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The activation of the dodecameric Ca2+/calmodulin dependent kinase II (CaMKII) holoenzyme is critical for the formation of memory. We now report that CaMKII has a remarkable property, which is that activation of the holoenzyme triggers the…
The electron-phonon coupling (EPC) is a ubiquitous interaction in condensed systems and plays a vital role in shaping the electronic properties of materials. Yet, achieving coherent manipulation of electron-phonon coupling has posed a…
Studying the conformations involved in the dimerization of cadherins is highly relevant to understand the development of tissue and its failure, which is associated with tumors and metastases. Experimental techniques, like X-ray…
Morphogenesis in animal development involves significant morphological transitions leading to the emerging body plan of a mature animal. Understanding how the collective physical processes drive robust morphological patterning requires a…
Protein structures can be encoded into binary sequences, these are used to define a Hamming distance in conformational space: the distance between two different molecular conformations is the number of different bits in their sequences.…
The role of fixed degrees of freedom in soft/granular matter systems has broad applicability and theoretical interest. Here we address questions of the geometrical role that a scaffolding of fixed particles plays in tuning the threshold…
The biological effects of electromagnetic fields on proteins remain controversial beyond well-established thermal mechanisms, particularly with respect to frequency-dependent responses. Here, we propose that electromagnetic waves can…
Understanding the coupling between structural phase transitions and thermal transport is essential for designing functional materials with tunable properties. Here, we investigate this interplay in CaSnF$_6$ by combining first-principles…
We find significant differences between degradation and healing at the surface or in the bulk for each of the different APbBr3 single crystals (A=CH3NH3+, methylammonium (MA); HC(NH2)2+, formamidinium (FA); and cesium, Cs+). Using 1- and…
The folding mechanism of the Villin headpiece (HP36) is studied by means of a novel approach which entails an initial coarse-grained Monte Carlo (MC) scheme followed by all-atom molecular dynamics (MD) simulations in explicit solvent. The…
The biological function of protein assemblies was conventionally equated with a unique three-dimensional protein structure and protein-specific interactions. However, in the past 20 years it was found that some assemblies contain long…
Biomolecular condensates are formed via liquid-liquid phase separation of proteins, often together with nucleic acids, typically driven by interactions between low-affinity binding sites. The computational study of such condensates that…
Medication recommendation systems play a crucial role in assisting clinicians with personalized treatment decisions. While existing approaches have made significant progress in learning medication representations, they suffer from two…
We use molecular dynamic simulations to investigate the relation between the presence of packing defects in a glass-former and the spontaneous cooperative motions called dynamic heterogeneity. For that purpose we use a simple diatomic…
Protein function does not solely depend on structure but often relies on dynamical transitions between distinct conformations. Despite this fact, our ability to characterize or predict protein dynamics is substantially less developed…
Making use of a simplified model for protein folding, it can be shown that conformations which are particularly stable when their energy is minimized with respect to amino acid sequence (in the sense that they display a large energy gap to…
Potassium (K-) channels catalyze K+ ion permeation across cellular membranes while simultaneously discriminating their permeation over Na+ ions by more than a factor of a thousand. Structural studies show bare K+ ions occupying the…
Heterogeneous catalysts based on sub-nanometer metal clusters often exhibit strongly size-dependent properties, and the addition or removal of a single atom can make all the difference. Identifying the most active species and deciphering…
Physics-informed neural networks (PINNs) have emerged as a powerful tool for solving physical systems described by partial differential equations (PDEs). However, their accuracy in dynamical systems, particularly those involving sharp…
The Finite Element Method (FEM) is a powerful modeling tool for predicting soft robots' behavior, but its computation time can limit practical applications. In this paper, a learning-based approach based on condensation of the FEM model is…