Related papers: Information-Thermodynamic Analysis of the DNA--RNA…
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…
Although RNAs play many cellular functions little is known about the dynamics and thermodynamics of these molecules. In principle, all-atom molecular dynamics simulations can investigate these issues, but with current computer facilities,…
For multilayer structures, interfacial failure is one of the most important elements related to device reliability. For cohesive zone modelling, traction-separation relations represent the adhesive interactions across interfaces. However,…
We discuss the physics of RNA as described by its secondary structure. We examine the static properties of a homogeneous RNA-model that includes pairing and base stacking energies as well as entropic costs for internal loops. For large…
We consider a Brownian particle confined by an external potential and subject to stochastic resetting to the origin. Motivated by the repetitive nature of the dynamics, we describe the process as a thermodynamic cycle of thermal expansion…
The translation of messenger RNA transcripts to proteins is commonly modeled as a one-dimensional totally asymmetric exclusion process with extended particles. Here we focus on the effects of premature termination of translation through the…
Many integrable stochastic particle systems in one space dimension (such as TASEP - totally asymmetric simple exclusion process - and its various deformations, with a notable exception of ASEP) remain integrable when we equip each particle…
We study the folding of RNA secondary structures with quenched sequence randomness by means of the constrained annealing method. A thermodynamic phase transition is induced by including the conformational weight of loop structures. In…
The transport and localization of RNA molecules, crucial for cellular function and development, involve a combination of diffusion and active transport mechanisms. Here, we are motivated by understanding the dynamics of RNA in Xenopus…
Nucleosome core particle is a dynamic structure -- DNA may transiently peel off the histone octamer surface due to thermal fluctuations or the action of chromatin remodeling enzymes. Partial DNA unwrapping enables easier access of…
Discriminating between correct and incorrect substrates is a core process in biology but how is energy apportioned between the conflicting demands of accuracy ($\mu$), speed ($\sigma$) and total entropy production rate ($P$)? Previous…
Ribonucleic acid (RNA) is involved in many regulatory and catalytic processes in the cell. The function of any RNA molecule is intimately related with its structure. In-line probing experiments provide valuable structural datasets for a…
For the canonical two-state model of transcription, we derive exact analytic expressions for the entropy production rate of transcription at steady state, and assess detailed balance breaking in transcription. Our analytics allow us to…
We call {\it monomer} a B-DNA base-pair and examine, analytically and numerically, electron or hole oscillations in monomer- and dimer-polymers, i.e., periodic sequences with repetition unit made of one or two monomers. We employ a…
Data-driven reachability analysis provides guaranteed outer approximations of reachable sets from input-state measurements, yet each propagation step requires a matrix-zonotope multiplication whose cost grows with the horizon length,…
Microscopic particle separation plays vital role in various scientific and industrial domains. In this Letter, we propose a universal non-equilibrium thermodynamic approach, employing the concept of Shortcuts to Isothermality, to realize…
We study a class of micromanipulation experiments, exemplified by the pulling apart of the two strands of double-stranded DNA (dsDNA). When the pulling force is increased to a critical value, an ``unzipping'' transition occurs. For random…
The two strands of the DNA double helix can be `unzipped' by application of 15 pN force. We analyze the dynamics of unzipping and rezipping, for the case where the molecule ends are separated and re-approached at constant velocity. For…
We report studies of the equilibrium and the dynamics of a general set of lattice models which capture the essence of the force-induced or mechanical DNA unzipping transition. Besides yielding the whole equilibrium phase diagram in the…
Templated copolymerization, in which information stored in the sequence of a heteropolymer template is copied into another polymer product, is the mechanism behind all known methods of genetic information transfer. A key aspect of templated…