Related papers: Thermodynamics of DNA loops with long-range correl…
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…
We examine the elastic model of short circular DNA. We obtain analytic expressions for configurations, elastic energy, twist and linking number of our solutions. We find the onset of the plectonemic transition. We suggest ways to use our…
The electronic properties of disordered systems have been the subject of intense study for several decades. Thermoelectric properties, such as thermopower and thermal conductivity, have been relatively neglected. A long standing problem is…
Transcriptional activity has been shown to relate to the organization of chromosomes in the eukaryotic nucleus and in the bacterial nucleoid. In particular, highly transcribed genes, RNA polymerases and transcription factors gather into…
We present experimental evidence for the different mechanisms driving the fluctuations of the local density of states (LDOS) in disordered photonic systems. We establish a clear link between the microscopic structure of the material and the…
This paper introduces the use of cable dynamics models as a means to explore the mechanics of DNA on long-length scales. It is on these length scales that DNA forms twisted and curved three-dimensional shapes known as supercoils and loops.…
We study the stochastic thermodynamics of an overdamped harmonic chain, which can be viewed equivalently as a 1D Rouse chain or as an approximate model of single file diffusion. We discuss mainly two levels of description of this system:…
One dimensional systems are under intense investigation, both from theoretical and experimental points of view, since they have rather peculiar characteristics which are of both conceptual and technological interest. We analyze the…
The responses of a $1+\epsilon $ dimensional directed path to temperature and to potential variations are calculated exactly, and are governed by the same scaling form. The short scale decorrelation (strong correlation regime) leads to the…
The formation of secondary structures by a random RNA sequence is studied as a model system for the sequence-structure problem omnipresent in biopolymers. Several toy energy models are introduced to allow detailed analytical and numerical…
We study how the influence of structural correlations in disordered systems manifests itself in experimentally measurable magnitudes, focusing on dc conductance of semiconductor superlattices with general potential profiles. We show that…
We numerically study the wetting (adsorption) transition of a polymer chain on a disordered substrate in 1+1 dimension.Following the Poland-Scheraga model of DNA denaturation, we use a Fixman-Freire scheme for the entropy of loops. This…
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…
We study the thermodynamic properties of a microscopic model of coupled oscillators that exhibits a dynamical phase transition from a desynchronized to a synchronized phase. We consider two different configurations for the thermodynamic…
The architecture of the eukaryotic genome is characterized by a high degree of spatial organization. Chromosomes occupy preferred territories correlated to their state of activity and, yet, displace their genes to interact with remote sites…
Short DNA linkers are increasingly being exploited for driving specific self-assembly of Brownian objects. DNA-functionalised colloids can assemble into ordered or amorphous materials with tailored morphology. Recently, the same approach…
Compressing or cooling a fluid typically enhances its static interparticle correlations. However, there are notable exceptions. Isothermal compression can reduce the translational order of fluids that exhibit anomalous waterlike trends in…
How a closed system thermalizes, especially in the absence of global conservation laws but in the presence of disorder and interactions, is one of the central questions in non-equilibrium statistical mechanics. We explore this for a…
Two-dimensional (2D) particulate aggregates formed due to competing interactions exhibit a range of non-equilibrium steady state morphologies from finite-size compact crystalline structures to non-compact string-like conformations. We…
Single-molecule experiments in which force is applied to DNA or RNA molecules have enabled important discoveries of nucleic acid properties and nucleic acid-enzyme interactions. These experiments rely on a model of the polymer…