Related papers: The Effect of Macromolecular Crowding, Ionic Stren…
It is now well established that the cell is a highly crowded environment. Yet, the effects of crowding on the dynamics of signaling pathways, gene regulation networks and metabolic networks are still largely unknown. Crowding can alter both…
An open question in deep clustering is how to understand what in the image is creating the cluster assignments. This visual understanding is essential to be able to trust the results of an inherently complex algorithm like deep learning,…
We describe a combination of all-atom simulations with CABS, a well-established coarse-grained protein modeling tool, into a single multiscale protocol. The simulation method has been tested on the C-terminal beta hairpin of protein G, a…
The affinity and specificity of protein-molecule binding directly impact functional outcomes, uncovering the mechanisms underlying biological regulation and signal transduction. Most deep-learning-based prediction approaches focus on…
To perform recognition, molecules must locate and specifically bind their targets within a noisy biochemical environment with many look-alikes. Molecular recognition processes, especially the induced-fit mechanism, are known to involve…
Biomolecular folding and function are often coupled. During molecular recognition events, one of the binding partners may transiently or partially unfold, allowing more rapid access to a binding site. We describe a simple model for this…
Calcium activation of striated muscle is known to exhibit a strongly cooperative dependency on calcium. Because the calcium receptor protein, troponin (Tn) is known to bind calcium non-cooperatively and has yet to be linked to a cooperative…
Growth in confined spaces can drive cellular populations through a jamming transition from a fluid-like state to a solid-like state. Experiments have found that jammed budding yeast populations can build up extreme compressive pressures…
The dynamics of many macromolecular machines is characterized by chemically-mediated structural changes that achieve large scale functional deployment through local rearrangements of constitutive protein sub-units. Motivated by recent high…
The extent of coupling between the folding of a protein and its binding to a substrate varies from protein to protein. Some proteins have highly structured native states in solution, while others are natively disordered and only fold fully…
Cryo-EM data processing typically focuses on the structure of the main conformational state under investigation and discards images that belong to other states. This approach can reach atomic resolution, but ignores vast amounts of valuable…
Compliant environments can mediate interactions between mechanically active cells like fibroblasts. Starting with a phenomenological model for the behaviour of single cells, we use extensive Monte Carlo simulations to predict non-trivial…
Here we present the first large scale investigation of electronic properties and correlated magnetism in Ce-based compounds accompanied by a systematic study of the electronic structure and 4f-hybridization function of a large body of Ce…
A major theme in constraint-based modeling is unifying experimental data, such as biochemical information about the reactions that can occur in a system or the composition and localization of enzyme complexes, with highthroughput data…
Calcium (Ca2+) signalling is one of the most important mechanisms of information propagation in the body. In embryogenesis the interplay between Ca2+ signalling and mechanical forces is critical to the healthy development of an embryo but…
Protein structure prediction models are now capable of generating accurate 3D structural hypotheses from sequence alone. However, they routinely fail to capture the conformational diversity of dynamic biomolecular complexes, often requiring…
Protein-mediated interactions are ubiquitous in the cellular environment, and particularly in the nucleus, where they are responsible for the structuring of chromatin. We show through molecular--dynamics simulations of a polymer surrounded…
Collagen fibers, an important component of the extracellular matrix (ECM), can both inhibit and promote cellular migration. {\it In-vitro} studies have revealed that the fibers' orientations are crucial to cellular invasion, while {\it…
Collective cell migration plays an essential role in various biological processes, such as development or cancer proliferation. While cell-cell interactions are clearly key determinants of collective cell migration -- in addition to…
Predictive models of thermodynamic properties of mixtures are paramount in chemical engineering and chemistry. Classical thermodynamic models are successful in generalizing over (continuous) conditions like temperature and concentration. On…