Related papers: Modeling Viral Capsid Assembly
A variety of models for the membrane-mediated interaction of particles in lipid membranes, mostly well-established in theoretical physics, is reviewed from a mathematical perspective. We provide mathematically consistent formulations in a…
Emergent phenomena share the fascinating property of not being obvious consequences of the design of the system in which they appear. This characteristic is no less relevant when attempting to simulate such phenomena, given that the outcome…
We examine the budding of a nanoscale particle through a lipid bilayer using molecular dynamics simulations, free energy calculations, and an elastic theory, with the aim of determining the extent to which equilibrium elasticity theory can…
We propose a description for the quasi-equilibrium self-assembly of small, single-stranded (ss) RNA viruses whose capsid proteins (CPs) have flexible, positively charged, disordered tails that associate with the negatively charged RNA…
A numerical method is presented for first-principle simulations of charged colloidal dispersions in electrolyte solutions. Utilizing a smoothed profile for colloid-solvent boundaries, efficient mesoscopic simulations are enabled for…
The kinetics of the self-assembly of nanocomponents into a virus, nanocapsule, or other composite structure is analyzed via a multiscale approach. The objective is to achieve predictability and to preserve key atomic-scale features that…
We present a simple kinetic model for the assembly of small single-stranded RNA viruses that can be used to carry out analytical packaging contests between different types of RNA molecules. The RNA selection mechanism is purely kinetic and…
This document presents a combinatorial framework for analyzing assembly systems using generating functions. We explore the theory through concrete examples, such as linear polymers, and develop recursive equations to characterize valid…
Realistic evolutionary fitness landscapes are notoriously difficult to construct. A recent cutting-edge model of virus assembly consists of a dodecahedral capsid with $12$ corresponding packaging signals in three affinity bands. This whole…
We review the recent literature on the simulation of the structure and deformation of amorphous glasses, including oxide and metallic glasses. We consider simulations at different length and time scales. At the nanometer scale, we review…
Cowpea chlorotic mottle virus (CCMV) is a widely used model for virus replication studies. A major challenge lies in distinguishing between the roles of the interaction between coat proteins and that between the coat proteins and the viral…
The molecular self-assembly of various structures such as micelles and vesicles has been the subject of comprehensive studies. Recently, a new approach to design these structures, the frame-guided assembly, has been developed to progress…
Highly symmetric nano-shells are found in many biological systems, such as clathrin cages and viral shells. Several studies have shown that symmetric shells appear in nature as a result of the free energy minimization of a generic…
Nanoparticles tethered with DNA strands are promising building blocks for bottom-up nanotechnology, and a theoretical understanding is important for future development. Here we build on approaches developed in polymer physics to provide…
Cells offer numerous inspiring examples where proteins and membranes combine to form complex structures that are key to intracellular compartmentalization, cargo transport, and specialization of cell morphology. Despite this wealth of…
Collective cell migration plays a central role in tissue development, morphogenesis, wound repair and cancer progression. With the growing realization that physical forces mediate cell motility in development and physiology, a key…
Cellular functions are established through biological evolution, but are constrained by the laws of physics. For instance, the physics of protein folding limits the lengths of cellular polypeptide chains. Consequently, many cellular…
In this work we study how a viral capsid can change conformation using techniques of Large Deviations Theory for stochastic differential equations. The viral capsid is a model of a complex system in which many units - the proteins forming…
A liquid crystal continuum modeling framework for icosahedra bacteriophage viruses is developed and tested. The main assumptions of the model are the chromonic columnar hexagonal structure of confined DNA, the high resistance to bending and…
We study viral transmission in crowds via the short-ranged airborne pathway using a purely model-based approach. Our goal is two-pronged. Firstly, we illustrate with a concrete and pedagogical case study how to estimate the risks of new…