Related papers: Distribution of volume, microvoid percolation, and…
Spatial heterogeneity is a hallmark of living systems, even at the molecular scale in individual cells. A key example is the partitioning of membrane-bound proteins via lipid domain formation or cytoskeleton-induced corralling. Yet the…
We present a model, based on symmetry and geometry, for proteins. Using elementary ideas from mathematics and physics, we derive the geometries of discrete helices and sheets. We postulate a compatible solvent-mediated emergent pairwise…
Recently, we presented a framework for understanding protein structure based on the idea that simple constructs of holding hands or touching of objects can be used to rationalize the common characteristics of globular proteins. We developed…
Understanding protein motion within the cell is crucial for predicting reaction rates and macromolecular transport in the cytoplasm. A key question is how crowded environments affect protein dynamics through hydrodynamic and direct…
We study the global distribution and morphology of dark matter voids in a LCDM universe using density fields generated by N-body simulations. Voids are defined as isolated regions of the low-density excursion set specified via density…
Percolation theory from statistical physics has been applied to several aspects of tumor progression. Tumor growth on percolation clusters has been used to model spatial expansion, vascular percolation to describe nutrient supply and…
We review recent developments in size separation in vibrated granular materials. Motivated by a need in industry to efficiently handle granular materials and a desire to make fundamental advances in non-equilibrium physics, experimental and…
Understanding how monomeric proteins fold under in vitro conditions is crucial to describing their functions in the cellular context. Significant advances both in theory and experiments have resulted in a conceptual framework for describing…
The protein folding problem must ultimately be solved on all length scales from the atomic up through a hierarchy of complicated structures. By analyzing the stability of the folding process using physics and mathematics, this paper shows…
Predicting segregation of granular materials composed of different-sized particles is a challenging problem. In this paper, we develop and implement a theoretical model that captures the interplay between advection, segregation, and…
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…
Localization properties of residue fluctuations in globular proteins are studied theoretically by using the Gaussian network model. Participation ratio for each residue fluctuation mode is calculated. It is found that the relationship…
We investigate experimentally the statistics of the free volume inside bidimensional granular packings, for two different kinds of grains and two levels of compaction. With the aim to gain new insight into the statistical description of…
In string percolation model, the study of colliding systems at high energies is based on a continuum percolation theory in two dimensions where the number of strings distributed in the surface of interest is strongly determined by the size…
Shortly after the determination of the first protein x-ray crystal structures, researchers analyzed their cores and reported packing fractions $\phi \approx 0.75$, a value that is similar to close packing equal-sized spheres. A limitation…
The mechanisms by which a protein's 3D structure can be determined based on its amino acid sequence have long been one of the key mysteries of biophysics. Often simplistic models, such as those derived from geometric constraints, capture…
Consider a Boolean model $\Sigma$ in $\R^d$. The centers are given by a homogeneous Poisson point process with intensity $\lambda$ and the radii of distinct balls are i.i.d.\ with common distribution $\nu$. The critical covered volume is…
The microstructure of coagulated colloidal particles, for which the inter-particle potential is described by the DLVO theory, is strongly influenced by the particles' surface potential. Depending on its value, the resulting microstructures…
The transport properties of disordered systems are known to depend critically on dimensionality. We study the diffusion coefficient of a quantum particle confined to a lattice on the surface of a tube, where it scales between the 1D and 2D…
We discuss the problem of proteasomal degradation of proteins. Though proteasomes are important for all aspects of the cellular metabolism, some details of the physical mechanism of the process remain unknown. We introduce a stochastic…