相关论文: Enzyme as Maxwell's Demon: Steady-state Deviation …
A diffusive process that is reset to its origin at random times, so-called stochastic resetting (SR), is an ubiquitous expedient in many natural systems . Yet, beyond its ability to improve the efficiency of target searching, SR is a true…
We study the enzymatic degradation of an elastic fiber under tension using an an isotropic random-walk model, coupled with binding-unbinding reactions that weaken the fiber. The fiber is represented by a chain of elastic springs in series,…
A novel mechanism of reaction-induced active molecular motion, not involving any kind of self-propulsion, is proposed and analyzed. Because of the momentum exchange with the surrounding solvent, conformational transitions in…
This paper starts with the investigation of the behaviour of a set of two subsystems which are able to exchange some internal quantity according to a given flux function. It is found that this sytem exhibit a bifurcation when the flux…
Biology achieves novel functions like error correction, ultra-sensitivity and accurate concentration measurement at the expense of free energy through Maxwell Demon-like mechanisms. The design principles and free energy trade-offs have been…
Molecular dynamics simulations are used to study the mechanism and kinetics of hydrated electron diffusion. The electron center of mass is found to exhibit Brownian-type behavior with a diffusion coefficient considerably greater than that…
Enzymes within biochemical pathways are often colocalized, yet the consequences of specific spatial enzyme arrangements remain poorly understood. We study the impact of enzyme arrangement on reaction efficiency within a reaction-diffusion…
In this paper, a new method to efficiently simulate diffusion controlled second order chemical reactions is derived and applied to site-specific DNA-binding proteins. The protein enters a spherical cell and propagates via two competing…
This work introduces a diffusion model for molecule generation in 3D that is equivariant to Euclidean transformations. Our E(3) Equivariant Diffusion Model (EDM) learns to denoise a diffusion process with an equivariant network that jointly…
Single-enzyme catalysis offers a promising approach for unravelling the dynamic behaviour of individual enzymes as they undergo a reaction, revealing the complex heterogeneity that is lost in the averaged ensembles. Here we demonstrate…
The relation between the theory of entanglement and thermodynamics is very tight: a thermodynamic theory of quantum entanglement, as well as the establishment of rigorous formal connections between the laws of thermodynamics and the…
We introduce a family of Maxwellian Demons for which correlations among information bearing degrees of freedom can be calculated exactly and in compact analytical form. This allows one to precisely determine Demon functional thermodynamic…
A demonic being, introduced by Maxwell, to miraculously create thermal non-equilibrium and violate the Second law of thermodynamics, has been among the most intriguing and elusive wishful concepts for over 150 years. Maxwell and his…
Recent 3D molecular generation methods primarily use asynchronous auto-regressive or synchronous diffusion models. While auto-regressive models build molecules sequentially, they're limited by a short horizon and a discrepancy between…
Frozen parametric disorder can lead to appearance of sets of localized convective currents in an otherwise stable (quiescent) fluid layer heated from below. These currents significantly influence the transport of an admixture (or any other…
An autonomous out of equilibrium Maxwell's demon is used to reverse the natural direction of the heat flux between two electric circuits kept at different temperatures and coupled by the electric thermal noise. The demon does not process…
Large Eddy Simulations with flamelet-based thermochemistry are used to investigate the behaviour of a premixed hydrogen-air flame stabilised by a bluff-body. Validation against experimental data is carried out first to demonstrate the…
We develop the theory of Energy Conserving Descent (ECD) and introduce ECDSep, a gradient-based optimization algorithm able to tackle convex and non-convex optimization problems. The method is based on the novel ECD framework of…
Masked diffusion models (MDMs) have achieved notable progress in modeling discrete data, while their potential in molecular generation remains underexplored. In this work, we explore their potential and introduce the surprising result that…
Building on a model introduced by Mandal and Jarzynski [Proc. Natl. Acad. Sci. U. S. A., {\bf 109}, (2012) 11641], we present a simple version of an autonomous reversible Maxwell's demon. By changing the entropy of a tape consisting of a…