Article
Biotechnology & Applied Microbiology
Rosanna Young, Matthew Haines, Marko Storch, Paul S. Freemont
Summary: Synthetic Biology is a rapidly growing interdisciplinary field that considers living systems as programmable at the genetic level, defining new platform technologies and methodological advances. A key concept driving the field is the Design-Build Test-Learn cycle, which provides a systematic framework for building new biological systems, with a major application area being biosynthetic pathway engineering requiring modular assembly of genetic elements and enzymes.
METABOLIC ENGINEERING
(2021)
Article
Biotechnology & Applied Microbiology
Gahyeon Ryu, Gi Bae Kim, Taeho Yu, Sang Yup Lee
Summary: The establishment of a bio-based circular economy is crucial for addressing the climate crisis and promoting sustainable development. Designing metabolic pathways for microbial cell factories is essential, and computer-supported tools and deep learning techniques can aid in pathway prediction and enzyme discovery. Leveraging these computational tools and strategies, particularly the capabilities of deep learning, has the potential to accelerate the advent of a bio-based circular economy.
METABOLIC ENGINEERING
(2023)
Article
Biotechnology & Applied Microbiology
Szu-Yi Hsu, Jihaeng Lee, Adam Sychla, Michael J. Smanski
Summary: Modern tools in DNA synthesis and assembly provide genetic engineers with precise control over the design of complex gene systems. However, there is a lack of systematic approaches to optimize the performance of genetic constructs. This study explores the use of a Plackett-Burman design to improve the production of a specific compound in Streptomyces.
METABOLIC ENGINEERING
(2023)
Review
Biochemistry & Molecular Biology
Yang Cheng, Xinyu Bi, Yameng Xu, Yanfeng Liu, Jianghua Li, Guocheng Du, Xueqin Lv, Long Liu
Summary: Optimizing metabolic pathways in microbial cell factories is crucial for efficient biotechnological production processes. Machine learning has been used to build data-driven models and accelerate development in areas such as genetic engineering and pathway optimization. This review discusses recent applications of machine learning in genome-scale metabolic model construction, enzyme engineering, and gene regulatory element design, as well as the limitations and potential solutions to these methods.
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL
(2023)
Article
Construction & Building Technology
Mingyang Pei, Mingxing Xu, Lingshu Zhong, Xiaobo Qu
Summary: The asymmetric demands of metro lines in megacities can lead to long passenger wait times and wasted vehicle capacity. To address this problem, a modular transit system (MTS) is proposed, which allows a metro fleet to be dynamically dissembled and assembled in identical modules on metro terminals. A nonlinear programming model is formulated, considering train power, greenhouse gas emissions, wind resistance, and operational economics. The model is linearized for fast solution. Numerical experiments based on Shenzhen Metro data demonstrate the model's viability and usefulness in terms of economic, low-carbon, and ecological consequences. The robustness of the proposed model and sensitivity analysis with different parameter values are also reported.
TUNNELLING AND UNDERGROUND SPACE TECHNOLOGY
(2023)
Article
Engineering, Electrical & Electronic
Quan Zhou, Yinglong He, Dezong Zhao, Ji Li, Yanfei Li, Huw Williams, Hongming Xu
Summary: This article proposes a new modular design method for hybrid powertrains using a modified accelerated particle swarm optimization (MAPSO) algorithm. The method determines the optimal combination of component specifications and control parameters, and a Pareto analysis is carried out for tradeoff determination. The MAPSO is verified as the best method and two different modular design methods are developed with it, with the simultaneous method showing better performance in terms of cost function and time savings compared to the two-level method.
IEEE TRANSACTIONS ON TRANSPORTATION ELECTRIFICATION
(2021)
Article
Automation & Control Systems
Nikita O. Starodubcev, Nikolay O. Nikitin, Elizaveta A. Andronova, Konstantin G. Gavaza, Denis O. Sidorenko, Anna Kalyuzhnaya
Summary: Generative design techniques have been widely applied in various fields, particularly in engineering, to automate initial stages of designing structures, minimizing routine work. However, existing approaches are limited by problem specificity and lack flexibility in method selection. To address these issues, a general approach named GEFEST (Generative Evolution For Encoded STructure) was proposed, providing sampling, estimation, and optimization principles for adaptable problem solutions. Experimental studies confirmed the effectiveness of GEFEST in coastal engineering, microfluidics, thermodynamics, and oil field planning, achieving improvements of 12%, 9%, 8%, and 7% respectively over baseline and state-of-the-art solutions.
ENGINEERING APPLICATIONS OF ARTIFICIAL INTELLIGENCE
(2023)
Article
Construction & Building Technology
Sheida Shahi, Patryk Wozniczka, Chris Rausch, Ian Trudeau, Carl Haas
Summary: This research proposes a methodology for generating modular design options for extensions of existing buildings by combining computational methods and modular construction, focusing on key architectural design metrics. A functional demonstration was conducted for the extension of Ken Soble Tower in Hamilton, Ontario to show the efficiency of developing and evaluating design options for improving existing residential infrastructure.
AUTOMATION IN CONSTRUCTION
(2021)
Article
Engineering, Chemical
Jorge L. Barrera, Joseph J. Hartvigsen, Michele Hollist, Jenna Pike, Ainsley Yarosh, Nicholas P. Fullilove, Victor A. Beck
Summary: Sustainable production of liquid fuels and feedstocks from atmospheric CO2 through carbon recycling technologies is necessary. Fischer-Tropsch (FT) reactors can provide liquid hydrocarbon fuels and feedstocks from reductive CO2 utilization. Smaller, modular reactors can be composed together to the specific scale of the emission source, yielding a flexible solution. Topology optimization is used to determine the cooling insert geometry that maximizes reactor productivity while preventing auto-thermal runaway in these modular reactors.
CHEMICAL ENGINEERING SCIENCE
(2023)
Article
Engineering, Multidisciplinary
Marek Tyburec, Martin Doskar, Jan Zeman, Martin Kruzik
Summary: This research addresses the topology optimization of modular structures and mechanisms by proposing a bi-level sequential strategy that combines free material design, clustering techniques, and topology optimization.
COMPUTER METHODS IN APPLIED MECHANICS AND ENGINEERING
(2022)
Review
Biochemical Research Methods
Woo Dae Jang, Gi Bae Kim, Yeji Kim, Sang Yup Lee
Summary: This paper reviews recent studies on AI-aided protein engineering and design, focusing on directed evolution that uses AI approaches to efficiently construct mutant libraries. Additionally, recent works on AI-aided pathway design strategies, including template-based and template-free approaches, are discussed.
CURRENT OPINION IN BIOTECHNOLOGY
(2022)
Article
Engineering, Industrial
Ling Chunyan, Lei Jingzhe, Kuo Way
Summary: This paper proposes an effective method to mitigate computational burden in reliability-based design optimization of modular systems. The method tackles coupling effects of modules using the individual module feasible approach and builds an alternative model for the probabilistic constraint function using Bayesian-inference-based support vector machine. The optimal decision scheme is obtained by solving the formulated conventional RBDO using the alternative model.
RELIABILITY ENGINEERING & SYSTEM SAFETY
(2022)
Article
Chemistry, Analytical
Gangpei Cai, Yuxin Huang, Bailiang Chen, Yuemin Shen, Xiaolu Shi, Bo Peng, Shengli Mi, Jiajun Huang
Summary: Modular integration of functional components on the chip and real-time alteration in the force direction of droplets optimizes centrifugal microfluidic systems and allows for passive components, compact modules, and high-throughput control. A novel centrifugal microfluidic system is introduced to improve chip control freedom and accuracy while facilitating the design and addition of passive functional components. The system is modularized to shorten design and optimization cycles and achieve chip reusability and multi-threaded control. Testing the nucleic acid purification and detection reactions on the modular chip verifies its feasibility for high-throughput nucleic acid screening.
Article
Engineering, Aerospace
Zijie Chen, Chuang Shi, Hongwei Guo, Rongqiang Liu, Zongquan Deng
Summary: This paper presents the design and study of a new type of planar antenna support mechanism. The mechanism offers advantages of good geometric stability and modular expansion. An equivalent model is established to verify its working performance, and the mechanism parameters are designed and optimized accordingly. A scaled-down prototype is developed to test the deployment performance.
AEROSPACE SCIENCE AND TECHNOLOGY
(2022)
Article
Engineering, Mechanical
Anubhav Dogra, Srikant Sekhar Padhee, Ekta Singla
Summary: The paper discusses the application of modular and reconfigurable manipulators in the service sector, focusing on customization. A new architectural design is proposed to achieve optimal reconfigurability for unconventional parameters, along with the development of a lighter and easier-to-connect modular design. Through assembling traditional and unconventional configurations, as well as conducting worst torque analyses, strategies for assembly combinations are provided.
JOURNAL OF MECHANICAL DESIGN
(2021)
Article
Chemistry, Applied
Claudia Amorim, Sara C. Silverio, Raquel F. S. Goncalves, Ana C. Pinheiro, Soraia Silva, Elisabete Coelho, Manuel A. Coimbra, Kristala L. J. Prather, Ligia R. Rodrigues
CARBOHYDRATE POLYMERS
(2019)
Article
Multidisciplinary Sciences
Jason T. Boock, Adam J. E. Freedman, Geoffrey A. Tompsett, Sarah K. Muse, Audrey J. Allen, Luke A. Jackson, Bernardo Castro-Dominguez, Michael T. Timko, Kristala L. J. Prather, Janelle R. Thompson
NATURE COMMUNICATIONS
(2019)
Article
Biochemical Research Methods
Aditya M. Kunjapur, Kristala L. J. Prather
ACS SYNTHETIC BIOLOGY
(2019)
Article
Biotechnology & Applied Microbiology
Kristina Haslinger, Kristala L. J. Prather
MICROBIAL CELL FACTORIES
(2020)
Article
Biochemical Research Methods
Christina Dinh, Xingyu Chen, Kristala L. J. Prather
ACS SYNTHETIC BIOLOGY
(2020)
Review
Biochemical Research Methods
Christina V. Dinh, Kristala L. J. Prather
CURRENT OPINION IN BIOTECHNOLOGY
(2020)
Article
Biotechnology & Applied Microbiology
Wesley Leoricy Marques, Lisa A. Anderson, Luis Sandoval, Michael A. Hicks, Kristala L. J. Prather
ENZYME AND MICROBIAL TECHNOLOGY
(2020)
Article
Biotechnology & Applied Microbiology
Kevin J. Fox, Kristala L. J. Prather
JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY
(2020)
Review
Biochemical Research Methods
Yuexuan Zu, Kristala L. J. Prather, Gregory Stephanopoulos
CURRENT OPINION IN BIOTECHNOLOGY
(2020)
Article
Biotechnology & Applied Microbiology
Kevin J. Fox, Kristala L. J. Prather
CURRENT OPINION IN CHEMICAL ENGINEERING
(2020)
Article
Biochemical Research Methods
Ana Vila-Santa, M. Ahsanul Islam, Frederico C. Ferreira, Kristala L. J. Prather, Nuno P. Mira
Summary: This study explores the potential of producing levulinic acid using microbial systems by assembling candidate biosynthetic pathways in Escherichia coli or Saccharomyces cerevisiae, based on computational tools and manual curation. Five pathways were identified as best candidates out of hundreds screened, showcasing the future potential of microbial production for value-added chemicals.
ACS SYNTHETIC BIOLOGY
(2021)
Review
Microbiology
Ana Vila-Santa, Fernao C. Mendes, Frederico C. Ferreira, Kristala L. J. Prather, Nuno P. Mira
Summary: Microbially produced carboxylic acids have the potential to replace oil-derived chemicals for more sustainable industrial processes. However, implementing this approach for certain carboxylic acids may be difficult, requiring the use of synthetic biology and computational tools to develop new production pathways.
Article
Agriculture, Multidisciplinary
Xiaoqiang Ma, Hong Liang, Qiuchi Pan, Kristala L. J. Prather, Anthony J. Sinskey, Gregory Stephanopoulos, Kang Zhou
Summary: Engineering microbes to produce isoprenoids faces limitations due to competition between product formation and cell growth. This study optimized the utilization pathway of isopentenols in Escherichia coli and successfully synthesized high yields of lycopene, beta-carotene, and R-(-)-linalool. These findings are important for cost-effective production of agri-food isoprenoids.
JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY
(2022)
Article
Multidisciplinary Sciences
May N. Taw, Jason T. Boock, Belen Sotomayor, Daniel Kim, Mark A. Rocco, Dujduan Waraho-Zhmayev, Matthew P. DeLisa
Summary: The study suggests that the Tat translocase may use molecular chaperones to monitor the conformational status of its substrates, with the TatB component playing a key role in sensing the folding state of Tat substrates.
SCIENTIFIC REPORTS
(2022)
Article
Biotechnology & Applied Microbiology
Jennifer Kaczmarek Nash, Kristala L. J. Prather
Summary: Recent work in biosensors has investigated the potential of high throughput searches through genetic libraries. However, similar to limitations in microbial systems, biosensors can face obstacles in their application. This study characterized a transcription-factor biosensor and explored its response to different MIOX homologs, finding that modifications to circuit architecture and culture conditions reduced variation and improved its application for separating closely related MIOX variants.
JOURNAL OF INDUSTRIAL MICROBIOLOGY & BIOTECHNOLOGY
(2023)
Review
Biochemical Research Methods
Pei-Ru Chen, Peng-Fei Xia
Summary: Carbon dioxide plays a crucial role in mitigating global climate change and supporting life on Earth. Synthetic biology and metabolic engineering offer a promising approach to enhance CO2 fixation by combining the advantages of autotrophic and heterotrophic organisms. This article reviews the current progress in constructing synthetic CO2 fixation pathways, discusses the underlying design principles and challenges, and provides insights into the future of carbon recycling through engineered synthetic carbon fixation pathways.
CURRENT OPINION IN BIOTECHNOLOGY
(2024)
