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Actin networks in certain single-celled organisms exhibit a complex pattern-forming dynamics that starts with the appearance of static spots of actin on the cell cortex. Spots soon become mobile, executing persistent random walks, and eventually give rise to traveling waves of actin. Here we describe a possible physical mechanism for this distinctive set of(More)
We introduce a "virtual-move" Monte Carlo algorithm for systems of pairwise-interacting particles. This algorithm facilitates the simulation of particles possessing attractions of short range and arbitrary strength and geometry, an important realization being self-assembling particles endowed with strong, short-ranged, and angularly specific ("patchy")(More)
When pulled along its axis, double-stranded DNA elongates abruptly at a force of approximately 65 pN. Two physical pictures have been developed to describe this overstretched state. The first proposes that strong forces induce a phase transition to a molten state consisting of unhybridized single strands. The second picture introduces an elongated(More)
We use computer simulations to investigate self-assembly in a system of model chaperonin proteins, and in an Ising lattice gas. We discuss the mechanisms responsible for rapid and efficient assembly in these systems, and we use measurements of dynamical activity and assembly progress to compare their propensities for kinetic trapping. We use the analytic(More)
We use computer simulation to study crystal-forming model proteins equipped with interactions that are both orientationally specific and nonspecific. Distinct dynamical pathways of crystal formation can be selected by tuning the strengths of these interactions. When the nonspecific interaction is strong, liquidlike clustering can precede crystallization;(More)
Protein complexes called rosettasomes self-assemble in solution to form large-scale filamentous and planar structures. The relative abundance of these aggregates varies abruptly with environmental conditions and sample composition. Our simulations of a model of patchy nanoparticles can reproduce this sharp crossover, but only if particles are allowed to(More)
Double-stranded DNA "overstretches" at a pulling force of about 65 pN, increasing in length by a factor of 1.7. The nature of the overstretched state is unknown, despite its considerable importance for DNA's biological function and technological application. Overstretching is thought by some to be a force-induced denaturation and by others to consist of a(More)
A quantitative understanding of nanocrystal phase transformations would enable more efficient energy conversion and catalysis, but has been hindered by difficulties in directly monitoring well-characterized nanoscale systems in reactive environments. We present a new in situ luminescence-based probe enabling direct quantification of nanocrystal phase(More)
Theories of phase change and self-assembly often invoke the idea of a "quasiequilibrium," a regime in which the nonequilibrium association of building blocks results nonetheless in a structure whose properties are determined solely by an underlying free energy landscape. Here we study a prototypical example of multicomponent self-assembly, a one-dimensional(More)
Three-dimensional protein structures usually contain regions of local order, called secondary structure, such as α-helices and β-sheets. Secondary structure is characterized by the local rotational state of the protein backbone, quantified by two dihedral angles called ϕ and ψ. Particular types of secondary structure can generally be described by a single(More)