Related papers: Theoretical and Experimental Investigations of DNA…
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…
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…
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…
The question of whether DNA conducts electric charges is intriguing to physicists and biologists alike. The suggestion that electron transfer/transport in DNA might be biologically important has triggered a series of experimental and…
The oxDNA model of DNA has been applied widely to systems in biology, biophysics and nanotechnology. It is currently available via two independent open source packages. Here we present a set of clearly-documented exemplar simulations that…
Stochastic dynamics of chemical reactions in a mutually repressing two-gene circuit is numerically simulated. The circuit has a rich variety of different states when the kinetic change of DNA status is slow. The stochastic switching…
We review statistical-mechanical theories of single-molecule micromanipulation experiments on nucleic acids. First, models for describing polymer elasticity are introduced. We then review how these models are used to interpret…
The structural flexibility of nucleic acids plays a key role in many fundamental life processes, such as gene replication and expression, DNA-protein recognition, and gene regulation. To obtain a thorough understanding of nucleic acid…
The thermodynamical stability of DNA minicircles is investigated by means of path integral techniques. Hydrogen bonds between base pairs on complementary strands can be broken by thermal fluctuations and temporary fluctuational openings…
The rapid progress in the field of molecular electronics has led to an increasing interest on DNA oligomers as possible components of electronic circuits at the nanoscale. For this, however, an understanding of charge transfer and transport…
Three coarse-grained models of the double-stranded DNA are proposed and compared in the context of mechanical manipulation such as twisting and various schemes of stretching. The models differ in the number of effective beads (between two…
Microscopic mechanisms of positive charge transfer in DNA remain unclear. A quantum state of electron hole in DNA is determined by the competition of a pi-stacking interaction $b$ smearing a charge between different base pairs and…
Complementary DNA strands in solution reliably hybridize to form stable duplexes. We study the kinetics of the hybridization process and the mechanisms by which two initially isolated strands come together to form a stable double helix. We…
DNA denaturation has long been a subject of intense study due to its relationship to DNA transcription and its fundamental importance as a nonlinear, structural transition. Many aspects of this phenomenon, however, remain poorly understood.…
While the thermodynamics of DNA hybridization is well understood, much less is known about the kinetics of this classic system. Filling this gap in our understanding has new urgency because DNA nanotechnology often depends critically on…
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…
The approach for the description of the DNA conformational transformations on the mesoscopic scales in the frame of the double helix is presented. Due to consideration of the joint motions of DNA structural elements along the conformational…
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 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…
Equations of State model relations between thermodynamic variables and are ubiquitous in scientific modelling, appearing in modern day applications ranging from Astrophysics to Climate Science. The three desired properties of a general…