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It is well-known that gene activation/deactivation dynamics may be a major source of randomness in genetic networks, also in the case of large concentrations of the transcription factors. In this work, we investigate the effect of realistic…
Factor analysis has proven to be a relevant tool for extracting tissue time-activity curves (TACs) in dynamic PET images, since it allows for an unsupervised analysis of the data. Reliable and interpretable results are possible only if…
We study theoretically the feasibility of using transverse electronic transport within a nanopore for rapid DNA sequencing. Specifically, we examine the effects of the environment and detection probes on the distinguishability of the DNA…
Spectrum analysis systems in online water quality testing are designed to detect types and concentrations of pollutants and enable regulatory agencies to respond promptly to pollution incidents. However, spectral data-based testing devices…
Intracellular transmission of information via chemical and transcriptional networks is thwarted by a physical limitation: the finite copy number of the constituent chemical species introduces unavoidable intrinsic noise. Here we provide a…
We present a maximum entropy framework to separate intrinsic and extrinsic contributions to noisy gene expression solely from the profile of expression. We express the experimentally accessible probability distribution of the copy number of…
We use particle dynamics simulations to probe the correlations between noise and dynamics in a variety of disordered systems, including superconducting vortices, 2D electron liquid crystals, colloids, domain walls, and granular media. The…
Even in the steady-state, the number of biomolecules in living cells fluctuates dynamically; and the frequency spectrum of this chemical fluctuation carries valuable information about the mechanism and the dynamics of the intracellular…
When modelling time series, it is common to decompose observed variation into a "signal" process, the process of interest, and "noise", representing nuisance factors that obfuscate the signal. To separate signal from noise, assumptions must…
Dirty paper coding (DPC) allows a transmitter to send information to a receiver in the presence of interference that is known (non-causally) to the transmitter. The original version of DPC was derived for the case where the noise and the…
Identifying concentrations of components from an observed mixture is a fundamental problem in signal processing. It has diverse applications in fields ranging from hyperspectral imaging to denoising biomedical sensors. This paper focuses on…
Noise induced decoherence is one of the main threats to large-scale quantum computation. In an attempt to assess the noise affecting a qubit we go beyond the standard steady-state solution of the transmission through a qubit-coupled cavity…
Based on the measurements of noise in gene expression performed during the last decade, it has become customary to think of gene regulation in terms of a two-state model, where the promoter of a gene can stochastically switch between an ON…
Predicting how genetic perturbations change cellular state is a core problem for building controllable models of gene regulation. Perturbations targeting the same gene can produce different transcriptional responses depending on their…
Given full or partial information about a collection of points that lie close to a union of several subspaces, subspace clustering refers to the process of clustering the points according to their subspace and identifying the subspaces. One…
Noise is source of ambiguity for fuzzy systems. Although being an important aspect, the effects of noise in fuzzy modeling have been little investigated. This paper presents a set of tests using three well-known fuzzy modeling algorithms.…
The ability of a quantum computer to reproduce or replicate the results of a quantum circuit is a key concern for verifying and validating applications of quantum computing. Statistical variations in circuit outcomes that arise from…
We study the theoretical performance of a combined approach to demodulation and decoding of binary continuous-phase modulated signals under repetition-like codes. This technique is motivated by a need to transmit packetized or framed data…
Organisms across all domains of life regulate the size of their cells. However, the means by which this is done is poorly understood. We study two abstracted "molecular" models for size regulation: inhibitor dilution and initiator…
MicroRNAs are small noncoding RNAs that regulate genes post-transciptionally by binding and degrading target eukaryotic mRNAs. We use a quantitative model to study gene regulation by inhibitory microRNAs and compare it to gene regulation by…