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- Volume 12, 2021
Annual Review of Chemical and Biomolecular Engineering - Volume 12, 2021
Volume 12, 2021
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Autobiography of Stanley I. Sandler
Vol. 12 (2021), pp. 1–13More LessI review my career from its academic beginning to my recent retirement. I grew up and studied chemical engineering in New York City. My initial failure to understand thermodynamics the way it had been taught, evidenced by the difficulty I had when starting graduate school, led me years later to write a textbook on the subject that is now in a fifth edition, in addition to other books I have written. My research areas have included molecular simulation, statistical- and quantum mechanical–based methods, and a variety of experimental thermodynamic measurements. In addition, I have been a consultant in traditional chemical engineering areas, as well in nontraditional areas, such as assisting in the design of a heat shield for interplanetary exploration, the destruction of armed chemical weapons, and the cleanup of nuclear weapons production facilities.
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Data Science in Chemical Engineering: Applications to Molecular Science
Vol. 12 (2021), pp. 15–37More LessChemical 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.
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Applications of Machine and Deep Learning in Adaptive Immunity
Vol. 12 (2021), pp. 39–62More LessAdaptive 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.
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Infochemistry and the Future of Chemical Information Processing
Vol. 12 (2021), pp. 63–95More LessNowadays, 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.
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Modeling Food Particle Systems: A Review of Current Progress and Challenges
Vol. 12 (2021), pp. 97–113More LessFor 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.
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Dynamic Interconversion of Metal Active Site Ensembles in Zeolite Catalysis
Vol. 12 (2021), pp. 115–136More LessCatalysis 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.
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Characterization of Nanoporous Materials
Vol. 12 (2021), pp. 137–162More LessDetailed analysis of textural properties, e.g., pore size and connectivity, of nanoporous materials is essential to identify correlations of these properties with the performance of gas storage, separation, and catalysis processes. The advances in developing nanoporous materials with uniform, tailor-made pore structures, including the introduction of hierarchical pore systems, offer huge potential for these applications. Within this context, major progress has been made in understanding the adsorption and phase behavior of confined fluids and consequently in physisorption characterization. This enables reliable pore size, volume, and network connectivity analysis using advanced, high-resolution experimental protocols coupled with advanced methods based on statistical mechanics, such as methods based on density functional theory and molecular simulation. If macro-pores are present, a combination of adsorption and mercury porosimetry can be useful. Hence, some important recent advances in understanding the mercury intrusion/extrusion mechanism are discussed. Additionally, some promising complementary techniques for characterization of porous materials immersed in a liquid phase are introduced.
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Emerging Biomedical Applications Based on the Response of Magnetic Nanoparticles to Time-Varying Magnetic Fields
Vol. 12 (2021), pp. 163–185More LessMagnetic nanoparticles are of interest for biomedical applications because of their biocompatibility, tunable surface chemistry, and actuation using applied magnetic fields. Magnetic nanoparticles respond to time-varying magnetic fields via physical particle rotation or internal dipole reorientation, which can result in signal generation or conversion of magnetic energy to heat. This dynamic magnetization response enables their use as tracers in magnetic particle imaging (MPI), an emerging biomedical imaging modality in which signal is quantitative of tracer mass and there is no tissue background signal or signal attenuation. Conversion of magnetic energy to heat motivates use in nanoscale thermal cancer therapy, magnetic actuation of drug release, and rapid rewarming of cryopreserved organs. This review introduces basic concepts of magnetic nanoparticle response to time-varying magnetic fields and presents recent advances in the field, with an emphasis on MPI and conversion of magnetic energy to heat.
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Nature-Inspired Chemical Engineering for Process Intensification
Vol. 12 (2021), pp. 187–215More LessA 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.
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Engineering Advances in Spray Drying for Pharmaceuticals
Vol. 12 (2021), pp. 217–240More LessSpray 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.
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Predictive Platforms of Bond Cleavage and Drug Release Kinetics for Macromolecule–Drug Conjugates
Vol. 12 (2021), pp. 241–261More LessMacromolecule–drug conjugates (MDCs) occupy a critical niche in modern pharmaceuticals that deals with the assembly and combination of a macromolecular carrier, a drug cargo, and a linker toward the creation of effective therapeutics. Macromolecular carriers such as synthetic biocompatible polymers and proteins are often exploited for their inherent ability to improve drug circulation, prevent off-target drug cytotoxicity, and widen the therapeutic index of drugs. One of the most significant challenges in MDC design involves tuning their drug release kinetics to achieve high spatiotemporal precision. This level of control requires a thorough qualitative and quantitative understanding of the bond cleavage event. In this review, we highlight specific research findings that emphasize the importance of establishing a precise structure–function relationship for MDCs that can be used to predict their bond cleavage and drug release kinetic parameters.
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RNA Engineering for Public Health: Innovations in RNA-Based Diagnostics and Therapeutics
Vol. 12 (2021), pp. 263–286More LessRNA is essential for cellular function: From sensing intra- and extracellular signals to controlling gene expression, RNA mediates a diverse and expansive list of molecular processes. A long-standing goal of synthetic biology has been to develop RNA engineering principles that can be used to harness and reprogram these RNA-mediated processes to engineer biological systems to solve pressing global challenges. Recent advances in the field of RNA engineering are bringing this to fruition, enabling the creation of RNA-based tools to combat some of the most urgent public health crises. Specifically, new diagnostics using engineered RNAs are able to detect both pathogens and chemicals while generating an easily detectable fluorescent signal as an indicator. New classes of vaccines and therapeutics are also using engineered RNAs to target a wide range of genetic and pathogenic diseases. Here, we discuss the recent breakthroughs in RNA engineering enabling these innovations and examine how advances in RNA design promise to accelerate the impact of engineered RNA systems.
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Bottom-Up Synthesis of Artificial Cells: Recent Highlights and Future Challenges
Vol. 12 (2021), pp. 287–308More LessThe 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.
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Phagosome–Bacteria Interactions from the Bottom Up
Vol. 12 (2021), pp. 309–331More LessWhen 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.
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Solid-Binding Proteins: Bridging Synthesis, Assembly, and Function in Hybrid and Hierarchical Materials Fabrication
Vol. 12 (2021), pp. 333–357More LessThere is considerable interest in the development of hybrid organic–inorganic materials because of the potential for harvesting the unique capabilities that each system has to offer. Proteins are an especially attractive organic component owing to the high amount of chemical information encoded in their amino acid sequence, their amenability to molecular and computational (re)design, and the many structures and functions they specify. Genetic installation of solid-binding peptides (SBPs) within protein frameworks affords control over the position and orientation of adhesive and morphogenetic segments, and a path toward predictive synthesis and assembly of functional materials and devices, all while harnessing the built-in properties of the host scaffold. Here, we review the current understanding of the mechanisms through which SBPs bind to technologically relevant interfaces, with an emphasis on the variables that influence the process, and highlight the last decade of progress in the use of solid-binding proteins for hybrid and hierarchical materials synthesis.
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Wearable and Implantable Soft Bioelectronics: Device Designs and Material Strategies
Vol. 12 (2021), pp. 359–391More LessHigh-performance wearable and implantable devices capable of recording physiological signals and delivering appropriate therapeutics in real time are playing a pivotal role in revolutionizing personalized healthcare. However, the mechanical and biochemical mismatches between rigid, inorganic devices and soft, organic human tissues cause significant trouble, including skin irritation, tissue damage, compromised signal-to-noise ratios, and limited service time. As a result, profuse research efforts have been devoted to overcoming these issues by using flexible and stretchable device designs and soft materials. Here, we summarize recent representative research and technological advances for soft bioelectronics, including conformable and stretchable device designs, various types of soft electronic materials, and surface coating and treatment methods. We also highlight applications of these strategies to emerging soft wearable and implantable devices. We conclude with some current limitations and offer future prospects of this booming field.
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Tough Double Network Hydrogel and Its Biomedical Applications
Vol. 12 (2021), pp. 393–410More LessSoft and wet hydrogels have many similarities to biological tissues, though their mechanical fragility had been one of the biggest obstacles in biomedical applications. Studies and developments in double network (DN) hydrogels have elucidated how to create tough gels universally based on sacrificial bond principles and opened a path for biomedical application of hydrogels in regenerative medicine and artificial soft connective tissues, such as cartilage, tendon, and ligament, which endure high tension and compression. This review explores a universal toughening mechanism for and biomedical studies of DN hydrogels. Moreover, because the term sacrificial bonds has been mentioned often in studies of bone tissues, consisting of biomacromolecules and biominerals, recent studies of gel–biomineral composites to understand early-stage osteogenesis and to simulate bony sacrificial bonds are also summarized.
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Polymer-Infiltrated Nanoparticle Films Using Capillarity-Based Techniques: Toward Multifunctional Coatings and Membranes
Vol. 12 (2021), pp. 411–437More LessPolymer-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.
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Stepping on the Gas to a Circular Economy: Accelerating Development of Carbon-Negative Chemical Production from Gas Fermentation
Vol. 12 (2021), pp. 439–470More LessOwing 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.
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Storage of Carbon Dioxide in Saline Aquifers: Physicochemical Processes, Key Constraints, and Scale-Up Potential
Vol. 12 (2021), pp. 471–494More LessCO2 storage in saline aquifers offers a realistic means of achieving globally significant reductions in greenhouse gas emissions at the scale of billions of tonnes per year. We review insights into the processes involved using well-documented industrial-scale projects, supported by a range of laboratory analyses, field studies, and flow simulations. The main topics we address are (a) the significant physicochemical processes, (b) the factors limiting CO2 storage capacity, and (c) the requirements for global scale-up.Although CO2 capture and storage (CCS) technology can be considered mature and proven, it requires significant and rapid scale-up to meet the objectives of the Paris Climate Agreement. The projected growth in the number of CO2 injection wells required is significantly lower than the historic petroleum industry drill rates, indicating that decarbonization via CCS is a highly credible and affordable ambition for modern human society. Several technology developments are needed to reduce deployment costs and to stimulate widespread adoption of this technology, and these should focus on demonstration of long-term retention and safety of CO2 storage and development of smart ways of handling injection wells and pressure, cost-effective monitoring solutions, and deployment of CCS hubs with associated infrastructure.
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Liquid–Liquid Chromatography: Current Design Approaches and Future Pathways
Vol. 12 (2021), pp. 495–518More LessSince its first appearance in the 1960s, solid support–free liquid–liquid chromatography has played an ever-growing role in the field of natural products research. The use of the two phases of a liquid biphasic system, the mobile and stationary phases, renders the technique highly versatile and adaptable to a wide spectrum of target molecules, from hydrophobic to highly polar small molecules to proteins. Generally considered a niche technique used only for small-scale preparative separations, liquid–liquid chromatography currently lags far behind conventional liquid–solid chromatography and liquid–liquid extraction in process modeling and industrial acceptance. This review aims to expose a broader audience to this high-potential separation technique by presenting the wide variety of available operating modes and solvent systems as well as structured, model-based design approaches. Topics currently offering opportunities for further investigation are also addressed.
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Dynamic Control of Metabolism
Vol. 12 (2021), pp. 519–541More LessMetabolic 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.
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Reactive Flows in Porous Media: Challenges in Theoretical and Numerical Methods
Vol. 12 (2021), pp. 543–571More LessWe 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.
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Recent Developments in Solvent-Based Fluid Separations
Vol. 12 (2021), pp. 573–591More LessThe most important developments in solvent-based fluid separations, separations involving at least one fluid phase, are reviewed. After a brief introduction and discussion on general solvent trends observed in all fields of application, several specific fields are discussed. Important solvent trends include replacement of traditional molecular solvents by ionic liquids and deep eutectic solvents and, more recently, increasing discussion around bio-based solvents in some application fields. Furthermore, stimuli-responsive systems are discussed; the most significant developments in this field are seen for CO2-switchable and redox-responsive solvents. Discussed fields of application include hydrocarbons separations, carbon capture, biorefineries, and metals separations. For all but the hydrocarbons separations, newly reported electrochemically mediated separations seem to offer exciting new windows of opportunities.
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Crystal Structure Prediction Methods for Organic Molecules: State of the Art
Vol. 12 (2021), pp. 593–623More LessThe prediction of the crystal structures that a given organic molecule is likely to form is an important theoretical problem of significant interest for the pharmaceutical and agrochemical industries, among others. As evidenced by a series of six blind tests organized over the past 2 decades, methodologies for crystal structure prediction (CSP) have witnessed substantial progress and have now reached a stage of development where they can begin to be applied to systems of practical significance. This article reviews the state of the art in general-purpose methodologies for CSP, placing them within a common framework that highlights both their similarities and their differences. The review discusses specific areas that constitute the main focus of current research efforts toward improving the reliability and widening applicability of these methodologies, and offers some perspectives for the evolution of this technology over the next decade.
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Small-Scale Phenomena in Reactive Bubbly Flows: Experiments, Numerical Modeling, and Applications
Vol. 12 (2021), pp. 625–643More LessImproving the yield and selectivity of chemical reactions is one of the challenging tasks in paving the way for a more sustainable and climate-friendly economy. For the industrially highly relevant gas–liquid reactions, this can be achieved by tailoring the timescales of mixing to the requirements of the reaction. Although this has long been known for idealized reactors and time- and space-averaged processes, considerable progress has been made recently on the influence of local mixing processes. This progress has become possible through joint research between chemists, mathematicians, and engineers. We present the reaction systems with adjustable kinetics that have been developed, which are easy to handle and analyze. We show examples of how the selectivity of competitive-consecutive reactions can be controlled via local bubble wake structures. This is demonstrated for Taylor bubbles and bubbly flows under technical conditions. Highly resolvednumerical simulations confirm the importance of the bubble wake structure for the performance of a particular chemical reaction and indicate tremendous potential for future process improvements.
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