{"title":"Phagosome-Bacteria Interactions from the Bottom Up.","authors":"Darshan M Sivaloganathan, Mark P Brynildsen","doi":"10.1146/annurev-chembioeng-090920-015024","DOIUrl":"https://doi.org/10.1146/annurev-chembioeng-090920-015024","url":null,"abstract":"<p><p>When attempting to propagate infections, bacterial pathogens encounter phagocytes that encase them in vacuoles called phagosomes. Within phagosomes, bacteria are bombarded with a plethora of stresses that often lead to their demise. However, pathogens have evolved numerous strategies to counter those host defenses and facilitate survival. Given the importance of phagosome-bacteria interactions to infection outcomes, they represent a collection of targets that are of interest for next-generation antibacterials. To facilitate such therapies, different approaches can be employed to increase understanding of phagosome-bacteria interactions, and these can be classified broadly as top down (starting from intact systems and breaking down the importance of different parts) or bottom up (developing a knowledge base on simplified systems and progressively increasing complexity). Here we review knowledge of phagosomal compositions and bacterial survival tactics useful for bottom-up approaches, which are particularly relevant for the application of reaction engineering to quantify and predict the time evolution of biochemical species in these death-dealing vacuoles. Further, we highlight how understanding in this area can be built up through the combination of immunology, microbiology, and engineering.</p>","PeriodicalId":8234,"journal":{"name":"Annual review of chemical and biomolecular engineering","volume":" ","pages":"309-331"},"PeriodicalIF":8.4,"publicationDate":"2021-06-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25529077","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":"Engineering Advances in Spray Drying for Pharmaceuticals.","authors":"John M Baumann, Molly S Adam, Joel D Wood","doi":"10.1146/annurev-chembioeng-091720-034106","DOIUrl":"https://doi.org/10.1146/annurev-chembioeng-091720-034106","url":null,"abstract":"<p><p>Spray drying is a versatile technology that has been applied widely in the chemical, food, and, most recently, pharmaceutical industries. This review focuses on engineering advances and the most significant applications of spray drying for pharmaceuticals. An in-depth view of the process and its use is provided for amorphous solid dispersions, a major, growing drug-delivery approach. Enhanced understanding of the relationship of spray-drying process parameters to final product quality attributes has made robust product development possible to address a wide range of pharmaceutical problem statements. Formulation and process optimization have leveraged the knowledge gained as the technology has matured, enabling improved process development from early feasibility screening through commercial applications. Spray drying's use for approved small-molecule oral products is highlighted, as are emerging applications specific to delivery of biologics and non-oral delivery of dry powders. Based on the changing landscape of the industry, significant future opportunities exist for pharmaceutical spray drying.</p>","PeriodicalId":8234,"journal":{"name":"Annual review of chemical and biomolecular engineering","volume":" ","pages":"217-240"},"PeriodicalIF":8.4,"publicationDate":"2021-06-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25529079","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}
Siddarth H Krishna, Casey B Jones, Rajamani Gounder
{"title":"Dynamic Interconversion of Metal Active Site Ensembles in Zeolite Catalysis.","authors":"Siddarth H Krishna, Casey B Jones, Rajamani Gounder","doi":"10.1146/annurev-chembioeng-092120-010920","DOIUrl":"https://doi.org/10.1146/annurev-chembioeng-092120-010920","url":null,"abstract":"<p><p>Catalysis science is founded on understanding the structure, number, and reactivity of active sites. Kinetic models that consider active sites to be static and noninteracting entities are routinely successful in describing the behavior of heterogeneous catalysts. Yet, active site ensembles often restructure in response to their external environment and even during steady-state catalytic turnover, sometimes requiring non-mean-field kinetic treatments to describe distance-dependent interactions among sites. Such behavior is being recognized more frequently in modern catalysis research, with the advent of experimental methods to quantify turnover rates with increasing precision, an expanding arsenal of operando characterization tools, and computational descriptions of atomic structure and motion at chemical potentials and timescales increasingly relevant to reaction conditions. This review focuses on dynamic changes to metal active site ensembles on zeolite supports, which are silica-based crystalline materials substituted with Al that generate binding sites for isolated and low-nuclearity metal site ensembles. Metal sites can become solvated and mobilized during reaction, facilitating interactions among sites that change their nuclearity and function. Such intersite communication can be regulated by the zeolite support, resulting in non-single-site and potentially non-mean-field kinetic behavior arising from mechanisms of catalytic action that combine elements of those canonically associated with homogeneous and heterogeneous catalysis.We discuss recent literature examples that document dynamic active site behavior in metal-zeolites and outline methodologies to identify and interpret such behavior. We conclude with our outlook on future research directions to develop this evolving branch of catalysis science and harness it for practical applications.</p>","PeriodicalId":8234,"journal":{"name":"Annual review of chemical and biomolecular engineering","volume":" ","pages":"115-136"},"PeriodicalIF":8.4,"publicationDate":"2021-06-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25567336","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}
R Bharath Venkatesh, Neha Manohar, Yiwei Qiang, Haonan Wang, Hong Huy Tran, Baekmin Q Kim, Anastasia Neuman, Tian Ren, Zahra Fakhraai, Robert A Riggleman, Kathleen J Stebe, Kevin Turner, Daeyeon Lee
{"title":"Polymer-Infiltrated Nanoparticle Films Using Capillarity-Based Techniques: Toward Multifunctional Coatings and Membranes.","authors":"R Bharath Venkatesh, Neha Manohar, Yiwei Qiang, Haonan Wang, Hong Huy Tran, Baekmin Q Kim, Anastasia Neuman, Tian Ren, Zahra Fakhraai, Robert A Riggleman, Kathleen J Stebe, Kevin Turner, Daeyeon Lee","doi":"10.1146/annurev-chembioeng-101220-093836","DOIUrl":"https://doi.org/10.1146/annurev-chembioeng-101220-093836","url":null,"abstract":"<p><p>Polymer-infiltrated nanoparticle films (PINFs) are a new class of nanocomposites that offer synergistic properties and functionality derived from unusually high fractions of nanomaterials. Recently, two versatile techniques,capillary rise infiltration (CaRI) and solvent-driven infiltration of polymer (SIP), have been introduced that exploit capillary forces in films of densely packed nanoparticles. In CaRI, a highly loaded PINF is produced by thermally induced wicking of polymer melt into the nanoparticle packing pores. In SIP, exposure of a polymer-nanoparticle bilayer to solvent vapor atmosphere induces capillary condensation of solvent in the pores of nanoparticle packing, leading to infiltration of polymer into the solvent-filled pores. CaRI/SIP PINFs show superior properties compared with polymer nanocomposite films made using traditional methods, including superb mechanical properties, thermal stability, heat transfer, and optical properties. This review discusses fundamental aspects of the infiltration process and highlights potential applications in separations, structural coatings, and polymer upcycling-a process to convert polymer wastes into useful chemicals.</p>","PeriodicalId":8234,"journal":{"name":"Annual review of chemical and biomolecular engineering","volume":" ","pages":"411-437"},"PeriodicalIF":8.4,"publicationDate":"2021-06-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"39071348","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}
Nikolay V Ryzhkov, Konstantin G Nikolaev, Artemii S Ivanov, Ekaterina V Skorb
{"title":"Infochemistry and the Future of Chemical Information Processing.","authors":"Nikolay V Ryzhkov, Konstantin G Nikolaev, Artemii S Ivanov, 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":" ","pages":"63-95"},"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}
Chowdhury Ashraf, Nisarg Joshi, David A C Beck, Jim Pfaendtner
{"title":"Data Science in Chemical Engineering: Applications to Molecular Science.","authors":"Chowdhury Ashraf, Nisarg Joshi, David A C Beck, 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":" ","pages":"15-37"},"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, 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":" ","pages":"543-571"},"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}
Cynthia Ni, Christina V Dinh, Kristala L J Prather
{"title":"Dynamic Control of Metabolism.","authors":"Cynthia Ni, Christina V Dinh, 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":" ","pages":"519-541"},"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":"Nature-Inspired Chemical Engineering for Process Intensification.","authors":"Marc-Olivier Coppens","doi":"10.1146/annurev-chembioeng-060718-030249","DOIUrl":"https://doi.org/10.1146/annurev-chembioeng-060718-030249","url":null,"abstract":"<p><p>A nature-inspired solution (NIS) methodology is proposed as a systematic platform for innovation and to inform transformative technology required to address Grand Challenges, including sustainable development. Scalability, efficiency, and resilience are essential to nature, as they are to engineering processes. They are achieved through underpinning fundamental mechanisms, which are grouped as recurring themes in the NIS approach: hierarchical transport networks, force balancing, dynamic self-organization, and ecosystem properties. To leverage these universal mechanisms, and incorporate them effectively into engineering design, adaptations may be needed to accommodate the different contexts of nature and engineering applications. Nature-inspired chemical engineering takes advantage of the NIS methodology for process intensification, as demonstrated here in fluidization, catalysis, fuel cell engineering, and membrane separations, where much higher performance is achieved by rigorously employing concepts optimized in nature. The same approach lends itself to other applications, from biomedical engineering to information technology and architecture.</p>","PeriodicalId":8234,"journal":{"name":"Annual review of chemical and biomolecular engineering","volume":" ","pages":"187-215"},"PeriodicalIF":8.4,"publicationDate":"2021-06-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"25549121","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}
Nick Fackler, Björn D Heijstra, Blake J Rasor, Hunter Brown, Jacob Martin, Zhuofu Ni, Kevin M Shebek, Rick R Rosin, Séan D Simpson, Keith E Tyo, Richard J Giannone, Robert L Hettich, Timothy J Tschaplinski, Ching Leang, Steven D Brown, Michael C Jewett, Michael Köpke
{"title":"Stepping on the Gas to a Circular Economy: Accelerating Development of Carbon-Negative Chemical Production from Gas Fermentation.","authors":"Nick Fackler, Björn D Heijstra, Blake J Rasor, Hunter Brown, Jacob Martin, Zhuofu Ni, Kevin M Shebek, Rick R Rosin, Séan D Simpson, Keith E Tyo, Richard J Giannone, Robert L Hettich, Timothy J Tschaplinski, Ching Leang, Steven D Brown, Michael C Jewett, 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":" ","pages":"439-470"},"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}