Related papers: Why is the DNA Denaturation Transition First Order…
We consider the large-time dynamics of one-dimensional processes involving adsorption and desorption of extended hard-core particles (dimers, trimers,\,$\cdots,k$-mers), while interacting through their constituent monomers. Desorption can…
The phase diagram of spins 1/2 embedded in a magnetic field mutually interacting antiferromagnetically is determined. Contrary to the ferromagnetic case where a second order quantum phase transition occurs, a first order transition is…
We study the evolution of the dynamics across a generic first order quantum phase transition in an interacting boson model of nuclei. The dynamics inside the phase coexistence region exhibits a very simple pattern. A classical analysis…
The denaturation of the double helix is a template for fundamental biological functions such as replication and transcription involving the formation of local fluctuational openings. The denaturation transition is studied for heterogeneous…
Nucleation and growth is the dominant relaxation mechanism driving first order phase transitions. In two-dimensional at systems nucleation has been applied to a wide range of problems in physics, chemistry and biology. Here we study…
First order quantum phase transitions (1QPTs) are signaled, in the thermodynamic limit, by discontinuous changes in the ground state properties. These discontinuities affect expectation values of observables, including spatial correlations.…
Conformational transitions are ubiquitous in biomolecular systems, have significant functional roles and are subject to evolutionary pressures. Here we provide a first theoretical framework for topological transition, i.e. conformational…
The $2$d orders are a sub class of causal sets, which is especially amenable to computer simulations. Past work has shown that the $2$d orders have a first order phase transition between a random and a crystalline phase. When coupling the…
DNA is subject to large deformations in a wide range of biological processes. Two key examples illustrate how such deformations influence the readout of the genetic information: the sequestering of eukaryotic genes by nucleosomes, and DNA…
A fluid in the NVT ensemble at T less than the critical temperature T_c and rho = N/V somewhat in excess of rho_coex (density of the saturated gas in the gas-liquid transition) is considered. For V->infinity, a macroscopic liquid droplet…
We generalize the Poland-Scheraga (PS) model to the case of a circular DNA, taking into account the twisting of the two strains around each other. Guided by recent single-molecule experiments on DNA strands, we assume that the torsional…
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…
We investigate the translocation of a single stranded DNA through a pore which fluctuates between two conformations, using coupled master equations. The probability density function of the first passage times (FPT) of the translocation…
Here we investigate how the positions of a condensed phase can be controlled by using concentration gradients of a regulator that influences phase separation. We consider a mean field model of a ternary mixture where a concentration…
We consider disordered models of pinning of directed polymers on a defect line, including (1+1)-dimensional interface wetting models, disordered Poland--Scheraga models of DNA denaturation and other (1+d)-dimensional polymers in interaction…
A double stranded DNA molecule when pulled with a force acting on one end of the molecule can become either partially or completely unzipped depending on the magnitude of the force F. For a random DNA sequence, the number M of unzipped base…
In the framework of the Poland Scheraga model of DNA denaturation, we derive a recursion relation for the partition function of double stranded DNA, allowing for mismatches between the two strands. This relation is studied numerically using…
The statistical physics of homogeneous DNA is investigated by the imaginary time path integral formalism. The base pair stretchings are described by an ensemble of paths selected through a macroscopic constraint, the fulfillement of the…
A statistical model of homopolymer DNA, coupling internal base pair states (unbroken or broken) and external thermal chain fluctuations, is exactly solved using transfer kernel techniques. The dependence on temperature and DNA length of the…
The connectivity of individual neurons of large neural networks determine both the steady state activity of the network and its answer to external stimulus. Highly diluted random networks have zero activity. We show that increasing the…