Special Issue "Principles of Modular Design and Control in Complex Systems"

A special issue of Processes (ISSN 2227-9717). This special issue belongs to the section "Biological Systems".

Deadline for manuscript submissions: 31 March 2020.

Special Issue Editor

Dr. Cong T. Trinh
E-Mail Website
Guest Editor
Department of Chemical and Biomolecular Engineering, The University of Tennessee, Knoxville, TN 37996, USA
Interests: systems and synthetic biology; metabolic engineering; computational biology; CRISPR technology; modular design; modular cell engineering; pathogen inactivation; bioenergy and biofuels; bioesters; microbial robustness

Special Issue Information

Dear Colleagues,

Modular design is at the core of modern engineering, which enables rapid, efficient, and reproducible construction and maintenance of complex systems across applications. Remarkably, modularity has recently been discovered as a governing principle in natural biological systems from genes to proteins to pathways to cells and microbial communities. The convergent knowledge of natural and engineered modular systems will be the key to drive modern biotechnology to address emergent challenges associated with health, food, energy, and the environment. This Special Issue calls for contributions across a broad range of disciplines that address recent experimental, computational and/or modeling advancements in modular design and control of complex systems.

Dr. Cong T. Trinh
Guest Editor

Manuscript Submission Information

Manuscripts should be submitted online at www.mdpi.com by registering and logging in to this website. Once you are registered, click here to go to the submission form. Manuscripts can be submitted until the deadline. All papers will be peer-reviewed. Accepted papers will be published continuously in the journal (as soon as accepted) and will be listed together on the special issue website. Research articles, review articles as well as short communications are invited. For planned papers, a title and short abstract (about 100 words) can be sent to the Editorial Office for announcement on this website.

Submitted manuscripts should not have been published previously, nor be under consideration for publication elsewhere (except conference proceedings papers). All manuscripts are thoroughly refereed through a single-blind peer-review process. A guide for authors and other relevant information for submission of manuscripts is available on the Instructions for Authors page. Processes is an international peer-reviewed open access monthly journal published by MDPI.

Please visit the Instructions for Authors page before submitting a manuscript. The Article Processing Charge (APC) for publication in this open access journal is 1400 CHF (Swiss Francs). Please note that for papers submitted after 30 June 2020 an APC of 1500 CHF applies. Submitted papers should be well formatted and use good English. Authors may use MDPI's English editing service prior to publication or during author revisions.

Keywords

  • Modular design
  • Modular control
  • Modular cell
  • Modular enzyme
  • Protein network
  • Gene regulatory network
  • Multiobjective optimization
  • Metabolic network analysis
  • Graph algorithms
  • Control theory

Published Papers (2 papers)

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Open AccessFeature PaperArticle
Comparison of Multi-Objective Evolutionary Algorithms to Solve the Modular Cell Design Problem for Novel Biocatalysis
Processes 2019, 7(6), 361; https://doi.org/10.3390/pr7060361 - 11 Jun 2019
Cited by 1
Abstract
A large space of chemicals with broad industrial and consumer applications could be synthesized by engineered microbial biocatalysts. However, the current strain optimization process is prohibitively laborious and costly to produce one target chemical and often requires new engineering efforts to produce new [...] Read more.
A large space of chemicals with broad industrial and consumer applications could be synthesized by engineered microbial biocatalysts. However, the current strain optimization process is prohibitively laborious and costly to produce one target chemical and often requires new engineering efforts to produce new molecules. To tackle this challenge, modular cell design based on a chassis strain that can be combined with different product synthesis pathway modules has recently been proposed. This approach seeks to minimize unexpected failure and avoid task repetition, leading to a more robust and faster strain engineering process. In our previous study, we mathematically formulated the modular cell design problem based on the multi-objective optimization framework. In this study, we evaluated a library of state-of-the-art multi-objective evolutionary algorithms (MOEAs) to identify the most effective method to solve the modular cell design problem. Using the best MOEA, we found better solutions for modular cells compatible with many product synthesis modules. Furthermore, the best performing algorithm could provide better and more diverse design options that might help increase the likelihood of successful experimental implementation. We identified key parameter configurations to overcome the difficulty associated with multi-objective optimization problems with many competing design objectives. Interestingly, we found that MOEA performance with a real application problem, e.g., the modular strain design problem, does not always correlate with artificial benchmarks. Overall, MOEAs provide powerful tools to solve the modular cell design problem for novel biocatalysis. Full article
(This article belongs to the Special Issue Principles of Modular Design and Control in Complex Systems)
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Review

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Open AccessFeature PaperReview
Modular Engineering of Biomass Degradation Pathways
Processes 2019, 7(4), 230; https://doi.org/10.3390/pr7040230 - 23 Apr 2019
Cited by 3
Abstract
Production of fuels and chemicals from renewable lignocellulosic feedstocks is a promising alternative to petroleum-derived compounds. Due to the complexity of lignocellulosic feedstocks, microbial conversion of all potential substrates will require substantial metabolic engineering. Non-model microbes offer desirable physiological traits, but also increase [...] Read more.
Production of fuels and chemicals from renewable lignocellulosic feedstocks is a promising alternative to petroleum-derived compounds. Due to the complexity of lignocellulosic feedstocks, microbial conversion of all potential substrates will require substantial metabolic engineering. Non-model microbes offer desirable physiological traits, but also increase the difficulty of heterologous pathway engineering and optimization. The development of modular design principles that allow metabolic pathways to be used in a variety of novel microbes with minimal strain-specific optimization will enable the rapid construction of microbes for commercial production of biofuels and bioproducts. In this review, we discuss variability of lignocellulosic feedstocks, pathways for catabolism of lignocellulose-derived compounds, challenges to heterologous engineering of catabolic pathways, and opportunities to apply modular pathway design. Implementation of these approaches will simplify the process of modifying non-model microbes to convert diverse lignocellulosic feedstocks. Full article
(This article belongs to the Special Issue Principles of Modular Design and Control in Complex Systems)
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