相关论文: Aggregate geometry in amyloid fibril nucleation

Ample experimental evidence has been accumulated demonstrating that the formation of monodispersed colloids proceeds through a more complex mechanism, than the generally excepted diffusional "burst nucleation" process. Instead, the…

Protein aggregation, linked to many of diseases, is initiated when monomers access rogue conformations that are poised to form amyloid fibrils. We show, using simulations of src SH3 domain, that mechanical force enhances the population of…

We employ Monte Carlo simulations to investigate the self-assembly of patchy colloidal dumbbells interacting via a modified Kern-Frenkel potential by probing the system concentration and dumbbell shape. We consider dumbbells consisting of…

The observation by Ke et al. [Science 338, 1177 (2012)] that large numbers of short, pre-designed DNA strands can assemble into three-dimensional target structures came as a great surprise, as no colloidal self-assembling system has ever…

Spontaneous self-assembly in molecular systems is a fundamental route to both biological and engineered soft matter. Simple micellisation, emulsion formation, and polymer mixing principles are well understood. However, the principles behind…

Large protein complexes are assembled from protein subunits to form a specific structure. In our theoretic work, we propose that assembly into the correct structure could be reliably achieved through an assembly line with a specific…

Peptides are recognized for their varied self-assembly behaviors, forming a wide array of structures and geometries, such as spheres, fibers, and hydrogels, each presenting a unique set of material properties. The functionalities of these…

Amphipathic peptides are considered promising antibiotics because of their ability to form pores in bacterial membranes. In two companion papers, we analyzed both experimentally and theoretically the mechanisms and consequences of the…

We systematically explore the self-assembly of semi-flexible polymers in deformable spherical confinement across a wide regime of chain stiffness, contour lengths and packing fractions by means of coarse-grained molecular dynamics…

In laboratory experiments, we studied collisions of ensembles of compact (filling factor 0.33) millimeter dust aggregates composed of micrometer quartz grains. We used cylindrical aggregates, triangular aggregates, square aggregates, and…

The classical approach to protein folding inspired by statistical mechanics avoids the high dimensional structure of the conformation space by using effective coordinates. Here we introduce a network approach to capture the statistical…

The assumption that similar structures have similar folding probabilities ($p_{fold}$) leads naturally to a procedure to evaluate $p_{fold}$ for every snapshot saved along an equilibrium folding-unfolding trajectory of a structured peptide…

Protein aggregation including the formation of dimers and multimers in solution, underlies an array of human diseases such as systemic amyloidosis which is a fatal disease caused by misfolding of native globular proteins damaging the…

Protein aggregation is of great importance in biology, e.g., in amyloid fibrillation. The aggregation processes that occur at the cellular scale must be highly stochastic in nature because of the statistical number fluctuations that arise…

Molecular dynamics simulations have been employed to study the formation of a physical (thermoreversible) gel by amphiphilic A-B-A triblock copolymers in aqueous solution. In order to mimic the structure of hydrogel-forming polypeptides…

We use numerical simulations to show how noninteracting hard particles binding to a deformable elastic shell may self-assemble into a variety of linear patterns. This is a result of the nontrivial elastic response to deformations of shells.…

We study geometric presentations of braid groups for particles that are constrained to move on a graph, i.e. a network consisting of nodes and edges. Our proposed set of generators consists of exchanges of pairs of particles on junctions of…

Assembled arrays of individual atoms with Rydberg-mediated interactions provide a powerful platform for the simulation of many-body spin Hamiltonians as well as the implementation of universal gate-based quantum information processing. We…

We study the thermodynamics and kinetics of folding for a small peptide. Our data rely on Monte Carlo simulations where the interactions among all atoms are taken into account. Monte Carlo kinetics is used to study folding of the peptide at…

We investigate the length distribution of self-assembled, long and stiff polymers at thermal equilibrium. Our analysis is based on calculating the partition functions of stiff polymers of variable lengths in the elastic regime. Our…