Related papers: Nonequilibrium sensing and its analogy to kinetic …
Based on a thermodynamic analysis of the kinetic model for the protein phosphorylation-dephosphorylation cycle, we study the ATP (or GTP) energy utilization of this ubiquitous biological signal transduction process. It is shown that the…
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…
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…
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…
Cooperativity arising from local interactions in equilibrium receptor systems provides gain, but does not increase sensory performance, as measured by the signal-to-noise ratio (SNR) due to a fundamental tradeoff between gain and intrinsic…
Cooperative interactions among sensory receptors provide a general mechanism to increase the sensitivity of signal transduction. In particular, bacterial chemotaxis receptors interact cooperatively to produce an ultrasensitive response to…
This paper exhibits the closed-loop design constraints using the non-analytic function theory. First, the paper generalizes the sensitivity integral for linear feedback systems with the non-analytic sensitivity function. Sensitivity…
A new type of cooperativity termed temporal cooperativity [Biophys. Chem. 105 585-593 (2003), Annu. Rev. Phys. Chem. 58 113-142 (2007)], emerges in the signal transduction module of phosphorylation-dephosphorylation cycle (PdPC). It…
Most sensory cells use surface receptors to detect environmental stimuli and initiate downstream signaling. Cooperative interactions among sensory receptors is known to play a crucial role in enhancing the sensitivity of biochemical…
We realize a nanoscale accelerometer exploiting the nonequilibrium dynamics of a nanoparticle near the quantum ground state. We explore the dynamics after quenching the trapping potential and find that rapid quenching provides an instance…
Adaptation is used by biological sensory systems to respond to a wide range of environmental signals, by adapting their response properties to the statistics of the stimulus in order to maximize information transmission. We derive rules of…
Kinetic proofreading mechanisms explain the extraordinary accuracy observed in central biological events in terms of the enhanced specificity of substrate selection networks under a nonequilibrium environment. The nonequilibrium steady…
Isotropization occurs on time scales much shorter than the thermal equilibration time. This is a crucial ingredient for the understanding of collision experiments of heavy nuclei or other nonequilibrium phenomena in complex many body…
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…
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…
As shown in previous work, in some cases closed quantum systems exhibit a non-conventional trade-off in performance and robustness in the sense that controllers with the highest fidelity can also provide the best robustness to parameter…
Of all sensor performance parameters, the conversion gain is arguably the most fundamental as it describes the conversion of photoelectrons at the sensor input into digital numbers at the output. Due in part to the emergence of deep…
Bacterial chemotaxis is controlled by the signalling of a cluster of receptors. A cooperative model is presented, in which coupling between neighbouring receptor dimers enhances the sensitivity with which stimuli can be detected, without…
The thermodynamic approach to non-equilibrium dynamics describes the state of macroscopic systems by means of a collection of intensities or intensive variables. The latter are by definition the differentials of the entropy with respect to…
T cell receptor signaling must operate reliably under tight time constraints. While assuming quite different mechanisms, two prominent models of T cell receptor activation, kinetic segregation and kinetic proofreading, both introduce a…