Related papers: Using biochemical circuits to approximately comput…
One key challenge in Artificial Life is designing systems that display an emergence of complex behaviors. Many such systems depend on a high-dimensional parameter space, only a small subset of which displays interesting dynamics. Focusing…
In this paper, we study the problem of transient signal analysis. A signal-dependent algorithm is proposed which sequentially identifies the countable sets of decay rates and expansion coefficients present in a given signal. We…
Power systems, including synchronous generator systems, are typical systems that strive for stable operation. In this article, we numerically study the fault transient process of a synchronous generator system based on the first benchmark…
Transcriptional networks represent one of the most extensively studied types of systems in synthetic biology. Although the completeness of transcriptional networks for digital logic is well-established, *analog* computation plays a crucial…
Statistical inference of genetic regulatory networks is essential for understanding temporal interactions of regulatory elements inside the cells. For inferences of large networks, identification of network structure is typical achieved…
In this paper, we propose a new method to identify biochemical reaction networks (i.e. both reactions and kinetic parameters) from heterogeneous datasets. Such datasets can contain (a) data from several replicates of an experiment performed…
Inferring gene regulatory networks is an important problem in systems biology. However, these networks can be hard to infer from experimental data because of the inherent variability in biological data as well as the large number of genes…
What is the frequency content of temporal logic formulas? That is, when we monitor a signal against a formula, which frequency bands of the signal are relevant to the logic and should be preserved, and which can be safely discarded? This…
We propose a new cross-correlation method that can recognize independent realizations of the same type of stochastic processes and can be used as a new kind of pattern recognition tool in biometrics, sensing, forensic, security and image…
Reconstructing transcriptional regulatory networks is an important task in functional genomics. Data obtained from experiments that perturb genes by knockouts or RNA interference contain useful information for addressing this reconstruction…
Biomolecular logic systems processing biochemical input signals and producing "digital" outputs in the form of YES/NO were developed for analysis of physiological conditions characteristic of liver injury, soft tissue injury and abdominal…
Parameterizing mathematical models of biological systems often requires fitting to stable periodic data. In cardiac electrophysiology this typically requires converging to a stable action potential through long simulations. We explore this…
In this paper, a set of Python methods is described that can be used to compute the frequency response of an arbitrary biochemical network given any input and output. Models can be provided in standard SBML or Antimony format. The code…
We propose a method to obtain phase portraits for stochastic systems. Starting from the Fokker-Planck equation, we separate the dynamics into a convective and a diffusive part. We show that stable and unstable fixed points of the convective…
Convection is a well-studied topic in fluid dynamics, yet it is less understood in the context of networks flows. Here, we incorporate techniques from topological data analysis (namely, persistent homology) to automate the detection and…
In many organisms the expression levels of each gene are controlled by the activation levels of known "Transcription Factors" (TF). A problem of considerable interest is that of estimating the "Transcription Regulation Networks" (TRN)…
We consider a quantum system that is being continuously monitored, giving rise to a measurement signal. From such a stream of data, information needs to be inferred about the underlying system's dynamics. Here we focus on hypothesis testing…
Sensitivity analysis of biochemical reactions aims at quantifying the dependence of the reaction dynamics on the reaction rates. The computation of the parameter sensitivities, however, poses many computational challenges when taking…
Recently it was demonstrated that long-lived quantum coherence exists during excitation energy transport in photosynthesis. It is a valid question up to which length, time and mass scales quantum coherence may extend, how to one may detect…
Living cells use readout molecules to record the state of receptor proteins, similar to measurements or copies in typical computational devices. But is this analogy rigorous? Can cells be optimally efficient, and if not, why? We show that,…