43 citations · 186 across the 15 of their papers we have counts for
15 papers
Impact of the RNA Binding Domain Localization of the Protein Shell on Virus Particle Stability
Mohammadamin Safdari, Siyu Li, Sanaz Panahandeh +2
The encapsulation of polyanions, whether single-stranded RNAs or synthetic polymers, is primarily driven by attractive electrostatic interactions between the positively charged, st…
General Solution for Elastic Networks on Arbitrary Curved Surfaces in the Absence of Rotational Symmetry
Yankang Liu, Siyu Li, Roya Zandi +1
Understanding crystal growth over arbitrary curved surfaces with arbitrary boundaries is a formidable challenge, stemming from the complexity of formulating non-linear elasticity u…
Switchable Conformation in Protein Subunits: Unveiling Assembly Dynamics of Icosahedral Viruses
Siyu Li, Guillaume Tresset, Roya Zandi
The packaging of genetic material within a protein shell, called the capsid, marks a pivotal step in the life cycle of numerous single-stranded RNA viruses. Understanding how hundr…
PyMembrane: A flexible framework for efficient simulations of elastic and liquid membranes
D. A. Matoz-Fernandez, Siyu Li, Monica Olvera de la Cruz +1
PyMembrane is a software package for simulating liquid and elastic membranes using a discretisation of the continuum description based on unstructured triangulated two-dimensional…
Biophysical Modeling of SARS-CoV-2 Assembly: Genome Condensation and Budding
Siyu Li, Roya Zandi
The COVID-19 pandemic caused by the Severe Acute Respiratory Syndrome Coronavirus 2 (SARS-CoV-2) has spurred unprecedented and concerted worldwide research to curtail and eradicate…
Virus Assembly Pathways inside a Host Cell
Sanaz Panahandeh, Siyu Li, Bogdan Dragnea +1
Simple RNA viruses self-assemble spontaneously and encapsulate their genome into a shell called the capsid. This process is mainly driven by the attractive electrostatic interactio…
Effect of the charge distribution of virus coat proteins on the length of packaged RNAs
Yinan Dong, Siyu Li, Roya Zandi
Single-stranded RNA viruses efficiently encapsulate their genome into a protein shell called the capsid. Electrostatic interactions between the positive charges in the capsid prote…
How a Virus Circumvents Energy Barriers to Form Symmetric Shells
Sanaz Panahandeh, Siyu Li, Laurent Marichal +3
Previous self-assembly experiments on a model icosahedral plant virus have shown that, under physiological conditions, capsid proteins initially bind to the genome through an en ma…
Ground States of Crystalline Caps: Generalized Jellium on Curved Space
Siyu Li, Roya Zandi, Alex Travesset +1
We study the structure and elastic energy of the ground states of crystalline caps conforming to a spherical surface. These ground states consist of positive disclination defects i…
Elasticity in Curved Topographies: Exact Theories and Linear Approximations
Siyu Li, Roya Zandi, Alex Travesset
Almost all available results in elasticity on curved topographies are obtained within either a small curvature expansion or an empirical covariant generalization that accounts for…
The equilibrium structure of self-assembled protein nano-cages
Sanaz Panahandeh, Siyu Li, Roya Zandi
Understanding how highly symmetric, robust, monodisperse protein cages self-assemble can have major applications in various areas of bio-nanotechnology, such as drug delivery, biom…
Why large icosahedral viruses need scaffolding proteins: The interplay of Gaussian curvature and disclination interactions
Siyu Li, Polly Roy, Alex Travesset +1
While small single stranded viral shells encapsidate their genome spontaneously, many large viruses, such as the Herpes virus or Infectious Bursal Disease Virus (IBDV), typically r…
The effect of RNA stiffness on the self-assembly of virus particles
Siyu Li, Gonca Erdemci-Tandogan, Paul van der Schoot +1
Under many in vitro conditions, some small viruses spontaneously encapsidate a single stranded (ss) RNA into a protein shell called the capsid. While viral RNAs are found to be com…
Self Consistent Field Theory of Virus Assembly
Siyu Li, Henri Orland, Roya Zandi
The Ground State Dominance Approximation(GSDA) has been extensively used to study the assembly of viral shells. In this work we employ the self-consistent field theory (SCFT) to in…
Impact of a non-uniform charge distribution on virus assembly
Siyu Li, Gonca Erdemci-Tandogan, Jef Wagner +2
Many spherical viruses encapsulate their genome in protein shells with icosahedral symmetry. This process is spontaneous and driven by electrostatic interactions between positive d…