Experimental and computational methods to highlight behavioural variations in TonB-dependent transporter expression in Pseudomonas aeruginosa versus siderophore concentration.

Iron is a key nutrient for bacterial growth. The source can be either heme or siderophore-Fe complexes. Siderophores are small molecules synthesized by bacteria to scavenge iron from the bacterial environment.

Calibration Methods for Time-to-Digital Converters.

In this paper, two of the most common calibration methods of synchronous TDCs, which are the bin-by-bin calibration and the average-bin-width calibration, are first presented and compared. Then, an innovative new robust calibration method for asynchronous TDCs is proposed and evaluated. Simulation results showed that: (i) For a synchronous TDC, the bin-by-bin calibration, applied to a histogram, does not improve the TDC's differential non-linearity (DNL); nevertheless, it improves its Integral Non-Linearity (INL), whereas the average-bin-width calibration significantly improves both the DNL and the INL.

Analytic modelling of passive microfluidic mixers.

This paper deals with a new analytical model for microfluidic passive mixers. Two common approaches already exist for such a purpose. On the one hand, the resolution of the advection-diffusion-reaction equation (ADRE) is the first one and the closest to physics.

Towards Tracking of Deep Brain Stimulation Electrodes Using an Integrated Magnetometer.

This paper presents a tracking system using magnetometers, possibly integrable in a deep brain stimulation (DBS) electrode. DBS is a treatment for movement disorders where the position of the implant is of prime importance. Positioning challenges during the surgery could be addressed thanks to a magnetic tracking.

Feasibility and reliability of sequential logic with gene regulatory networks.

Gene regulatory networks exhibiting Boolean behaviour, e.g. AND, OR or XOR, have been routinely designed for years.

A Label-Free Optical Detection of Pathogens in Isopropanol as a First Step towards Real-Time Infection Prevention.

The detection of pathogens is a major public health issue. Every year, thousands of people die because of nosocomial infections. It is therefore important to be able to detect possible outbreaks as early as possible, especially in the hospital environment.

Efficient Modeling and Simulation of Space-Dependent Biological Systems.

We recently demonstrated the possibility to model and to simulate biological functions using hardware description languages (HDLs) and associated simulators traditionally used for microelectronics. Nevertheless, those languages are not suitable to model and simulate space-dependent systems described by partial differential equations. However, in more and more applications space- and time-dependent models are unavoidable.

Modeling and simulation of biological systems using SPICE language.

The article deals with BB-SPICE (SPICE for Biochemical and Biological Systems), an extension of the famous Simulation Program with Integrated Circuit Emphasis (SPICE). BB-SPICE environment is composed of three modules: a new textual and compact description formalism for biological systems, a converter that handles this description and generates the SPICE netlist of the equivalent electronic circuit and NGSPICE which is an open-source SPICE simulator. In addition, the environment provides back and forth interfaces with SBML (System Biology Markup Language), a very common description language used in systems biology.

[Application of microelectronics CAD tools to synthetic biology].

Synthetic biology is an emerging science that aims to create new biological functions that do not exist in nature, based on the knowledge acquired in life science over the last century. Since the beginning of this century, several projects in synthetic biology have emerged. The complexity of the developed artificial bio-functions is relatively low so that empirical design methods could be used for the design process.

GeNeDA: An Open-Source Workflow for Design Automation of Gene Regulatory Networks Inspired from Microelectronics.

The topic of this article is the development of an open-source automated design framework for synthetic biology, specifically for the design of artificial gene regulatory networks based on a digital approach. In opposition to other tools, GeNeDA is an open-source online software based on existing tools used in microelectronics that have proven their efficiency over the last 30 years. The complete framework is composed of a computation core directly adapted from an Electronic Design Automation tool, input and output interfaces, a library of elementary parts that can be achieved with gene regulatory networks, and an interface with an electrical circuit simulator.

Modeling biology with HDL languages: a first step toward a genetic design automation tool inspired from microelectronics.

Nowadays, synthetic biology is a hot research topic. Each day, progresses are made to improve the complexity of artificial biological functions in order to tend to complex biodevices and biosystems. Up to now, these systems are handmade by bioengineers, which require strong technical skills and leads to nonreusable development.

A general framework improving teaching ligand binding to a macromolecule.

The interaction of a ligand with a macromolecule has been modeled following different theories. The tenants of the induced fit model consider that upon ligand binding, the protein-ligand complex undergoes a conformational change. In contrast, the allosteric model assumes that only one among different coexisting conformers of a given protein is suitable to bind the ligand optimally.

A game-of-life like simulator for design-oriented modeling of BioBricks in synthetic biology.

This paper deals with the development of a new simulator that will be very helpful to establish new accurate and predictive design-oriented models for the BioBricks used in synthetic biology. The simulator uses the principle of the game-of-life: molecules can move on a grid and, at every iteration, binding and dissociation rules are applied when two molecules are on same node. The principle is elementary but it can highlight interesting biological phenomenon.

Synthetic biology methodology and model refinement based on microelectronic modeling tools and languages.

In microelectronics, the design of new systems is based on a proven time-tested design flow. The goal of this paper is to determine to what extend this design flow can be adapted to biosystem design. The presented methodology is based on a top-down approach and consists of starting with a behavioral description of the system to progressively refine it to its final low-level system representation, composed of DNA parts.