Related papers: Simultaneous Design of Microbe and Bioreactor
Biotechnology offers many opportunities for the sustainable manufacturing of valuable products. The toolbox to optimize bioprocesses includes \textit{extracellular} process elements such as the bioreactor design and mode of operation,…
Molecular circuits capable of autonomous learning could unlock novel applications in fields such as bioengineering and synthetic biology. To this end, existing chemical implementations of neural computing have mainly relied on emulating…
Design of next generation computer systems should be supported by simulation infrastructure that must achieve a few contradictory goals such as fast execution time, high accuracy, and enough flexibility to allow comparison between large…
Optimal biomarker combinations for treatment-selection can be derived by minimizing total burden to the population caused by the targeted disease and its treatment. However, when multiple biomarkers are present, including all in the model…
Bilevel optimization problems are a class of challenging optimization problems, which contain two levels of optimization tasks. In these problems, the optimal solutions to the lower level problem become possible feasible candidates to the…
The capacity to predict and control bioprocesses is perhaps one of the most important objectives of biotechnology. Computational simulation is an established methodology for the design and optimization of bioprocesses, where the finite…
Model-assisted interval designs such as the Keyboard design are transparent and easy to implement in phase I oncology trials. However, interim decisions based solely on data from the current dose may overlook informative signals from…
Molecular docking is a key computational tool utilized to predict the binding conformations of small molecules to protein targets, which is fundamental in the design of novel drugs. Despite recent advancements in geometric deep…
In this article the most fundamental decomposition-based optimization method - block coordinate search, based on the sequential decomposition of problems in subproblems - and building performance simulation programs are used to reason about…
We address the question of optimization of the microalgal biomass long term productivity in the framework of production in photobioreactors under the influence of day/night cycles. For that, we propose a simple bioreactor model accounting…
Biomolecular computers, along with quantum computers, may be a future alternative for traditional, silicon-based computers. Main advantages of biomolecular computers are massive parallel processing of data, expanded capacity of storing…
In many applications, including Stackelberg games, machine learning, and power systems \cite{Mackay2018Selftuning,Heinrich1952The,Wang2021Bi-Level}, the decisions in a minimax optimization problem can be constrained by a solution to an…
The design of biological systems is hindered by uncertainty arising from both intrinsic stochasticity of biomolecular reactions and variability across laboratory or experimental conditions. In this work, we present a sequential framework to…
This paper is centered on using chemical reaction as a computational metaphor for simultaneously solving problems. An artificial chemical reactor that can simultaneously solve instances of three unrelated problems was created. The reactor…
In cancer biomarker development, a key objective is to evaluate whether a new biomarker, when combined with an established one, improves early cancer detection compared to using the established biomarker alone. Incremental value is often…
Neuromorphic engineering concentrates the efforts of a large number of researchers due to its great potential as a field of research, in a search for the exploitation of the advantages of the biological nervous system and the brain as a…
Bayesian Optimization is a very effective tool for optimizing expensive black-box functions. Inspired by applications developing and characterizing reaction chemistry using droplet microfluidic reactors, we consider a novel setting where…
Artificial RNA molecules with novel functionality have many applications in synthetic biology, pharmacy and white biotechnology. The de novo design of such devices using computational methods and prediction tools is a resource-efficient…
Basic block reordering is an important step for profile-guided binary optimization. The state-of-the-art goal for basic block reordering is to maximize the number of fall-through branches. However, we demonstrate that such orderings may…
To facilitate rational molecular and materials design, this research proposes an integrated computational framework that combines stochastic simulation, ab initio quantum chemistry, and molecular docking. The suggested workflow allows…