相关论文: Information-Thermodynamic Analysis of the DNA--RNA…
Nucleic acids have been regarded as stiff polymers with long-range flexibility and generally modeled using elastic rod models of polymer physics. Notwithstanding, investigations carried out over the past few years on single fragments of…
DNA hybridization is a fundamental reaction with wide-ranging applications in biotechnology. The nearest-neighbor (NN) model provides the most reliable description of the energetics of duplex formation. Most DNA thermodynamics studies have…
We study the force-induced unfolding of random disordered RNA or single-stranded DNA polymers. The system undergoes a second order phase transition from a collapsed globular phase at low forces to an extensive necklace phase with a…
Using Brownian dynamics simulations, we study the migration of long charged chains in an electrophoretic microchannel device consisting of an array of microscopic entropic traps with alternating deep regions and narrow constrictions. Such a…
Using a combination of theory and computer simulations, we study the translocation of an RNA molecule, pulled through a solid-state nanopore by an optical tweezer, as a method to determine its secondary structure. The resolution with which…
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…
The fidelity of DNA replication by DNA polymerase (DNAP) has long been an important issue in biology. While numerous experiments have revealed details of the molecular structure and working mechanism of DNAP which consists of both a…
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…
DNA renaturation is the recombination of two complementary single strands to form a double helix. It is experimentally known that renaturation proceeds through the formation of a double stranded nucleus of several base pairs (the rate…
We study the statistical mechanics of RNA secondary structures designed to have an attraction between two different types of structures as a model system for heteropolymer aggregation. The competition between the branching entropy of the…
The efficiency of path sampling simulations can be improved considerably using the approach of path swapping. For this purpose, we have devised a new algorithmic procedure based on the transition interface sampling technique. In the same…
Information-to-energy conversion with feedback measurement stands as one of the most intriguing aspects of the thermodynamics of information in the nanoscale. To date, experiments have focused on feedback protocols for work extraction. Here…
Being a dual purpose enzyme, the DNA polymerase is responsible for elongation of the newly formed DNA strand as well as cleaving the erroneous growth in case of a misincorporation. The efficiency of replication depends on the coordination…
Small-angle X-ray scattering (SAXS) experiments are increasingly used to probe RNA structure. A number of \emph{forward models} that relate measured SAXS intensities and structural features, and that are suitable to model either…
The process of RNA base fraying (i.e. the transient opening of the termini of a helix) is involved in many aspects of RNA dynamics. We here use molecular dynamics simulations and Markov state models to characterize the kinetics of RNA…
Using force as a probe to map the folding landscapes of RNA molecules has become a reality thanks to major advances in single molecule pulling experiments. Although the unfolding pathways under tension are complicated to predict studies in…
We explore and quantify the physical and biochemical mechanisms that may be relevant in the regulation of translation. After elongation and detachment from the 3' termination site of mRNA, parts of the ribosome machinery can diffuse back to…
We study the dynamics of overdamped Brownian particles diffusing in conservative force fields and undergoing stochastic resetting to a given location with a generic space-dependent rate of resetting. We present a systematic approach…
Experimental studies of the thermal denaturation of DNA yield a strong indication that the transition is first order. This transition has been theoretically studied since the early sixties, mostly within an approach in which the microscopic…
Several important biological processes are initiated by the binding of a protein to a specific site on the DNA. The strategy adopted by a protein, called transcription factor (TF), for searching its specific binding site on the DNA has been…