Related papers: On the ion-mediated interaction between protein an…
A dynamical mean-field theory is developed to analyze stochastic single-cell dynamics of gene expression. By explicitly taking account of nonequilibrium and nonadiabatic features of the DNA state fluctuation, two-time correlation functions…
Single T4-DNA molecules were confined in rectangular-shaped channels with a depth of 300 nm and a width in the range 150-300 nm casted in a poly(dimethylsiloxane) nanofluidic chip. The extensions of the DNA molecules were measured with…
The pair interaction between two stiff parallel linear DNA molecules depends not only on the distance between their axes but on their azimuthal orientation. The positional and orientational order in columnar B-DNA assemblies in solution is…
As a key molecule of Life, Deoxyribonucleic acid (DNA) is the focus of numbers of investigations with the help of biological, chemical and physical techniques. From a physical point of view, both experimental and theoretical works have…
Positions of protons in DNA hydrogen bonds are fundamental for the fidelity of the replication process. Because the hydrogen bond is partially covalent the electronic structure of DNA plays an important role in the replication process.…
In order to characterize the mechanisms governing the diffusion of particles in biological scenarios, it is essential to accurately determine their diffusive properties. To do so, we propose a machine learning method to characterize…
The theory of elastic rods can be used to describe certain geometric and topological properties of the DNA molecules. A similar effective field theory approach was previously suggested to describe the conformations and dynamics of proteins.…
Rich data and powerful machine learning models allow us to design drugs for a specific protein target \textit{in silico}. Recently, the inclusion of 3D structures during targeted drug design shows superior performance to other target-free…
The evolutionary reason for the increase in gene length from archaea to prokaryotes to eukaryotes observed in large scale genome sequencing efforts has been unclear. We propose here that the increasing complexity of protein-protein…
Simple elastic network models of DNA were developed to reveal the structure-dynamics relationships for several nucleotide sequences. First, we propose a simple all-atom elastic network model of DNA that can explain the profiles of…
Phase separation in biomolecular mixtures can result from multiple physical interactions, which may act either complementarily or antagonistically. In the case of protein-nucleic acid mixtures, charge plays a key role but can have…
The possibility for proteins to aggregate in different superstructures, i.e. large-scale polymorphism, has been widely observed, but an understanding of the physico-chemical mechanisms behind it is still out of reach. Here we present a…
The CRISPR/Cas9 system acts as the prokaryotic immune system and has important applications in gene editing. The protein Cas9 is one of its crucial components. The role of Cas9 is to search for specific target sequences on the DNA and…
Network science has become an essential interdisciplinary tool for understanding complex biological systems. However, because these systems undergo continuous, often stimulus-driven changes in both structure and function, traditional static…
A recent experiment [Sadoon AA, Wang Y. 2018 Phys. Rev. E 98, 042411] has revealed that nucleoid associated proteins (i.e., DNA-binding proteins) exhibit highly heterogeneous diffusion processes in bacteria where not only the diffusion…
Motivated by a question about the sensitivity of knots' diffusive motion to the actual sequence of nucleotides placed on a given DNA, here we study a simple model of a sequence-reading diffusion on a stretched chain with a frozen sequence…
Heat-induced mobility of nucleosomes along DNA is an experimentally well-studied phenomenon. A recent experiment shows that the repositioning is modified in the presence of minor-groove binding DNA ligands. We present here a stochastic…
We develop a theoretical framework on the mechanism of combinatorial binding of transcription factors (TFs) with their specific binding sites on DNA. We consider three possible mechanisms viz. monomer, hetero-oligomer and coordinated…
Microscopic mechanisms of positive charge transfer in DNA remain unclear. A quantum state of electron hole in DNA is determined by the competition of the pi-stacking interaction $b$ sharing a charge between different base pairs and the…
From a nanoscience perspective, cellular processes and their reduced in vitro imitations provide extraordinary examples for highly robust few or single molecule reaction pathways. A prime example are biochemical reactions involving DNA…