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A numerical method is presented for first-principle simulations of charged colloidal dispersions in electrolyte solutions. Utilizing a smoothed profile for colloid-solvent boundaries, efficient mesoscopic simulations are enabled for…
We consider the homogenisation of a coupled reaction-diffusion process in a porous medium with evolving microstructure. A concentration-dependent reaction rate at the interface of the pores with the solid matrix induces a…
Chemically powered self-propelled colloids generate a motor force by converting locally a source of energy into directed motion, a process that has been explored both in experiments and in computational models. The use of active colloids as…
We present a multi-scale simulation of early stage of DNA damages by the indirect action of hydroxyl ($^\bullet$OH) free radicals generated by electrons and protons. The computational method comprises of interfacing the Geant4-DNA Monte…
Dynamical polydispersity in single-particle properties, for example a fluctuating particle size, shape, charge density, etc., is intrinsic to responsive colloids (RCs), such as biomacromolecules or microgels, but is typically not resolved…
Many recent studies of liquid-liquid phase separation in biology focus on phase separation as a dynamic control mechanism for cellular function, but it can also result in complex mesoscopic structures. We primarily investigate a model…
We study the depletion-induced self-assembly of indented colloids. Using state-of-the-art Monte Carlo simulation techniques that treat the depletant particles explicitly, we demonstrate that colloids assemble by a lock-and-key mechanism,…
Computational methods for designing interactions between colloidal particles that induce self-assembly have received much attention for their promise to discover tailored materials. However, it often remains a challenge to translate…
The approach for the description of the DNA conformational transformations on the mesoscopic scales in the frame of the double helix is presented. Due to consideration of the joint motions of DNA structural elements along the conformational…
We review theoretical explanation of mechanisms of control of uniformity in growth of nanosize particles and colloids. The nanoparticles are synthesized as nanocrystals, by burst nucleation from solution. The colloids are self-assembled by…
Stochastic models of reaction-diffusion systems are important for the study of biochemical reaction networks where species are present in low copy numbers or if reactions are highly diffusion limited. In living cells many such systems…
Self-assembly, the process by which interacting components form well-defined and often intricate structures, is typically thought of as a spontaneous process arising from equilibrium dynamics. When a system is driven by external…
We study the computational complexity of the recently proposed nubot model of molecular-scale self-assembly. The model generalises asynchronous cellular automata to have non-local movement where large assemblies of molecules can be pushed…
DNA nanotechnology promises to provide controllable self-assembly on the nanoscale, allowing for the design of static structures, dynamic machines and computational architectures. In this article I review the state-of-the art of DNA…
The specificity and thermal reversibility of DNA interactions have enabled the self-assembly of crystal structures, self-replicating materials and colloidal molecules. Grafting DNA onto liquid interfaces of emulsions leads to exciting new…
DNA is an astonishing material that can be used as a molecular building block to construct periodic arrays and devices with nanoscale accuracy and precision. Here, we present simple bead-spring model of DNA nanostars having three, four and…
The recently introduced method of excess collisions (MEC) is modified to estimate diffusion-controlled reaction times inside systems of arbitrary size. The resulting MEC-E equations contain a set of empirical parameters, which have to be…
This study presents a theoretical model for a self-replicating mechanical system inspired by biological processes within living cells and supported by computer simulations. The model decomposes self-replication into core components, each of…
Soft materials (e.g., enveloped viruses, liposomes, membranes and supercooled liquids) simultaneously deform or display collective behaviors, while undergoing atomic scale vibrations and collisions. While the multiple space-time character…
In order to replicate within their cellular host, many viruses have developed self-assembly strategies for their capsids which are sufficiently robust as to be reconstituted in vitro. Mathematical models for virus self-assembly usually…