Related papers: Computing the Frequency Response of Biochemical Ne…
New advances in nano sciences open the door for scientists to study biological processes on a microscopic molecule-by-molecule basis. Recent single-molecule biophysical experiments on enzyme systems, in particular, reveal that enzyme…
Interacting biological systems at all organizational levels display emergent behavior. Modeling these systems is made challenging by the number and variety of biological components and interactions (from molecules in gene regulatory…
Stochastic reaction networks are mathematical models with a wide range of applications in biochemistry, ecology, and epidemiology, and are often complex to analyze. Except for some special cases, it is generally difficult to predict how the…
Mathematical methods provide useful framework for the analysis and design of complex systems. In newer contexts such as biology, however, there is a need to both adapt existing methods as well as to develop new ones. Using a combination of…
Stochastic models are often used to help understand the behavior of intracellular biochemical processes. The most common such models are continuous time Markov chains (CTMCs). Parametric sensitivities, which are derivatives of expectations…
Power system coherency refers to the phenomenon that machines in a power network exhibit similar frequency responses after disturbances, and is foundational for model reduction and control design. Despite abundant empirical observations,…
Chemical reactions are often associated with an energy barrier along the reaction pathway which hinders the spontaneity of the reaction. Changing the energy barrier along the reaction pathway allows one to modulate the performance of a…
In this work the robustness of a feedback optimization scheme is discussed. Previously known results in literature, on the convergence to local optima of the optimization problem of interest, are extended to the case where the sensitivities…
Bifurcations leading to complex dynamical behaviour of non-linear systems are often encountered when the characteristics of feedback circuits in the system are varied. In systems with many unknown or varying parameters, it is an…
How smart can a micron-sized bag of chemicals be? How can an artificial or real cell make inferences about its environment? From which kinds of probability distributions can chemical reaction networks sample? We begin tackling these…
New checkable criteria for persistence of chemical reaction networks are proposed, which extend and complement those obtained by the authors in previous work. The new results allow the consideration of reaction rates which are time-varying,…
Bayesian methods which utilize Bayes' theorem to update the knowledge of desired parameters after each measurement, are used in a wide range of quantum science. For various applications in quantum science, efficiently and accurately…
We realize a biochemical filtering process by introducing a buffer in a biocatalytic signal-transduction logic system based on the function of an enzyme, esterase. The input, ethyl butyrate, is converted into butyric acid-the output signal,…
This paper studies a system of Ordinary Differential Equations modeling a chemical reaction network and derives from it a simulation tool mimicking Loss of Function and Gain of Function mutations found in cancer cells. More specifically,…
Living cells encode and transmit information in the temporal dynamics of biochemical components. Gaining a detailed understanding of the input-output relationship in biological systems therefore requires quantitative measures that capture…
Flow cytometry (FCM) is an analytic technique that is capable of detecting and recording the emission of fluorescence and light scattering of cells or particles (that are collectively called "events") in a population. A typical FCM…
Compartmentalization of biochemical processes underlies all biological systems, from the organelle to the tissue scale. Theoretical models to study the interplay between noisy reaction dynamics and compartmentalization are sparse, and…
Based on the theory of stochastic chemical kinetics, the inherent randomness and stochasticity of biochemical reaction networks can be accurately described by discrete-state continuous-time Markov chains. The analysis of such processes is,…
Amperometry is a commonly used electrochemical method for studying the process of exocytosis in real-time. Given the high precision of recording that amperometry procedures offer, the volume of data generated can span over several hundreds…
Whisking is a rhythmic and adaptive behavior that rodents use to probe and interact with their environment, and the frequency of movement reflects both sensorimotor processing and internal brain states. A robust and traditional method of…