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The emergence upon cooling of an ordered solid phase from a liquid is a remarkable example of self-assembly, which has also major practical relevance. Here, we use a recently developed committor-based enhanced sampling method [Kang et al.,…
Self-assembly processes in biological and synthetic biomolecular systems are often governed by the spatial separation of biochemical processes. While previous work has focused on optimizing self-assembly through fine-tuned reaction…
Statistical aspects of the dynamics of chaotic scattering in the classical model of $\alpha$-cluster nuclei are studied. It is found that the dynamics governed by hyperbolic instabilities which results in an exponential decay of the…
Self-assembly is a ubiquitous process in synthetic and biological systems, broadly defined as the spontaneous organization of multiple subunits (e.g. macromolecules, particles) into ordered multi-unit structures. The vast majority of…
The Eigen model is a prototypical toy model of evolution that is synonymous with the so-called error catastrophe: when mutation rates are sufficiently high, the genetic variant with the largest replication rate does not occupy the largest…
Recent theoretical studies have shown that demographic stochasticity can greatly increase the tendency of asexually reproducing phenotypically diverse organisms to spontaneously evolve into localised clusters, suggesting a simple mechanism…
A central problem in population ecology is understanding the consequences of stochastic fluctuations. Analytically tractable models with Gaussian driving noise have led to important, general insights, but they fail to capture rare,…
Nucleation is the rate-determining step in the kinetics of many self-assembly processes. However, the importance of nucleation in the kinetics of DNA-origami self-assembly, which involves both the binding of staple strands and the folding…
Conventional wisdom suggests that environmental noise drives populations toward extinction. In contrast, we report a paradoxical phenomenon in which stochasticity reverses a deterministic tipping point, thereby preventing collapse. Using a…
The inverse problem of designing component interactions to target emergent structure is fundamental to numerous applications in biotechnology, materials science, and statistical physics. Equally important is the inverse problem of designing…
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…
In biological materials, strong binding despite an applied load force is often based on clusters of dynamic bonds that share the load. Different macroscopic behaviors have been described depending on whether the load is shared locally or…
We use computer simulations to study a model, first proposed by Wales [1], for the reversible and monodisperse self-assembly of simple icosahedral virus capsid structures. The success and efficiency of assembly as a function of…
Despite recent developments in management theory, maintaining a manufacturing schedule remains difficult because of production delays and fluctuations in demand and supply of materials. The response of manufacturing systems to such…
In the self-assembly process which drives the formation of cellular membranes, micelles, and capsids, a collection of separated subunits spontaneously binds together to form functional and more ordered structures. In this work, we study the…
We investigate extinction of a long-lived self-regulating stochastic population, caused by intrinsic (demographic) noise. Extinction typically occurs via one of two scenarios depending on whether the absorbing state n=0 is a repelling…
Self-closing assembly is prone to polymorphism due to thermally-excited bending fluctuations, which permit the formation of off-target assemblies at the point of self-closure. One way to overcome this source of polymorphism is to use…
We study the steady state of an assembly of microtubules in a confined volume, analogous to the situation inside a cell where the cell boundary forms a natural barrier to growth. We show that the dynamical equations for growing and…
Majumder, Reif and Sahu have presented a stochastic model of reversible, error-permitting, two-dimensional tile self-assembly, and showed that restricted classes of tile assembly systems achieved equilibrium in (expected) polynomial time.…
The crystallization of complex, concentrated alloys can result in atomic-level short-range order, composition gradients, and phase separation. These features govern the properties of the resulting alloy. While nucleation and growth in…