Related papers: Digital clocks: simple Boolean models can quantita…
Living systems regulate many aspects of their behavior through periodic oscillations of molecular concentrations, which function as `biochemical clocks.' These clocks are intrinsically subject to thermal fluctuations, so that the duration…
To model biological systems using networks, it is desirable to allow more than two levels of expression for the nodes and to allow the introduction of parameters. Various modeling and simulation methods addressing these needs using Boolean…
Boolean Delay Equations (BDEs) are semi-discrete dynamical models with Boolean-valued variables that evolve in continuous time. Systems of BDEs can be classified into conservative or dissipative, in a manner that parallels the…
Embedding efficient calculation instructions into biochemical system has always been a research focus in synthetic biology. One of the key problems is how to sequence the chemical reaction modules that act as units of computation and make…
Circadian rhythmicity lies at the center of various important physiological and behavioral processes in mammals, such as sleep, metabolism, homeostasis, mood changes and more. It has been shown that this rhythm arises from self-sustained…
Boolean networks are powerful mathematical tools for modeling the qualitative dynamics of genetic regulation. Yet inferred models often generate spurious attractors that lack biological viability. In this paper, we propose a parsimonious…
Biological rhythms are generated by pacemaker organs, such as the heart pacemaker organ (the sinoatrial node) and the master clock of the circadian rhythms (the suprachiasmatic nucleus), which are composed of a network of autonomously…
For years, we have been building models of gene regulatory networks, where recent advances in molecular biology shed some light on new structural and dynamical properties of such highly complex systems. In this work, we propose a novel…
Differential equation-based physiological models of sleep-wake networks describe sleep-wake regulation by simulating the activity of wake- and sleep-promoting neuronal populations and the modulation of these populations by homeostatic and…
Biochemical circadian rhythm oscillations play an important role in many signalling mechanisms. In this work, we explore some of the biophysical mechanisms responsible for sustaining robust oscillations by constructing a minimal but…
Circadian clocks ubiquitous in life forms ranging bacteria to multi-cellular organisms, often exhibit intrinsic temperature compensation; the period of circadian oscillators is maintained constant over a range of physiological temperatures,…
Our daily social and political life is more and more impacted by social networks. The functioning of our living bodies is deeply dependent on biological regulation networks such as neural, genetic, and protein networks. And the physical…
We observe deterministic chaos in a simple network of electronic logic gates that are not regulated by a clocking signal. The resulting power spectrum is ultra-wide-band, extending from dc to beyond 2 GHz. The observed behavior is…
Quantum Hamiltonian Computing is a recent approach that uses quantum systems, in particular a single molecule, to perform computational tasks. Within this approach, we present explicit methods to construct logic gates using two different…
Living organisms need to be sensitive to a changing environment while also ignoring uninformative environmental fluctuations. Here, we show that the circadian clock in \textit{Synechococcus elongatus} can naturally tune its environmental…
We propose a static and a dynamic approach to model biological signaling networks, and show how each can be used to answer relevant biological questions. For this we use the two different mathematical tools of Propositional Logic and…
We explore a definition of complexity based on logic functions, which are widely used as compact descriptions of rules in diverse fields of contemporary science. Detailed numerical analysis shows that (i) logic complexity is effective in…
The KaiABC circadian clock from cyanobacteria is the only known three-protein oscillatory system which can be reconstituted outside the cell and which displays sustained periodic dynamics in various molecular state variables. Despite many…
Biological oscillators are very diverse but can be classified based on dynamical motifs such as the types of feedback loops present. The S. Elongatus circadian clock is a remarkable phosphorylation-based oscillator that can be reconstituted…
In this paper, we present the Difference- Based Causality Learner (DBCL), an algorithm for learning a class of discrete-time dynamic models that represents all causation across time by means of difference equations driving change in a…