Related papers: Multicriteria global optimization for biocircuit d…
Synthetic biology is a recent area of biological engineering, whose aim is to provide cells with novel functionalities. A number of important results regarding the development of control circuits in synthetic biology have been achieved…
Innovation in synthetic biology often still depends on large-scale experimental trial-and-error, domain expertise, and ingenuity. The application of rational design engineering methods promise to make this more efficient, faster, cheaper…
With the ever increasing complexity of specifications, manual sizing for analog circuits recently became very challenging. Especially for innovative, large-scale circuits designs, with tens of design variables, operating conditions and…
Real-life engineering optimization problems need Multiobjective Optimization (MOO) tools. These problems are highly nonlinear. As the process of Multiple Criteria Decision-Making (MCDM) is much expanded most MOO problems in different…
The rapid advances in the field of optimization methods in many pure and applied science pose the difficulty of keeping track of the developments as well as selecting an appropriate technique that best suits the problem in-hand. From a…
In order to design broadband extreme ultraviolet multilayers with many objectives, the multiobjective genetic algorithm and the multiobjective genetics algorithm with reference direction have been improved and combined used. The certain…
The potential of synthetic biology techniques for designing complex cellular circuits able to solve complicated computations opens a whole domain of exploration, beyond experiments and theory. Such cellular circuits could be used to carry…
Real-world decision and optimization problems, often involve constraints and conflicting criteria. For example, choosing a travel method must balance speed, cost, environmental footprint, and convenience. Similarly, designing an industrial…
The complex regulatory dynamics of a biological network can be succinctly captured using discrete logic models. Given even sparse time-course data from the system of interest, previous work has shown that global optimization schemes are…
This article focuses on the optimization of a complex system which is composed of several subsystems. On the one hand, these subsystems are subject to multiple objectives, local constraints as well as local variables, and they are…
Architecture optimization is the process of automatically generating design options, typically to enhance software's quantifiable quality attributes, such as performance and reliability. Multi-objective optimization approaches have been…
We address the problem of synthetic gene design using Bayesian optimization. The main issue when designing a gene is that the design space is defined in terms of long strings of characters of different lengths, which renders the…
Artificial neurons built on synthetic gene networks have potential applications ranging from complex cellular decision-making to bioreactor regulation. Furthermore, due to the high information throughput of natural systems, it provides an…
Many chemical and biological experiments involve multiple treatment factors and often it is convenient to fit a nonlinear model in these factors. This nonlinear model can be mechanistic, empirical or a hybrid of the two. Motivated by…
In multidisciplinary optimization the designer needs to find solution to optimization problems which include a number of usually contradicting criteria. Such a problem is mathematically related to the field of nonlinear vector optimization…
Genetic circuit design is a well-studied problem in synthetic biology. Ever since the first genetic circuits -- the repressilator and the toggle switch -- were designed and implemented, many advances have been made in this area of research.…
Computer-aided design for synthetic biology promises to accelerate the rational and robust engineering of biological systems; it requires both detailed and quantitative mathematical and experimental models of the processes to (re)design,…
Insufficient performance of optimization approaches for fitting of mathematical models is still a major bottleneck in systems biology. In this manuscript, the reasons and methodological challenges are summarized as well as their impact in…
Purpose: To develop a multi-criteria optimization framework for image guided radiotherapy. Methods: An algorithm is proposed for a multi-criteria framework for the purpose of patient setup verification decision processes. Optimal patient…
Artificial synthesis of DNA molecules is an essential part of the study of biological mechanisms. The design of a synthetic DNA molecule usually involves many objectives. One of the important objectives is to eliminate short sequence…