Related papers: Fine structures of Intrinsically Disordered Protei…
Intrinsically disordered regions (IDRs) of proteins mediate sequence-specific interactions underlying diverse cellular processes, including the formation of biomolecular condensates. Although IDRs strongly influence condensate compositions,…
We present a scaled particle density functional study of two-dimensional binary mixtures of hard convex particles with one or both species being ellipses. In particular, we divide our study into two parts. The first part is devoted to the…
Predicting the physical interaction of proteins is a cornerstone problem in computational biology. New classes of learning-based algorithms are actively being developed, and are typically trained end-to-end on protein complex structures…
We review the development of thermodynamic protein hydropathic scaling theory, starting from backgrounds in mathematics and statistical mechanics, and leading to biomedical applications. Darwinian evolution has organized each protein family…
We studied equilibrium systems composed of wedge-shaped monodisperse molecules using hard-particle Monte Carlo simulations. Each model molecule was made up of six colinear tangent spheres with linearly decreasing diameters. Thus, the shape…
Mineralization of bone and teeth involves interactions between biomolecules and hydroxyapatite. Associated complex interfaces and processes remain difficult to analyze at the 1 to 100 nm scale using current laboratory techniques, and prior…
We present a unified scaling theory for the structural behavior of polymers embedded in a disordered energy substrate. An optimal polymer configuration is defined as the polymer configuration that minimizes the sum of interacting energies…
Many essential cellular processes, including cell division and the establishment of cell polarity during embryogenesis, are regulated by pattern-forming proteins. These proteins often need to bind to a substrate, such as the cell membrane,…
How do living cells achieve sufficient abundances of functional protein complexes while minimizing promiscuous non-functional interactions? Here we study this problem using a first-principle model of the cell whose phenotypic traits are…
In recent years, Adiabatic Connection Interpolations developed within Density Functional Theory (DFT) have been found to provide satisfactory performances in the calculation of interaction energies when used with Hartree-Fock (HF)…
The probability of two loci, separated by a certain genome length, being in contact can be inferred using the Chromosome Conformation Capture (3C) method and related Hi-C experiments. How to go from the contact map, a matrix listing the…
We consider a particle in one dimension submitted to amplitude and phase disorder. It can be mapped onto the complex Burgers equation, and provides a toy model for problems with interplay of interferences and disorder, such as the NSS model…
This is the second paper of a series of three investigating, by numerical means, the geometric and mechanical properties of spherical bead packings under isotropic stresses. We study the effects of varying the applied pressure P (from 1 or…
Active matter systems, from self-propelled colloids to motile bacteria, are characterized by the conversion of free energy into useful work at the microscopic scale. They involve physics beyond the reach of equilibrium statistical…
In this study, we present a systematic computational investigation to analyze the long debated crystal stability of two well known aspirin polymorphs, labeled as Form I and Form II. Specifically, we developed a strategy to collect training…
We study the equilibrium properties of a single flexible homopolymers where consecutive monomers are represented by impenetrable hard spherical beads tangential to each other, and non-consecutive monomers interact via a square-well…
We introduce the so called DeepParticle method to learn and generate invariant measures of stochastic dynamical systems with physical parameters based on data computed from an interacting particle method (IPM). We utilize the expressiveness…
Biopolymers are characterized by heterogeneous interactions, and usually perform their biological tasks forming contacts within domains of limited size. Combining polymer theory with a replica approach, we study the scaling properties of…
This article investigates the properties of a few interacting particles trapped in a few wells and how these properties change under adiabatic tuning of interaction strength and inter-well tunneling. While some system properties are…
Controlling electrochemical reactivity requires a detailed understanding of the charging behavior and thermodynamics of the electrochemical interface. Experiments can independently probe the overall charge response of the electrochemical…