相关论文: Simultaneous Design of Microbe and Bioreactor
Constraint-based optimization of microbial strains and model-based bioprocess design have been used extensively to enhance yields in biotechnological processes. However, strain and process optimization are usually carried out in sequential…
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…
Microbial consortia offer significant biotechnological advantages over monocultures for bioproduction. However, industrial deployment is hampered by the lack of scalable architectures to ensure stable coexistence between populations.…
Designing synthetically accessible molecules and recommending analogs to unsynthesizable molecules are important problems for accelerating molecular discovery. We reconceptualize both problems using ideas from program synthesis. Drawing…
Microalgae are an important source of precursors (e.g. lipids) for a variety of biosynthetic processes (e.g. biofuel production). Their co-culturing with other organisms providing essential substrates for growth may reduce cost and provide…
The high energy consumption of electronic data processors, together with physical challenges limiting their further improvement, has triggered intensive interest in alternative computation paradigms. Here we focus on network-based…
This paper evaluates the cost competitiveness of microreactors in today's electricity markets, with a focus on uncertainties in reactor costs. A Genetic Algorithm (GA) is used to optimize key technical parameters, such as reactor capacity,…
The stochastic simulation of biological systems is an increasingly popular technique in bioinformatics. It often is an enlightening technique, which may however result in being computational expensive. We discuss the main opportunities to…
To create efficient-high performing processes, one must find an optimal design with its corresponding controller that ensures optimal operation in the presence of uncertainty. When comparing different process designs, for the comparison to…
The aim of this chapter is to provide a brief introduction into the basics of a top-down multilevel tumor dynamics modeling method primarily based on discrete entity consideration and manipulation. The method is clinically oriented, one of…
A key problem toward the use of microorganisms as bio-factories is reaching and maintaining cellular communities at a desired density and composition so that they can efficiently convert their biomass into useful compounds. Promising…
Dynamic flux balance analysis of a bioreactor is based on the coupling between a dynamic problem, which models the evolution of biomass, feeding substrates and metabolites, and a linear program, which encodes the metabolic activity inside…
Finite element simulations are essential in biomechanics, enabling detailed modeling of tissues and organs. However, architectural inefficiencies in current hardware and software stacks limit performance and scalability, especially for…
We report an experimental evaluation of the "input-output surface" for a biochemical AND gate. The obtained data are modeled within the rate-equation approach, with the aim to map out the gate function and cast it in the language of logic…
To overcome the brittleness limitation of ceramics, various toughening mechanisms have been proposed. Some of the most remarkable, especially for oxides, include the tetragonal-to-monoclinic phase transformation leading to crack shielding…
Information processing relying on biochemical interactions in the cellular environment is essential for biological organisms. The implementation of molecular computational systems holds significant interest and potential in the fields of…
Our brain consists of biological neurons encoding information through accurate spike timing, yet both the architecture and learning rules of our brain remain largely unknown. Comparing to the recent development of backpropagation-based…
Neutronic calculations for reactors are a daunting task when using Monte Carlo (MC) methods. As high-performance computing has advanced, the simulation of a reactor is nowadays more readily done, but design and optimization with multiple…
In this paper, we present a novel kinetic growth model for the micro-organism \textit{Methylococcus capsulatus} (Bath) that couples growth and pH. We apply growth kinetics in a model for single-cell protein production in a laboratory-scale…
Given a metabolic network in terms of its metabolites and reactions, our goal is to efficiently compute the minimal knock out sets of reactions required to block a given behaviour. We describe an algorithm which improves the computation of…