Related papers: The dynamics of viruslike capsid assembly and disa…
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 one-dimensional triplet contact process with diffusion (TCPD) model has been studied using fast multispin GPU Monte Carlo simulations. In particular, the particle density \rho and the density of pairs of neighboring particles \rho_p…
Significantly higher transmissibility of SARS CoV-2 (2019) compared to SARS CoV (2003) can be attributed to mutations of structural proteins (Spike S, Nucleocapsid N, Membrane M, and Envelope E) and the role played by non-structural…
Smectic-A monolayers self-assembled in aqueous solutions of chiral fd viruses and a polymer depletant have been shown to exhibit a variety of structures including large, flat disks and twisted ribbons. The virus particles twist near the…
Aggregation of animal cells in culture comprises a series of motility, collision and adhesion processes of basic relevance for tissue engineering, bioseparations, oncology research and \textit{in vitro} drug testing. In the present paper, a…
Capillary condensation of water is ubiquitous in nature and technology. It routinely occurs in granular and porous media, can strongly alter such properties as adhesion, lubrication, friction and corrosion, and is important in many…
We consider the random clique complex process - the process of clique complexes induced by the complete graph with i.i.d. Uniform edge weights. We investigate the evolution of the Betti numbers of the clique complex process in the critical…
We develop the elastic theory for inversion-asymmetric tethered membranes and use it to identify and study their possible phases. Asymmetry in a tethered membrane causes spontaneous curvature, which in general depends upon the local…
We present a class of cooperative sequential adsorption models on a Cayley tree with constant and variable attachment rates and their possible applications for ionic self-assembly of thin films and drug encapsulation of nanoparticles. Using…
We resolve difficulties in training and sampling from a discrete generative model by learning a smoothed energy function, sampling from the smoothed data manifold with Langevin Markov chain Monte Carlo (MCMC), and projecting back to the…
Self-assembly of proteins into amyloid aggregates is an important biological phenomenon associated with human diseases such as Alzheimer's disease. Amyloid fibrils also have potential applications in nano-engineering of biomaterials. The…
Folding and aggregation of proteins, the interaction between proteins and membranes, as well as the adsorption of organic soft matter to inorganic solid substrates belong to the most interesting challenges in understanding structure and…
Folding of the triangular lattice in a discrete three-dimensional space is investigated numerically. Such ``discrete folding'' has come under through theoretical investigation, since Bowick and co-worker introduced it as a simplified model…
While recent advances in AI have transformed protein structure prediction, protein function is also strongly influenced by the thermodynamic and kinetic features encoded in its underlying free-energy surface. Here, we propose a…
Motivated by observations in sequence data of herpesviruses, we introduce a multi-locus model for the joint evolution of different genotypes in a virus population that is distributed across a population of hosts. In the model, virus…
Biological condensates are assemblies of proteins and nucleic acids that form membraneless compartments in cells and play essential roles in cellular functions. In many cases they exhibit the physical properties of liquid droplets that…
The envelopes covering bacterial cytoplasm possess remarkable elastic properties. They are rigid enough to resist large pressures while being flexible enough to adapt to growth under environmental constraints. Similarly, the virus shells…
Self-assembly kinetics is usually described by approaches which assume that the shape of the aggregates has a definite form (e.g., spherical, cylindrical, cubic, etc), however that is unlikely to be the case in many finite-sized…
Molecule- and particle-based simulations provide the tools to test, in microscopic detail, the validity of classical nucleation theory. In this endeavour, determining nucleation mechanisms and rates for phase separation requires an…
Developing antiviral drugs is an exigent task since viruses mutate to overcome the effect of antiviral drugs. As a result, the efficacy of most antiviral drugs is short-lived. To include this effect, we modify the Neumann and Dahari model.…