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We study topological properties of large scale structure in a set of scale free N-body simulations using the genus and percolation curves as topological characteristics. Our results show that as gravitational clustering advances, the…
Many researches have been working on the protein folding problem from more than half century. Protein folding is indeed one of the major unsolved problems in science. In this work, we discuss a model for the simulation of protein…
A voxelization based post-processing algorithm is proposed to analyze the packing of non-spherical particle assemblies simulated using the Discrete Element Method. Voxelization of the particle data allows for isolating the geometric…
Volume density is a key physical quantity controlling the evolution of the interstellar medium (ISM) and star formation, but it cannot be accessed directly by observations of molecular clouds. We aim at estimating the volume density…
Chemical space which encompasses all stable compounds is unfathomably large and its dimension scales linearly with the number of atoms considered. The success of machine learning methods suggests that many physical quantities exhibit…
A steadily growing computational power is employed to perform molecular dynamics simulations of biological macromolecules, which represents at the same time an immense opportunity and a formidable challenge. In fact, large amounts of data…
What are the structural determinants of protein sequence evolution? A number of site-specific structural characteristics have been proposed, most of which are broadly related to either the density of contacts or the solvent accessibility of…
While all the information required for the folding of a protein is contained in its amino acid sequence, one has not yet learnt how to extract this information so as to predict the detailed, biological active, three-dimensional structure of…
A two-dimensional, transient, multi-scale modeling approach is presented for predicting the magnitude and rate of percolation segregation for binary mixtures of granular material in a rotating drum and conical hopper. The model utilizes…
A fundamental task in kernel methods is to pick nodes and weights, so as to approximate a given function from an RKHS by the weighted sum of kernel translates located at the nodes. This is the crux of kernel density estimation, kernel…
We present a statistical mechanics treatment of the stability of globular proteins which takes explicitly into account the coupling between the protein and water degrees of freedom. This allows us to describe both the cold and the warm…
Granular materials segregate spontaneously due to differences in particle size, shape, density and flow behaviour. In this paper we experimentally investigate density-difference-driven segregation for a range of density ratios and a range…
Resolving the structural variability of proteins is often key to understanding the structure-function relationship of those macromolecular machines. Single particle analysis using Cryogenic electron microscopy (CryoEM), combined with…
Descriptors that characterize the geometry and topology of the pore space of porous media are intimately linked to their transport properties. We quantify such descriptors, including pore-size functions and the critical pore radius…
Background: Many attempts have been made to resolve in time the folding of model proteins in computer simulations. Different computational approaches have emerged. Some of these approaches suffer from the insensitivity to the geometrical…
Voids are a prominent feature of the galaxy distribution but their quantitative study is hindered by the lack of a precise definition of what constitutes a void. Here we propose a definition of voids in point distributions that uses methods…
Inside a cell, heterotypic proteins assemble in inhomogeneous, crowded systems where the abundance of these proteins vary with cell types. While some protein complexes form putative structures that can be visualized with imaging, there are…
A simple and surprisingly accurate description of spectral diffusion in deeply frozen globular proteins is constructed directly using the concept of ultrametricity of protein dynamics. Earlier the similar concept has been used for…
The functionality of proteins is related to their structure in the native state. Protein structures are made up of emergent building blocks of helices and almost planar sheets. A simple coarse-grained geometrical model of a flexible tube…
We investigate the upscaling of diffusive transport parameters as function of pore scale material structure using a stochastic framework. We focus on sub-REV (representative elementary volume) scale where the complexity of pore space…