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Many essential cellular processes, including cell division and the establishment of cell polarity during embryogenesis, are regulated by pattern-forming proteins. These proteins often need to bind to a substrate, such as the cell membrane,…
We shall construct a class of nonlinear reaction-diffusion equations starting from an infinitesimal algebraic skeleton. Our aim is to explore the possibility of an algebraic foundation of integrability properties and of stability of…
Modeling of biomolecular systems plays an essential role in understanding biological processes, such as ionic flow across channels, protein modification or interaction, and cell signaling. The continuum model described by the…
We present a theoretical model for the evolution of mixture concentrations in a micro-pervaporation device, similar to those recently presented experimentally. The described device makes use of the pervaporation of water through a thin PDMS…
Recent developments in lipid membrane models for simulations are reviewed. To reduce computational costs, various coarse-grained molecular models have been proposed. Among them, implicit solvent (solvent-free) molecular models are…
This paper concerns multiphase models of tumor growth in interaction with a surrounding tissue, taking into account also the interplay with diffusible nutrients feeding the cells. Models specialize in nonlinear systems of possibly…
We propose a novel approach for predicting protein-peptide interactions using a bi-modal transformer architecture that learns an inter-facial joint distribution of residual contacts. The current data sets for crystallized protein-peptide…
Research in cell biology is steadily contributing new knowledge about many different aspects of physiological processes like polymerization, both with respect to the involved molecular structures as well as their related function.…
A unifying framework to describe dense flows of dry, deformable grains is proposed. Perturbative analysis of a granular temperature equation describing flows with contact stresses, supported by the recovery of the nonlocal granular fluidity…
Many mathematical models for biological phenomena, such as the spread of diseases, are based on reaction-diffusion equations for densities of interacting cell populations. We present a consistent derivation of reaction-diffusion equations…
Relatively short peptides, such as toxins and antimicrobial-peptides, are known to insert themselves into cell membranes. On the basis of simple bead-spring models for the membrane lipids, the peptide, and water, detailed processes of the…
We investigate the use of an extension of rule-based modelling for cellular signalling to create a structured space of model variants. This enables the incremental development of rule sets that start from simple mechanisms and which, by a…
Interactions mediated by the cell membrane between inclusions, such as membrane proteins or antimicrobial peptides, play important roles in their biological activity. They also constitute a fascinating challenge for physicists, since they…
Particle stabilized emulsions are ubiquitous in the food and cosmetics industry, but our understanding of the influence of microscopic fluid-particle and particle-particle interactions on the macroscopic rheology is still limited. In this…
Cell division is a process that involves many biochemical steps and complex biophysical mechanisms. To simplify the understanding of what triggers cell division, three basic models that subsume more microscopic cellular processes associated…
Numerous cellular functions rely on protein$\unicode{x2013}$protein interactions. Efforts to comprehensively characterize them remain challenged however by the diversity of molecular recognition mechanisms employed within the proteome. Deep…
The effective mixing behavior of solutes in porous media is fundamentally connected to the development of a local mixing interface between the two initial solutions, which is characterized by a complex lamellar structure. The deformation of…
We introduce the BioBeta Framework, a meta-model for both protein-level and membrane-level interactions of living cells. This formalism aims to provide a formal setting where to encode, compare and merge models at different abstraction…
We formulate a model for the dynamic growth of a membrane developing in a flow as the result of a precipitation reaction, a situation inspired by recent microfluidic experiments. The precipitating solid introduces additional forces on the…
A recently introduced numerical scheme for calculating self-diffusion coefficients of solid objects embedded in lipid bilayer membranes is extended to enable calculation of hydrodynamic interactions between multiple objects. The method is…