Related papers: Multifarious Assembly Mixtures: Systems Allowing R…
We study two mechanisms for the formation of protein patterns near membranes of living cells by mathematical modelling. Self-assembly of protein domains by electrostatic lipid-protein interactions is contrasted with self-organization due to…
Recent advances in Foundation Models for Materials Science are poised to revolutionize the discovery, manufacture, and design of novel materials with tailored properties and responses. Although great strides have been made, successes have…
High-throughput computational materials design promises to greatly accelerate the process of discovering new materials and compounds, and of optimizing their properties. The large databases of structures and properties that result from…
Many biological and synthetic materials self-assemble into helical or twisted aggregates. The shape is determined by a complex interplay between elastic forces and the orientation and chirality of the constituent molecules. We study this…
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…
The use of reduced models for investigating the self-assembly dynamics underlying protein shell formation in spherical viruses is described. The spontaneous self-assembly of these polyhedral, supramolecular structures, in which icosahedral…
The kinetics of the self-assembly of nanocomponents into a virus, nanocapsule, or other composite structure is analyzed via a multiscale approach. The objective is to achieve predictability and to preserve key atomic-scale features that…
The accurate assembly of the system matrix is an important step in any code that solves partial differential equations on a mesh. We either explicitly set up a matrix, or we work in a matrix-free environment where we have to be able to…
Self-assembly is ubiquitous in nature, particularly in biology, where it underlies the formation of protein quaternary structure and protein aggregation. Quaternary structure assembles deterministically and performs a wide range of…
In the age of artificial intelligence and biotechnology, a unified understanding of technology and biology is critically needed but still lacking. A cornerstone of such unification is evolvable design. I present a formalism, called goal…
We formulate statistical-mechanical inverse methods in order to determine optimized interparticle interactions that spontaneously produce target many-particle configurations. Motivated by advances that give experimentalists greater and…
We investigate general properties of non-deterministic self-assembly with asymmetric interactions, using a computational model and DNA tile assembly experiments. By contrasting symmetric and asymmetric interactions we show that the latter…
Structural hierarchy, in which materials possess distinct features on multiple length scales, is ubiquitous in nature; diverse biological materials, such as bone, cellulose, and muscle, have as many as ten hierarchical levels. Structural…
Equilibrium self-assembly and conventional materials processing techniques fall far short of mimicking dynamic self-actuating processes that are commonplace throughout biology. To bridge the gap between living and synthetic matter, we study…
In this paper, we present high-level overviews of tile-based self-assembling systems capable of producing complex, infinite, aperiodic structures known as discrete self-similar fractals. Fractals have a variety of interesting mathematical…
Isotropic pairwise interactions that promote the self assembly of complex particle morphologies have been discovered by inverse design strategies derived from the molecular coarse-graining literature. While such approaches provide an avenue…
Interaction between dipolar forces, such as permanent magnets, generally leads to the formation of one-dimensional chains and rings. We investigated whether it was possible to let dipoles self-assemble into three-dimensional structures by…
In this paper we generalize a methodology [T. E. Ouldridge, A. A. Louis, and J. P. K. Doye, J. Phys.: Condens. Matter {\bf 22}, 104102 (2010)] for dealing with the inference of bulk properties from small simulations of self-assembling…
Obtaining a rigorous and reliable method for linking computer simulations of polymer blends and composites at different length scales of interest is a highly desirable goal in soft matter physics. In this paper a multiscale modeling…
Allosteric interactions occur when binding at one part of a complex affects the interactions at another part. Allostery offers a high degree of control in multi-species processes, and these interactions play a crucial role in many…