Related papers: Dynamic control of catalysis within biological cel…

In this paper, we adopt results in nonlinear time series analysis for causal inference in dynamical settings.~Our motivation is policy analysis with panel data, particularly through the use of "synthetic control" methods. These methods…

In this thesis we present a mathematical model describing the population dynamics of molecules in an artificial chemistry where large molecules can be produced by successive ligation of pairs of smaller molecules. The chemistry contains a…

Enzymes within biochemical pathways are often colocalized, yet the consequences of specific spatial enzyme arrangements remain poorly understood. We study the impact of enzyme arrangement on reaction efficiency within a reaction-diffusion…

Cells rely on the ability to sense and respond to small spatial differences in chemoattractant concentrations for survival. There is growing evidence that this is accomplished by setting the signaling system near the threshold for…

Collective oscillation of cells in a population has been reported under diverse biological contexts and with vastly different molecular constructs. Could there be common principles similar to those that govern spontaneous oscillation in…

A dynamic model for cell differentiation is studied, where cells with internal chemical reaction dynamics interact with each other and replicate. It leads to spontaneous differentiation of cells and determination, as is discussed in the…

Eukaryotic transcription generally occurs in bursts of activity lasting minutes to hours; however, state-of-the-art measurements have revealed that many of the molecular processes that underlie bursting, such as transcription factor binding…

Spatiotemporal pattern formation in a product-activated enzymic reaction at high enzyme concentrations is investigated. Stochastic simulations show that catalytic turnover cycles of individual enzymes can become coherent and that complex…

The bottom-up construction of synthetic cells is one of the most intriguing and interesting research arenas in synthetic biology. Synthetic cells are built by encapsulating biomolecules inside lipid vesicles (liposomes), allowing the…

Bacterial assemblies exhibit rich collective behaviors that control their biological functions, making them a relevant object of study from an active matter physics perspective. Dense bacterial suspensions self-organize into distinct…

The century-long Michaelis-Menten rate law and its modifications in the modeling of biochemical rate processes stand on the assumption that the concentration of the complex of interacting molecules, at each moment, rapidly approaches an…

We study molecular dynamics within populations of diffusively coupled cells under the assumption of fast diffusive exchange. As a technical tool, we propose conditions on boundedness and ultimate boundedness for systems with a singular…

This paper presents a framework for automatic synthesis of a control sequence for multi-agent systems governed by continuous linear dynamics under timed constraints. First, the motion of the agents in the workspace is abstracted into…

We study a class of Stochastic Differential Equations (SDEs) with jumps modeling multistage Michaelis--Menten enzyme kinetics, in which a substrate is sequentially transformed into a product via a cascade of intermediate complexes. These…

The spontaneous generation of electrical activity underpins a number of essential physiological processes, and is observed even in tissues where specialized pacemaker cells have not been identified. The emergence of periodic oscillations in…

Biological molecular machines are enzymes that simultaneously catalyze two processes, one donating free energy and second accepting it. Recent studies show that most native protein enzymes have a rich stochastic dynamics that often…

We propose a dynamical theory of how the chemical energy stored in a battery generates the electromotive force (emf). In this picture, the battery's half-cell acts as an engine, cyclically extracting work from its underlying chemical…

Production of chemicals from engineered organisms in a batch culture involves an inherent trade-off between productivity, yield, and titer. Existing strategies for strain design typically focus on designing mutations that achieve the…

The dynamics of active matter driven by interacting molecular motors has a non-potential structure at the local scale. However, we show that there exists a quasi-potential effectively describing the collective self-organization of the…

We have theoretically studied the effect of deterministic temporal control of spontaneous emission in a dynamic optical microcavity. We propose a new paradigm in light emission: we envision an ensemble of two-level emitters in an…