Biological Physics
Conformation of a protein (CorA) is examined in a matrix with mobile solute constituents as a function of solute-residue interaction strength (f) by a coarse-grained model with a Monte Carlo simulation. Solute particles are found to reach…
The proper functions of tissues depend on the ability of cells to withstand stress and maintain shape. Central to this process is the cytoskeleton, comprised of three polymeric networks: F-actin, microtubules, and intermediate filaments.…
The formation and proliferation of protein aggregates play a central role in a number of devastating neuro-degenerative diseases. Many experimental studies indicate that the ability of existing aggregates to replicate is a key property in…
Protein-protein interaction (PPI) networks have been used to investigate the influence of SARS-CoV-2 viral proteins on the function of human cells, laying out a deeper understanding of COVID--19 and providing ground for drug repurposing…
The emergence of longer information-carrying and functional nucleotide polymers from random short strands was a major stepping stone at the dawn of life. But the formation of those polymers under temperature oscillation required some form…
Liquid liquid phase separation (LLPS) mediated by pi-cation bonds between tyrosine and arginine residues are of biological importance. To understand the interactions between proteins in the condensed phase in close analogy to complex…
As the question of the origins of eukaryotes comes closer to an answer, the interactions between the archaeal ancestor to eukaryotes and environmental, molecular, bacterial, other influences and symbionts have become increasingly relevant.…
Upon stimulation, plants elicit electrical signals that can travel within a cellular network analogous to the animal nervous system. It is well-known that in the human brain, voltage changes in certain regions result from concerted…
During migration cells exhibit a rich variety of seemingly random migration patterns, which makes unraveling the underlying mechanisms that control cell migration a daunting challenge. For efficient migration cells require a mechanism for…
The mitotic spindle lies at the heart of the spatio-temporal control over cellular components during cell division. The spindle consists of microtubules, which are not only crosslinked by motor proteins but also by passive binding proteins.…
Multi-step assembly of individual protein building blocks is key to the formation of essential higher-order structures inside and outside of cells. Optical tweezers is a technique well suited to investigate the mechanics and dynamics of…
We study numerically the behaviour of a mixture of a passive isotropic fluid and an active polar gel, in the presence of a surfactant favouring emulsification. Focussing on parameters for which the underlying free energy favours the…
We previously introduced a conformational sampling method, a multi-dimensional virtual-system coupled molecular dynamics (mD-VcMD), to enhance conformational sampling of a biomolecular system by computer simulations. Here, we present a new…
This work addresses the question of the interplay of DNA demixing and supercoiling in bacterial cells. Demixing of DNA from other globular macromolecules results from the overall repulsion between all components of the system and leads to…
As the places where most of the fuel of the cell, namely ATP, is synthesized, mitochondria are crucial organelles in eukaryotic cells. The shape of the invaginations of the mitochondria inner membrane, known as cristae, has been identified…
Kinesin motors can induce a buckling instability in a microtubule with a fixed minus end. Here we show that by modifying the surface with a protein-repellent functionalization and using clusters of kinesin motors, the microtubule can…
Motile human-skin fibroblasts form macroscopic swirling patterns when grown to confluence on a culture dish. In this paper, we investigate the effect of coating the culture-dish surface with collagen on the resulting pattern, using…
Analyte translocation involves three phases: (i) diffusion in the loading solution; (ii) capture by the pore; (iii) threading. The capture process remains poorly characterized because it cannot easily be visualized or inferred from indirect…
We investigated melting transitions in biological membranes in their native state that include their membrane proteins. These membranes originated from \textit{E. coli}, \textit{B. subtilis}, lung surfactant and nerve tissue from the spinal…
Living systems regulate many aspects of their behavior through periodic oscillations of molecular concentrations, which function as `biochemical clocks.' These clocks are intrinsically subject to thermal fluctuations, so that the duration…