Related papers: Target search on a dynamic DNA molecule
Previous numerical investigations of an one-dimensional DNA model with an extended modified coupling constant by transcripting enzyme are integrated to longer time and demonstrated explicitly the trapping of breathers by DNA chains with…
We explore the consequences of very high dimensionality in the dynamical landscape of protein folding. Consideration of both typical range of stabilising interactions, and folding rates themselves, leads to a model of the energy…
Genetic stability is a key factor in maintaining, survival and reproduction of biological cells. It relies on many processes, but one of the most important is a {\it homologous recombination}, in which the repair of breaks in…
In this paper we propose a novel theoretical framework for interpreting long-range dynamical correlations unveiled in proteins through NMR measurements. The theoretical rationale relies on the hypothesis that correlated motions in proteins…
The speed of site-specific binding of transcription factor (TFs) proteins with genomic DNA seems to be strongly retarded by the randomly occurring sequence traps. Traps are those DNA sequences sharing significant similarity with the…
2D display is a fast and economical way of visualizing polymorphism and comparing genomes, which is based on the separation of DNA fragments in two steps, according first to their size and then to their sequence composition. In this paper,…
Evolutionary search via the quality-diversity (QD) paradigm can discover highly performing solutions in different behavioural niches, showing considerable potential in complex real-world scenarios such as evolutionary robotics. Yet most QD…
As the structural databases continue to expand, efficient methods are required to search similar structures of the query structure from the database. There are many previous works about comparing protein 3D structures and scanning the…
A variety of experimental techniques have improved the 2D and 3D spatial resolution that can be extracted from \emph{in vivo} single-molecule measurements. This enables researchers to quantitatively infer the magnitude and directionality of…
Motivation: Thanks to the recent advances in structural biology, nowadays three-dimensional structures of various proteins are solved on a routine basis. A large portion of these contain structural repetitions or internal symmetries. To…
The understanding of dynamics and functioning of biological membranes and in particular of membrane embedded proteins is one of the most fundamental problems and challenges in modern biology and biophysics. In particular the impact of…
Many proteins carry out their biological functions by forming the characteristic tertiary structures. Therefore, the search of the stable states of proteins by molecular simulations is important to understand their functions and…
We use nucleosome maps obtained by high-throughput sequencing to study sequence specificity of intrinsic histone-DNA interactions. In contrast with previous approaches, we employ an analogy between a classical one-dimensional fluid of…
The diffusive arrival of transcription factors at the promoter sites on the DNA sets a lower bound on how accurately a cell can regulate its protein levels. Using results from the literature on diffusion-influenced reactions, we derive an…
In recent years machine learning (ML) took bio- and cheminformatics fields by storm, providing new solutions for a vast repertoire of problems related to protein sequence, structure, and interactions analysis. ML techniques, deep neural…
We propose a data-directed paradigm (DDP) to search for new physics. Focusing on the data without using simulations, exclusive selections which exhibit significant deviations from known properties of the standard model can be identified…
The problem is area-restricted search for targets using an autonomous mobile sensing platform. Detection is imperfect: the probability of detection depends on the range to the target, while the probability of false detections is non-zero.…
This paper aims at a comprehensive understanding on the novel elastic property of double-stranded DNA (dsDNA) discovered very recently through single-molecule manipulation techniques. A general elastic model for double-stranded biopolymers…
Collective coordinate and direct numerical integration methods are applied to the analysis of a one-dimensional DNA model. A modification of the coupling constant in an extended region is found to be less selective towards the breather it…
Accurate prediction of drug-target interactions is critical for advancing drug discovery. By reducing time and cost, machine learning and deep learning can accelerate this laborious discovery process. In a novel approach, BarlowDTI, we…