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Model-driven analysis of biophysical phenomena is gaining increased attention and utility for medical imaging applications. In magnetic resonance imaging (MRI), the availability of well-established models for describing the relations…
The main objective of a statistical mechanical calculation is drawing the phase diagram of a many-body system. In this respect, discrete systems offer the clear advantage over continuum systems of an easier enumeration of microstates,…
Computer simulations of coarse-grained molecular models for amphiphilic systems can provide insight into the the structure of amphiphiles at interfaces. They can help to identify the factors that determine the phase behavior, and they can…
The accurate, reliable and efficient numerical approximation of multi-physics processes in heterogeneous porous media with varying media coefficients that include fluid flow and structure interactions is of fundamental importance in energy,…
The determination of potentials of mean force for solute insertion in a membrane by means of all-atom molecular dynamics simulations is often hampered by sampling issues. A multiscale approach to conformational sampling was recently…
Biological cells are built up from many different constituents of varying size and stiffness which all contribute to the cell's mechanical properties. Despite this heterogeneity, in the analysis of experimental measurements such as atomic…
Atomistic modelling of phase transitions, chemical reactions, or other rare events that involve overcoming high free energy barriers usually entails prohibitively long simulation times. Introducing a bias potential as a function of an…
The phase diagram of soft spheres with size dispersion has been studied by means of an optimized Monte Carlo algorithm which allows to equilibrate below the kinetic glass transition for all sizes distribution. The system ubiquitously…
Recovering 3D phase features of complex, multiple-scattering biological samples traditionally sacrifices computational efficiency and processing time for physical model accuracy and reconstruction quality. This trade-off hinders the rapid…
All-atom molecular dynamics has been recently proven a useful tool for the study of supramolecular polymers. While the high resolution offered by the atomistic models may allow for deep comprehension of the assembled structure, obtaining a…
The biological membrane, which compartmentalizes the cell and its organelles, exhibit wide variety of macroscopic shapes of varying morphology and topology. A systematic understanding of the relation of membrane shapes to composition,…
Biological cells utilize membranes and liquid-like droplets, known as biomolecular condensates, to structure their interior. The interaction of droplets and membranes, despite being involved in several key biological processes, is so far…
Advanced algorithms are necessary to obtain faster-than-real-time dynamic simulations in a number of different physical problems that are characterized by widely disparate time scales. Recent advanced dynamic Monte Carlo algorithms that…
To minimise systematic errors in Monte Carlo simulations of charged particles, long range electrostatic interactions have to be calculated accurately and efficiently. Standard approaches, such as Ewald summation or the naive application of…
Hybrid modeling provides an effective solution to cope with multiple time scales dynamics in systems biology. Among the applications of this method, one of the most important is the cell cycle regulation. The machinery of the cell cycle,…
The phase diagram of water harbours many mysteries: some of the phase boundaries are fuzzy, and the set of known stable phases may not be complete. Starting from liquid water and a comprehensive set of 50 ice structures, we compute the…
Molecular simulations of the forced unfolding and refolding of biomolecules or molecular complexes allow to gain important kinetic, structural and thermodynamic information about the folding process and the underlying energy landscape. In…
Conservative and non-conservative phase-field models are considered for the numerical simulation of lateral phase separation and coarsening in biological membranes. An unfitted finite element method is devised for these models to allow for…
A new homogenization approach for the simulation of multi-phase flows in heterogeneous porous media is presented. It is based on the lattice Boltzmann method and combines the grayscale with the multi-component Shan-Chen method. Thus, it…
MARTINI is a popular coarse-grained force-field that is mainly used in molecular dynamics (MD) simulations. It is based on the ``Lego'' approach where intermolecular interactions between coarse-grained beads representing chemical units of…