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Oscillation is an important cellular process that regulates timing of different vital life cycles. However, in the noisy cellular environment, oscillations can be highly inaccurate due to phase fluctuations. It remains poorly understood how…
Principal component analysis (PCA) is one of the most powerful tools in machine learning. The simplest method for PCA, the power iteration, requires $\mathcal O(1/\Delta)$ full-data passes to recover the principal component of a matrix with…
Linear dynamical systems are canonical models for learning-based control of plants with uncertain dynamics. The setting consists of a stochastic differential equation that captures the state evolution of the plant understudy, while the true…
Synchronization with noise is important for understanding biophysical processes at nano- and micro-meter scales, such as neuronal firing and flagellar rotations. To understand the energetics of these processes, stochastic thermodynamics…
We present a computer-assisted approach to coarse-graining the evolutionary dynamics of a system of nonidentical oscillators coupled through a (fixed) network structure. The existence of a spectral gap for the coupling network graph…
Probabilistic Cellular Automata are a generalization of Cellular Automata. Despite their simple definition, they exhibit fascinating and complex behaviours. The stationary behaviour of these models changes when model parameters are varied,…
Modeling stochasticity in gene regulatory networks is an important and complex problem in molecular systems biology. To elucidate intrinsic noise, several modeling strategies such as the Gillespie algorithm have been used successfully. This…
Models of active nematics in biological systems normally require complexity arising from the hydrodynamics involved at the microscopic level as well as the viscoelastic nature of the system. Here we show that a minimal, space-independent,…
Many biological systems are governed by difference equations and exhibit discrete-time dynamics. Examples include the size of a population when generations are non-overlapping, and the incidence of a disease when infections are recorded at…
Circadian rhythms regulate the physiology and behavior of humans and animals. Despite advancements in understanding these rhythms and predicting circadian phases at the transcriptional level, predicting circadian phases from proteomic data…
Given non-sequential snapshots from instances of a dynamical system, we design a compressed sensing based algorithm that reconstructs the dynamical system. On the theoretical side, we show that: (1) successful reconstruction is possible…
Chemical reactions in cell are subject to intense stochastic fluctuations. An important question is how the fundamental physiological behavior of cell is kept stable against those noisy perturbations. In this paper a stochastic model of…
Biochemical oscillation systems often consist of negative feedback loops with repressive transcription regulation. Such systems have distinctive characteristics in comparison with ordinary chemical systems: i) the numbers of molecules…
Stochastic oscillations in individual cells are usually characterized by a non-monotonic power spectrum with an oscillatory autocorrelation function. Here we develop an analytical approach of stochastic oscillations in a minimal hybrid…
Stochastic thermodynamics as reviewed here systematically provides a framework for extending the notions of classical thermodynamics like work, heat and entropy production to the level of individual trajectories of well-defined…
Circadian rhythms are endogenous 24-hour oscillations that regulate physiology, metabolism, sleep-wake cycles, and cellular homeostasis. Drosophila melanogaster, a genetically tractable model organism, has played a foundational role in…
The design of biological systems is hindered by uncertainty arising from both intrinsic stochasticity of biomolecular reactions and variability across laboratory or experimental conditions. In this work, we present a sequential framework to…
Equilibrating proteins and other biomacromolecules is cardinal for molecular dynamics simulation of such biological systems in which they perform free dynamics without any externally-applied mechanical constraint, until thermodynamic…
Pancreatic $\beta-$cells regulate insulin secretion through complex oscillations, which are vital for glucose control and diabetes research. In this paper, an existing mathematical model of $\beta-$cell dynamics is analyzed using a…
Biochemical oscillations are prevalent in living organisms. Systems with a small number of constituents cannot sustain coherent oscillations for an indefinite time because of fluctuations in the period of oscillation. We show that the…