Related papers: Formal Analysis of the Biological Circuits using H…
One of the challenges in Synthetic Biology is to design circuits with increasing levels of complexity. While circuits in Biology are complex and subject to natural tradeoffs, most synthetic circuits are simple in terms of the number of…
Higher-order quantum theory is an extension of quantum theory where one introduces transformations whose input and output are transformations, thus generalizing the notion of channels and quantum operations. The generalization then goes…
We present a method for logical specification of the behavior of a system based on the specification of its components and for representing and specifying the effect of a class of communication "signaling pathways" among them. Variations in…
Recent years have witnessed the growing scholarly interest in the next-generation general-purpose computers. Various innovative computing modes have been proposed, such as optical, quantum phenomena, and DNA-based modes. Sequential logic…
Synthetic biologists have made great progress over the past decade in developing methods for modular assembly of genetic sequences and in engineering biological systems with a wide variety of functions in various contexts and organisms.…
Systems Biology has emerged in the last years as a new holistic approach based on the global understanding of cells instead of only being focused on their individual parts (genes or proteins), to better understand the complexity of human…
We advocate here the use of computational logic for systems biology, as a \emph{unified and safe} framework well suited for both modeling the dynamic behaviour of biological systems, expressing properties of them, and verifying these…
Building circuits and studying their behavior in cells is a major goal of systems and synthetic biology. Synthetic biology enables the precise control of cellular states for systems studies, the discovery of novel parts, control strategies,…
Functions of chemical composition are complex and discrete in nature making it impossible to optimize them with gradient methods. Genetic algorithms, which do not use derivative information, are used to maximize the thermal conductivity of…
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…
The Laplace transform is an algebraic method that is widely used for analyzing physical systems by either solving the differential equations modeling their dynamics or by evaluating their transfer function. The dynamics of the given system…
The study of biological systems witnessed a pervasive cross-fertilization between experimental investigation and computational methods. This gave rise to the development of new methodologies, able to tackle the complexity of biological…
At the heart of many contemporary theories of life is the concept of biological self-organisation: organisms have to continuously produce and maintain the conditions of their own existence in order to stay alive. The way in which these…
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…
The last decade has witnessed a surge of theoretical and computational models to describe the dynamics of complex gene regulatory networks, and how these interactions can give rise to multistable and heterogeneous cell populations. As the…
Both experimental and computational biology is becoming increasingly automated. Laboratory experiments are now performed automatically on high-throughput machinery, while computational models are synthesized or inferred automatically from…
We advocates here the use of (mathematical) logic for systems biology, as a unified framework well suited for both modeling the dynamic behaviour of biological systems, expressing properties of them, and verifying these properties. The…
The design of genetic networks with specific functions is one of the major goals of synthetic biology. However, constructing biological devices that work "as required" remains challenging, while the cost of uncovering flawed designs…
Over the past decade, a number of quantum processes have been proposed which are logically consistent, yet feature a cyclic causal structure. However, there is no general formal method to construct a process with an exotic causal structure…
Transcriptional networks represent one of the most extensively studied types of systems in synthetic biology. Although the completeness of transcriptional networks for digital logic is well-established, *analog* computation plays a crucial…