Related papers: Bridging scales in a multiscale pattern-forming sy…
Chemical reactions inside cells are generally considered to happen within fixed-size compartments. Needless to say, cells and their compartments are highly dynamic. Thus, such stringent assumptions may not reflect biochemical reality, and…
Friction is ubiquitous in daily life, from nanoscale machines to large engineering components. By probing the intricate interplay between system parameters and frictional behavior, scientists seek to unveil the underlying mechanisms that…
Understanding the (de)mixing behavior of multicomponent lipid bilayers is an important step towards unraveling the nature of spatial composition heterogeneities in cellular membranes and their role in biological function. We use…
Quantum nanosystems such as graphene nanoribbons or superconducting nanoparticles are studied via a multiscale approach. Long space-time dynamics is derived using a perturbation expansion in the ratio of the nearest-neighbor distance to a…
Granular systems are not always homogeneous and can be composed of grains with very different mechanical properties. To improve our understanding of the behavior of real granular systems, in this experimental study, we compress 2D…
We study pattern formation in a chemotaxis model of bacteria and soil carbon dynamics as an example system where transient dynamics can give rise to pattern formation outside of Turing unstable regimes. We use a detailed analysis of the…
Vegetation patterns are a characteristic feature of semi-arid regions. On hillsides these patterns occur as stripes running parallel to the contours. The Klausmeier model, a coupled reaction-advection-diffusion system, is a deliberately…
Two coarse-grained models which capture some universal characteristics of stripe forming systems are stud- ied. At high temperatures, the structure factors of both models attain their maxima on a circle in reciprocal space, as a consequence…
Models for the microstructure evolution during hot rolling are reviewed. The basic macroscopic phenomena related to recrystallization are summarized. Constitutive models based on semi empirical equations are compared to more sophisticated…
In recent years, several particle-based stochastic simulation algorithms (PSSA) have been developed to study the spatially resolved dynamics of biochemical networks at a molecular scale. A challenge all these approaches have to address is…
Coarse-grained molecular models of proteins permit access to length and time scales unattainable by all-atom models and the simulation of processes that occur on long-time scales such as aggregation and folding. The reduced resolution…
We show that cluster expansions (CE), previously used to model solid-state materials with binary or ternary configurational disorder, can be extended to the protein design problem. We present a generalized CE framework, in which properties…
Coarse-grained (CG) force field methods for molecular systems are a crucial tool to simulate large biological macromolecules and are therefore essential for characterisations of biomolecular systems. While state-of-the-art deep learning…
We have performed multicanonical computer simulations of a small system of short protein-like heteropolymers and found that their aggregation transition possesses similarities to first-order phase separation processes. Not being a phase…
Elastic filaments are vital to biological, physical and engineering systems, from cilia driving fluid in the lungs to artificial swimmers and micro-robotics. Simulating slender structures requires intricate balance of elastic, body, active,…
Transitions between different conformational states are ubiquitous in proteins, being involved in signaling, catalysis and other fundamental activities in cells. However, modeling those processes is extremely difficult, due to the need of…
In this thesis, we develop multiscale models for particle simulations in population dynamics. These models are characterised by prescribing particle motion on two spatial scales: microscopic and macroscopic. At the microscopic level, each…
Quantitative modeling of post-transcriptional regulation process is a challenging problem in systems biology. A mechanical model of the regulatory process needs to be able to describe the available spatio-temporal protein concentration and…
A multiscale scheme combining molecular dynamics (MD) and microscopic phase-field theory is proposed to study the structural phase transformations in solids with inhomogeneous strain field. The approach calculates strain response based on…
The size distribution of grains is a fundamental characteristic of polycrystalline solids. In the absence of deformation, the grain-size distribution is controlled by normal grain growth. The canonical model of normal grain growth,…