Related papers: An intermediate phase in DNA melting
We propose a dynamical model for the secondary structure of DNA, which is based on the finite stacking enthalpies used in thermodynamics calculations. In this model, the two strands can separate and the bases are allowed to rotate…
We analyze the possible transition patterns exhibited by an effective non-relativistic field model describing interacting binary homogeneous dilute Bose gases whose overall potential is repulsive. We evaluate the temperature dependence of…
By extending the classical Peyrard-Bishop model, we are able to obtain a fully analytical description for the mechanical resistance of DNA under stretching at variable values of temperature, number of base pairs and intrachains and…
Native membranes of biological cells display melting transitions of their lipids at a temperature of 10-20 degrees below body temperature. Such transitions can be observed in various bacterial cells, in nerves, in cancer cells, but also in…
Despite numerous attempts, the understanding of the thermal denaturation of DNA is still a challenge due to the lack of structural data at the transition since standard experimental approaches to DNA melting are made in solution and do not…
We find that both continuous and discontinuous hexatic-liquid transitions can happen in the melting of two-dimensional solids of soft-core disks. For three typical model systems, Hertzian, harmonic, and Gaussian-core models, we observe the…
Recent theoretical predictions on DNA mechanical separation induced by pulling forces are numerically tested within a model in which self-avoidance for DNA strands is fully taken into account. DNA strands are described by interacting pairs…
Inner core translation, with solidification on one hemisphere and melting on the other, provides a promising basis for understanding the hemispherical dichotomy of the inner core, as well as the anomalous stable layer observed at the base…
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…
A theory of condensation and resolubilization of a dilute DNA solution with growing concentration of multivalent cations, N is suggested. It is based on a new theory of screening of a macroion by multivalent cations, which shows that due to…
First-order phase transition in a highly correlated electron system can manifest as a dynamic phenomenon. The presence of multiple domains of the coexisting phases average out the dynamical effects making it nearly impossible to predict the…
The closure of long equilibrated denaturation bubbles in DNA is studied using Brownian dynamics simulations. A minimal mesoscopic model is used where the double-helix is made of two interacting bead-spring freely rotating strands, with a…
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…
Our understanding of various states of matter usually relies on the assumption of thermodynamic equilibrium. However, the transitions between different phases of matter can be strongly affected by non-equilibrium phenomena. Here we…
When pulled along its axis, double-stranded DNA elongates abruptly at a force of about 65 pN. Two physical pictures have been developed to describe this overstretched state. The first proposes that strong forces induce a phase transition to…
We investigate the characteristics of two dimensional melting in simple atomic systems via isobaric-isothermal ($NPT$) and isochoric-isothermal ($NVT$) molecular dynamics simulations with special focus on the effect of the range of 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…
The mechanical separation of the double helical DNA structure induced by forces pulling apart the two DNA strands (``unzipping'') has been the subject of recent experiments. Analytical results are obtained within various models of…
Understanding the melting of short DNA sequences probes DNA at the scale of the genetic code and raises questions which are very different from those posed by very long sequences, which have been extensively studied. We investigate this…
The distance-resolved effective interaction potential between two parallel DNA molecules is calculated by computer simulations with explicit tetravalent counterions and monovalent salt. Adding counterions first yields an attractive minimum…