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The port-Hamiltonian framework is a structure-preserving modeling approach that preserves key physical properties such as energy conservation and dissipation. When subsystems are modeled as port-Hamiltonian systems (pHS) with linearly…
A polymer chain tethered to a surface may be compact or extended, adsorbed or desorbed, depending on interactions with the surface and the surrounding solvent. This leads to a rich phase diagram with a variety of transitions. To investigate…
The structure of membrane-active peptides and their interaction with lipid bilayers can be studied in oriented lipid membranes deposited on solid substrates. Such systems are desirable for a number of surface-sensitive techniques. Here we…
The qualitative solvent- and temperature-dependent conformational behavior of a peptide in the proximity of solid substrates with different adsorption properties is investigated by means of a simple lattice model. The resulting pseudophase…
Multibody dynamics simulation plays an important role in various fields, including mechanical engineering, robotics, and biomechanics. Setting up computational models however becomes increasingly challenging as systems grow in size and…
Polymer chains undergoing a continuous adsorption-desorption transition are studied through extensive computer simulations. A three-dimensional self-avoiding walk lattice model of a polymer chain grafted onto a surface has been treated for…
This article examines the dynamic phase transitions and pattern formations attributed to binary systems modeled by the Cahn-Hilliard equation. In particular, we consider a two-dimensional lattice structure and determine how different…
The port-Hamiltonian modelling framework allows for models that preserve essential physical properties such as energy conservation or dissipative inequalities. If all subsystems are modelled as port-Hamiltonian systems and the inputs are…
We propose and study a model for the equilibrium statistical mechanics of a pressurised semiflexible polymer ring. The Hamiltonian has a term which couples to the algebraic area of the ring and a term which accounts for bending…
We consider a lattice model of a semiflexible homopolymer chain in a bad solvent. Beside the temperature $T$, this model is described by (i) a curvature energy $\varepsilon_h$, representing the stiffness of the chain (ii) a…
By means of extensive replica-exchange simulations of generic coarse-grained models for helical polymers, we systematically investigate the structural transitions into all possible helical phases for flexible and semiflexible elastic…
In this paper we extend the Gaussian self-consistent method to permit study of the equilibrium and kinetics of conformational transitions for heteropolymers with any given primary sequence. The kinetic equations earlier derived by us are…
Protein folding, peptide aggregation and crystallization, as well as adsorption of molecules on soft or solid substrates have an essential feature in common: In all these processes, structure formation is guided by a collective, cooperative…
An atomic protein model with a minimalistic potential is developed and then tested on an alpha-helix and a beta-hairpin, using exactly the same parameters for both peptides. We find that melting curves for these sequences to a good…
Protein structure is generally conceptualized as the global arrangement or of smaller, local motifs of helices, sheets, and loops. These regular, recurring secondary structural elements have well-understood and standardized definitions in…
Hydrogen as a fuel plays a crucial role in driving the transition to net zero greenhouse gas emissions. To realise its potential, obtaining a means of efficient storage is paramount. One solution is using metal hydrides, owing to their good…
We present a novel Monte Carlo simulation of protein folding, in which all heavy atoms are represented as interacting hard spheres. This model includes all degrees of freedom relevant to folding - all sidechain and backbone torsions - and…
A lattice model of a hetero-polymer with random hydrophilic-hydrophobic charges interacting with the solvent is introduced, whose continnuum counterpart has been proposed by T. Garel, L. Leibler and H. Orland {J. Phys. II France 4, 2139…
We build a transient multidimensional multiphysical model based on continuum theories, involving the coupled mechanical, thermal and electrochemical phenomena occurring simultaneously in the discharge or charge of lithium-ion batteries. The…
A multiphysics modeling approach for heat conduction in metal hydride powders is presented, including particle shape distribution, size distribution, granular packing structure, and effective thermal conductivity. A statistical geometric…