Related papers: Fine structures of Intrinsically Disordered Protei…
Soft particles such as microgels and core-shell particles can undergo significant and anisotropic deformations when adsorbed to a liquid interface. This, in turn, leads to a complex phase behavior upon compression. Here we develop a…
Allosteric (long-range) interactions can be surprisingly strong in proteins of biomedical interest. Here we use bioinformatic scaling to connect prior results on nonsteroidal anti-inflammatory drugs to promising new drugs that inhibit…
Polyphenols and proteins are essential biomolecules that influence food functionality and, by extension, human health. Their interactions -- hereafter referred to as PhPIs (polyphenol-protein interactions) -- affect key processes such as…
We study a one-dimensional classical system of $N$ particles confined within a harmonic trap. Interactions among these particles are dictated by a pairwise potential $V(x)$, where $x$ is the separation between two particles. Each particle…
We investigate one-dimensional harmonically trapped two-component systems for repulsive interaction strengths ranging from the non-interacting to the strongly interacting regime for Fermi-Fermi mixtures. A new and powerful mapping between…
We investigate the ground-state phase diagram of the spinless Haldane-Hubbard model in the presence of quenched disorder, contrasting results obtained from both exact diagonalization as well as density matrix renormalization group, applied…
We present an extended structural study of globular complexes made by mixing a positively charge protein (lysozyme) and a negatively charged polyelectrolyte (PSS). We study the influence of all the parameters that may act on the structure…
Identifying interacting partners from two sets of protein sequences has important applications in computational biology. Interacting partners share similarities across species due to their common evolutionary history, and feature…
The mechanical response of intrinsically disordered proteins (IDPs) and polyampholyte (PA) chains is vital for understanding their biological functions and designing functional materials. We investigate the force-extension behavior of a PA…
Current methods for investigation of receptor - ligand interactions in drug discovery are based on three-dimensional complementarity of receptor and ligand surfaces, and they include pharmacophore modelling, QSAR, molecular docking etc.…
We develop a multi-scale approach to simulate hydrated nanobio systems under realistic condi- tions (e.g., nanoparticles and protein solutions at physiological conditions over time-scales up to hours). We combine atomistic simulations of…
In this work we study the tertiary structure of ionic surfactants when the pH in the system is modified using electrostatic dissipative particle dynamics simulations (DPD). The dependence with pH and kind of surfactant is presented. Our…
We present a minimal model for simulating dynamics of assorted lipid assemblies in a computationally efficient manner. Our model is particle-based and consists of coarse-grained beads put together on a modular platform to give generic…
The mechanical properties of a disordered heterogeneous medium depend, in general, on a complex interplay between multiple length scales. Connecting local interactions to macroscopic observables, such as stiffness or fracture, is thus…
To confer high specificity and affinity in binding, contacts at interfaces between two interacting macromolecules are expected to exhibit pair preferences for types of atoms or residues. Here we quantify these preferences by measuring the…
Computation of biological processes creates great promise for everyday life and great challenges for physical scientists. Simulations of molecular dynamics appeal to biologists as a natural extension of structural biology. Once biologists…
Molecular dynamics simulations are used to investigate the conformations of a single polymer chain, represented by the Kremer-Grest bead-spring model, in a solution with a Lennard-Jones liquid as the solvent when the interaction strength…
Random heteropolymers do not display the typical equilibrium properties of globular proteins, but are the starting point to understand the physics of proteins and, in particular, to describe their non-native states. So far, they have been…
The paper develops the stiffness relationship between the movements and forces among a system of discrete interacting grains. The approach is similar to that used in structural analysis, but the stiffness matrix of granular material is…
We consider a simple random walk of length $N$, denoted by $(S_{i})_{i\in \{1,...,N\}}$, and we define $(w_i)_{i\geq 1}$ a sequence of centered i.i.d. random variables. For $K\in\N$ we define $((\gamma_i^{-K},...,\gamma_i^K))_{i\geq 1}$ an…