Related papers: Minimum energy paths for conformational changes of…
From the analysis of sizes of approximately 130 small icosahedral viruses we find that there is a typical structural capsid protein, having a mean diameter of 5 nm and a mean thickness of 3 nm, with more than two thirds of the analyzed…
We study the behavior of atomistic models in general dimensions under uniaxial tension and investigate the system for critical fracture loads. We rigorously prove that in the discrete-to-continuum limit the minimal energy satisfies a…
A pentagonal order formed by 360 proteins in the bovine papilloma viral capsid and structures of some smaller viral capsids are considered from a unified point of view based on the Landau crystallization theory. To simulate the capsid…
We analyze the large deviations for a discrete energy Kac-like walk. In particular, we exhibit a path, with probability exponentially small in the number of particles, that looses energy.
The Caspar-Klug classification of viruses whose protein shell, called viral capsid, exhibits icosahedral symmetry, has recently been extended to incorporate viruses whose capsid proteins are exclusively organised in pentamers. The approach,…
The distribution of inequivalent geometries occurring during self-assembly of the major capsid protein in thermodynamic equilibrium is determined based on a master equation approach. These results are implemented to characterize the…
The coat proteins of many viruses spontaneously form icosahedral capsids around nucleic acids or other polymers. Elucidating the role of the packaged polymer in capsid formation could promote biomedical efforts to block viral replication…
We introduce a variational approximation to the microscopic dynamics of rare conformational transitions of macromolecules. Within this framework it is possible to simulate on a small computer cluster reactions as complex as protein folding,…
The Vlasov-Fokker-Planck equation describes the evolution of the probability density of the position and velocity of particles under the influence of external confinement, interaction, friction, and stochastic force. It is well-known that…
The time evolution of many physical, chemical, and biological systems can be modelled by stochastic transitions between the minima of the potential energy surface describing the system of interest. We show that in cases where there are two…
A variational modeling framework for hydraulically induced fracturing of elastic-plastic solids is developed in the present work. The developed variational structure provides a global minimization problem. While fracture propagation is…
Spontaneous structural rearrangements play a central role in the organization and function of complex biomolecular systems. In principle, physics-based computer simulations like Molecular Dynamics (MD) enable us to investigate these…
The small scale structure opens a window to constrain the dynamical properties of Dark Matter. Here we study the clustering of warm dark matter (WDM) in a semi-analytical approach and compared the linear power spectrum of WDM with cold dark…
We construct path integrals for stochastic hybrid reaction-diffusion (RD) processes, in which the reaction terms depend on the discrete state of a randomly switching environment. We proceed by spatially discretizing a given RD system and…
Employing molecular dynamics simulations of jammed soft particles, we study microscopic responses of force-chain networks to quasi-static isotropic (de)compressions. We show that not only contacts but also interparticle gaps between the…
We study the self-assembly behaviour of patchy particles with `protein-like' interactions that can be considered as a minimal model for the assembly of viral capsids and other shell-like protein complexes. We thoroughly explore the…
We present a rigorously formulated, novel operator-based framework that merges ideas from condensed matter physics, continuum mechanics, and quantum-inspired theory to analyze collective virion behavior in complex environments. By modeling…
The possibility to simulate the properties of many-body open quantum systems with a large number of degrees of freedom is the premise to the solution of several outstanding problems in quantum science and quantum information. The challenge…
Minimal models of active and driven particles have recently been used to elucidate many properties non-equilibrium systems. However, the relation between energy consumption and changes in the structure and transport properties of these…
We investigate fracture and fragmentation of solids due to impact at low energies using a two-dimensional dynamical model of granular solids. Simulating collisions of two solid discs we show that, depending on the initial energy, the…