Related papers: Density waves, dodecahedral geometry and structure…
We present a top-down approach to the study of the dynamics of icosahedral virus capsids, in which each protein is approximated by a point mass. Although this represents a rather crude coarse-graining, we argue that it highlights several…
We carry out a coarse-grained molecular dynamics simulation of phospholipid vesicles with transmembrane proteins. We measure the mean and Gaussian curvatures of our protein-embedded vesicles and quantitatively show how protein clusters…
Landau's phenomenological theory of Fermi liquids is a fundamental paradigm in many-body physics that has been remarkably successful in explaining the properties of a wide range of interacting fermion systems, such as liquid helium-3,…
The influence of quadrupolar interactions on the structure of small clusters is investigated by adding a point quadrupole of variable strength to the Lennard-Jones potential. Competition arises between sheet-like arrangements of the…
We explore the possibility for the native state of a protein being inherently a multi-conformation state in an ab initio coarse-grained model. Based on the Wang-Landau algorithm, the complete free energy landscape for the designed sequence…
We use computer simulations to study a model, first proposed by Wales [1], for the reversible and monodisperse self-assembly of simple icosahedral virus capsid structures. The success and efficiency of assembly as a function of…
We investigate the spatial structure of cohesive granular matter with spheres floating at an air-liquid interface that form disordered close packings with pores in between. The interface is slowly lowered in a conical container to uniformly…
A new method to construct quasicrystalline lattices is proposed. It is based on Landau crystallization theory. Like well-known cut and projection methods our approach deals with N dimensional crystallography, but we don't need any…
The Witting configuration with 40 complex rays was suggested as a possible reformulation of Penrose model with two spin-3/2 systems based on geometry of dodecahedron and used for analysis of nonlocality and contextuality in quantum…
A general Landau's free energy functional is used to study the dynamics of crystallization during liquid-solid Spinodal Decomposition (SD). The strong length scale selectivity imposed during the early stage of SD induces the appearance of…
We study cholesteric order in liquid crystal shells with planar degenerate anchoring. We observe that the bipolar and radial configurations intensively reported for bulk droplets have a higher degree of complexity when the liquid crystal is…
Suspensions of hard core spherical particles of diameter $D$ with inter-core connectivity range $\delta$ can be described in terms of random geometric graphs, where nodes represent the sphere centers and edges are assigned to any two…
Simple RNA viruses self-assemble spontaneously and encapsulate their genome into a shell called the capsid. This process is mainly driven by the attractive electrostatic interaction between the positive charges on capsid proteins and the…
In analytical models of structure formation, protohalos are routinely assumed to be peaks of the smoothed initial density field, with the smoothing filter being spherically symmetric. This works reasonably well for identifying a protohalo's…
The original Thomson problem of "spherical crystallography" seeks the ground state of electron shells interacting via the Coulomb potential; however one can also study crystalline ground states of particles interacting with other…
We present a theoretical study of the folding of small proteins inside confining potentials. Proteins are described in the framework of an effective potential model which contains the Ramachandran angles as degrees of freedom and does not…
Understanding how particles are arranged on the sphere is not only central to numerous physical, biological, and materials systems but also finds applications in mathematics and in analysis of geophysical and meteorological measurements. In…
Hypothesis: Anisotropic rod particles in capillary suspensions form complex network structures with distinctive orientation patterns and rheological properties that differ significantly from spherical particle systems. By identifying the…
We study the optimal packing of short, hard spherocylinders confined to lie tangential to a spherical surface, using simulated annealing and molecular dynamics simulations. For clusters of up to twelve particles, we map out the changes in…
Spin-polarized reconstruction of the v=1 quantum Hall edge is accompanied by a spatial modulation of the charge density along the edge. We find that this is also the case for finite quantum Hall droplets: current spin density functional…