Related papers: Quantifying fluctuations in reversible enzymatic c…
Quantum fluctuations are fundamental in quantum technologies, affecting computing, sensing, cryptography, and thermodynamics. These include fluctuations in the variation of energy, charge, and other observables driven by interactions with…
Many processes in biology, from the regulation of gene expression in bacteria to memory in the brain, involve switches constructed from networks of biochemical reactions. Crucial molecules are present in small numbers, raising questions…
Natural systems are remarkably robust and resilient, maintaining essential functions despite variability, uncertainty, and hostile conditions. Understanding these nonlinear, dynamic behaviours is challenging because such systems involve…
The theory of biochemical processes needs simple but realistic models of phenomena underlying microscopic dynamics of proteins. Many experiments performed in the 1980s have demonstrated that within the protein native state, apart from usual…
Exploiting the information provided by the molecular noise of a biological process has proven to be valuable in extracting knowledge about the underlying kinetic parameters and sources of variability from single cell measurements. However,…
Chemical and biological networks can describe a wide variety of processes, from gene regulatory networks to biochemical oscillations. Modeled by chemical master equations, these processes are inherently stochastic, as fluctuations dominate…
Thermodynamics constrains the flow of matter in a reaction network to occur through routes along which the Gibbs energy decreases, implying that viable steady-state flux patterns should be void of closed reaction cycles. Identifying and…
Scaling analysis exploiting timescale separation has been one of the most important techniques in the quantitative analysis of nonlinear dynamical systems in mathematical and theoretical biology. In the case of enzyme catalyzed reactions,…
We study the effects of intrinsic noise on chemical reaction systems, which in the deterministic limit approach a limit cycle in an oscillatory manner. Previous studies of systems with an oscillatory approach to a fixed point have shown…
Stochastic transitions between discrete microscopic states play an important role in many physical and biological systems. Often, these transitions lead to fluctuations on a macroscopic scale. A classic example from neuroscience is the…
We investigate the stochastic dynamics of a thermal machine realized by a fast-driven Otto cycle. By employing a stochastic approach, we find that system coherences strongly affect fluctuations depending on the thermodynamic current.…
We study the sum of first passage times along an arbitrary cycle made up of N>2 states of a small physical system. We show that, if the system is at thermodynamic equilibrium, this sum follows the same probability distribution regardless of…
Understanding how systems respond to external perturbations is a fundamental challenge in physics, particularly for non-equilibrium and non-stationary processes. The fluctuation-dissipation theorem provides a complete framework for…
Cells must continuously sense and respond to time-varying environmental stimuli. These signals are transmitted and processed by biochemical signalling networks. However, the biochemical reactions making up these networks are intrinsically…
We study the fluctuations of generic currents in multi-terminal, multi-channel quantum transport settings. In the quantum regime, these fluctuations and the resulting precision differ strongly depending on whether the device is of fermionic…
Time-irreversible stochastic processes are frequently used in natural sciences to explain non-equilibrium phenomena and to design efficient stochastic algorithms. Our main goal in this thesis is to analyse their dynamics by means of large…
All clocks, classical or quantum, are open non equilibrium irreversible systems subject to the constraints of thermodynamics. Using examples I show that these constraints necessarily limit the performance of clocks and that good clocks…
Many of the chemical reactions that take place within a living cell are irreversible. Due to evolutionary pressures, the number of allowable reactions within these systems are highly constrained and thus the resulting metabolic networks…
Fluctuations of thermodynamic quantities become non-negligible and play an important role when the system size is small. We develop finite-time thermodynamics of fluctuations in microscopic heat engines whose environmental temperature and…
Many molecular junctions display stochastic telegraphic switching between two distinct current values, which is therefore an important source of fluctuations in nanoscale quantum transport. We investigate electronic fluctuations arising via…