Related papers: Interplay of energy, dissipation, and error in kin…
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…
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…
We use ideas from kinetic proofreading, an error-correcting mechanism in biology, to identify new kinetic regimes in non-equilibrium systems. These regimes are defined by the sensitivity of the occupancy of a state of the system to a change…
Biological processes such as DNA replication, RNA transcription, and protein translation show remarkable speed and accuracy in selecting the right substrate from pools of chemically identical molecules. This result is obtained by…
Biological processes that are able to discriminate between different molecules consume energy and dissipate heat. They operate at different levels of fidelity and speed, and as a consequence there exist fundamental trade-offs between these…
We study biochemical reaction networks capable of product discrimination inspired by biological proofreading mechanisms. At equilibrium, product discrimination, the selective formation of a "correct" product with respect to an "incorrect…
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…
The critical role of energy consumption in biological systems including T cell discrimination process has been investigated in various ways. The kinetic proofreading(KPR) in T cell recognition involving different levels of energy…
To mitigate errors induced by the cell's heterogeneous noisy environment, its main information channels and production networks utilize the kinetic proofreading (KPR) mechanism. Here, we examine two extensively-studied KPR circuits, DNA…
The promise of chemical computation lies in controlling systems incompatible with traditional electronic micro-controllers, with applications in synthetic biology and nano-scale manufacturing. Computation is typically embedded in…
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…
The study of motility control by smart agents offers a promising platform for systematically exploring the fundamental physical constraints underlying the functioning of bio-inspired micro-machines operating far from equilibrium. Here, we…
Discriminating between correct and incorrect substrates is a core process in biology but how is energy apportioned between the conflicting demands of accuracy ($\mu$), speed ($\sigma$) and total entropy production rate ($P$)? Previous…
In this paper we study the relation between the property of detailed balance and the ability of discriminating between different ligands for a class of stochastic models of kinetic proofreading. We prove the existence of a critical amount…
Physical systems driven away from equilibrium by an external controller dissipate heat to the environment; the excess entropy production in the thermal reservoir can be interpreted as a "cost" to transform the system in a finite time. The…
Chemical processes in closed systems are poorly controllable since they always relax to equilibrium. Living systems avoid this fate and give rise to a much richer diversity of phenomena by operating under nonequilibrium conditions. Recent…
Kinetic energy equipartition is a premise for many deterministic and stochastic molecular dynamics methods that aim at sampling a canonical ensemble. While this is expected for real systems, discretization errors introduced by the numerical…
Living cells use readout molecules to record the state of receptor proteins, similar to measurements or copies in typical computational devices. But is this analogy rigorous? Can cells be optimally efficient, and if not, why? We show that,…
Quantitative studies of cell metabolism are often based on large chemical reaction network models. A steady state approach is suited to analyze phenomena on the timescale of cell growth and circumvents the problem of incomplete experimental…