Related papers: A Coarse-Grained Simulation Model for Self-Assembl…
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…
In contrast to most self-assembling synthetic materials, which undergo unbounded growth, many biological self-assembly processes are self-limited. That is, the assembled structures have one or more finite dimensions that are much larger…
We study the effects of the optical binding force on wavelength sized colloidal particles free to move in a counter-propagating beam. This work is motivated by the concept of using optical binding to direct the assembly of large numbers of…
The associative interaction, such as hydrogen bonding, can bring about versatile functionalities to polymer systems, which has been investigated by tremendous researches, but the fundamental understanding on association process is still…
Understanding the role of self-propulsion on the conformational properties of active filamentous objects has relevance in biology. In this context, we consider a flexible bead-spring model polymer for which along with both attractive and…
The self-assembly of polyhedral shells, each constructed from 60 trapezoidal particles, is simulated using molecular dynamics. The spatial organization of the component particles in this shell is similar to the capsomer proteins forming the…
Phase separation within polymer networks plays a central role in shaping the structure and mechanics of both synthetic materials and living cells, including the formation of biomolecular condensates within cytoskeletal networks. Previous…
Molecular dynamics simulations have been performed on pure liquid water, aqueous solutions of sodium chloride, and polymer solutions exposed to a strong external electric field with the goal to gain molecular insight into the structural…
By means of multicanonical computer simulations, we investigate thermodynamic properties of the aggregation of interacting semiflexible polymers. We analyze a mesoscopic bead-stick model, where nonbonded monomers interact via Lennard-Jones…
We develop a method for simulating colloidal suspensions using multiparticle collision dynamics (MPCD) with a discrete particle model represented as a rigid body. The key steps for incorporating the rigid-body constraints are to thermalize…
Molecular motors are essential to the living, they generate additional fluctuations that boost transport and assist assembly. Self-propelled colloids, that consume energy to move, hold similar potential for the man-made assembly of…
In this work, we develop a two-component coarse-grained molecular dynamics (CGMD) model for simulating the erythrocyte membrane. This proposed model possesses the key feature of combing the lipid bilayer and the erythrocyte cytoskeleton,…
Macroscopic properties of suspensions, such as those composed of globular particles (e.g., colloidal or macromolecular), can be tuned by controlling the equilibrium aggregation of the particles. We examine how aggregation -- and, hence,…
We demonstrate a simple method by which time-dependent interactions can be exploited to improve self-assembly in colloidal systems. We apply this method to two systems: a model colloid with short-ranged attractive potentials that undergoes…
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…
Polypeptides can self-assemble into hierarchically organized fibrils consisting of a stack of individually folded polypeptides driven together by hydrophobic interaction. Using a coarse grained model, we systematically studied this…
Molecular dynamics simulations are used to investigate the conformations of a single polymer chain, represented by the Kremer-Grest bead-spring model, in a solution with a Lennard-Jones liquid as the solvent when the interaction strength…
We perform numerical simulations of isolated, partially active polymers, driven out-of-equilibrium by a fraction of their monomers. We show that, if the active beads are all gathered in a contiguous block, the position of the section along…
Colloidal dispersions are prized as model systems to understand basic properties of materials, and are central to a wide range of industries from cosmetics to foods to agrichemicals. Among the key developments in using colloids to address…
In the presence of a non-adsorbing polymer, monodisperse rod-like colloids assemble into one-rod-length thick liquid-like monolayers, called colloidal membranes. The density of the rods within a colloidal membrane is determined by a balance…