Related papers: Designing biological circuits: from principles to …
Bacteria have been a source of inspiration for the design of evolutionary algorithms. At the beginning of the 20th century synthetic biology was born, a discipline whose goal is the design of biological systems that do not exist in nature,…
This paper reviews the design of regulation loops for power converters. Power converter control being a vast domain, it does not aim to be exhaustive. The objective is to give a rapid overview of the main synthesis methods in both…
In the context of studying periodic processes, this paper investigates first under which conditions switching affine systems in the plane generate stable limit cycles. Based on these conditions, a design methodology is proposed by which the…
In this letter, we analyze a genetic toggle switch recently studied in the literature where the expression of two repressor proteins can be tuned by controlling two different inputs, namely the concentration of two inducer molecules in the…
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…
This paper surveys foundation models for AI-enabled biological design, focusing on recent developments in applying large-scale, self-supervised models to tasks such as protein engineering, small molecule design, and genomic sequence design.…
Quantum computing leverages the unique properties of qubits and quantum parallelism to solve problems intractable for classical systems, offering unparalleled computational potential. However, the optimization of quantum circuits remains…
Reversible logic has applications in various research areas including low-power design and quantum computation. In this paper, a rule-based optimization approach for reversible circuits is proposed which uses both negative and positive…
A central goal of synthetic biology is to design sophisticated synthetic cellular circuits that can perform complex computations and information processing tasks in response to specific inputs. The tremendous advances in our ability to…
We describe a conceptual design of a distributed classifier formed by a population of genetically engineered microbial cells. The central idea is to create a complex classifier from a population of weak or simple classifiers. We create a…
Many biological systems approach physical limits to their performance, motivating the idea that their behavior and underlying mechanisms could be determined by such optimality. Nevertheless, optimization as a predictive principle has only…
The genetic repressilator circuit consists of three transcription factors, or repressors, which negatively regulate each other in a cyclic manner. This circuit was synthetically constructed on plasmids in {\it Escherichia coli} and was…
The manual design of analog circuits is a tedious task of parameter tuning that requires hours of work by human experts. In this work, we make a significant step towards a fully automatic design method that is based on deep learning. The…
Embedding efficient command operation into biochemical system has always been a research focus in synthetic biology. One of the key problems is how to sequence the chemical reactions that act as units of computation. The answer is to design…
Identity, response to external stimuli, and spatial architecture of a living system are central topics of molecular biology. Presently, they are largely seen as a result of the interplay between a gene repertoire and the regulatory…
With the completion of human genome mapping, the focus of scientists seeking to explain the biological complexity of living systems is shifting from analyzing the individual components (such as a particular gene or biochemical reaction) to…
Quantum computers are considered as a future alternative to circumvent the heat dissipation problem of VLSI circuits. The synthesis of reversible circuits is a very promising area of study considering the expected further technological…
In this paper, we consider the problem of optimal exogenous control of gene regulatory networks. Our approach consists in adapting an established reinforcement learning algorithm called the fitted Q iteration. This algorithm infers the…
Genetic Algorithms are widely used in many different optimization problems including layout design. The layout of the shelves play an important role in the total sales metrics for superstores since this affects the customers' shopping…
Synchronous generators and inverter-based resources are complex systems with dynamics that cut across multiple intertwined physical domains and control loops. Modeling individual generators and inverters is, in itself, a very involved…