Related papers: Self-Organized Criticality: A Guide to Water-Prote…
This paper reports about an approach to the classification of proteins' primary structures taking advantage of the Self Organizing Maps algorithm and of a numerical coding of the aminoacids based upon their physico-chemical properties.…
High-resolution structural information on membrane proteins is essential for understanding cell biology and for structure-based design of new medical drugs and drug delivery strategies. X-ray diffraction (XRD) can provide {\AA}ngstrom-level…
The formation of naturally-derived materials with wet stable fibrous architectures is paramount in order to mimic the features of tissues at the molecular and microscopic scale. Here, we investigated the formation of wet-spun fibres based…
The increasing interest in photoactivated proteins as natural replacement of standard inorganic materials in photocells drives to the compared analysis of bacteriorhodopsin and proteorhodopsin, two widely diffused proteins belonging to the…
We develop a multi-scale approach to simulate hydrated nanobio systems under realistic condi- tions (e.g., nanoparticles and protein solutions at physiological conditions over time-scales up to hours). We combine atomistic simulations of…
We apply dynamic mode decomposition (DMD) and proper orthogonal decomposition (POD) methods to flows in highly-heterogeneous porous media to extract the dominant coherent structures and derive reduced-order models via Galerkin projection.…
Behavioural differences across organisms, whether healthy or pathological, are closely tied to the structure of their neural circuits. Yet, the fine-scale synaptic changes that give rise to these variations remain poorly understood, in part…
A novel scheme is introduced to capture the spatial correlations of consecutive amino acids in naturally occurring proteins. This knowledge-based strategy is able to carry out optimally automated subdivisions of protein fragments into…
The ability to detect out-of-distribution (OOD) samples is vital to secure the reliability of deep neural networks in real-world applications. Considering the nature of OOD samples, detection methods should not have hyperparameters that…
The interactions of a protein, its phase behavior, and ultimately, its ability to function, are all influenced by the interactions between the protein and its hydration waters. Here we study proteins with a variety of sizes, shapes,…
Membrane proteins constitute a large portion of the human proteome and perform a variety of important functions as membrane receptors, transport proteins, enzymes, signaling proteins, and more. The computational studies of membrane proteins…
The supra-molecular structure of a liquid is strongly connected to its dynamics which in turn controls macroscopic properties such as viscosity. Consequently, detailed knowledge about how this structure changes with temperature is essential…
Various microorganisms and some mammalian cells are able to swim in viscous fluids by performing nonreciprocal body deformations, such as rotating attached flagella or by distorting their entire body. In order to perform chemotaxis, i.e. to…
We study the behavior of five proteins at the air-water and oil-water interfaces by all-atom molecular dynamics. The proteins are found to get distorted when pinned to the interface. This behavior is consistent with the phenomenological way…
Though the problem of sequence-reversed protein folding is largely unexplored, one might speculate that reversed native protein sequences should be significantly more foldable than purely random heteropolymer sequences. In this article, we…
We review and further develop an analytical model that describes how thermodynamic constraints on the stability of the native state influence protein evolution in a site-specific manner. To this end, we represent both protein sequences and…
Ongoing advancements in computer vision, particularly in pattern recognition and scene classification, have enabled new applications in environmental monitoring. Deep learning now offers non-contact methods for assessing water quality and…
Mesoscale water-hydrophobic interfaces are of fundamental importance in multiple disciplines, but their molecular properties have remained elusive for decades due to experimental complications and alternate theoretical explanations.…
We investigate dynamical coupling between water and amino acid side-chain residues in solvation dynamics by selecting residues often used as natural probes, namely tryptophan, tyrosine and histidine, located at different positions on…
Based on overall 3D structure, proteins may be grouped into two broad categories, namely, globular proteins (spheroproteins), and elongated or rod-shaped proteins (RSP). The former comprises a significant majority of proteins. This work…