Related papers: Structurally specific thermal fluctuations identif…
DNA looping participates in transcriptional regulation, for instance, by allowing distal binding sites to act synergistically. Here we study this process and compare different regulatory mechanisms based on repression with and without…
We use a coarse-grained model of DNA-functionalized particles to understand the role of DNA chain length on their self-assembly. We find that the increasing chain length for a given particle size decreases the propensity to form ordered…
Steady progress in the miniaturization of structures and devices has reached a scale where thermal fluctuations become relevant and it is thus important to understand how such fluctuations affect their mechanical stability. Here, we…
We report an experimental and theoretical analysis of the energy exchanged between two conductors kept at different temperature and coupled by the electric thermal noise. Experimentally we determine, as functions of the temperature…
There is increasing evidence that protein binding to specific sites along DNA can activate the reading out of genetic information without coming into direct physical contact with the gene. There also is evidence that these distant but…
The genomic DNA of most bacteria is significantly underwound, which constrains the DNA molecule to adopt a branched plectoneme geometry. Moreover, biological functions like replication and transcription require that the two DNA strands be…
The imaginary time path integral formalism is applied to a nonlinear Hamiltonian for a short fragment of heterogeneous DNA with a stabilizing solvent interaction term. Torsional effects are modeled by a twist angle between neighboring base…
We report a theoretical study of the thermopower of single-molecule junctions, with focus on phenyl-based molecular junctions. In contrast to prior studies, thermal fluctuations of the torsional angle between the phenyl rings and variations…
Noise in the expression of a gene produces fluctuations in the concentration of the gene product. These fluctuations can interfere with optimal function or can be exploited to generate beneficial diversity between cells; gene expression…
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 properties of slow crack growth in brittle materials are analyzed both theoretically and experimentally. We propose a model based on a thermally activated rupture process. Considering a 2D spring network submitted to an external load…
We perform Brownian dynamics simulations of semiflexible colloidal sheets with hydrodynamic interactions and thermal fluctuations in shear flow. As a function of the ratio of bending rigidity to shear energy (a dimensionless quantity we…
Intrinsic transcriptional noise induced by operator fluctuations is investigated with a simple spin like stochastic model. The effects of transcriptional fluctuations in protein synthesis is probed by coupling transcription and translation…
The electrical conductance of molecular junctions may strongly depend on the temperature, and weakly on molecular length, under two distinct mechanisms: phase-coherent resonant conduction, with charges proceeding via delocalized molecular…
Fluctuation Theorems are central in stochastic thermodynamics, as they allow for quantifying the irreversibility of single trajectories. Although they have been experimentally checked in the classical regime, a practical demonstration in…
In eukaryotic genomes, nucleosomes function to compact DNA and to regulate access to it both by simple physical occlusion and by providing the substrate for numerous covalent epigenetic tags. While nucleosome positions in vitro are…
Genes are connected in complex networks of interactions where often the product of one gene is a transcription factor that alters the expression of another. Many of these networks are based on a few fundamental motifs leading to switches…
We discuss the thermodynamic behaviour near the force induced unzipping transition of a double stranded DNA in two different ensembles. The Y-fork is identified as the coexisting phases in the fixed distance ensemble. From finite size…
A class of nucleosome remodeling motors translocate nucleosomes, to which they are attached, toward the middle of DNA chain in the presence of ATP during in vitro experiments. Such a biological activity is likely based on a physical…
Plectonemes are intertwined helically looped domains which form when a DNA molecule is supercoiled, i.e. over- or under-wounded. They are ubiquitous in cellular DNA and their physical properties have attracted significant interest both from…