Morgan Madec

University of Strasbourg | UNISTRA · Laboratoire ICube

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...

Significant progress has been made in the development of magnetic micromanipulation for minimally invasive surgery. The development of systems to localize millimeter-sized robots during magnetic manipulation without line-of-sight detection remains, however, a challenging task. In this study, we focused on the development of a tracking system aiming...

Miniaturized NMR (Nuclear Magnetic Resonance) devices are a trend in the industry because they allow a flexible use within a range of applications that would be otherwise not feasible with standard NMR equipment. However, one of the main obstacles in the development of miniaturized NMR systems is the availability of a static magnetic field B <sub...

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. However, ADRE is a partial differential equation that requires finite element simulatio...

This paper describes an alternative to high-field electromagnetic tracking system, by using low consumption generator and high-performance magnetic sensors. Monotonically varying magnetic fields over three positions are created to produce magnetic field gradients, which encode each spatial point uniquely. Millimetric size sensors capable of measuri...

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. The system proposed in this paper,...

Gene regulatory networks exhibiting Boolean behaviour, e.g. AND, OR or XOR, have been routinely designed for years. However, achieving more sophisticated functions, such as control or computation, usually requires sequential circuits or so-called state machines. For such a circuit, outputs depend both on inputs and the current state of the system....

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. Various pathogen detection techniques have already been demonstrated. However, most of them r...

Mastering the basics of theoretical and experimental aspects of fluidics and biology is an obvious requirement for the design and evaluation of micro/nano biosystems. This chapter provides a review of the physics of micro/nano fluidics systems as well as basics of biochemistry and biological functions. It also gives detailed information on common e...

The topic of this paper is the development of biological models for 3D reaction-diffusion phenomena that can be used in any circuit electronic design automation environment for the simulation of biosensors. Biological systems that involve such 3D phenomena are described by partial differential equations. Our approach consists in discretizing these...

The design of biosystems, biosensors, and lab-on-chips is an important field of investigation since the beginning of this century. The miniaturization and the integration constraints make the design of such systems challenging, and it is no longer possible to uncouple biology (or biochemistry) from the rest of the system. The interest of extending...

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 mo...

A procedure of extracting a closed-form user-friendly I-V equation for short channel carbon nanotube field-effect transistors (CNFET) in the saturation region is presented by employing a relation between CNFET parameters meeting the experimental results. The methodology is based on the Stanford model and ballistic relation of one channel CNFET. In...

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...

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...

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 thei...

Synthetic biology aims at reinvesting theoretical knowledge from various do-mains (biology, engineering, microelectronics) for the development of new bio-logical functions. Concerning the design of such functions, the classical trial-error approach is expensive and time consuming. Computer-aided design is therefore of key interest in this field. As...

Vertical Hall-effect devices (VHDs) are CMOS integrated sensors dedicated to the measurement of magnetic field in the plane of the chip. At low frequency performances are severely reduced by the 1/f noise. We recently proposed a theoretical study which confirm the capability of the spinning current technique to lower the 1/f noise on Low-Voltage VH...

We recently demonstrated that it is possible to model and to simulate biological functions using hardware description languages (and associated simulators) traditionally used for micro-electronics. The main drawback of these languages is that they do not support partial differential equations. However, for several applications in biology, space-dep...

Research and development in life sciences domain brings every day many innovations. Some of them have been enabled (or improved) by the micro-electronics. Several examples are described in this paper. A big challenge in the design of such systems is that the biological part cannot be uncoupled from the rest of the system during the design process....

Synthetic biology is a new field of biotechnology which aims to apply engineering design processes for the development of new artificial biological functions. In this domain, the development of automated design tools is a big challenge. This paper deals with a new approach based on the description of elementary biological mechanisms through fuzzy l...

Vertical Hall-effect devices are CMOS integrated sensors designed for the measurement of magnetic field in the plane of the chip. In such devices, systematic offset is a major issue which limits their performance. We recently developed a design-oriented compact model for such devices. In this paper, the model is improved and used to study the main...

The paper presents a high level model of a Lab-On-Chip to detect micro-pollutants in drinking water, using an analog hardware description language (VHDL-AMS). The Lab-On-Chip is composed by a micro-fluidic system, a biological reaction and a detection system. Simulation results of Lab-On-Chip model are validated by comparison to experiment and nume...

Synthetic biology is an emerging field at the interface between biotechnology and engineering sciences. It aims at designing new biological functions by assembling elementary parts (DNA sequences) based on design approaches inspired from those used for the design of complex microsystems. The development of efficient tools to support the design is t...

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. Besides, scientific...

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 suit...

The Vertical Hall Device integrable in a shallow N-well, and thus compatible with Low-Voltage CMOS processes, i.e. the LV-VHD, was proposed five years ago. Its layout is similar to the layout of the HV-VHD, i.e. the conventional 5-contact VHD integrated in the deep N-well of High-Voltage processes. However, in the LV-VHD, the Hall voltage is picked...

Synthetic biology, or biological engineering, is a new science which may take advantage of the know-how of engineering science in order to build new in-vivo biological functions. The complete design process implies lots of modeling and simulation tasks. The design flow for this technology uses “digital” models at high level of abstraction as well a...

The topic of this paper is to develop an open-source framework to help bio-engineers through the different stages of a top-down design process for new artificial biosystems (synthetic biology). The presented tools address the upstream stages of the design, starting from a high-level behavioral description of the targeted biological function and end...

The goal of this work is the improvement of an existing design-oriented model of the 5-contact vertical Hall-effect sensor integrated in CMOS technology. Such a model should facilitate the work of designers, permitting them to simulate the sensor, the biasing and processing electronics together with the same electrical simulator. In this paper, foc...

A compact model of a cross-shaped horizontal integrated Hall-effect sensor is presented in this paper. Compared to existing models, reliability is improved, especially to simulate systems in which biasing and measurement circuits are not independent. The Hall device model core, already published, is based on a network of six non-linear resistances...

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 tw...

Synthetic bio-systems become increasingly more complex and their development is lengthy and expensive. In the same way, in microelectronics, the design process of very complex circuits has benefited from many years of experience. It is now partly automated through Electronic Design Automation tools. Both areas present analogies that can be used to...

With the high complexity of current digital circuits, the use of gate-level models during the design process is mandatory. For standard CMOS technologies, designers assemble standard cells for which the gate-level model is provided by the founderies. For a given technology, the temporal parameters (such as propagation delays) are constants that can...

The topic of this work is the building of a design-oriented compact model of vertical Hall-effect sensors integrated in CMOS technologies. The use of such a model should facilitate the work of integrated sensors designers, permitting them to simulate the sensor, the biasing and processing electronics together with the same electrical simulator. In...

In this letter, we propose to introduce the notion of equivalent capacitance and to generalize the so-called equivalent-thickness concept to model arbitrary shapes of lightly doped nonplanar multigate MOSFETs, without the need to introduce any unphysical parameter. These definitions, which merely map a multigate geometry into the symmetric double-g...

In this letter, we propose to introduce the notion of equivalent capacitance and to generalize the so-called equivalent-thickness concept to model arbitrary shapes of lightly doped nonplanar multigate MOSFETs, without the need to introduce any unphysical parameter. These definitions, which merely map a multigate geometry into the symmetric double-g...

The paper describes a new design-oriented compact model for horizontal Hall effect devices. This model is based on the physics of semi-conductor and is simplified according to some assumptions verified through experimental results and/or numerical simulations. Compared to existing models, it has the advantage to take most of the first-order effects...

The development of computer-aided design tools for synthetic biology is currently a hot research topic. However the field is not mature enough to provide a generic, adaptable and reliable tool for potential applications. The purpose of this paper is to present a system designers approach. We highlight, through the work carried out by our team in re...

Hall-sensors integrated in CMOS technology are good candidates for the design of low-cost magnetometers. However, one of their major limitations is the 0-field offset, and it is essential to take this effect into account in the very early steps of the design process. For this purpose, we recently developed a new compact model for horizontal cross-s...

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...

Synthetic biology is a science resulting from the connection between biotechnology and engineering sciences. It aims to design and build new biological systems and functions. The ability to design a new biological function according to given specifications includes many steps. One of the big issues is to formalize a design methodology and to develo...

Synthetic biology is an emerging area of biotechnology for which main applications are in the field of Health and Environment. However, it suffers from a lack of adapted CAD tools and methodology in order to fulfill efficiently and quickly to the needs of these domains. In this paper, the strong relationship between circuits design in microelectron...

A new compact model of a cross-shaped horizontal integrated Hall-effect sensor is presented in this paper. Compared to existing models, the model reliability is improved, especially for designs in which the bias and the measurement circuits are not independent. The Hall device model uses six subcomponents, each modeling the non-linear resistance du...

The potential application range of spintronic devices is wide. However, few works were carried out in the field of compact modeling of such devices. The lack of compact models dramatically increases the design complexity of circuits using spintronic devices. In this paper, focus is made on magnetic tunnel junctions (MTJs). It is presented in a set...

The potential application range of spintronic devices is wide. However, a few works were carried out in the field of compact modeling of such devices. The lack of compact models dramatically increases the design complexity of circuits using spintronic devices. In this paper, focus is made on magnetic tunnel junctions (MTJs). It is presented in a se...

The paper presents an innovative approach for the modeling and simulation of heterogeneous biological systems based on SystemC-AMS, an open-source C++ extension to the OSCI SystemC Standard. After some basic notions on synthetic biology, an analogy is drawn between this active field of research and nanoelectronics. The paper then presents the Syste...

The paper presents an innovative approach for the modeling and simulation of heterogeneous biological systems based on SystemC-AMS, an open-source C++ extension to the OSCI SystemC Standard. After some basic notions on synthetic biology, an analogy is drawn between this active field of research and nanoelectronics. The paper then presents the Syste...

In this paper, the potential of microelectronic design methods in synthetic biology is analyzed. Synthetic biology is an emerging domain, which aims to combine biology and genetics knowledge with engineering methods in order to design new biological systems. The argument is illustrated by a case study on a specific biodevice, which is modeled and s...

In this paper, we present a FinFET compact model and its associated parameter extraction methodology. This explicit model accounts for all major small geometry effects and allows accurate simulations of both n- and p-type FinFETs. The model core is physics-based (long-channel model) and some semiempirical corrections are introduced in order to accu...

Image rendering of spatial light modulators (SLMs) is often degraded by various effects. Some efficient methods to get around non-uniformity, nonlinearity, and remanence and improve image rendering are presented. Optical laboratory results are presented for an analog ferroelectric liquid-crystal SLM using a high-speed camera. Focus is made on a pre...

This paper presents a new driving method allowing fast analogue light modulation with bistable ferroelectric liquid crystals (FLC). The method is evaluated using a functional virtual prototyping design flow. First, a surface stabilized binary FLC cell is modeled in VHDL-AMS language on the basis of well-known theories of FLC. Some physical and envi...

A new compact model of a magnetic tunnel junction (MTJ) is presented in this paper. This model is intended to describe the behavior of a MTJ and to take the magnetic as well as the non-linear electronic transport phenomena into account. It should be suitable for circuits simulation and thus, it must be simple (no finite element approach, analytical...

This paper presents a hybrid processor dedicated to the reconstruction algorithm in multislice spiral computed tomography. The described architecture focuses on the advanced single-slice rebinning algorithm, which is a basic 2-D-to-3-D rebinning method developed in 2000. The hybrid processor is composed of four cores (rebinning, filtering, backproj...

Filtered backprojection (FBP) is the basic operation of image reconstruction algorithms in tomography. It is widely used but very time-consuming. We propose a new implementation, based on an optoelectronic architecture, providing a speedup of about two orders of magnitude over a classical digital implementation. The realization of the optical core,...

The tendency today is to replace high-dynamic light modulators by high-speed binary ones (of which the micromirror is the best example). This kind of spatial light modulators (SLM) fulfils all the present needs in displays. They are used in optical communications as binary systems and also in display applications (video projectors) with temporal mu...

Optical processing can be used to speed up some algorithms of image reconstruction from tomodensitometric data provided by volume exploration systems. This may be of high interest in order to meet the needs of future assisted therapy systems. Two systems are described in this document, corresponding to the two main steps of the above mentioned algo...

Résumé Le traitement optique de l'information est une alternative aux processeurs classiques connue depuis plus de 50 ans. Il n'a pas encore eu l'essor que l'on attendait, faute principalement à un manque de matériel adapté (afficheurs, capteurs, …). Cet article démontre, exemples à l'appui, comment les processeurs à base d'optique vont pouvoir pro...