Related papers: Mechanism for the stabilization of protein cluster…
Spherical confinement can act either stabilizing or destabilizing on the collapsed state of a semi-flexible polymer. General free-energy arguments suggest that the order of the unconstrained collapse transition is the distinguishing factor:…
We investigate regular configurations of a small number of particles settling under gravity in a viscous fluid. The particles do not touch each other and can move relative to each other. The dynamics is analyzed in the point-particle…
A framework is presented for understanding the common character of proteins. Proteins are linear chain molecules. However, the simple model of a polymer viewed as spheres tethered together does not account for many of the observed…
A theory of clustering of inertial particles advected by a turbulent velocity field caused by an instability of their spatial distribution is suggested. The reason for the clustering instability is a combined effect of the particles inertia…
We investigate the formation of cluster crystals with multiply occupied lattice sites on a spherical surface in systems of ultra-soft particles interacting via repulsive, bounded pair potentials. Not all interactions of this kind lead to…
We have performed large-scale Lennard-Jones molecular dynamics simulations of homogeneous vapor-to-liquid nucleation, with $10^9$ atoms. This large number allows us to resolve extremely low nucleation rates, and also provides excellent…
Proteins are biological polymers that underlie all cellular functions. The first high-resolution protein structures were determined by x-ray crystallography in the 1960s. Since then, there has been continued interest in understanding and…
Motivated by experimental and numerical studies revealing that discoidal high-density lipoprotein (HDL) particles may adopt flat elliptical and nonplanar saddle-like configurations, it is hypothesized that these might represent stabilized…
We report numerical investigations of a three-dimensional model of diffusive growth of fine particles, the internal structure of which corresponds to different crystal lattices. A growing cluster (particle) is immersed in, and exchanges…
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…
Membrane proteins often form dimers and higher-order oligomers whose stability and spatial organization depend sensitively on their lipid environment. To investigate the physical principles underlying this coupling, we employ a lattice…
Single domain proteins are thought to be tightly packed. The introduction of voids by mutations is often regarded as destabilizing. In this study we show that packing density for single domain proteins decreases with chain length. We find…
We make use of the previously developed formalism for a monomer ensemble and include angular dependence of the segments of the polymer chains thus described. In particular we show how to deal with stiffness when the polymer chain is…
The settling of heavy spherical particles in a column of quiescent fluid is investigated. The performed experiments cover a range of Galileo numbers ($110 \leq \text{Ga} \leq 310$) for a fixed density ratio of $\Gamma = \rho_p/\rho_f =…
In the context of the standard model of particle physics, there is a definite upper limit to the density of stable compact stars. However, if there is a deeper layer of constituents, below that of quarks and leptons, stability may be…
We investigate the properties of clusters formed from two connected $\mathrm{Ge_{m}}$ cage-like clusters, such as experimentally synthesized $\mathrm{Au_3Ge_{18}^{5-}}$, using first-principles DFT methods. We focus particularly on…
This article uses a combination of three ideas from simulation to establish a nearly optimal polynomial upper bound for the joint density of the stable process and its associated supremum at a fixed time on the entire support of the joint…
The dilute fluid phase of model globular proteins is studied. The model possesses a fluid-fluid transition buried within the fluid-crystal coexistence region, as do some globular proteins. If this fluid-fluid transition is not buried deep…
Particles confined in droplets are called compound particles. They are encountered in various biological and soft matter systems. Hydrodynamics can play a decisive role in determining the configuration and stability of these multiphase…
We present a new stabilization technique for multiscale convection diffusion problems. Stabilization for these problems has been a challenging task, especially for the case with high Peclet numbers. Our method is based on a constraint…