Related papers: Distribution of volume, microvoid percolation, and…
Proteins are complex biomolecules that perform a variety of crucial functions within living organisms. Designing and generating novel proteins can pave the way for many future synthetic biology applications, including drug discovery.…
We present an in-depth analysis of the geometrical percolation behavior in the continuum of random assemblies of hard oblate ellipsoids of revolution. Simulations where carried out by considering a broad range of aspect-ratios, from spheres…
We study how the dynamics of a drying front propagating through a porous medium are affected by small-scale correlations in material properties. For this, we first present drying experiments in micro-fluidic micro-models of porous media.…
The intrinsic volumes are measures of the content of a convex body. This paper uses probabilistic and information-theoretic methods to study the sequence of intrinsic volumes of a convex body. The main result states that the intrinsic…
Protein structure prediction and folding are fundamental to understanding biology, with recent deep learning advances reshaping the field. Diffusion-based generative models have revolutionized protein design, enabling the creation of novel…
A region of two-dimensional space has been filled randomly with large number of growing circular discs allowing only a `slight' overlapping among them just before their growth stop. More specifically, each disc grows from a nucleation…
Coarse-grained (CG) molecular dynamics simulations enable efficient exploration of protein conformational ensembles. However, reconstructing atomic details from CG structures (backmapping) remains a challenging problem. Current approaches…
We test the universal finite-size scaling of the cluster mass order parameter in two-dimensional (2D) isotropic and directed continuum percolation models below the percolation threshold by computer simulations. We found that the simulation…
We introduce a new method for stacking voids and deriving their profile that greatly increases the potential of voids as a tool for precision cosmology. Given that voids are highly non-spherical and have most of their mass at their edge,…
In living cells, proteins combine 3D bulk diffusion and 1D sliding along the DNA to reach a target faster. This process is known as facilitated diffusion, and we investigate its dynamics in the physiologically relevant case of confined DNA.…
We study quantum percolation which is described by a tight-binding Hamiltonian containing only off-diagonal hopping terms that are generally in quenched binary disorder (zero or one). In such a system, transmission of a quantum particle is…
In this paper the excluded volume of binary similar hyperparticles with small size difference in D-dimensional Euclidean spaces R2, R3, and R4 is studied using two different statistical geometry approaches. These geometric approaches,…
Protein structure prediction is pivotal for understanding the structure-function relationship of proteins, advancing biological research, and facilitating pharmaceutical development and experimental design. While deep learning methods and…
In the course of evolution, proteins show a remarkable conservation of their three-dimensional structure and their biological function, leading to strong evolutionary constraints on the sequence variability between homologous proteins. Our…
It is not merely the position of residues that are of utmost importance in protein function and stability, but the interactions between them. We illustrate, by using a network construction on a set of 595 non-homologous proteins, that…
We present a general analytical procedure for computing the number density of voids with radius above a given value within the context of gravitational formation of the large scale structure of the universe out of Gaussian initial…
Protein folding, peptide aggregation and crystallization, as well as adsorption of molecules on soft or solid substrates have an essential feature in common: In all these processes, structure formation is guided by a collective, cooperative…
By means of a simple model system, the total volume fluctuations of a tapped granular material in the steady state are studied. In the limit of a system with a large number of particles, they are found to be Gaussian distributed, and…
We simulate the bond and site percolation models on several three-dimensional lattices, including the diamond, body-centered cubic, and face-centered cubic lattices. As on the simple-cubic lattice [Phys. Rev. E, \textbf{87} 052107 (2013)],…
In the first work of this series [physics/0204035] it was shown that the conformational space of a molecule could be described to a fair degree of accuracy by means of a central hyperplane arrangement. The hyperplanes divide the espace into…