Related papers: Probabilistic Model to Treat Flexibility in Molecu…
Employing molecular dynamics simulations of jammed soft particles, we study microscopic responses of force-chain networks to quasi-static isotropic (de)compressions. We show that not only contacts but also interparticle gaps between the…
The contact process is a non-equilibrium Hamiltonian model that, even in one dimension, lacks an exact solution and has been extensively studied via Monte Carlo simulations, both in steady-state and time-dependent scenarios. Although the…
The inelastic hard sphere model of granular material is simple, easily accessible to theory and simulation, and captures much of the physics of granular media. It has three drawbacks, all related to the approximation that collisions are…
Systems which consist of many localized constituents interacting with each other can be represented by complex networks. Consistently, network science has become highly popular in vast fields focusing on natural, artificial and social…
The calculation of thermodynamic properties of biochemical systems typically requires the use of resource-intensive molecular simulation methods. One example thereof is the thermodynamic profiling of hydration sites, i.e. high-probability…
This thesis deals with shape optimization for contact mechanics. More specifically, the linear elasticity model is considered under the small deformations hypothesis, and the elastic body is assumed to be in contact (sliding or with Tresca…
We introduce an approximate model for predicting the net contact wrench between nominally rigid objects for use in simulation, control, and state estimation. The model combines and generalizes two ideas: a bed of springs (an "elastic…
We study and predict the interfacial tension, solubility parameters and Flory-Huggins parameters of binary mixtures as functions of pressure and temperature, using multiscale numerical simulation. A mesoscopic approach is proposed for…
Chromosomes are crumpled polymer chains further folded into a sequence of stochastic loops via loop extrusion. While extrusion has been verified experimentally, the particular means by which the extruding complexes bind DNA polymer remains…
We investigate a diffusive motion of a system of interacting Brownian particles in quasi-one-dimensional micropores. In particular, we consider a semi-infinite 1D geometry with a partially absorbing boundary and the hard-core inter-particle…
We develop a model to describe the properties of random assemblies of polydisperse hard spheres. We show that the key features to describe the system are (i) the dependence between the free volume of a sphere and the various coordination…
A fundamental step in the rational design of vascular targeted particles is the firm adhesion at the blood vessel walls. Here, a combined Lattice Boltzmann Immersed Boundary model is presented for predicting the near wall dynamics of…
The increasing number of protein-based metamaterials demands reliable and efficient theoretical and computational methods to study the physicochemical properties they may display. In this regard, we develop a simulation strategy based on…
Polymer entanglements lead to complicated topological constraints and interactions between neighbouring chains in a dense solution or melt. Entanglements can be treated in a mean field approach, within the famous reptation model, since they…
We develop a simple but rigorous model of protein-protein association kinetics based on diffusional association on free energy landscapes obtained by sampling configurations within and surrounding the native complex binding funnels. Guided…
A molecular theory of liquid water is identified and studied on the basis of computer simulation of the TIP3P model of liquid water. This theory would be exact for models of liquid water in which the intermolecular interactions vanish…
Sensitivity analysis of a numerical model, for instance simulating physical phenomena, is useful to quantify the influence of the inputs on the model responses. This paper proposes a new sensitivity index, based upon the modification of the…
The study of almost surely discrete random probability measures is an active line of research in Bayesian nonparametrics. The idea of assuming interaction across the atoms of the random probability measure has recently spurred significant…
We study the problem of rapidly identifying contact dynamics of unknown objects in partially known environments. The key innovation of our method is a novel formulation of the contact dynamics estimation problem as the joint estimation of…
Changes in the mechanical properties of granular materials, induced by variations in the intrinsic compressibility of the particles, are investigated by means of numerical simulations based on the combination of the Finite Element and…