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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. For this purpose, we investigated a new modeling approach to simulate molecular diffusion on a mesoscopic scale still based on HDL. Our work relies on previous investigations on an electrothermal simulation tool for integrated circuits, and analogies that can be drawn between electronics, thermodynamics, and biology. The tool is composed of four main parts: a simple but efficient mesher that divides space into parallelepipeds (or rectangles in 2D) of adaptable size, a set of interconnected biological models, a SPICE simulator that handles the model and Python scripts that interface the different tools. Simulation results obtained with our tool have been validated on simple cases for which an analytical solution exists and compared with experimental data gathered from literature. Compared with existing approaches, our simulator has three main advantages: a very simple algorithm providing a direct interface between the diffusion model and biological model of each cell, the use of a powerful and widely proven simulation core (SPICE) and the ability to interface biological models with other domains of physics, enabling the study of transdisciplinary systems.

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. Each of these modules is an extension of microelectronics tools and concepts: ODIN II, ABC, the Verilog language, SPICE simulator, and SystemC-AMS. GeNeDA is first validated on a benchmark of several combinatorial circuits. The results highlight the importance of the part library. Then, this framework is used for the design of a sequential circuit including a biological state machine.

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 fields that share the same design approach, such as microelectronics, have already overcome several issues and designers succeed in building extremely complex systems with many evolved functions. On the other hand, in systems engineering and more specifically in microelectronics, the development of the domain has been promoted by both the improvement of technological processes and electronic design automation tools. The work presented in this paper paves the way for the adaptation of microelectronics design tools to synthetic biology. Considering the similarities and differences between the synthetic biology and microelectronics, the milestones of this adaptation are described. The first one concerns the modeling of biological mechanisms. To do so, a new formalism is proposed, based on an extension of the generalized Kirchhoff laws to biology. This way, a description of all biological mechanisms can be made with languages widely used in microelectronics. Our approach is therefore successfully validated on specific examples drawn from the literature.

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. To preserve accuracy and simplicity, the design flow relies on refined models of biological mechanisms, which can be expressed by the hardware description languages and simulation tools traditionally used in microelectronics. A case study, the complete modeling of a priority encoder, is presented to demonstrate the effectiveness of the method., (Copyright © 2011 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.)

An explicit model is proposed for lightly doped FinFETs, which is valid and continuous in all operating regimes for channel lengths down to 25 nm, Fin widths down to 3 nm and Fin heights down to 50 nm with a single set of parameters. Short-channel effects, subthreshold slope degradation, drain-induced barrier lowering, drain saturation voltage with saturation, channel length modulation and quantum mechanical effects are taken into consideration by these studies.

This paper examines aspects of design technology required to explore advanced logic-circuit design using carbon nanotube field-effect transistor (CNTFET) devices. An overview of current types of CNTFETs is given and highlights the salient characteristics of each. Compact modeling issues are addressed and new models are proposed implementing: 1) a physics-based calculation of energy conduction sub-band minima to allow a realistic analysis of the impact of CNT helicity and radius on the dc characteristics; 2) descriptions of ambipolar behavior in Schottky-barrier CNTFETs and ambivalence in double-gate CNTFETs (DG-CNTFETs). Using the available models, the influence of the parameters on the device characteristics were simulated and analyzed. The exploitation of properties specific to CNTFETs to build functions inaccessible to MOSFETs is also described, particularly with respect to the use of DG-CNTFETs in fine-grain reconfigurable logic. Index Terms--Circuit simulation, carbon nanotube field-effect transistor (CNTFET), compact model, reconfigurable logic gates.

A simple, physics-based and continuous model for the quantum effects and polydepletion in deep-submicrometer MOSFETs with very thin gate oxide thickness is presented. The model offers simple relationships among effective electrical parameters and physical device parameters, providing insight into the physical phenomena.

An analytical one-dimensional thermoelectrical model for the power MOSFET transistor (VDMOS transistor) has been developed and implemented in the Saber circuit simulator. The device temperature becomes an interactive variable during the simulation. The model results in the combination of the electrical model of the device with a thermal network which models the different material layers crossed by the heat flow from the silicon chip to the heatsink (conduction phenomenon), and also takes into account the radiation and convection phenomena. The accuracy of the model is evaluated with electrical and thermal characterizations, and with a validation circuit. Index Terms - Characterization, CAD, modeling, power MOSFET transistor, thermal behavior, thermal dissipation, thermo-electrical interactions.

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. BB-SPICE has been developed in order to bridge the gap between the simulation of biological systems on the one hand and electronics circuits on the other hand. Thus, it is suitable for applications at the interface between both domains, such as development of design tools for synthetic biology and for the virtual prototyping of biosensors and lab-on-chip. Simulation results obtained with BB-SPICE and COPASI (an open-source software used for the simulation of biochemical systems) have been compared on a benchmark of models commonly used in systems biology. Results are in accordance from a quantitative viewpoint but BB-SPICE outclasses COPASI by 1 to 3 orders of magnitude regarding the computation time. Moreover, as our software is based on NGSPICE, it could take profit of incoming updates such as the GPU implementation, of the coupling with powerful analysis and verification tools or of the integration in design automation tools (synthetic biology). [ABSTRACT FROM AUTHOR]