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Bacterial communities such as biofilms are widely recognised as being important for survival and persistence of bacteria in harsh environments. Mechanistic models of biofilm growth indicate that the way in which the surface is seeded can…
The understanding, and even the description of protein folding is impeded by the complexity of the process. Much of this complexity can be described and understood by taking a statistical approach to the energetics of protein conformation,…
The adhesion of biomembranes is mediated by the binding of membrane-anchored receptor and ligand proteins. The proteins can only bind if the separation between apposing membranes is sufficiently close to the length of the protein complexes,…
The spatial organization of complex biochemical reactions is essential for the regulation of cellular processes. Membrane-less structures called foci containing high concentrations of specific proteins have been reported in a variety of…
We perform simulations of a system containing simple model proteins and a polymer representing chromatin. We study the interplay between protein-protein and protein-chromatin interactions, and the resulting condensates which arise due to…
We use mesoscale simulations to gain insight into the digestion of biopolymers by studying the break-up dynamics of polymer aggregates (boluses) bound by physical cross-links. We investigate aggregate evolution, establishing that the…
The adsorbate dynamics during simultaneous action of desorption and lateral adsorbate diffusion is studied in a simple lattice-gas model by kinetic Monte Carlo simulations. It is found that the action of the coverage-conserving diffusion…
Neither of the two prevalent theories, namely thermodynamic stability and kinetic stability, provides a comprehensive understanding of protein folding. The thermodynamic theory is misleading because it assumes that free energy is the…
Molecular simulations and biophysical experiments can be used to provide independent and complementary insights into the molecular origin of biological processes. A particularly useful strategy is to use molecular simulations as a modelling…
We present a statistical mechanics approach to the protein folding problem. We first review some of the basic properties of proteins, and introduce some physical models to describe their thermodynamics. These models rely on a random…
Hypothesis: A broad range of phenomena, such as emulsification and emulsion stability, foam formation or liquid evaporation, are closely related to the dynamics of adsorbing colloidal particles. Elucidation of the mechanisms implied is key…
The protein dynamics are common and important for their biological functions and properties, the study of which usually involves time-consuming molecular dynamics (MD) simulations in silico. Recently, generative models has been leveraged as…
Several recent imaging experiments access the equilibrium density profiles of interacting particles confined to a two-dimensional substrate. When these particles are in a fluid phase, we show that such data yields precise information…
Bacteria often develop distinct phenotypes to adapt to environmental stress. In particular, they can produce biofilms, dense communities of bacteria that live in a complex extracellular matrix. Bacterial biofilms provide a safe haven from…
As an example of topic where biology and physics meet, we present the issue of protein folding and stability, and the development of thermodynamics-based bioinformatics tools that predict the stability and thermal resistance of proteins and…
To interpret molecular dynamics simulations of biomolecular systems, systematic dimensionality reduction methods are commonly employed. Among others, this includes principal component analysis (PCA) and time-lagged independent component…
Stretching of a protein by a fluid flow is compared to that in a force-clamp apparatus. The comparison is made within a simple topology-based dynamical model of a protein in which the effects of the flow are implemented using Langevin…
Grand canonical Monte Carlo simulations are used to explore the metastable fluid-fluid coexistence curve of the modified Lennard-Jones model of globular proteins of ten Wolde and Frenkel (Science, v277, 1975 (1997)). Using both mixed-field…
The lifetime of protein domains and ligand-receptor complexes under force is crucial for mechanosensitive functions, while many aspects of how force affects the lifetime still remain poorly understood. Here, we report a new analytical…
A model system inspired by recent experiments on the dynamics of a folded protein under the influence of a sinusoidal force is investigated and found to replicate many of the response characteristics of such a system. The essence of the…