Related papers: Work Distribution for Unzipping Processes
The transport of nanoparticles (NPs) in polymer networks, as a typical simplified model describing various structures in living systems, is profoundly important in biomedical engineering and nanotechnology. Predicting the effective…
We propose a regularization framework inspired by thermodynamic work for guiding pre-trained probability flow generative models (e.g., continuous normalizing flows or diffusion models) by minimizing excess work, a concept rooted in…
The statistical physics of homogeneous DNA is investigated by the imaginary time path integral formalism. The base pair stretchings are described by an ensemble of paths selected through a macroscopic constraint, the fulfillement of the…
Although partition temperature derived using the Darwin-Fowler method is exact for simple scenarios, the derivation for complex systems might reside on specific approximations whose viability is not ensured if the thermodynamic limit is not…
PDZ domains are typical examples of binding motifs mediating the formation of protein-protein assemblies in many different cells. A quantitative characterization of the mechanisms intertwining structure, chemistry and dynamics with the PDZ…
We consider the weakly asymmetric limit of simple exclusion process with drift to the left, starting from step Bernoulli initial data with $\rho_-<\rho_+$ so that macroscopically one has a rarefaction fan. We study the fluctuations of the…
The twisting deformation of mechanically stretched DNA molecules is studied by a coarse grained Hamiltonian model incorporating the fundamental interactions that stabilize the double helix and accounting for the radial and angular base pair…
We investigated how the finiteness of the length of the sequence affects the phase transition that takes place at DNA melting temperature. For this purpose, we modified the Transfer Integral method to adapt it to the calculation of both…
RNA's diversity of structures and functions impacts all life forms since primordia. We use calorimetric force spectroscopy to investigate RNA folding landscapes in previously unexplored low-temperature conditions. We find that Watson-Crick…
Understanding the motion of particles with ligand-receptors is important for biomedical applications and material design. Yet, even among a single design, the prototypical DNA-coated colloids, seemingly similar micrometric particles hop or…
We consider in this paper, a few important issues in non-equilibrium work fluctuations and their relations to equilibrium free energies. First we show that Jarzynski identity can be viewed as a cumulant expansion of work. For a switching…
A simple expression for the non-equilibrium distribution function in ultra-fast transient processes is proposed. Postulating its dependence on temporal derivatives of the equilibrium integrals of motion, non-equilibrium analogues of the…
Quantum thermal states are known to be passive, as required by the second law of thermodynamics. This paper investigates the potential for work extraction by coupling a thermal bath to a qubit of either spin, fermionic, or topological type,…
We introduce a sequence-dependent parametrization for a coarse-grained DNA model [T. E. Ouldridge, A. A. Louis, and J. P. K. Doye, J. Chem. Phys. 134, 085101 (2011)] originally designed to reproduce the properties of DNA molecules with…
We consider an arbitrary translationally invariant chain model with nearest neighbors interaction and satisfying periodic boundary condition. The approach developed here allows a thermodynamic description of the chain model directly in…
We propose a scenario for the prebiotic co-evolution of RNA and of fast folding proteins with large entropy gaps as observed today. We show from very general principles that the folding and unfolding of the proteins synthesized by RNA can…
We study theoretically the unzipping of a double stranded DNA from a condensed globule state by an external force. At constant force, we find that the double stranded DNA unzips an at critical force Fc and the number of unzipped monomers M…
Large-scale three dimensional molecular dynamics simulations of hopper flow are presented. The flow rate of the system is controlled by the width of the aperture at the bottom. As the steady-state flow rate is reduced, the force…
We construct and study an extended random matrix model of RNA (polymer) folding. A perturbation which acts on all the nucleotides in the chain is added to the action of the RNA partition function. The effect of this perturbation on the…
Experimental variables of optical tweezers instrumentation that affect RNA folding/unfolding kinetics were investigated. A model RNA hairpin, P5ab, was attached to two micron-sized beads through hybrid RNA/DNA handles; one bead was trapped…