相关论文: Entropy Transfer and Dynamics of Allostery in Prot…
We investigate entropy transport for universal scaling phenomena in closed quantum many-body systems far from equilibrium. From spatially resolved experimental data of a spinor Bose gas, we demonstrate that entropy decreases on…
Allostery commonly refers to the mechanism that regulates protein activity through the binding of a molecule at a different, usually distal, site from the orthosteric site. The omnipresence of allosteric regulation in nature and its…
Over the last few years, machine learning unlocked previously infeasible features for compression, such as providing guarantees for users' privacy or tailoring compression to specific data statistics (e.g., satellite images or audio…
We propose a protein model based on a hierarchy of constraints that force the protein to follow certain pathways when changing conformation. The model exhibits a first order phase transition, cooperativity and is exactly solvable. It also…
The process of protein folding from an unfolded state to a biologically active, folded conformation is governed by many parameters e.g the sequence of amino acids, intermolecular interactions, the solvent, temperature and chaperon…
Electrostatic interactions fundamentally govern the structure, stability, and dynamics of charged (bio)matter, yet the impact of heterogeneous and anisotropic charge distributions on the behavior of protein solutions remains elusive. Here,…
In many problems in data mining and machine learning, data items that need to be clustered or classified are not points in a high-dimensional space, but are distributions (points on a high dimensional simplex). For distributions, natural…
The stochastic entropy generated during the evolution of a system interacting with an environment may be separated into three components, but only two of these have a non-negative mean. The third component of entropy production is…
Allostery is a form of protein regulation, where ligands that bind sites located apart from the active site can modify the activity of the protein. The molecular mechanisms of allostery have been extensively studied, because allosteric…
Many measurements on soft condensed matter (e.g., biological and materials) systems track low-dimensional observables projected from the full system phase space as a function of time. Examples are dynamic structure factors, spectroscopic…
Proteins experience a wide variety of conformational dynamics that can be crucial for facilitating their diverse functions. How is the intrinsic flexibility required for these motions encoded in their three-dimensional structures? Here, the…
The conventional assumption that the self-diffusion coefficient of a small tracer can be obtained by a local and instantaneous application of Einstein's relation in a temperature field with spatial and temporal heterogeneity is revisited.…
Repeat proteins are made with tandem copies of similar amino acid stretches that fold into elongated architectures. Due to their symmetry, these proteins constitute excellent model systems to investigate how evolution relates to structure,…
Transfer entropy in information theory was recently demonstrated [Phys. Rev. E 102, 012404 (2020)] to enable us to elucidate the interaction domain among interacting elements solely from an ensemble of trajectories. There, only pairs of…
Allosteric interactions in DNA are crucial for various biological processes. These interactions are quantified by measuring the change in free energy as a function of the distance between the binding sites for two ligands. Here we show that…
While allostery is of paramount importance for protein regulation, the underlying dynamical process of ligand (un)binding at one site, resulting time evolution of the protein structure, and change of the binding affinity at a remote site is…
Long distance excitation energy transfer between a donor and an acceptor embedded in a polymer chain is usually assumed to occur via the Forster mechanism which predicts a 1/R^6 distance dependence of the transfer rate, where R is the…
Transfer entropy has been used to quantify the directed flow of information between source and target variables in many complex systems. While transfer entropy was originally formulated in discrete time, in this paper we provide a framework…
In the paper the memory effect in the system consisting from a trajectory of process and an environment is considered. The environment is presented by scalar potential and noise. The evolution of system is interpreted as process of the…
The length distribution of proteins measured in amino acids follows the CoHSI (Conservation of Hartley-Shannon Information) probability distribution. In previous papers we have verified various predictions of this using the Uniprot database…