Related papers: Modelling toehold-mediated RNA strand displacement
Following nuclear decay, a daughter atom in a solid will "stay in place" if the recoil energy is less than the threshold for displacement. At high temperature, it may subsequently undergo long-range diffusion or some other kind of atomic…
We develop a dynamical theory of heat transfer between two nano systems. In particular, we consider the resonant heat transfer between two nanoparticles due to the coupling of localized surface modes having a finite spectral width. We model…
Solid-state nanopores are single molecule sensors that measure changes in ionic current as charged polymers such as DNA pass through. Here, we present comprehensive experiments on the length, voltage and salt dependence of the frequency of…
Because of the potential link between -1 programmed ribosomal frameshifting and response of a pseudoknot (PK) RNA to force, a number of single molecule pulling experiments have been performed on PKs to decipher the mechanism of programmed…
The competition between toroidal and rod-like conformations as possible ground states for DNA condensation is studied as a function of the stiffness, the length of the DNA and the form of the long-range interactions between neighboring…
RNA molecules exhibit various biological functions intrinsically dependent on their diverse ecosystem of highly flexible structures. This flexibility arises from complex hydrogen-bonding networks defined by canonical and non-canonical base…
Several experiments on tagged molecules or particles in living systems suggest that they move anomalously slow - their mean squared displacement (MSD) increase slower than linearly with time. Leading models aimed at understanding these…
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…
Renaturation of complementary single strands of DNA is one of the important processes that requires better understanding in the view of molecular biology and biological physics. Here we develop a stochastic dynamical model on the DNA…
Nuclear reaction rates are one of the most important ingredients in describing how stars evolve. The study of the nuclear reactions involved in different astrophysical sites is thus mandatory to address most questions in nuclear…
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…
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 denaturation dynamics of a long double-stranded DNA is studied by means of a model of the Poland-Scheraga type. We note that the linking of the two strands is a locally conserved quantity, hence we introduce local updates that respect…
Recent experiments showed that multiple copies of the molecular machine RNA polymerase (RNAP) can efficiently synthesize mRNA collectively in the active state of the promoter. However, environmentally-induced promoter repression results in…
In the coordinate representation of thermofield dynamics, we investigate the thermalized displaced squeezed thermal state which involves two temperatures successively. We give the wavefunction and the matrix element of the density operator…
In this work we present a plasmonic platform capable of trapping nano-objects as small as 100 nm in two different spatial configurations. The switch between the two trapping states, localized on the tip and on the outer wall of a vertical…
We review the basic concepts and tools for mechanically unzipping RNA hairpins using force spectroscopy. By pulling apart the ends of an RNA molecule using optical tweezers, it is possible to measure the folding free energy at varying…
RNA polymerase (RNAP) is a mobile molecular workshop that polymerizes a RNA molecule by adding monomeric subunits one by one, while moving step by step on the DNA template itself. Here we develop a theoretical model by incorporating the…
In-situ powder diffraction was used to study the annealing of dislocations in the archetypal hydrogen absorbers Pd and LaNi5. The relationship between dislocations and trapped hydrogen was explored using thermally induced desorption. It was…
The temperature dependence of DNA flexibility is studied in the presence of stretching and unzipping forces. Two classes of models are considered. In one case the origin of elasticity is entropic due to the polymeric correlations, and in…