Related papers: Charge Transfer Database for Bio-molecule Tight Bi…

The observed correlations between pairs of homologous protein sequences are typically explained in terms of a Markovian dynamic of amino acid substitution. This model assumes that every location on the protein sequence has the same…

The trend to fabricate electrical circuits on nanoscale dimensions has led to impressive progress in the field of molecular electronics in the last decade. A theoretical description of molecular contacts as the building blocks of future…

Due to inherent complexity active transport presents a landmark hurdle for oral absorption properties prediction. We present a novel approach carrier-mediated drug absorption parameters calculation based on entirely different paradigm than…

Accurate quantification of protein-nanoparticle interactions is essential for applications in nanobiotechnology, nanomedicine, and drug delivery. Motivated by recent computational and experimental work, we combine coarse-grained united-atom…

An essential aspect for adequate predictions of chemical properties by machine learning models is the database used for training them. However, studies that analyze how the content and structure of the databases used for training impact the…

Atomic-scale charge transport properties are not only of significant fundamental interest but also highly relevant for numerous technical applications. However, experimental methods which are capable of detecting charge transport at the…

The mechanisms by which a protein's 3D structure can be determined based on its amino acid sequence have long been one of the key mysteries of biophysics. Often simplistic models, such as those derived from geometric constraints, capture…

In this work we present a system based on a Deep Learning approach, by using a Convolutional Neural Network, capable of classifying protein chains of amino acids based on the protein description contained in the Protein Data Bank. Each…

In this paper, we consider the statistical analysis of a protein interaction network. We propose a Bayesian model that uses a hierarchy of probabilistic assumptions about the way proteins interact with one another in order to: (i) identify…

We consider multi-chain protein native structures and propose a criterion that determines whether two chains in the system are entangled or not. The criterion is based on the behavior observed by pulling at both temini of each chain…

Molecular devices, as future electronics, seek low-resistivity contacts for the energy saving. At the same time, the contacts should intensify desired properties of tailored electronic elements. In this work, we focus our attention on two…

Partial atomic charges are a useful and intuitive concept for understanding molecular properties and chemical reaction mechanisms, showing how changes in molecular geometry can affect the flow of electronic charge within a molecule.…

We present a detailed analysis of the mechanism of the primary charge separation process in bacterial photosynthesis using real-time path integrals. Direct computer simulations as well as an approximate analytical theory have been employed…

We report the electronic transport properties of a new photo-addressable molecular switch. The switching process relies on a new concept based on linear {\pi}-conjugated dynamic systems, in which the geometry and hence the electronic…

Predicting structural and energetic properties of a molecular system is one of the fundamental tasks in molecular simulations, and it has use cases in chemistry, biology, and medicine. In the past decade, the advent of machine learning…

Functional protein-protein interactions are crucial in most cellular processes. They enable multi-protein complexes to assemble and to remain stable, and they allow signal transduction in various pathways. Functional interactions between…

Different aspects of protein folding are illustrated by simplified polymer models. Stressing the diversity of side chains (residues) leads one to view folding as the freezing transition of an heteropolymer. Technically, the most common…

In the present work, we review the fundamental methods which have been developed in the last few years for classifying into families and clans the distribution of amino acids in protein databases. This is done through functions of random…

The response of proteins to chemical reactions or impulsive excitation that occurs within the molecule has fascinated chemists for decades. In recent years ultrafast X-ray studies have provided ever more detailed information about the…

In Heisenberg models with exchange anisotropy, transverse spin components are not conserved and can decay not only by transport, but also by dephasing. Here we utilize ultracold atoms to simulate the dynamics of 1D Heisenberg spin chains,…