Related papers: Information-Thermodynamic Analysis of the DNA--RNA…
Brownian computers utilize thermal fluctuations as a resource for computation and hold promise for achieving ultra-low-energy computations. However, the lack of a statistical direction in Brownian motion necessitates the incorporation of…
Metrics for indirectly predicting the folding rates of RNA sequences are of interest. In this letter, we introduce a simple metric of RNA structural complexity, which accounts for differences in the energetic contributions of RNA base…
Lipid membranes in a physiological context cannot be understood without taking into account their mobile environment. Here, we report on a high energy-resolution neutron backscattering study to investigate slow motions on nanosecond time…
In this work, we study the nonequilibrium statistical properties of the relaxation dynamics of a nanoparticle trapped in a harmonic potential. We report an exact time-dependent analytical solution to the Langevin dynamics that arises from…
The Minimum Rate of Dissipation Principle (MRDP) affirms that, for time-independent boundary conditions, a thermodynamic system evolves towards a steady-state with the least possible dissipation. In this note, examples of diffusion…
The purpose of this work is to extend the Geant4-DNA Monte Carlo toolkit to include electron interactions with the four DNA bases using a set of cross sections recently implemented in Geant-DNA CPA100 models and available for liquid water.…
We propose a statistical mechanics model for DNA melting in which base stacking and pairing are explicitly introduced as distinct degrees of freedom. Unlike previous approaches, this model describes thermal denaturation of DNA secondary…
Models for RNA secondary structures (the topology of folded RNA) without pseudo knots are disordered systems with a complex state-space below a critical temperature. Hence, a complex dynamical (glassy) behavior can be expected, when…
By exerting mechanical force it is possible to unfold/refold RNA molecules one at a time. In a small range of forces, an RNA molecule can hop between the folded and the unfolded state with force-dependent kinetic rates. Here, we introduce a…
Nowadays different experimental techniques, such as single molecule or relaxation experiments, can provide dynamic properties of biomolecular systems, but the amount of detail obtainable with these methods is often limited in terms of time…
The mechanical properties of molecules are today captured by single molecule manipulation experiments, so that polymer features are tested at a nanometric scale. Yet devising mathematical models to get further insight beyond the commonly…
We show how single-molecule unzipping experiments can provide strong evidence that the zero-force melting transition of long molecules of natural dsDNA should be classified as a phase transition of the higher-order type (continuous). We…
The closure dynamics of a pre-equilibrated DNA denaturation bubble is studied using both Brownian dynamics simulations and an analytical approach. The numerical model consists of two semi-flexible interacting single strands (ssDNA) and a…
We extend the principles of information thermodynamics to study energy and information exchanges between coupled systems composed of one part undergoing a Markov jump process and another underdamped diffusion. We derive integral fluctuation…
Stochastically gated interfaces play an important role in a variety of cellular diffusion processes. Examples include intracellular transport via stochastically gated ion channels and pores in the plasma membrane of a cell, intercellular…
We present an extensive theoretical investigation of the mechanical unzipping of double-stranded DNA under the influence of an applied force. In the limit of long polymers, there is a thermodynamic unzipping transition at a critical force…
RNA folding is a kinetic process governed by the competition of a large number of structures stabilized by the transient formation of base pairs that may induce complex folding pathways and the formation of misfolded structures. Despite of…
Messenger RNA translation is often studied by means of statistical-mechanical models based on the Asymmetric Simple Exclusion Process (ASEP), which considers hopping particles (the ribosomes) on a lattice (the polynucleotide chain). In this…
The ability to generate and recognize sequential data is fundamental for autonomous systems operating in dynamic environments. Inspired by the key principles of the brain-predictive coding and the Bayesian brain-we propose a novel…
We present and characterize a method to accelerate the relaxation of a Brownian object between two distinct equilibrium states. Instead of relying on a deterministic time-dependent control parameter, we use stochastic resetting to guide and…