Related papers: Modeling Viral Capsid Assembly
Understanding how highly symmetric, robust, monodisperse protein cages self-assemble can have major applications in various areas of bio-nanotechnology, such as drug delivery, biomedical imaging and gene therapy. We develop a model to…
The simulated self-assembly of molecular building blocks into functional complexes is a key area of study in computational biology and materials science. Self-assembly simulations of proteins using physically-motivated potentials for…
Computer simulation is an important tool for scientific progress, especially when lab experiments are either extremely costly and difficult or lack the required resolution. However, all of the simulation methods come with limitations. In…
This study aims at finding a method for constructing molecular dynamics like models using the formalism of cellular automata for fast simulation of fluid dynamic systems (including compressible phenomena). In as much as the results…
In this paper the problems of the retrospective analysis of models with time-varying structure are considered. These models include contamination models with randomly switching parameters and multivariate classification models with an…
Understanding interactions between microparticles and lipid membranes is of increasing importance, especially for unraveling the influence of microplastics on our health and environment. Here, we study how a short-ranged adhesive force…
In living cells, proteins self-assemble into large functional structures based on specific interactions between molecularly complex patches. Due to this complexity, protein self-assembly results from a competition between a large number of…
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…
A summary is given of the mechanical characteristics of virus contaminants and the transmission via droplets and aerosols. The ordinary and partial differential equations describing the physics of these processes with high fidelity are…
We introduce and analyze the problem of the compilation of decision models from a decision-theoretic perspective. The techniques described allow us to evaluate various configurations of compiled knowledge given the nature of evidential…
Merging has become a widespread way to cheaply combine individual models into a single model that inherits their capabilities and attains better performance. This popularity has spurred rapid development of many new merging methods, which…
Understanding protein self-assembly is important for many biological and industrial processes. Proteins can self-assemble into crystals, filaments, gels, and other amorphous aggregates. The final forms include virus capsids and condensed…
Micrometre sized colloidal particles can be viewed as large atoms with tailorable size, shape and interactions. These building blocks can assemble into extremely rich structures and phases, in which the thermal motions of particles can be…
There is growing recognition in both the experimental and modelling literature of the importance of spatial structure to the dynamics of viral infections in tissues. Aided by the evolution of computing power and motivated by recent…
A set of programs for the numerical simulation of the diffusion decomposition processes was developed by using simulation methods, kinetic and particle method. The complex has been validated on the model system Ni-Al by the growth of -phase…
Biomolecular condensates self-assemble when proteins and nucleic acids spontaneously demix to form droplets within the crowded intracellular milieu. This simple mechanism underlies the formation of a wide variety of membraneless…
There is significant interest in using existing repositories of biological entities, relationships, and models to automate biological model assembly and extension. Current methods aggregate human-curated biological information into…
The desire to create cell-like models for fundamental science and applications has spurred extensive effort towards creating giant unilamellar vesicles (GUVs). However, a route to selectively self-assemble GUVs in bulk has remained elusive.…
An algorithm of particle-in-cell simulations is described and tested to aid further the actual design of simple vircators working on axially symmetric modes. The methods of correction of the numerical solution, have been chosen and jointly…
In self-assembly processes, kinetic trapping effects often hinder the formation of thermodynamically stable ordered states. In a model of viral capsid assembly and in the phase transformation of a lattice gas, we show how simulations in a…