Related papers: Patchy Particles Design: From Floppy Modes to Slop…
Dynamic models of biochemical networks typically consist of sets of non-linear ordinary differential equations involving states (concentrations or amounts of the components of the network) and parameters describing the reaction kinetics.…
Inverse design can be a useful strategy for discovering interactions that drive particles to spontaneously self-assemble into a desired structure. Here, we extend an inverse design methodology--relative entropy optimization--to determine…
We consider several patchy particle models that have been proposed in literature and we investigate their candidate crystal structures in a systematic way. We compare two different algorithms for predicting crystal structures: (i) an…
We model and study the patterns created through the interaction of collectively moving self-propelled particles (SPPs) and elastically tethered obstacles. Simulations of an individual-based model reveal at least three distinct large-scale…
We study the self-assembly behaviour of patchy particles with `protein-like' interactions that can be considered as a minimal model for the assembly of viral capsids and other shell-like protein complexes. We thoroughly explore the…
Patchy colloids are promising candidates for building blocks in directed self-assembly. To be successful the surface patterns need to both be simple enough to be synthesized, while feature-rich enough to cause the colloids to self-assemble…
A series of simulations aimed at elucidating the self-assembly dynamics of spherical virus capsids is described. This little-understood phenomenon is a fascinating example of the complex processes that occur in the simplest of organisms.…
Throughout the physical sciences, entropy stands out as a pivotal but enigmatic concept that, in materials design, often takes a backseat to energy. Here, we demonstrate how to precisely engineer entropy to achieve desired colloidal…
We explore the relationship among model fidelity, experimental design, and parameter estimation in sloppy models. We show that the approximate nature of mathematical models poses challenges for experimental design in sloppy models. In many…
We explore the use of templated self-assembly to facilitate the formation of complex target structures made from patchy particles. First, we consider the templating of high-symmetry shell structures around a spherical core particle. We find…
One of the fundamental goals of nanotechnology is to exploit selective and directional interactions between molecules to design particles that self-assemble into desired structures, from capsids, to nano-clusters, to fully formed crystals…
A major goal in nanoscience and nanotechnology is the self-assembly of any desired complex structure with a system of particles interacting through simple potentials. To achieve this objective, intense experimental and theoretical efforts…
Stochastic partition models tailor a product space into a number of rectangular regions such that the data within each region exhibit certain types of homogeneity. Due to constraints of partition strategy, existing models may cause…
A broad class of blocked or jammed configurations of particles on the one-dimensional lattice can be characterized in terms of local rules involving only the lengths of clusters of particles (occupied sites) and of holes (empty sites).…
The ability to control forces between sub-micron-scale building blocks offers considerable potential for designing new materials through self-assembly. A typical paradigm is to first identify a particular (crystal) structure that has some…
We study the ordered equilibrium structures of patchy particles where the patches are located on the surface of the colloid such that they form a regular tetrahedron. Using optimization techniques based on ideas of evolutionary algorithms…
Fabrication of diamond structures by self-assembly is a fundamental challenge in making three-dimensional photonic crystals. We simulate a system of model hard particles with attractive patches and show that they can self-assemble into a…
We introduce SAFT-P, a plaquette-level extension of Statistical Associating Fluid Theory for patchy particles. By treating local clusters as associating superparticles and contracting their free energy back to monomer densities, SAFT-P…
In living cells, proteins self-assemble into large functional structures based on specific interactions between molecularly complex patches. Due to this complexity, protein self-assembly results from a competition between a large number of…
Open lattices are characterized by low volume-fraction arrangements of building blocks, low coordination number, and open spaces between building blocks. The self-assembly of these lattices faces the challenge of mechanical instability due…