travesset, Alex2022 · 7 citationsPhysical review letters. 2022;129(8):088001
The Dynamics of Viruslike Capsid Assembly and Disassembly.35792573 · Timmermans, Suzanne B P E, Ramezani, Alireza, Montalvo, Toni et al.2022 · 39 citationsJournal of the American Chemical Society. 2022;144(28):12608-12612
A Chemical-mechanical Coupled Model Predicts Roles of Spatial Distribution of Morphogen in Maintaining Tissue Growth10.1101/2022.06.28.497907v1 · Ramezani, A., Britton, S., Zandi, R. et al.2022 · 0 citationsbioRxiv
Virus Assembly Pathways inside a Host Cell2202.09736v1 · Sanaz Panahandeh, Siyu Li, Bogdan Dragnea et al.2022 · 41 citationsACS Nano 2022, 16, 1, 317-327
De novo endocytic clathrin coats develop curvature at early stages of their formation.34774130 · Willy, Nathan M, Ferguson, Joshua P, Akatay, Ata et al.2021 · 55 citationsDevelopmental cell. 2021;56(22):3146-3159.e5
Relationships between RNA topology and nucleocapsid structure in a model icosahedral virus.34418368 · Marichal, Laurent, Gargowitsch, Laetitia, Rubim, Rafael Leite et al.2021 · 15 citationsBiophysical journal. 2021;120(18):3925-3936
Effect of electric fields on the director field and shape of nematic tactoids.34271629 · Safdari, Mohammadamin, Zandi, Roya, van der Schoot, Paul2021 · 9 citationsPhysical review. E. 2021;103(6-1):062703
Virus Mechanics under Molecular Crowding.33577322 · Zeng, Cheng, Scott, Liam, Malyutin, Andrey et al.2021 · 15 citationsThe journal of physical chemistry. B. 2021;125(7):1790-1798
Effect of the charge distribution of virus coat proteins on the length of packaged RNAs.33466113 · Dong, Yinan, Li, Siyu, Zandi, Roya2024 · 13 citationsPhysical review. E. 2020;102(6-1):062423
Role of combined cell membrane and wall mechanical properties regulated by polarity signals in cell budding.33085651 · Tsai, Kevin, Britton, Samuel, Nematbakhsh, Ali et al.2021 · 8 citationsPhysical biology. 2020;17(6):065011
How a Virus Circumvents Energy Barriers to Form Symmetric Shells.32115940 · Panahandeh, Sanaz, Li, Siyu, Marichal, Laurent et al.2021 · 63 citationsACS nano. 2020;14(3):3170-3180
Investigation of HIV-1 Gag binding with RNAs and lipids using Atomic Force Microscopy.32015565 · Chen, Shaolong, Xu, Jun, Liu, Mingyue et al.2020 · 8 citationsPloS one. 2020;15(2):e0228036
Ground States of Crystalline Caps: Generalized Jellium on Curved Space.31702180 · Li, Siyu, Zandi, Roya, Travesset, Alex et al.2019 · 40 citationsPhysical review letters. 2019;123(14):145501
Endocytic Clathrin Coats Develop Curvature at Early Stages of Their Formation10.1101/715219v2 · Willy, N., Ferguson, J., Silahli, S. et al.2019 · 9 citationsbioRxiv
Elasticity in curved topographies: Exact theories and linear approximations.31330662 · Li, Siyu, Zandi, Roya, Travesset, Alex2019 · 17 citationsPhysical review. E. 2019;99(6-1):063005
The equilibrium structure of self-assembled protein nano-cages.30516220 · Panahandeh, Sanaz, Li, Siyu, Zandi, Roya2018 · 48 citationsNanoscale. 2018;10(48):22802-22809
Measurement of entropic force from polymers attached to a pyramidal tip.30524055 · Liu, Mingyue, Xu, Jun, Zandi, Roya et al.2019 · 1 citationJournal of physics. Condensed matter : an Institute of Physics journal. 2019;31(7):075102
Why large icosahedral viruses need scaffolding proteins.30301797 · Li, Siyu, Roy, Polly, Travesset, Alex et al.2018 · 106 citationsProceedings of the National Academy of Sciences of the United States of America. 2018;115(43):10971-10976
Why large icosahedral viruses need scaffolding proteins: The interplay of Gaussian curvature and disclination interactions1809.01809v1 · Siyu Li, Polly Roy, Alex Travesset et al.2018 · 0 citationsarXiv
Foreword.29671097 · Zandi, Roya, Micheletti, Cristian, Podgornik, Rudolf2018 · 0 citationsJournal of biological physics. 2018;44(2):117
The different faces of mass action in virus assembly.29616429 · van der Holst, Bart, Kegel, Willem K, Zandi, Roya et al.2018 · 6 citationsJournal of biological physics. 2018;44(2):163-179
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