Related papers: Protein container disassembly pathways depend on g…

Protein folding and design are major biophysical problems, the solution of which would lead to important applications especially in medicine. Here a novel protein model capable of simultaneously provide quantitative protein design and…

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…

Biofilms are antibiotic-resistant bacterial aggregates that grow on moist surfaces and can trigger hospital-acquired infections. They provide a classical example in biology where the dynamics of cellular communities may be observed and…

Three-dimensional discrete numerical simulation is used to investigate the properties of close-packed frictionless granular assemblies as a function of particle polydispersity and shape. Unlike some experimental results, simulations show…

The question of how stiff polymers are able to pack into small containers is particularly relevant to the study of DNA packaging in viruses. A reduced version of the problem based on coarse-grained representations of the main components of…

The statistical mechanics of a treelike polymer in a confining volume is relevant to the packaging of the genome in RNA viruses. Making use of the mapping of the grand partition function of this system onto the statistical mechanics of a…

Lattice-model simulations and experiments of some small proteins suggest that folding is essentially controlled by a few conserved contacts. Residues of these conserved contacts form the minimum set of native contacts needed to ensure…

Nature creates diverse proteins through a 'divide and assembly' strategy. Inspired by this idea, we introduce ProteinWeaver, a two-stage framework for protein backbone design. Our method first generates individual protein domains and then…

Bacterial microcompartments are large, roughly icosahedral shells that assemble around enzymes and reactants involved in certain metabolic pathways in bacteria. Motivated by microcompartment assembly, we use coarse-grained computational and…

Predicting the growth of large cracks in brittle materials is a fundamental unresolved problem in fracture mechanics. Under out-of-plane shear loading, an initially planar crack may fragment into multiple cracks, forming an echelon crack…

The field of complex self-assembly is moving toward the design of multi-particle structures consisting of thousands of distinct building blocks. To exploit the potential benefits of structures with such `addressable complexity,' we need to…

In this paper, we analyse a model for the growth of three-dimensional walled cells. In this model the biomechanical expansion of the cell is coupled with the geometry of its wall. We consider that the density of building material depends on…

Protein aggregation in cell membrane is vital for the majority of biological functions. Recent experimental results suggest that transmembrane domains of proteins such as $\alpha$-helices and $\beta$-sheets have different structural…

A reduced model, which can fold both helix and sheet structures, is proposed to study the problem of protein folding. The goal of this model is to find an unbiased effective potential that has included the effects of water and at the same…

A geometric analysis of protein folding, which complements many of the models in the literature, is presented. We examine the process from unfolded strand to the point where the strand becomes self-interacting. A central question is how it…

Using large deviation theory and principles of stochastic optimal control, we show that rare molecular dynamics trajectories conditioned on assembling a specific target structure encode a set of interactions and external forces that lead to…

Molecular simulations of the self-assembly of cone-shaped particles with specific, attractive interactions are performed. Upon cooling from random initial conditions, we find that the cones self assemble into clusters and that clusters…

We investigate the transport properties of a complex porous structure with branched fractal architectures formed due to the gradual deposition of dimers in a model of multilayer adsorption. We thoroughly study the interplay between the…

Motivated by recent experiments on the rod-like virus bacteriophage fd, confined to circular and annular domains, we present a theoretical study of structural transitions in these geometries. Using the continuum theory of nematic liquid…

There have been several studies suggesting that protein structures solved by NMR spectroscopy and x-ray crystallography show significant differences. To understand the origin of these differences, we assembled a database of high-quality…