Annual review of chemical and biomolecular engineering最新文献

{"title":"Data Science in Chemical Engineering: Applications to Molecular Science.","authors":"Chowdhury Ashraf,&nbsp;Nisarg Joshi,&nbsp;David A C Beck,&nbsp;Jim Pfaendtner","doi":"10.1146/annurev-chembioeng-101220-102232","DOIUrl":"https://doi.org/10.1146/annurev-chembioeng-101220-102232","url":null,"abstract":"<p><p>Chemical engineering is being rapidly transformed by the tools of data science. On the horizon, artificial intelligence (AI) applications will impact a huge swath of our work, ranging from the discovery and design of new molecules to operations and manufacturing and many areas in between. Early adoption of data science, machine learning, and early examples of AI in chemical engineering has been rich with examples of molecular data science-the application tools for molecular discovery and property optimization at the atomic scale. We summarize key advances in this nascent subfield while introducing molecular data science for a broad chemical engineering readership. We introduce the field through the concept of a molecular data science life cycle and discuss relevant aspects of five distinct phases of this process: creation of curated data sets, molecular representations, data-driven property prediction, generation of new molecules, and feasibility and synthesizability considerations.</p>","PeriodicalId":8234,"journal":{"name":"Annual review of chemical and biomolecular engineering","volume":null,"pages":null},"PeriodicalIF":8.4,"publicationDate":"2021-06-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25469451","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Reactive Flows in Porous Media: Challenges in Theoretical and Numerical Methods.","authors":"Anthony J C Ladd,&nbsp;Piotr Szymczak","doi":"10.1146/annurev-chembioeng-092920-102703","DOIUrl":"https://doi.org/10.1146/annurev-chembioeng-092920-102703","url":null,"abstract":"<p><p>We review theoretical and computational research, primarily from the past 10 years, addressing the flow of reactive fluids in porous media. The focus is on systems where chemical reactions at the solid-fluid interface cause dissolution of the surrounding porous matrix, creating nonlinear feedback mechanisms that can often lead to greatly enhanced permeability. We discuss insights into the evolution of geological forms that can be inferred from these feedback mechanisms, as well as some geotechnical applications such as enhanced oil recovery, hydraulic fracturing, and carbon sequestration. Until recently, most practical applications of reactive transport have been based on Darcy-scale modeling, where averaged equations for the flow and reactant transport are solved. We summarize the successes and limitations of volume averaging, which leads to Darcy-scale equations, as an introduction to pore-scale modeling. Pore-scale modeling is computationally intensive but offers new insights as well as tests of averaging theories and pore-network models. We include recent research devoted to validation of pore-scale simulations, particularly the use of visual observations from microfluidic experiments.</p>","PeriodicalId":8234,"journal":{"name":"Annual review of chemical and biomolecular engineering","volume":null,"pages":null},"PeriodicalIF":8.4,"publicationDate":"2021-06-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25531603","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Dynamic Control of Metabolism.","authors":"Cynthia Ni,&nbsp;Christina V Dinh,&nbsp;Kristala L J Prather","doi":"10.1146/annurev-chembioeng-091720-125738","DOIUrl":"https://doi.org/10.1146/annurev-chembioeng-091720-125738","url":null,"abstract":"<p><p>Metabolic engineering reprograms cells to synthesize value-added products. In doing so, endogenous genes are altered and heterologous genes can be introduced to achieve the necessary enzymatic reactions. Dynamic regulation of metabolic flux is a powerful control scheme to alleviate and overcome the competing cellular objectives that arise from the introduction of these production pathways. This review explores dynamic regulation strategies that have demonstrated significant production benefits by targeting the metabolic node corresponding to a specific challenge. We summarize the stimulus-responsive control circuits employed in these strategies that determine the criterion for actuating a dynamic response and then examine the points of control that couple the stimulus-responsive circuit to a shift in metabolic flux.</p>","PeriodicalId":8234,"journal":{"name":"Annual review of chemical and biomolecular engineering","volume":null,"pages":null},"PeriodicalIF":8.4,"publicationDate":"2021-06-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25533031","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Infochemistry and the Future of Chemical Information Processing.","authors":"Nikolay V Ryzhkov,&nbsp;Konstantin G Nikolaev,&nbsp;Artemii S Ivanov,&nbsp;Ekaterina V Skorb","doi":"10.1146/annurev-chembioeng-122120-023514","DOIUrl":"https://doi.org/10.1146/annurev-chembioeng-122120-023514","url":null,"abstract":"<p><p>Nowadays, information processing is based on semiconductor (e.g., silicon) devices. Unfortunately, the performance of such devices has natural limitations owing to the physics of semiconductors. Therefore, the problem of finding new strategies for storing and processing an ever-increasing amount of diverse data is very urgent. To solve this problem, scientists have found inspiration in nature, because living organisms have developed uniquely productive and efficient mechanisms for processing and storing information. We address several biological aspects of information and artificial models mimicking corresponding bioprocesses. For instance, we review the formation of synchronization patterns and the emergence of order out of chaos in model chemical systems. We also consider molecular logic and ion fluxes as information carriers. Finally, we consider recent progress in infochemistry, a new direction at the interface of chemistry, biology, and computer science, considering unconventional methods of information processing.</p>","PeriodicalId":8234,"journal":{"name":"Annual review of chemical and biomolecular engineering","volume":null,"pages":null},"PeriodicalIF":8.4,"publicationDate":"2021-06-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38849714","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Modeling Food Particle Systems: A Review of Current Progress and Challenges.","authors":"Lennart Fries","doi":"10.1146/annurev-chembioeng-121820-081524","DOIUrl":"https://doi.org/10.1146/annurev-chembioeng-121820-081524","url":null,"abstract":"<p><p>For many years, food engineers have attempted to describe physical phenomena such as heat and mass transfer in food via mathematical models. Still, the impact and benefits of computer-aided engineering are less established in food than in most other industries today. Complexity in the structure and composition of food matrices are largely responsible for this gap. During processing of food, its temperature, moisture, and structure can change continuously, along with its physical properties. We summarize the knowledge foundation, recent progress, and remaining limitations in modeling food particle systems in four relevant areas: flowability, size reduction, drying, and granulation and agglomeration. Our goal is to enable researchers in academia and industry dealing with food powders to identify approaches to address their challenges with adequate model systems or through structural and compositional simplifications. With advances in computer simulation capacity, detailed particle-scale models are now available for many applications. Here, we discuss aspects that require further attention, especially related to physics-based contact models for discrete-element models of food particle systems.</p>","PeriodicalId":8234,"journal":{"name":"Annual review of chemical and biomolecular engineering","volume":null,"pages":null},"PeriodicalIF":8.4,"publicationDate":"2021-06-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25520083","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Stepping on the Gas to a Circular Economy: Accelerating Development of Carbon-Negative Chemical Production from Gas Fermentation.","authors":"Nick Fackler,&nbsp;Björn D Heijstra,&nbsp;Blake J Rasor,&nbsp;Hunter Brown,&nbsp;Jacob Martin,&nbsp;Zhuofu Ni,&nbsp;Kevin M Shebek,&nbsp;Rick R Rosin,&nbsp;Séan D Simpson,&nbsp;Keith E Tyo,&nbsp;Richard J Giannone,&nbsp;Robert L Hettich,&nbsp;Timothy J Tschaplinski,&nbsp;Ching Leang,&nbsp;Steven D Brown,&nbsp;Michael C Jewett,&nbsp;Michael Köpke","doi":"10.1146/annurev-chembioeng-120120-021122","DOIUrl":"https://doi.org/10.1146/annurev-chembioeng-120120-021122","url":null,"abstract":"<p><p>Owing to rising levels of greenhouse gases in our atmosphere and oceans, climate change poses significant environmental, economic, and social challenges globally. Technologies that enable carbon capture and conversion of greenhouse gases into useful products will help mitigate climate change by enabling a new circular carbon economy. Gas fermentation usingcarbon-fixing microorganisms offers an economically viable and scalable solution with unique feedstock and product flexibility that has been commercialized recently. We review the state of the art of gas fermentation and discuss opportunities to accelerate future development and rollout. We discuss the current commercial process for conversion of waste gases to ethanol, including the underlying biology, challenges in process scale-up, and progress on genetic tool development and metabolic engineering to expand the product spectrum. We emphasize key enabling technologies to accelerate strain development for acetogens and other nonmodel organisms.</p>","PeriodicalId":8234,"journal":{"name":"Annual review of chemical and biomolecular engineering","volume":null,"pages":null},"PeriodicalIF":8.4,"publicationDate":"2021-06-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"38893887","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Applications of Machine and Deep Learning in Adaptive Immunity.","authors":"Margarita Pertseva,&nbsp;Beichen Gao,&nbsp;Daniel Neumeier,&nbsp;Alexander Yermanos,&nbsp;Sai T Reddy","doi":"10.1146/annurev-chembioeng-101420-125021","DOIUrl":"https://doi.org/10.1146/annurev-chembioeng-101420-125021","url":null,"abstract":"<p><p>Adaptive immunity is mediated by lymphocyte B and T cells, which respectively express a vast and diverse repertoire of B cell and T cell receptors and, in conjunction with peptide antigen presentation through major histocompatibility complexes (MHCs), can recognize and respond to pathogens and diseased cells. In recent years, advances in deep sequencing have led to a massive increase in the amount of adaptive immune receptor repertoire data; additionally, proteomics techniques have led to a wealth of data on peptide-MHC presentation. These large-scale data sets are now making it possible to train machine and deep learning models, which can be used to identify complex and high-dimensional patterns in immune repertoires. This article introduces adaptive immune repertoires and machine and deep learning related to biological sequence data and then summarizes the many applications in this field, which span from predicting the immunological status of a host to the antigen specificity of individual receptors and the engineering of immunotherapeutics.</p>","PeriodicalId":8234,"journal":{"name":"Annual review of chemical and biomolecular engineering","volume":null,"pages":null},"PeriodicalIF":8.4,"publicationDate":"2021-06-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25590351","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Bottom-Up Synthesis of Artificial Cells: Recent Highlights and Future Challenges.","authors":"Ivan Ivanov,&nbsp;Sebastián López Castellanos,&nbsp;Severo Balasbas,&nbsp;Lado Otrin,&nbsp;Nika Marušič,&nbsp;Tanja Vidaković-Koch,&nbsp;Kai Sundmacher","doi":"10.1146/annurev-chembioeng-092220-085918","DOIUrl":"https://doi.org/10.1146/annurev-chembioeng-092220-085918","url":null,"abstract":"<p><p>The bottom-up approach in synthetic biology aims to create molecular ensembles that reproduce the organization and functions of living organisms and strives to integrate them in a modular and hierarchical fashion toward the basic unit of life-the cell-and beyond. This young field stands on the shoulders of fundamental research in molecular biology and biochemistry, next to synthetic chemistry, and, augmented by an engineering framework, has seen tremendous progress in recent years thanks to multiple technological and scientific advancements. In this timely review of the research over the past decade, we focus on three essential features of living cells: the ability to self-reproduce via recursive cycles of growth and division, the harnessing of energy to drive cellular processes, and the assembly of metabolic pathways. In addition, we cover the increasing efforts to establish multicellular systems via different communication strategies and critically evaluate the potential applications.</p>","PeriodicalId":8234,"journal":{"name":"Annual review of chemical and biomolecular engineering","volume":null,"pages":null},"PeriodicalIF":8.4,"publicationDate":"2021-06-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39071350","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Phenolic Profile and Biological Properties of Momordica charantia","authors":"Z. Khalid, S. M. Hassan, Shahzad Sharif Mughal, S. K. Hassan, Huma Hassan","doi":"10.11648/J.CBE.20210601.13","DOIUrl":"https://doi.org/10.11648/J.CBE.20210601.13","url":null,"abstract":"M. charantia is an important medicinal plant belongs to family cucurbitaceae. It originates from India, Malasiya and is widely spread all over tropical, subtropical and warm temperate regions of the world. This research work has been designed to evaluate the antioxidant, antimicrobial and toxicological potential of M. charantia. The antifungal and antioxidant components of M. charantia leaves, seeds and peels were extracted by using four solvent systems (80% methanol, 80% ethanol, 100% methanol and 100% ethanol) andleaves presented maximum extract yield (22.7 g/100g DW) in 80% methanolic solvent system. Phytochemical analysis of M. Charantia leaves, seeds and peels extracts performed in terms of total phenolic and total flavonoid contents, showed that 80% methanolic leaves extract offered highest total phenolic contents (47.1 mg GAE/g DW), whereas80% ethanolic leaves gave maximum total flavonoid contents (67.3 mg CE/g DW). The phenolic contents were also analysed by HPLC. Antioxidant activity was determined by DPPH radical scavenging activity and measure of reducing power. Results revealed that 80% methanolic leaves extract showed highest radical scavenging activity and reducing potential. Antimicrobial activity of M. charantia leaves, seeds and peels was investigated by Disc Diffusion Method and Minimum Inhibitory Concentration (MIC). Results showed that 80% methanolic extract of leaves exhibited highest antibacterial and antifungal potential against P. multocida (30 mm DIZ) and A. paraciticus (28 mm DIZ), respectively. Cytotoxicity analysis was performed on BHK-21 cell by adopting the MTT assay. The cytotoxicity activity of the 80% methanolic extract of leaves was evaluated by noticing the cell survival percentage (53.4%). Overall results of the present study showed that 80% methanolic leaves extracts of M. charantia possesses very good antioxidant, antimicrobial and cytotoxic properties.","PeriodicalId":8234,"journal":{"name":"Annual review of chemical and biomolecular engineering","volume":null,"pages":null},"PeriodicalIF":8.4,"publicationDate":"2021-03-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"89240171","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

{"title":"Resistance Rate Distribution of MDR-TB Among Pulmonary Tuberculosis Patients Attending NAUTH and St Patrick’s Hospital Mile 4 Abakiliki in Southeast Nigeria","authors":"Chinenye Esther Okoro-Ani, C. Akujobi, I. Udoh, S. Ibhawaegbele, C. Ezema, U. Ezeugwu, O. Dozie-Nwakile, A. Okpe","doi":"10.11648/J.CBE.20210601.11","DOIUrl":"https://doi.org/10.11648/J.CBE.20210601.11","url":null,"abstract":"Tuberculosis, one of the oldest recorded human afflictions, is still one of the biggest killers among the infectious diseases, despite the worldwide use of a live attenuated vaccine and several antibiotics. This study was designed to assess the resistance rate distribution of MDR-TB among pulmonary tuberculosis patients attending Nnamdi Azikiewe University Teaching Hospital (NAUTH) Nnewi and St Patrick’s Hospital Mile 4 Abakaliki in the Southeast Nigeria. Patients with persistent cough for over two weeks were screened by Ziehl-Neelsen (ZN) technique for the presence of acid fast bacilli (AFB) in their sputum and a total of 103 patients with AFB positive sputum samples were recruited. The positive sputum samples were subjected to Xpert MTB/RIF assay (GeneXpert®, Cepheid USA) and culture on Lowestein Jensen medium for 42 days at 37°C. Drug susceptibility testing was done on the isolates using the nitrate reduction assay (NRA). Xpert MTB/RIF assay detected MTB in 83 (80.6%) samples out of which 45 (67.2%) were rifampicin resistant. Sixty-seven (80.7%) of the isolates were resistant to at least one of the first-line drugs. Primary resistance was 91% while 19.4%, 35.8%, 22.4% and 22.4% of the isolates were resistant to one, two, three and four drugs respectively. Isoniazid had the highest rate of resistance (57.8%) while Ethambutol had the least (34.9%) and 30 (44.8%) of the resistant isolates were MDR. Smoking (P=.002), gender (P=.002) and history of TB treatment (P=.012) were significantly associated with drug resistance. Educational status was significantly associated with MDR-TB (P=.020). NAUTH and St Patrick’s hospital had MDR-TB rates of 38.9% and 46.9% respectively. The findings of this study indicate high prevalence of MDR-TB among patients with pulmonary TB in the study sites and this portrays a menace to adequate TB control. Prompt diagnosis of TB, adequate patient compliance to therapy and increased awareness and mass education is recommended.","PeriodicalId":8234,"journal":{"name":"Annual review of chemical and biomolecular engineering","volume":null,"pages":null},"PeriodicalIF":8.4,"publicationDate":"2021-03-22","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"83928750","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":2,"RegionCategory":"工程技术","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}