相关论文: Kinetic Proofreading and the Limits of Thermodynam…
Due to large fluctuations in cellular environments, transfer of information in biological processes without regulation is inherently error-prone. The mechanistic details of error-reducing mechanisms in biological copying processes have been…
Cellular signaling, crucial for biological processes like immune response and homeostasis, relies on specificity and fidelity in signal transduction to accurately respond to stimuli amidst biological noise. Kinetic proofreading (KPR) is a…
Many biological processes discriminate between correct and incorrect substrates through the kinetic proofreading mechanism which enables lower error at the cost of higher energy dissipation. Elucidating physicochemical constraints for…
In the immune system, T cells can quickly discriminate between foreign and self ligands with high accuracy. There is evidence that T-cells achieve this remarkable performance utilizing a network architecture based on a generalization of…
Kinetic theory and thermodynamics are applied to DNA polymerases with exonuclease activity, taking into account the dependence of the rates on the previously incorportated nucleotide. The replication fidelity is shown to increase…
The high accuracy exhibited by biological information transcription processes is due to kinetic proofreading, i.e., by a mechanism which reduces the error rate of the information-handling process by driving it out of equilibrium. We provide…
Stability and efficiency are mutually exclusive in a thermodynamic process, e.g. in a thermal machine. Any effort to reduce the fluctuations of a certain output quantity is necessarily accompanied by an increase of entropy production,…
Key enzymatic processes in biology use the nonequilibrium error correction mechanism called kinetic proofreading to enhance their specificity. Kinetic proofreading typically requires several dedicated structural features in the enzyme, such…
We study stochastic copying schemes in which discrimination between a right and a wrong match is achieved via different kinetic barriers or different binding energies of the two matches. We demonstrate that, in single-step reactions, the…
We review the trade-offs between speed, fluctuations, and thermodynamic cost involved with biological processes in nonequilibrium states, and discuss how optimal these processes are in light of the universal bound set by the thermodynamic…
Thermodynamic uncertainty relations (TURs) set fundamental bounds on the fluctuation and dissipation of stochastic systems. Here, we examine these bounds, in experiment and theory, by exploring the entire phase space of a cyclic information…
Gene expression is controlled primarily by interactions between transcription factor proteins (TFs) and the regulatory DNA sequence, a process that can be captured well by thermodynamic models of regulation. These models, however, neglect…
Universal relations that characterize the fluctuations of nonequilibrium systems are of fundamental importance. The thermodynamic and kinetic uncertainty relations impose upper bounds on the precision of currents solely by total entropy…
From a recent geometric generalization of Thermodynamic Uncertainty Relations (TURs) we derive novel upper bounds on the nonlinear response of an observable of an arbitrary system undergoing a change of probabilistic state. Various…
Polymerases are protein enzymes that move along nucleic acid chains and catalyze template-based polymerization reactions during gene transcription and replication. The polymerases also substantially improve transcription or replication…
Kinetic proofreading is an error correction mechanism present in the processes of the central dogma and beyond, and typically requires the free energy of nucleotide hydrolysis for its operation. Though the molecular players of many…
Thermodynamic Uncertainty Relations (TURs) set universal bounds linking current fluctuations to entropy production in nonequilibrium steady states. Their multidimensional generalization (MTUR) introduces matrix inequalities connecting…
To ensure faithful information transmission, cells utilize nonequilibrium drives to reduce errors. Kinetic proofreading is a classic mechanism known to sharpen ligand discrimination by T lymphocytes. It remains an open question whether the…
The thermodynamic uncertainty relations (TURs) provide lower bounds on the entropy production (EP) of a system in terms of the statistical precision of an arbitrary current in that system. All conventional TURs derived so far have concerned…
Thermodynamic uncertainty relations (TURs) represent a benchmark result in nonequilibrium physics that allows to place fundamental lower bounds on the noise-to-signal ratio (precision) of currents in nanoscale devices. Originally formulated…