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We explain the physical basis of a model for small globular proteins with water interactions. The water is supposed to access the protein interior in an "all-or-none" manner during the unfolding of the protein chain. As a consequence of…
The soft condensed matter of biological organisms exhibits atomic motions whose properties depend strongly on temperature and hydration conditions. Due to the superposition of rapidly fluctuating alternative motions at both very low…
We present for the first time a complex network approach to the study of the electrical properties of single protein devices. In particular, we consider an electronic nanobiosensor based on a G-protein coupled receptor. By adopting a coarse…
Apart from being the gateway for all access to the eukaryotic genome, chromatin has in recent years been identified as carrying an epigenetic code regulating transcriptional activity. The detailed knowledge of this code contrasts the…
One approach for solving interacting many-fermion systems is the configuration-interaction method, also sometimes called the interacting shell model, where one finds eigenvalues of the Hamiltonian in a many-body basis of Slater determinants…
Explainable and interpretable unsupervised machine learning helps understand the underlying structure of data. We introduce an ensemble analysis of machine learning models to consolidate their interpretation. Its application shows that…
We study the effect of membrane proteins on the shape, composition and thermodynamic stability of the surrounding membrane. When the coupling between membrane composition and curvature is strong enough the nearby composition and shape both…
An ubiquitous property of biological sensory systems is adaptation: a step increase in stimulus triggers an initial change in a biochemical or physiological response, followed by a more gradual relaxation toward a basal, pre-stimulus level.…
Protein-ligand modeling underpins computational drug discovery and molecular design. Existing protein-ligand benchmarks typically evaluate whether a protein and ligand interact and how strongly they bind, through tasks such as binary…
Protein-Protein Interaction Networks aim to model the interactome, providing a powerful tool for understanding the complex relationships governing cellular processes. These networks have numerous applications, including functional…
The interaction of fluid membranes with a scaffold, which can be a planar surface or a more complex structure, is intrinsic to a number of systems - from artificial supported bilayers and vesicles to cellular membranes. In principle, these…
Cytoskeletons are self-organized networks based on polymerized proteins: actin, tubulin, and driven by motor proteins, such as myosin, kinesin and dynein. Their positive Darwinian evolution enables them to approach optimized functionality…
We show that a recent reformulation of hydrodynamic equations for a large class of models consisting of q-dits on a graph with short range interactions is sufficient for understanding chaotic behavior. Any such system consists of large…
Geometric and structural constraints greatly restrict the selection of folds adapted by protein backbones, and yet, folded proteins show an astounding diversity in functionality. For structure to have any bearing on function, it is thus…
Allosteric (long-range) interactions can be surprisingly strong in proteins of biomedical interest. Here we use bioinformatic scaling to connect prior results on nonsteroidal anti-inflammatory drugs to promising new drugs that inhibit…
We present a geometrical analysis of the protrusion statistics of side chains in more than 4,000 high-resolution protein structures. We employ a coarse-grained representation of the protein backbone viewed as a linear chain of C{\alpha}…
Proteins are the fundamental macromolecules that play diverse and crucial roles in all living matter and have tremendous implications in healthcare, manufacturing, and biotechnology. Their functions are largely determined by the sequences…
The ability of a protein to recognise multiple independent target conformations was demonstrated in [1]. Here we consider the recognition of correlated configurations, which we apply to funnel design for a single conformation. The maximum…
To test the potential of using amino acid abundances as a biosignature at icy ocean worlds, we investigate whether primordial amino acids (accreted or formed by early aqueous processes) could persist until the present time. By examining the…
When two surfaces are brought into contact and slide against each other, junctions are formed at the interface. The dynamics of formation, rupture and evolution of these junctions governs the tribological response of the macro-contact.…