Related papers: Mechanical limits of viral capsids
Many physical systems can be modelled as parameter-dependent variational problems. In numerous cases, multiple equilibria co-exist, requiring the evaluation of their stability, and the monitoring of transitions between them. Generally, the…
We implement molecular dynamics simulations in canonical ensemble to study the effect of confinement on a $2d$ crystal of point particles interacting with an inverse power law potential proportional to $r^{-12}$ in a narrow channel. This…
In this paper we present a three-dimensional discrete model governing the deformation of a viral capsid, modelled as a regular icosahedron and subjected not to cross a given flat rigid surface on which it initially lies in correspondence of…
Understanding how virus capsids assemble around their nucleic acid (NA) genomes could promote efforts to block viral propagation or to reengineer capsids for gene therapy applications. We develop a coarse-grained model of capsid proteins…
Soft, amorphous solids such as tissues, foams, and emulsions are composed of deformable particles. However, the effect of single-particle deformability on the collective behavior of soft solids is still poorly understood. We perform…
The kinetics for the assembly of viral proteins into a population of capsids can be measured in vitro with size exclusion chromatography or dynamic light scattering, but extracting mechanistic information from these studies is challenging.…
A series of simulations aimed at elucidating the self-assembly dynamics of spherical virus capsids is described. This little-understood phenomenon is a fascinating example of the complex processes that occur in the simplest of organisms.…
We develop coarse-grained models that describe the dynamic encapsidation of functionalized nanoparticles by viral capsid proteins. We find that some forms of cooperative interactions between protein subunits and nanoparticles can…
Cells and other soft particles are often forced to flow in confined geometries in both laboratory and natural environments, where the elastic deformation induces an additional drag and pressure drop across the particle. In contrast with…
We present a simple method for accessing the elastic properties of microscopic deformable particles. This method is based on measuring the pressure-induced deformation of soft particles as they are forced through a tapered glass…
Polymorphism has been observed in viral capsid assembly, demonstrating the ability of identical protein dimers to adopt multiple geometries under the same solution conditions. A well-studied example is the hepatitis B virus (HBV), which…
The formation of a viral capsid -- the highly-ordered protein shell that surrounds the genome of a virus -- is the canonical example of self-assembly. The capsids of many positive-sense RNA viruses spontaneously assemble from in vitro…
We use computer simulations to study a model, first proposed by Wales [1], for the reversible and monodisperse self-assembly of simple icosahedral virus capsid structures. The success and efficiency of assembly as a function of…
Mechanical characteristics of single biological cells are used to identify and possibly leverage interesting differences among cells or cell populations. Fluidity---hysteresivity normalized to the extremes of an elastic solid or a viscous…
We develop a class of models with which we simulate the assembly of particles into T1 capsid-like objects using Newtonian dynamics. By simulating assembly for many different values of system parameters, we vary the forces that drive…
Elucidating the interplay of stress and geometry is a fundamental scientific question arising in multiple fields. In this work, we investigate the geometric frustration of crystalline caps confined on the sphere in both elastic and plastic…
Induced by proteins within the cell membrane or by differential growth, heating, or swelling, spontaneous curvatures can drastically affect the morphology of thin bodies and induce mechanical instabilities. Yet, the interaction of…
We study an elasticity model for compressed protein monolayers or particle rafts at a liquid interface. Based on the microscopic view of hard-core particles with soft shells, a bead-spring model is formulated and analyzed in terms of…
In the present paper, a fiber bundle model in (1+1)-dimensions that simulates the rupture process of a fibrous material pulled by an uniaxial force F is analyzed. In this model the load of a broken fiber is shifted in equal portions onto…
The protein shells, or capsids, of all sphere-like viruses adopt icosahedral symmetry. In the present paper we propose a statistical thermodynamic model for viral self-assembly. We find that icosahedral symmetry is not expected for viral…