Related papers: Digital clocks: simple Boolean models can quantita…
Algorithms for the synchronisation of clocks across networks are both common and important within distributed systems. We here address not only the formal modelling of these algorithms, but also the formal verification of their behaviour.…
Periodic patterns in dynamical behaviours of biological models described by simple form differential delay equations are studied. Mathematical models are given by a class of scalar delay differential equations with a multiplicative time…
While existing mathematical descriptions can accurately account for phenomena at microscopic scales (e.g. molecular dynamics), these are often high-dimensional, stochastic and their applicability over macroscopic time scales of physical…
The main difficulty when modelling gene networks is the identification of the parameters that govern their dynamics. It is particularly difficult for models in which time is continuous: parameters have real values which cannot be…
Nonlinear oscillations are commonly observed in complex systems far from equilibrium, such as living organisms. These oscillations are essential for sustaining vital processes, like neuronal firing, circadian rhythms, and heartbeats. In…
Boolean networks are a popular modeling framework in computational biology to capture the dynamics of molecular networks, such as gene regulatory networks. It has been observed that many published models of such networks are defined by…
We investigate the evolution of Boolean networks subject to a selective pressure which favors robustness against noise, as a model of evolved genetic regulatory systems. By mapping the evolutionary process into a statistical ensemble and…
Quantum hydrodynamics is a formulation of quantum mechanics based on the probability density and flux (current) density of a quantum system. It can be used to define trajectories which allow for a particle-based interpretation of quantum…
We investigate the expressive power of neural networks from the point of view of descriptive complexity. We study neural networks that use floating-point numbers and piecewise polynomial activation functions from two perspectives: 1) the…
Intrinsically disordered protein regions (IDRs) are found across all domains of life and are characterized by a lack of stable 3D structure. Nevertheless, IDRs play critical roles in the most tightly regulated cellular processes, including…
Advances in data collection using inexpensive sensors have enabled monitoring the performance of dynamic systems, and to implement appropriate control actions to improve their performance. Moreover, engineering systems often operate under…
Ultradian rhythms - quasi-rhythmic fluctuations in behavior and physiology with periods shorter than 24 hours - are observed across various organisms, including humans. Despite their role in key biological processes such as sleep…
The dynamic emulation of non-linear deterministic computer codes where the output is a time series, possibly multivariate, is examined. Such computer models simulate the evolution of some real-world phenomenon over time, for example models…
Noise-based logic, by utilizing its multidimensional logic hyperspace, has significant potential for low-power parallel operations in beyond-Moore-chips. However universal gates for Boolean logic thus far had to rely on either time…
Simulations are vital for understanding and predicting the evolution of complex molecular systems. However, despite advances in algorithms and special purpose hardware, accessing the timescales necessary to capture the structural evolution…
The generating functional method is employed to investigate the synchronous dynamics of Boolean networks, providing an exact result for the system dynamics via a set of macroscopic order parameters. The topology of the networks studied and…
Active biological molecules present a powerful, yet largely untapped, opportunity to impart autonomous regulation to materials. Because these systems can function robustly to regulate when and where chemical reactions occur, they have the…
How does soil pollution affect a plant's circadian clock? Are there any differences between how the clock reacts when exposed to different concentrations of elements of the periodic table? If so, can we characterise these differences? We…
This thesis aims at the logical analysis of discrete processes, in particular of such generated by gene regulatory networks. States, transitions and operators from temporal logics are expressed in the language of Formal Concept Analysis. By…
Sleep is essential for the maintenance of the brain and the body, yet many features of sleep are poorly understood and mathematical models are an important tool for probing proposed biological mechanisms. The most well-known mathematical…