Related papers: Bubbles, clusters and denaturation in genomic DNA:…
We have measured the temperature driven denaturing, or melting transition in poly d(A)-poly d(T) DNA oligomers of various lengths in different buffer conditions. Our findings are in clear disagreement with two state, reaction kinetics…
We generalize the particle-conserving dynamics method of de las Heras et al. [J. Phys. Condens. Matter: 28, 24404 (2016).] to binary mixtures and apply this to hard rods in one dimension. Considering the case of one species consisting of…
We propose a statistical mechanics model for DNA melting in which base stacking and pairing are explicitly introduced as distinct degrees of freedom. Unlike previous approaches, this model describes thermal denaturation of DNA secondary…
High-density DNA arrays, used to monitor gene expression at a genomic scale, have produced vast amounts of information which require the development of efficient computational methods to analyze them. The important first step is to extract…
In many fields, researchers are interested in large and complex biological processes. Two important examples are gene expression and DNA methylation in genetics. One key problem is to identify aberrant patterns of these processes and…
DNA is an astonishing material that can be used as a molecular building block to construct periodic arrays and devices with nanoscale accuracy and precision. Here, we present simple bead-spring model of DNA nanostars having three, four and…
The relationship of base pair openings to DNA flexibility is examined. Published experimental data on the temperature dependence of the persistence length by two different groups are well described in terms of an inhomogeneous Kratky-Porot…
Diffusion probabilistic models have achieved remarkable success in generative tasks across diverse data types. While recent studies have explored alternative degradation processes beyond Gaussian noise, this paper bridges two key diffusion…
A method is presented that allows exact calculations of fragment multiplicity distributions for a canonical ensemble of non-interacting clusters. Fragmentation properties are shown to depend on only a few parameters. Fragments are shown to…
In this Letter, we investigate the link between thermal denaturation and mechanical unzipping for two models of DNA, namely the Dauxois-Peyrard-Bishop model and a variant thereof we proposed recently. We show that the critical line that…
Cells regulate gene expression in part by forming DNA-protein condensates in the nucleus. While existing theories describe the equilibrium size and stability of such condensates, their dynamics remain less understood. Here, we use…
We use the "magnetic tweezers" technique to reveal the structural transitions that DNA undergoes in the force-torsion space. In particular, we focus on regions corresponding to negative supercoiling. These regions are characterized by the…
We show that a mesoscale model, with a minimal number of parameters, can well describe the thermomechanical and mechanochemical behavior of homogeneous DNA at thermal equilibrium under tension and torque. We predict critical temperatures…
We develop a phenomenological statistical model for dilute star matter at finite temperature, in which free nucleons are treated within a mean-field approximation and nuclei are considered to form a loosely interacting cluster gas. Its…
Many researches demonstrated that the DNA methylation, which occurs in the context of a CpG, has strong correlation with diseases, including cancer. There is a strong interest in analyzing the DNA methylation data to find how to distinguish…
A theory for thermomechanical behavior of homogeneous DNA at thermal equilibrium predicts critical temperatures for denaturation under torque and stretch, phase diagrams for stable B--DNA, supercoiling, optimally stable torque, and the…
Thermal denaturation of DNA is often studied with coarse-grained models in which native sequential base pairing is mimicked by the existence of attractive interactions only between monomers at the same position along strands (Poland and…
This review focuses on Direct numerical simulations (DNS) of turbulent flows laden with droplets or bubbles. DNS of these flows are more challenging than those of flows laden with solid particles due to the surface deformation in the…
DNA hybridization is a fundamental reaction with wide-ranging applications in biotechnology. The nearest-neighbor (NN) model provides the most reliable description of the energetics of duplex formation. Most DNA thermodynamics studies have…
We studied how the inhomogeneity of a sequence affects the phase transition that takes place at DNA melting. Unlike previous works, which considered thermodynamic quantities averaged over many different inhomogeneous sequences, we focused…