Related papers: Protein structural variation in computational mode…
Networked systems display complex patterns of interactions between a large number of components. In physical networks, these interactions often occur along structural connections that link components in a hard-wired connection topology,…
The possibility of deriving the contact potentials between amino acids from their frequencies of occurence in proteins is discussed in evolutionary terms. This approach allows the use of traditional thermodynamics to describe such…
The topology of nanoporous metals is crucial for determining their mechanical response. In this work, we generated 6,000 gold and 422 silver nanoporous structures and calculated three components of elastic modulus with Molecular Dynamics…
We propose a framework to model elastic properties of polycrystals by coupling crystal orientational degrees of freedom with elastic strains. Our model encodes crystal symmetries and takes into account explicitly the strain compatibility…
Isomorphs are curves in the thermodynamic phase diagram along which structure and dynamics are invariant to a good approximation. There are two main ways to trace out isomorphs, the configurational-adiabat method and the…
Despite the importance of a thermodynamically stable structure with a conserved fold for protein function, almost all evolutionary models neglect site-site correlations that arise from physical interactions between neighboring amino acid…
Determining protein structures at an atomic level remains a significant challenge in structural biology. We introduce $\texttt{RecCrysFormer}$, a hybrid model that exploits the strengths of transformers with the aim of integrating…
$\alpha$-helices stand out as common and relatively invariant secondary structural elements of proteins. However, $\alpha$-helices are not rigid bodies and their deformations can be significant in protein function ({\it e.g.} coiled coils).…
The multifractal detrended fluctuation analysis of time series is able to reveal the presence of long-range correlations and, at the same time, to characterize the self-similarity of the series. The rich information derivable from the…
Long, flexible physical filaments are naturally tangled and knotted, from macroscopic string down to long-chain molecules. The existence of knotting in a filament naturally affects its configuration and properties, and may be very stable or…
The study of neuronal morphology is important not only for its potential relationship with neuronal dynamics, but also as a means to classify diverse types of cells and compare than among species, organs, and conditions. In the present…
Convolutional neural networks are increasingly being used to analyze and classify material microstructures, motivated by the possibility that they will be able to identify relevant microstructural features more efficiently and impartially…
Gel electrophoresis is a powerful experimental method to probe the topology of DNA and other biopolymers. While there is a large body of experimental work which allows us to accurately separate different topoisomers of a molecule, a full…
A model for studying the ultrametricity of the energy landscape in a disordered heteropolymer is presented. It is treated as a simplified model of a protein molecule in which amino acid residues are modeled as point masses. Pairwise…
Inorganic crystal materials have broad application potential due to excellent physical and chemical properties, with elastic properties (shear modulus, bulk modulus) crucial for predicting materials' electrical conductivity, thermal…
The generation of protein crystals is necessary for the study of protein molecular function and structure. This is done empirically by processing large numbers of crystallization trials and inspecting them regularly in search of those with…
Biological molecular machines are proteins that operate under isothermal conditions hence are referred to as free energy transducers. They can be formally considered as enzymes that simultaneously catalyze two chemical reactions: the free…
Electrostatic interactions fundamentally govern the structure, stability, and dynamics of charged (bio)matter, yet the impact of heterogeneous and anisotropic charge distributions on the behavior of protein solutions remains elusive. Here,…
A fundamental goal of research in molecular biology is to understand protein structure. Protein crystallography is currently the most successful method for determining the three-dimensional (3D) conformation of a protein, yet it remains…
Automated identification of protein conformational states from simulation of an ensemble of structures is a hard problem because it requires teaching a computer to recognize shapes. We adapt the naive Bayes classifier from the machine…