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Stochasticity is both exploited and controlled by cells. Although the intrinsic stochasticity inherent in biochemistry is relatively well understood, cellular variation, or 'noise', is predominantly generated by interactions of the system…
Auto-regulatory feedback loops are one of the most common network motifs. A wide variety of stochastic models have been constructed to understand how the fluctuations in protein numbers in these loops are influenced by the kinetic…
Actigraphy has been widely used for the analysis of circadian rhythm. Current practice applies regression analysis to data from multiple days to estimate the circadian phase. This paper presents a filtering method for online processing of…
In this dissertation, we study temporally stochasticity in cellular automata and the behavior of such cellular automata. The work also explores the computational ability of such cellular automaton that illustrates the computability of…
We introduce a stochastic model of coupled genetic oscillators in which chains of chemical events involved in gene regulation and expression are represented as sequences of Poisson processes. We characterize steady states by their…
Wet-lab experiments, in which the dynamics within living cells are observed, are usually costly and time consuming. This is particularly true if single-cell measurements are obtained using experimental techniques such as flow-cytometry or…
Modeling dynamical biological systems is key for understanding, predicting, and controlling complex biological behaviors. Traditional methods for identifying governing equations, such as ordinary differential equations (ODEs), typically…
The temporal behaviour of segmentation clock oscillations show phase synchrony via mean field like coupling of delta protein restricting to nearest neighbours only, in a configuration of cells arranged in a regular three dimensional array.…
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…
Biological oscillations are periodic changes in various signaling processes crucial for the proper functioning of living organisms. These oscillations are modeled by ordinary differential equations, with coefficient variations leading to…
The bloom clock is a space-efficient, probabilistic data structure designed to determine the partial order of events in highly distributed systems. The bloom clock, like the vector clock, can autonomously detect causality violations by…
Understanding the relationship between spontaneous stochastic fluctuations and the topology of the underlying gene regulatory network is of fundamental importance for the study of single-cell stochastic gene expression. Here by solving the…
Oja's rule [Oja, Journal of mathematical biology 1982] is a well-known biologically-plausible algorithm using a Hebbian-type synaptic update rule to solve streaming principal component analysis (PCA). Computational neuroscientists have…
Molecular dynamics is one of the most commonly used approaches for studying the dynamics and statistical distributions of many physical, chemical, and biological systems using atomistic or coarse-grained models. It is often the case,…
The digital nature of genes combined with the associated low copy numbers of proteins regulating them is a significant source of stochasticity, which affects the phase of biochemical oscillations. We provide a theoretical framework for…
To successfully navigate chemical gradients, microorganisms need to predict how the ligand concentration changes in space. Due to their limited size, they do not take a spatial derivative over their body length but rather a temporal…
Modeling biological rhythms helps understand the complex principles behind the physical and psychological abnormalities of human bodies, to plan life schedules, and avoid persisting fatigue and mood and sleep alterations due to the…
Rhythmic data are ubiquitous in the life sciences. Biologists need reliable statistical tests to identify whether a particular experimental treatment has caused a significant change in a rhythmic signal. When these signals display…
Oscillatory chemical reactions often serve as a timing clock of cellular processes in living cells. The temporal dynamics of protein concentration levels is thus of great interest in biology. Here we propose a theoretical framework to…
A dynamic logic method was developed to analyze molecular networks of cells by combining Kauffman and Thomas's logic operations with molecular interaction parameters. The logic operations characterize the discrete interactions between…