Related papers: How do particles with complex interactions self-as…
The self-assembly of polymer grafted nanoparticles is more and more used in the field of functional materials. However, there is still a lack of analysis on the dynamic transformation paths of different self-assembly morphologies, which…
Membrane proteins and lipids can self-assemble into membrane protein polyhedral nanoparticles (MPPNs). MPPNs have a closed spherical surface and a polyhedral protein arrangement, and may offer a new route for structure determination of…
Using a coarse-grained model, self-organized assembly of proteins (e.g. CorA and its inner segment iCorA) is studied by examining quantities such as contact profile, radius of gyration, and structure factor as a function of protein…
A major challenge facing existing sequential Monte-Carlo methods for parameter estimation in physics stems from the inability of existing approaches to robustly deal with experiments that have different mechanisms that yield the results…
Studying physical mechanisms and common geometric principles underlying known spherical packings is crucial for rational design of synthetic nanocontainers. Here we model the growth of small spherical shells containing n<72 identical…
Patchy particles have proven to be a prominent model for studying the self-assembly behavior of various systems, ranging from finite clusters to bulk crystal assemblies, and from synthetic colloidal particles to viruses. The patchy particle…
Polymer-grafted nanoparticles are versatile building blocks that self-assemble into a rich diversity of mesostructures. Coarse-grained molecular simulations have commonly accompanied experiments by resolving structure formation pathways and…
An extremely broad and important class of phenomena in nature involves the settling and aggregation of matter under gravitation in fluid systems. Some examples include: sedimenting marine snow particles in lakes and oceans (central to…
Self-propelled particles can spontaneously form dense phases from a dilute suspension in a process referred to as motility-induced phase separation. The properties of the out-of-equilibrium structures that are formed are governed by the…
Field induced assembly of reconfigurable structures with complex hierarchical configurations has recently become an area of intense research with the promise for exciting applications in programmable self-assembly and nano/microstructure…
Peptides and proteins exhibit a common tendency to assemble into highly ordered fibrillar aggregates, whose formation proceeds in a nucleation-dependent manner that is often preceded by the formation of disordered oligomeric assemblies.…
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…
Just like atoms combine into molecules, colloids can self-organize into predetermined structures according to a set of design principles. Controlling valence -- the number of inter-particle bonds -- is a prerequisite for the assembly of…
The ability to control the crystallization behaviour (including its absence) of particles, be they biomolecules such as globular proteins, inorganic colloids, nanoparticles, or metal atoms in an alloy, is of both fundamental and…
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…
Accurately modeling and designing protein complex structures is a central problem in computational structural biology, with broad implications for understanding cellular function and developing therapeutics. This thesis investigates two…
We simulate structural phase behavior of polymer-grafted colloidal particles by molecular Monte Carlo technique. Interparticle potential, which has a finite repulsive square-step outside a rigid core of the colloid, was previously confirmed…
The formation of quasi-spherical cages from protein building blocks is a remarkable self-assembly process in many natural systems, where a small number of elementary building blocks are assembled to build a highly symmetric icosahedral…
The spontaneous organization of particles at the boundary between two fluids is a common occurrence. Scientists have extensively investigated various internal and external factors to manipulate and guide these self-assembly processes. This…
Patchy particles is the name given to a large class of systems of mesoscopic particles characterized by a repulsive core and a discrete number of short-range and highly directional interaction sites. Numerical simulations have contributed…