Related papers: The Effect of Macromolecular Crowding, Ionic Stren…
Cell migration is crucial to many physiological and pathological processes. During migration, a cell adapts its morphology, including the overall morphology and nucleus morphology, in response to various cues in complex microenvironments,…
Development of high strength carbon fibers (CFs) requires an understanding of the relationship between the processing conditions, microstructure and resulting properties. We developed a molecular model that combines kinetic Monte Carlo…
Mobile genetic elements like conjugative plasmids play a crucial role in shaping the genetic content and population dynamics of bacterial species. Bacterial populations often contain not one, but multiple co-circulating MGEs, which modify…
The physical and chemical environment inside cells is of fundamental importance to all life but has traditionally been difficult to determine on a subcellular basis. Here we combine cutting-edge genomically integrated FRET biosensing to…
Proteins and other macromolecules exist not in a single state but as dynamic ensembles of interconverting conformations, which are essential for catalysis, allosteric regulation, and molecular recognition. While AI-based structure…
Collective cell migration in 3D extracellular matrix (ECM) is crucial to many physiological and pathological processes. Migrating cells can generate active pulling forces via actin filament contraction, which are transmitted to the ECM…
Cells are dynamic systems characterized by temporal variations in biophysical properties such as stiffness and contractility. Recent studies show that the recruitment and release of actin filaments into and out of the cell cortex - a…
The mechanosensitivity of cells, which determines how they are able to respond to mechanical signals received from their environment, is crucial for the functioning of all biological systems. In experiments, cells placed on cyclically…
We present the assembly category assessment in the 13th edition of the CASP community-wide experiment. For the second time, protein assemblies constitute an independent assessment category. Compared to the last edition we see a clear uptake…
Intracellular calcium is regulated in part by the release of Ca$^{2+}$ ions from the endoplasmic reticulum via inositol-4,5-triphosphate receptor (IP$_3$R) channels (among other possibilities such as RyR and L-type calcium channels). The…
High-content cellular imaging, transcriptomics, and proteomics data provide rich and complementary views on the molecular layers of biology that influence cellular states and function. However, the biological determinants through which…
Via event-driven molecular dynamics simulations we study kinetics of clustering in assemblies of inelastic particles in various space dimensions. We consider two models, viz., the ballistic aggregation model (BAM) and the freely cooling…
Recent findings suggest that shell protein distribution and morphology of bacterial microcompartments regulate the chemical fluxes facilitating reactions which dictate their biological function. We explore how the morphology and component…
The Extra-Cellular-Matrix (ECM) is a complex interconnected 3D network that provides structural support for the cells and tissues and defines organ architecture key for their healthy functioning. However, the intimate mechanisms by which…
We present a computational microscopy analysis (targeted molecular dynamics simulations) of the structure and performance of conductive metal organic framework (MOF) electrodes in supercapacitors with room temperature ionic liquids. The…
In multi-resolution simulations, different system components are simultaneously modelled at different levels of resolution, these being smoothly coupled together. In the case of enzyme systems, computationally expensive atomistic detail is…
Predicting how protein mutations affect drug binding remains a major challenge, particularly when the mutations are distal from the binding site. In this study, we introduce a coupled simulation workflow that combines long-time-scale…
Antibody binding site prediction plays a pivotal role in computational immunology and therapeutic antibody design. Existing sequence or structure methods rely on single-view features and fail to identify antibody-specific binding sites on…
The synthetic actin network arouses great interest as bio-material due to its soft and wet nature that mimics many biological scaffolding structures. Inside the cell, the actin network is regulated by tens of actin-binding proteins (ABP's),…
Cell membranes interact with a myriad of curvature-active proteins that control membrane morphology and are responsible for mechanosensation and mechanotransduction. Some of these proteins, such as those containing BAR domains, are curved…