Related papers: Quantitative Aspects, Engineering and Optimization…
Metagenomics sequencing is routinely applied to quantify bacterial abundances in microbiome studies, where the bacterial composition is estimated based on the sequencing read counts. Due to limited sequencing depth and DNA dropouts, many…
During last years theoretical works shed new light and proposed new hypothesis on the mechanisms which regulate the time behaviour of biological populations in different natural systems. Despite of this, the role of environmental variables…
For a general sensory system following an external stochastic signal, we introduce the sensory capacity. This quantity characterizes the performance of a sensor: sensory capacity is maximal if the instantaneous state of the sensor has as…
Technological advancements in miniaturization and wireless communications are yielding more affordable and versatile sensors and, in turn, more applications in which a network of sensors can be actively managed to best support overall…
The zymase activity of the yeast Saccharomyces Cerevisiae is sensitive to environmental parameters and is therefore used as a microbiological sensor for water quality assessment, ecotoxicological characterization or environmental…
Dynamical systems modeling, particularly via systems of ordinary differential equations, has been used to effectively capture the temporal behavior of different biochemical components in signal transduction networks. Despite the recent…
Signal transduction, or signal-processing capability, is a fundamental property of nature that manifests universally across systems of different scales -- from quantum behaviour to the biological. This includes the detection of…
Living cell signaling systems include multistep biochemical signaling reaction cascades (BSCs) comprising modifications of molecular signaling proteins. Substantial data on BSCs have been accumulated in the field of molecular biology and…
Microbes are everywhere, including in and on our bodies, and have been shown to play key roles in a variety of prevalent human diseases. Consequently, there has been intense interest in the design of bacteriotherapies or "bugs as drugs,"…
We address the problem of parameter estimation in models of systems biology from noisy observations. The models we consider are characterized by simultaneous deterministic nonlinear differential equations whose parameters are either taken…
Robustness and sensitivity of responses generated by cell signaling networks has been associated with survival and evolvability of organisms. However, existing methods analyzing robustness and sensitivity of signaling networks ignore the…
Escherichia coli has long been used as a model organism due to the extensive experimental characterization of its pathways and molecular components. Take chemotaxis as an example, which allows bacteria to sense and swim in response to…
Bacteria often develop distinct phenotypes to adapt to environmental stress. In particular, they can produce biofilms, dense communities of bacteria that live in a complex extracellular matrix. Bacterial biofilms provide a safe haven from…
Electrotactile feedback is a promising method for delivering haptic sensations, but challenges such as the naturalness of sensations hinder its adoption in commercial devices. In this study, we introduce a novel device that enables the…
Bacterial chemotactic sensing converts noisy chemical signals into running and tumbling. We analyze the static sensing limits of mixed Tar/Tsr chemoreceptor clusters in individual Escherichia coli cells using a heterogeneous…
An active area of research interest is the inference of ecological models of complex microbial communities. Inferring such ecological models entails understanding the interactions between microbes and how they affect each other's growth.…
Biological systems sense and extract information from fluctuating signals while operating under energetic constraints and limited resolution. We introduce a general chemical model in which a sensor, coupled to a signaling pathway activated…
Computation of biological processes creates great promise for everyday life and great challenges for physical scientists. Simulations of molecular dynamics appeal to biologists as a natural extension of structural biology. Once biologists…
Biological cells are often found to sense their chemical environment near the single-molecule detection limit. Surprisingly, this precision is higher than simple estimates of the fundamental physical limit, hinting towards active sensing…
This paper presents a novel methodology for modeling memristive biosensing within COMSOL Multiphysics, focusing on critical performance metrics such as antigen-antibody binding concentration and output resistive states. By studying the…