Related papers: Intrinsic Defect Formation in Peptide Self-Assembl…
We present fast simulation methods for the self-assembly of complex shapes in two dimensions. The shapes are modeled via a general boundary curve and interact via a standard volume term promoting overlap and an interpenetration penalty. To…
The persistent dynamics in systems out of equilibrium, particularly those characterized by annihilation and creation of topological defects, is known to involve complicated spatiotemporal processes and is deemed difficult to control. Here…
We show that geometric frustration in a broad class of deformable and naturally curved, shell-like colloidal particles gives rise to self-limiting assembly of finite-sized stacks that far exceed particle dimensions. When inter-particle…
Peculiarities of the defect modes of cholesteric liquid crystals (CLCs) with an isotropic/anisotropic defect inside are investigated. The influence of the defect layer thickness and its anisotropy of refraction, the influence of the system…
Spherical particles confined to a sphere surface cannot pack densely into a hexagonal lattice without defects. In this study, we use hard particle Monte Carlo simulations to determine the effects of continuously deformable shape anisotropy…
In this paper the characteristic matrix method is used to study the propagation of electromagnetic waves through one-dimensional lossy photonic crystals composed of negative and positive refractive index material layers with symmetric and…
Motivated by the observations of intracellular phase separations and the wetting of cell membranes by protein droplets, we study the nonequilibrium surface wetting by Monte Carlo simulations of a lattice gas model involving particle…
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…
We report on the self-assembly of inverse patchy colloids (IPC) using Monte Carlo simulations in two-dimensions. The IPC model considered in this work corresponds to either bipolar colloids or colloids decorated with complementary DNA on…
We elucidate the origin of large differences (two-fold or more) in the fixed-node errors between the first- vs second-row systems for single-configuration trial wave functions in quantum Monte Carlo calculations. This significant difference…
We study the patterns generated in finite-time sweeps across symmetry-breaking bifurcations in individual-based models. Similar to the well-known Kibble-Zurek scenario of defect formation, large-scale patterns are generated when model…
Cultured stem cells have become a standard platform not only for regenerative medicine and developmental biology but also for biophysical studies. Yet, the characterization of cultured stem cells at the level of morphology and macroscopic…
In these lectures, I review cosmological phase transitions and the topological aspects of spontaneous symmetry breaking. I then discuss the formation of walls, strings and monopoles during phase transitions including lattice based studies…
Nonlinear plastic modes (NPMs) are collective displacements that are indicative of imminent plastic instabilities in elastic solids. In this work we formulate the atomistic theory that describes the reversible evolution of NPMs and their…
We describe several unexpected phenomena, caused by a solid-solid phase transition (gel-to-crystal) typical for all main classes of lipid substances - phospholipids, triglycerides, diglycerides, alkanes, etc. We discovered that this…
We use computer simulations to investigate self-assembly in a system of model chaperonin proteins, and in an Ising lattice gas. We discuss the mechanisms responsible for rapid and efficient assembly in these systems, and we use measurements…
The hallmark feature of polymorphic systems is their ability to assemble into many possible structures at the same thermodynamic state. Designer polymorphic materials can in principle be engineered via programmable self-assembly, but the…
The errors arising in ab initio density functional theory studies of semiconductor point defects using the supercell approximation are analyzed. It is demonstrated that a) the leading finite size errors are inverse linear and inverse cubic…
The necking instability is a precursor to tensile failure and rupture of materials. A quasistatically loaded free-standing uniaxial specimen typically exhibits necking at a single location, corresponding to a long wavelength bifurcation…
Membrane deformation inside living cells is crucial for the proper shaping of various intracellular organelles and is necessary during the fission/fusion processes that allow membrane recycling and transport (e.g. endocytosis). Proteins…