Related papers: Duplex-single strand denaturing transition in DNA …
Charge transfer along the base-pair stack in DNA is modeled in terms of thermally-assisted tunneling between adjacent base pairs. Central to our approach is the notion that tunneling between fluctuating pairs is rate-limited by the…
The melting of a homopolymer double-stranded (ds) deoxyribonucleic acid (DNA) in the dilute limit is studied numerically in the presence of an attractive and impenetrable surface on a simple cubic lattice. The two strands of the DNA are…
We separate double stranded lambda phage DNA by applying a fixed force at a constant temperature ranging from 15C to 50C, and measure the minimum force required to separate the two strands, providing the first experimental determination of…
We have simulated structure and dynamics of water in the grooves of a DNA duplex using moleculear dynamics simulations. We find signatures of a dynamical transition in both translational and orientational dynamics of water molecules in both…
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…
We use a recently developed coarse-grained model to simulate the overstretching of duplex DNA. Overstretching at 23C occurs at 74 pN in the model, about 6-7 pN higher than the experimental value at equivalent salt conditions. Furthermore,…
A model of dipolar dimer liquid (DDL) on a two-dimensional lattice has been proposed. We found that at high density and low temperature, it has a partially ordered phase which we called glacia phase. The glacia phase transition can be…
We evaluate, by means of molecular dynamics simulations employing a realistic DNA coarse-grained model, the phase behaviour and the structural and dynamic properties of tetravalent DNA nanostars, i.e. nanoconstructs completely made of DNA.…
The closure dynamics of a pre-equilibrated DNA denaturation bubble is studied using both Brownian dynamics simulations and an analytical approach. The numerical model consists of two semi-flexible interacting single strands (ssDNA) and a…
Temperature and angular momentum dependence of the quadrupole deformation is studied in the middle of the sd-shell for 28Si and 27Si isotopes using the spherical shell model approach. The shell model calculations have been performed using…
We employ two Tight-Binding (TB) approaches to study the electronic structure and hole or electron transfer in B-DNA monomer polymers and dimer polymers made up of $N$ monomers (base pairs): (I) at the base-pair level, using the on-site…
We predict a novel temperature-driven phase transition of DNA below the melting transition. The additional, intermediate phase exists for repetitive sequences, when the two strands have different lengths. In this phase, the excess bases of…
The dilatometric investigation in the temperature range of 2-28K shows that a first-order polyamorphous transition occurs in the orientational glasses based on C60 doped with H2, D2 and Xe. A polyamorphous transition was also detected in…
Standard DNA melting curves record the separation of the two strands versus temperature, but they do not provide any information on the location of the opening. We introduce an experimental method which adds a new dimension to the melting…
Circular double stranded DNA has different topological states which are defined by their linking numbers. Equilibrium distribution of linking numbers can be obtained by closing a linear DNA into a circle by ligase. Using Monte Carlo…
Motivated by experiments on doped transition metal oxides, this paper considers the interplay of interactions, disorder, kinetic energy and temperature in a simple system. An ensemble of two-site Anderson-Hubbard model systems has already…
Kittel's 1D model represents a natural DNA with two strands as a (molecular) zipper, which may separated as the temperature is varied. We define multidimensional version of this model on a Cayley tree and study the set of Gibbs measures. We…
Phase transitions in 1/4-filled quasi-one-dimensional molecular conductors are studied theoretically on the basis of extended Hubbard chains including electron-lattice interactions coupled by interchain Coulomb repulsion. We apply the…
When double-stranded DNA molecules are heated, or exposed to denaturing agents, the two strands get separated. The statistical physics of this process has a long history, and is commonly described in term of the Poland-Scheraga (PS) model.…
A unifying theory of the denaturation transition of DNA, driven by temperature T or induced by an external mechanical torque Gamma is presented. Our model couples the hydrogen-bond opening and the untwisting of the helicoidal molecular…