Related papers: Digital clocks: simple Boolean models can quantita…
Simulating Hamiltonian dynamics is one of the most fundamental and significant tasks for characterising quantum materials. Recently, a series of quantum algorithms employing block-encoding of Hamiltonians have succeeded in providing…
Boolean automata networks (aka Boolean networks) are space-time discrete dynamical systems, studied as a model of computation and as a representative model of natural phenomena. A collection of simple entities (the automata) update their…
The development of new techniques to quantitatively measure gene expression in cells has shed light on a number of systems that display oscillations in protein concentration. Here we review the different mechanisms which can produce…
We formulate a mathematical model for daily activities of a cow (eating, lying down, and standing) in terms of a piecewise affine dynamical system. We analyze the properties of this bovine dynamical system representing the single animal and…
Biomedical signals carry signature rhythms of complex physiological processes that control our daily bodily activity. The properties of these rhythms indicate the nature of interaction dynamics among physiological processes that maintain a…
Typical properties of computing circuits composed of noisy logical gates are studied using the statistical physics methodology. A growth model that gives rise to typical random Boolean functions is mapped onto a layered Ising spin system,…
Compared with time independent Hamiltonians, the dynamics of generic quantum Hamiltonians $H(t)$ are complicated by the presence of time ordering in the evolution operator. In the context of digital quantum simulation, this difficulty…
A driven linear oscillator and a feedback mechanism are two necessary elements of any classical periodic clock. Here, we introduce a novel, fully quantum clock using a driven oscillator in the quantum regime and coherent quantum feedback.…
We show that noise-induced oscillations in a gene circuit model display stochastic coherence, that is, a maximum in the regularity of the oscillations as a function of noise amplitude. The effect is manifest as a system-size effect in a…
We have developed a coarse-grained formulation for modeling the dynamic behavior of cells quantitatively, based on stochasticity and heterogeneity, rather than on biochemical reactions. We treat each reaction as a continuous-time stochastic…
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…
The significant role of epigenetic mechanisms within natural systems has become increasingly clear. This paper uses a recently presented abstract, tunable Boolean genetic regulatory network model to explore aspects of epigenetics. It is…
The process of calibrating computer models of natural phenomena is essential for applications in the physical sciences, where plenty of domain knowledge can be embedded into simulations and then calibrated against real observations. Current…
Describing dynamic medical systems using machine learning is a challenging topic with a wide range of applications. In this work, the possibility of modeling the blood glucose level of diabetic patients purely on the basis of measured data…
We advocate here the use of computational logic for systems biology, as a \emph{unified and safe} framework well suited for both modeling the dynamic behaviour of biological systems, expressing properties of them, and verifying these…
Deep learning is computationally intensive, with significant efforts focused on reducing arithmetic complexity, particularly regarding energy consumption dominated by data movement. While existing literature emphasizes inference, training…
Boolean networks with canalizing functions are used to model gene regulatory networks. In order to learn how such networks may behave under evolutionary forces, we simulate the evolution of a single Boolean network by means of an adaptive…
Molecular circadian clocks, that are found in all nucleated cells of mammals, are known to dictate rhythms of approximately 24 hours (circa diem) to many physiological processes. This includes metabolism (e.g., temperature, hormonal blood…
Causal ordering of key events in the cell cycle is essential for proper functioning of an organism. Yet, it remains a mystery how a specific temporal program of events is maintained despite ineluctable stochasticity in the biochemical…
Autonomous circadian clocks drive daily rhythms in physiology and behaviour. A network of coupled neurons, the suprachiasmatic nucleus (SCN), serves as a robust self-sustained circadian pacemaker. Synchronization of this timer to the…