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An analytical expression is derived for the transition path time distribution for a one-dimensional particle crossing of a parabolic barrier. Two cases are analyzed: (i) A non-Markovian process described by a generalized Langevin equation…
The concept of allostery in which macromolecules switch between two different conformations is a central theme in biological processes ranging from gene regulation to cell signaling to enzymology. Allosteric enzymes pervade metabolic…
The century-long Michaelis-Menten rate law and its modifications in the modeling of biochemical rate processes stand on the assumption that the concentration of the complex of interacting molecules, at each moment, rapidly approaches an…
We show that in the generic situation where a biological network, e.g. a protein interaction network, is in fact a subnetwork embedded in a larger "bulk" network, the presence of the bulk causes not just extrinsic noise but also memory…
This paper was presented in poster form at and in the proceedings of the QCMC 2008. It is a summary of a fuller paper to appear separately. The classical product state capacity of a noisy quantum channel with memory is investigated. A…
We comprehensively investigate two distinct mechanisms leading to memory loss of non-Gaussian correlations after switching off the interactions in an isolated quantum system undergoing out-of-equilibrium dynamics. The first mechanism is…
We propose to model the dynamics of metabolic networks from a systems biology point of view by four dynamical structure elements: potential function, transverse matrix, degradation matrix, and stochastic force. These four elements are…
Transient and equilibrium synchronizations in complex neuronal networks as a consequence of dynamics induced by having sources placed at specific neurons are investigated. The basic integrate-and-fire neuron is adopted, and the dynamics is…
We used various analytical and numerical techniques to elucidate signal propagation in a small enzymatic cascade which is subjected to external and internal noise. The nonlinear character of catalytic reactions, which underlie protein…
The transfer tensor method is a versatile tool for analyzing and propagating general open quantum systems. It captures in a compact manner all memory effects in a non-Markovian system through a straightforward transformation of a set of…
Adaptive physical and biological systems continually process fluctuating information from their environments. When the environment is nonstationary, inference itself becomes a nonequilibrium process with thermodynamic cost. We analyse a…
An increasing body of evidence suggests that the trial-to-trial variability of spiking activity in the brain is not mere noise, but rather the reflection of a sampling-based encoding scheme for probabilistic computing. Since the precise…
The opening or closing mechanism of a voltage-gated ion channel is triggered by the potential difference crossing the cell membrane in the nervous system. Based on this picture, we model the ion channel as a nanoscale two-terminal ionic…
The non-Markovianity of an arbitrary open quantum system is analyzed in reference to the multi-time statistics given by its monitoring at discrete times. On the one hand, we exploit the hierarchy of inhomogeneous transfer tensors, which…
We report short-term memory formation in a nonlinear dynamical system with many degrees of freedom. The system ``remembers'' a sequence of impulses for a transient period, but it coarsens and eventually ``forgets'' nearly all of them. The…
Metabolic heterogeneity is widely recognised as the next challenge in our understanding of non-genetic variation. A growing body of evidence suggests that metabolic heterogeneity may result from the inherent stochasticity of intracellular…
Modeling the dynamics of non-stationary stochastic systems requires balancing the representational power of deep learning with the mathematical transparency of classical models. While classical Markov transition operators provide explicit,…
Quantification of information content and its temporal variation in intracellular calcium spike trains in neurons helps one understand functions such as memory, learning, and cognition. Such quantification could also reveal pathological…
The first passage times for enzymatic turnovers in non-equilibrium steady state display a statistical symmetry property related to non-equilibrium fluctuation theorems, that makes it possible to extract the chemical driving force from…
Biochemical reactions are fundamentally noisy at a molecular scale. This limits the precision of reaction networks, but also allows fluctuation measurements which may reveal the structure and dynamics of the underlying biochemical network.…