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To study the fluctuations and dynamics in chemical reaction processes, stochastic differential equations based on the rate equation involving chemical concentrations are often adopted. When the number of molecules is very small, however,…
Noisy fluctuations are ubiquitous in complex systems. They play a crucial or delicate role in the dynamical evolution of gene regulation, signal transduction, biochemical reactions, among other systems. Therefore, it is essential to…
Biochemical reactions are fundamentally noisy at a molecular scale. This limits the precision of reaction networks, but also allows fluctuation measurements which may reveal the structure and dynamics of the underlying biochemical network.…
Understanding the phase behavior of mixtures with many components is important in many contexts, including as a key step toward a physics-based description of intracellular compartmentalization. Here, we study the instabilities of a mixture…
Timing is essential for many cellular processes, from cellular responses to external stimuli to the cell cycle and circadian clocks. Many of these processes are based on gene expression. For example, an activated gene may be required to…
Stochasticity in gene expression can result in fluctuations in gene product levels. Recent experiments indicated that feedback regulation plays an important role in controlling the noise in gene expression. A quantitative understanding of…
A natural phenomenon occurring in a living system is an outcome of the dynamics of the specific biological network underlying the phenomenon. The collective dynamics have both deterministic and stochastic components. The stochastic nature…
Understanding computational capabilities of simple biological circuits, such as the regulatory circuits of single-cell organisms, remains an active area of research. Recent theoretical work has shown that a simple regulatory architecture…
Feedback is a most important concept in control systems, its main purpose is to deal with internal and/or external uncertainties in dynamical systems, by using the on-line observed information. Thus, a fundamental problem in control theory…
Biomolecular condensates are small droplets forming spontaneously in biological cells via phase separation. They play a role in many cellular processes, but it is unclear how cells control them. Cellular regulation often relies on…
Stochastic simulation is a widely used method for estimating quantities in models of chemical reaction networks where uncertainty plays a crucial role. However, reducing the statistical uncertainty of the corresponding estimators requires…
Biological machines like molecular motors and enzymes operate in dynamic cycles representable as stochastic flows on networks. Current stochastic dynamics describes such flows on fixed networks. Here, we develop a scalable approach to…
Fractional killing in response to drugs is a hallmark of non-genetic cellular heterogeneity. Yet how individual lineages evade drug treatment, as observed in bacteria and cancer cells, is not quantitatively understood. We analyse a…
Cellular signaling networks have evolved to cope with intrinsic fluctuations, coming from the small numbers of constituents, and the environmental noise. Stochastic chemical kinetics equations govern the way biochemical networks process…
Feedback regulation in biochemical systems is fundamental to homeostasis, with failure causing disease or death. Recent work has found that cooperation between feedback and buffering---the use of reservoirs of molecules to maintain…
The number of molecules involved in a cell or subcellular structure is sometimes rather small. In this situation, ordinary macroscopic-level fluctuations can be overwhelmed by non-negligible large fluctuations, which results in drastic…
The application of a random modulation of a system parameter usually increases decoherence effects. Here we show how, employing an appropriate stochastic modulation, it is instead possible to preserve the quantum coherence of a system.
Liquid mixtures of many interacting components often exhibit numerous coexisting types of droplets. An exciting example is the cytosol of biological cells, where diverse droplets, called condensates, are essential for cellular function.…
A central goal of synthetic biology is the design of molecular controllers that can manipulate the dynamics of intracellular networks in a stable and accurate manner. To address the fact that detailed knowledge about intracellular networks…
The diversity of cell populations is regulated by extracellular and intracellular variability. The latter includes genetic, epigenetic and stochastic variability, all contributing to the experimentally observed heterogeneity in response to…