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Inspired by recent successes using single-stranded DNA tiles to produce complex structures, we develop a two-step coarse-graining approach that uses detailed thermodynamic calculations with oxDNA, a nucleotide-based model of DNA, to…
Parallelism of tight-binding molecular dynamics simulations is presented by means of the order-N electronic structure theory with the Wannier states, recently developed (J. Phys. Soc. Jpn. 69,3773 (2000)). An application is tested for…
Colloidal building blocks with re-configurable shapes and dynamic interactions can exhibit unusual self-assembly behaviors and pathways. In this work, we consider the phase behavior of colloids coated with surface-mobile polymer brushes…
Colloidal particles can create reconfigurable nanomaterials, with applications such as color-changing, self-repairing, and self-regulating materials and reconfigurable drug delivery systems. However, top-down methods for manipulating…
The design space for a self-assembled multicomponent objects ranges from a solution in which every building block is unique to one with the minimum number of distinct building blocks that unambiguously define the target structure. Using a…
Understanding multibody interactions between colloidal particles out of equilibrium has a profound impact on dynamical processes such as colloidal self assembly. However, traditional colloidal interactions are effectively quasi-static on…
In many virus families, tens to thousands of proteins assemble spontaneously into a capsid (protein shell) while packaging the genomic nucleic acid. This review summarizes recent advances in computational modeling of these dynamical…
This computational study introduces a theoretical framework for practical, electrochemical fuel generation displaying exponential product yields as functions of time. Exponential reaction scaling is simulated through an autocatalytic cycle…
DNA self-assembly is an important tool that has a wide range of applications such as building nanostructures, the transport of target virotherapies, and nano-circuitry. Tools from graph theory can be used to encode the biological process of…
We survey our research on modeling the mechanisms of control of uniformity in growth of nanosize and colloid particles. The former are produced as nanocrystals, by burst-nucleation from solution. The latter, colloid-size particles, are…
We propose that genetic encoding of self-assembling components greatly enhances the evolution of complex systems and provides an efficient platform for inductive generalization, i.e. the inductive derivation of a solution to a problem with…
Self-assembly of complex and functional materials remains a grand challenge in soft material science. Efficient assembly depends on a delicate balance between thermodynamic and kinetic effects, requiring fine-tuning affinities and…
Many processes can correspond to reactive impregnation in porous solids. These processes are usually numerically computed by classical methods like finite element method, finite volume method, etc. The disadvantage of these methods remains…
Many stochastic processes in the physical and biological sciences can be modelled as Brownian dynamics with multiplicative noise. However, numerical integrators for these processes can lose accuracy or even fail to converge when the…
Complex colloidal cluster morphologies are desirable for the fabrication of advanced materials, such as photonic crystals and meta-materials, and can be formed through evaporation-driven packing. By coupling lattice Boltzmann and discrete…
The evolution of an initially prepared distribution of micron sized colloidal particles, trapped at a fluid interface and under the action of their mutual capillary attraction, is analyzed by using Brownian dynamics simulations. At a…
Concentrated solutions of short blunt-ended DNA duplexes, down to 6 base pairs, are known to order into the nematic liquid crystal phase. This self-assembly is due to the stacking interactions between the duplex terminals that promotes…
An important goal of self-assembly is to achieve a preprogrammed structure with high fidelity. Here, we control the valence of DNA-functionalized emulsions to make linear and branched model polymers, or `colloidomers'. The distribution of…
We study the problem of the self-assembly of nanoparticles (NPs) into finite mesoscopic structures with a programmed local morphology and complex overall shape. Our proposed building blocks are NPs directionally-functionalized with DNA. The…
Simulations of macromolecular diffusion and adsorption in confined environments can offer valuable mechanistic insights into numerous biophysical processes. In order to model solutes at atomic detail on relevant time scales, Brownian…