Related papers: Using biochemical circuits to approximately comput…
This article introduces an algorithm to compute the persistent homology of a filtered complex with various coefficient fields in a single matrix reduction. The algorithm is output-sensitive in the total number of distinct persistent…
Mean-field molecular dynamics based on path integrals is used to approximate canonical quantum observables for particle systems consisting of nuclei and electrons. A computational bottleneck is the sampling from the Gibbs density of the…
Spectrograms visualize the frequency components of a given signal which may be an audio signal or even a time-series signal. Audio signals have higher sampling rate and high variability of frequency with time. Spectrograms can capture such…
Regulation of gene expression is the consequence of interactions between the promoter of the gene and the transcription factors (TFs). In this paper, we explore the features of a genetic network where the TFs (activators and repressors)…
Analyzing synthesis pathways for target molecules in a chemical reaction network annotated with information on the kinetics of individual reactions is an area of active study. This work presents a computational methodology for searching for…
Gene regulatory networks play a crucial role in controlling an organism's biological processes, which is why there is significant interest in developing computational methods that are able to extract their structure from high-throughput…
The process of biomarker discovery is typically lengthy and costly, involving the phases of discovery, qualification, verification, and validation before clinical evaluation. Being able to efficiently identify the truly relevant markers in…
Physical selectors (lasers choosing a mode, Ising machines settling on a ground state, condensates occupying a spin state) produce high-dimensional signatures at the moment of decision: full field amplitudes, multimode interference…
A stochastic flow network is a directed graph with incoming edges (inputs) and outgoing edges (outputs), tokens enter through the input edges, travel stochastically in the network, and can exit the network through the output edges. Each…
In order to find the outcome probabilities of quantum mechanical systems like the optical networks underlying Boson sampling, it is necessary to be able to compute the permanents of unitary matrices, a computationally hard task. Here we…
The problem of detecting a binding site -- a substring of DNA where transcription factors attach -- on a long DNA sequence requires the recognition of a small pattern in a large background. For short binding sites, the matching probability…
We demonstrate that failure of time-invariance assumption in the modeling of electrochemical systems by equivalent circuits can lead to the formation of low frequency "inductive loops" that manifest themselves as positive imaginary parts of…
We study the problem of system identification for stochastic continuous-time dynamics, based on a single finite-length state trajectory. We present a method for estimating the possibly unstable open-loop matrix by employing properly…
This report proposes a novel framework for a rigorous robustness analysis of stochastic biochemical systems. The technique is based on probabilistic model checking. We adapt the general definition of robustness introduced by Kitano to the…
A common approach to quantifying DNA involves repeated cycles of DNA amplification. This approach, employed by the polymerase chain reaction (PCR), produces outputs that are corrupted by amplification noise, making it challenging to…
In the past few decades, the development of fluorescent technologies and microscopic techniques has greatly improved scientists' ability to observe real-time single-cell activities. In this paper, we consider the filtering problem associate…
Stochastic dynamics of chemical reactions in a mutually repressing two-gene circuit is numerically simulated. The circuit has a rich variety of different states when the kinetic change of DNA status is slow. The stochastic switching…
Transcription factors (TFs) play a vital role in the regulation of gene expression thereby making them critical to many cellular processes. In this study, we used graph machine learning methods to create a compendium of TF cascades using…
Organisms gain by anticipating future changes in the environment. Those environmental changes often follow stochastic trends. The greater the slope of the trend, the more likely the trend's momentum carries the future trend in the same…
In this paper, we propose stochastic structure-preserving schemes to compute the effective diffusivity for particles moving in random flows. We first introduce the motion of particles using the Lagrangian formulation, which is modeled by…