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AIChE J 2021 Mar 18;67(3):e17026. Epub 2020 Sep 18.

Department of Chemical and Biomolecular Engineering Penn Institute for Computational Science, University of Pennsylvania Philadelphia Philadelphia USA.

Research problems in the domains of physical, engineering, biological sciences often span multiple time and length scales, owing to the complexity of information transfer underlying mechanisms. Multiscale modeling (MSM) and high-performance computing (HPC) have emerged as indispensable tools for tackling such complex problems. We review the foundations, historical developments, and current paradigms in MSM. Read More

AIChE J 2021 Mar 14:e17250. Epub 2021 Mar 14.

Department of Chemical Engineering Massachusetts Institute of Technology Cambridge Massachusetts USA.

While facial coverings reduce the spread of SARS-CoV-2 by viral filtration, masks capable of viral inactivation by heating can provide a complementary method to limit transmission. Inspired by reverse-flow chemical reactors, we introduce a new virucidal face mask concept driven by the oscillatory flow of human breath. The governing heat and mass transport equations are solved to evaluate virus and CO transport. Read More

AIChE J 2021 Mar 7;67(3):e17101. Epub 2020 Nov 7.

Department of Chemical and Biomolecular Engineering North Carolina State University Raleigh North Carolina USA.

Determining the structure of the (oligomeric) intermediates that form during the self-assembly of amyloidogenic peptides is challenging because of their heterogeneous and dynamic nature. Thus, there is need for methodology to analyze the underlying molecular structure of these transient species. In this work, a combination of fluorescence quenching, photo-induced crosslinking (PIC) and molecular dynamics simulation was used to study the assembly of a synthetic amyloid-forming peptide, Aβ. Read More

AIChE J 2021 Jan 2;67(1):e17067. Epub 2020 Oct 2.

Department of Chemical Engineering and Chemistry, Micro Flow Chemistry and Process Technology Eindhoven University of Technology Eindhoven The Netherlands.

Liquid-phase adsorption has hardly been established in micro-flow, although this constitutes an industrially vital method for product separation. A micro-flow UV-photo isomerization process converts -cyclooctene partly into -cyclooctene, leaving an isomeric mixture. cyclooctene adsorption and thus separation was achieved in a fixed-bed micro-flow reactor, packed with AgNO/SiO powder, while the -isomer stays in the flow. Read More

AIChE J 2020 Mar 11;66(3). Epub 2019 Jun 11.

Department of Chemical Engineering, University of Michigan, Ann Arbor, Michigan.

Despite promising developments in computational tools, peptide-class II MHC (MHCII) binding predictors continue to lag behind their peptide-class I MHC counterparts. Consequently, peptide-MHCII binding is often evaluated experimentally using competitive binding assays, which tend to sacrifice throughput for quantitative binding detail. Here, we developed a high-throughput semiquantitative peptide-MHCII screening strategy termed microsphere-assisted peptide screening (MAPS) that aims to balance the accuracy of competitive binding assays with the throughput of computational tools. Read More

AIChE J 2020 Oct 6;66(10). Epub 2020 Jul 6.

Artie McFerrin Department of Chemical Engineering, Texas A&M University, College Station, TX 77843, USA.

Support Vector Machines (SVMs) based optimization framework is presented for the data-driven optimization of numerically infeasible Differential Algebraic Equations (DAEs) without the full discretization of the underlying first-principles model. By formulating the stability constraint of the numerical integration of a DAE system as a supervised classification problem, we are able to demonstrate that SVMs can accurately map the boundary of numerical infeasibility. The necessity of this data-driven approach is demonstrated on a 2-dimensional motivating example, where highly accurate SVM models are trained, validated, and tested using the data collected from the numerical integration of DAEs. Read More

AIChE J 2019 Dec 16;65(12). Epub 2019 Oct 16.

Chemical and Biomolecular Engineering, University of Delaware, Newark DE, 19716.

Many cell behaviors are significantly affected by cell culture geometry, though it remains unclear which geometry from two- to three-dimensional (2D to 3D) culture is appropriate for probing a specific cell function and mimicking native microenvironments. Toward addressing this, we established a 2.5D culture geometry, enabling initial cell spreading while reducing polarization to bridge between 2D and 3D geometries, and examined the responses of wound healing cells, human pulmonary fibroblasts, within it. Read More

AIChE J 2020 Mar 9;66(3). Epub 2019 Oct 9.

Department of Pharmaceutical Sciences, Biointerfaces Institute, University of Michigan, Ann Arbor, Michigan.

Engineered proteins are being widely developed and employed in applications ranging from enzyme catalysts to therapeutic antibodies. Directed evolution, an iterative experimental process composed of mutagenesis and library screening, is a powerful technique for enhancing existing protein activities and generating entirely new ones not observed in nature. However, the process of accumulating mutations for enhanced protein activity requires chemical and structural changes that are often destabilizing, and low protein stability is a significant barrier to achieving large enhancements in activity during multiple rounds of directed evolution. Read More

AIChE J 2020 Mar 19;66(3). Epub 2019 Nov 19.

Department of Molecular Biosciences, The University of Texas at Austin, Austin, TX 78712.

We used the molecular modeling program Rosetta to identify clusters of amino acid substitutions in antibody fragments (scFvs and scAbs) that improve global protein stability and resistance to thermal deactivation. Using this methodology, we increased the melting temperature (T) and resistance to heat treatment of an antibody fragment that binds to the hemagglutinin protein (anti-HA33). Two designed antibody fragment variants with two amino acid replacement clusters, designed to stabilize local regions, were shown to have both higher T compared to the parental scFv and importantly, to retain full antigen binding activity after 2 hours of incubation at 70 °C. Read More

AIChE J 2018 Dec 11;64(12):4182-4186. Epub 2018 Jun 11.

Department of Chemical and Biomolecular Engineering, University of California, Los Angeles, CA90095, United States.

AIChE J 2018 Dec 8;64(12):4308-4318. Epub 2018 Sep 8.

Department of Chemistry, Haverford College, Haverford PA 19041, USA.

The successful engineering of biosynthetic pathways hinges on understanding the factors that influence acyl carrier protein (ACP) stability and function. The stability and structure of ACPs can be influenced by the presence of divalent cations, but how this relates to primary sequence remains poorly understood. As part of a course-based undergraduate research experience, we investigated the thermostability of type II polyketide synthase (PKS) ACPs. Read More

AIChE J 2019 Feb 5;65(2):629-639. Epub 2018 Oct 5.

Dept. of Chemical and Biological Engineering, Illinois Institute of Technology, Chicago, IL 60616.

Erroneous information from sensors affect process monitoring and control. An algorithm with multiple model identification methods will improve the sensitivity and accuracy of sensor fault detection and data reconciliation (SFD&DR). A novel SFD&DR algorithm with four types of models including outlier robust Kalman filter, locally weighted partial least squares, predictor-based subspace identification, and approximate linear dependency-based kernel recursive least squares is proposed. Read More

AIChE J 2018 Dec 12;64(12):4351-4360. Epub 2018 Oct 12.

Nancy E. and Peter C. Meinig School of Biomedical Engineering, Cornell University, Ithaca, NY, 14853, USA.

The combination of cell culture models with microscale technology has fostered emergence of cell-based microphysiological models, also known as organ-on-a-chip systems. Body-on-a-chip systems, which are multi-organ systems on a chip to mimic physiological relations, enable recapitulation of organ-organ interactions and potentially whole-body response to drugs, as well as serve as models of diseases. Chemical reaction engineering principles can be applied to understanding complex reactions inside the cell or human body, which can be treated as a multi-reactor system. Read More

AIChE J 2019 Aug 9;65(8). Epub 2019 May 9.

Bioengineering Department, Northeastern University, Boston, Massachusetts.

While it is known that cancer cell interactions with vascular endothelial cells (ECs) drive metastatic cancer cell extravasation from blood vessels into secondary tumor sites, the mechanisms of action are still poorly understood. Here, we tested the hypothesis that neuraminidase-induced degradation of EC surface glycocalyx (GCX), particularly the sialic acid (SA) residue components of the GCX, will substantially increase metastatic cancer cell attachment to ECs. To our knowledge, our study is the first to isolate the role of GCX SA residues in cancer cell attachment to the endothelium, which were found to be differentially affected by the presence of neuraminidase and to indeed regulate metastatic cancer cell homing to ECs. Read More

AIChE J 2018 Dec 21;64(12):4319-4330. Epub 2018 Sep 21.

Chemistry, Engineering and Medicine for Human Health, Stanford University, Stanford CA 94305.

Plant natural products have served as a prominent source of medicines throughout human history, and are still used today as clinically-approved pharmaceuticals. However, many medicinal plants that produce useful compounds are slow-growing or recalcitrant to cultivation, making it difficult to investigate the underlying genetic/enzymatic machinery responsible for biosynthesis. To better understand the metabolism of bioactive natural products in slow-growing medicinal plants, we used DO labeling and LC-MS-based metabolomics to explore the biosynthesis of medically-relevant alkaloids in three plant species. Read More

AIChE J 2018 Nov 7;64(11):3803-3816. Epub 2018 Sep 7.

Wolfson School of Mechanical, Electrical and Manufacturing Engineering Loughborough University Loughborough Leicestershire, LE11 3TU U.K.

A novel lignocellulosic biomass pretreatment reactor has been designed and tested to investigate pretreatment efficacy of miscanthus grass. The reactor was designed to optimize the transfer of highly oxidative species produced by dielectric barrier discharge plasma to the liquid phase immediately after generation, by arranging close proximity of the plasma to the gas-liquid interface of microbubbles. The reactor produced a range of reactive oxygen species and reactive nitrogen species, and the rate of production depended on the power source duty cycle and the temperature of the plasma. Read More

AIChE J 2018 Dec 11;64(12):4255-4262. Epub 2018 Jul 11.

Department of Chemical and Biomolecular Engineering, University of California, Berkeley, 2151 Berkeley Way, Berkeley, CA 94720.

The alkyne functionality has attracted much interest due to its diverse chemical and biological applications. We recently elucidated an acyl carrier protein (ACP)-dependent alkyne biosynthetic pathway, however, little is known about ACP interactions with the alkyne biosynthetic enzymes, an acyl-ACP ligase (JamA) and a membrane-bound bi-functional desaturase/acetylenase (JamB). Here, we showed that JamB has a more stringent interaction with ACP than JamA. Read More

AIChE J 2018 Dec 9;64(12):4247-4254. Epub 2018 Aug 9.

Delaware Biotechnology Institute, University of Delaware, Newark, DE 19711.

Complete, accurate genome assemblies are necessary to design targets for genetic engineering strategies. Successful gene knockdowns and knockouts in Chinese hamster ovary (CHO) cells may prevent the expression of difficult-to-remove host cell proteins (HCPs). HCPs, if not removed, can cause problems in stability, safety, and efficacy of the biotherapeutic. Read More

AIChE J 2018 Dec 22;64(12):4229-4236. Epub 2018 Aug 22.

Dept. of Chemical and Biological Engineering, University of Wisconsin-Madison, Madison, WI 53706.

Antibodies that target the blood-brain barrier (BBB) are of particular interest for the treatment of neurological diseases. Here, we screened a phage display single-chain antibody (scFv) library by brain perfusion in an attempt to isolate scFv that target the rat BBB. After four rounds of screening, the resulting antibody pool remained highly complex and discrete clonal sampling did not identify any scFvs capable of binding to the rat BBB. Read More

AIChE J 2019 Mar 18;65(3):992-1005. Epub 2018 Dec 18.

Artie McFerrin Dept. of Chemical Engineering, Texas A&M University, College Station, Texas 77843.

In this article, we present (1) a feature selection algorithm based on nonlinear support vector machine (SVM) for fault detection and diagnosis in continuous processes and (2) results for the Tennessee Eastman benchmark process. The presented feature selection algorithm is derived from the sensitivity analysis of the dual C-SVM objective function. This enables simultaneous modeling and feature selection paving the way for simultaneous fault detection and diagnosis, where feature ranking guides fault diagnosis. Read More

AIChE J 2019 ;65

Applied Chemicals and Materials Division, National Institute of Standards and Technology, Boulder, Colorado.

Two-dimensional cross-sections of the phase envelopes of fluid mixtures-in particular isotherms, isobars, and isopleths-are often computed point-by-point by incrementing a so-called marching variable and solving the equilibrium conditions at each step. The marching variable is usually pressure, temperature, or a mole fraction, depending on the application. These isolines, however, can have rather complicated shapes, so that a simple unidirectional "sweep" of the marching variable often gives merely a part of the desired isoline. Read More

AIChE J 2019 ;66

Department of Chemical Engineering and Materials Science, University of Minnesota, 412 Washington Avenue SE, Minneapolis, Minnesota 55455-0132, United States.

In this work, batch-adsorption experiments and molecular simulations are employed to probe the adsorption of binary mixtures containing ethanol or a linear alkane-1,n-diol solvated in water or ethanol onto silicate-1. Since the batch-adsorption experiments require an additional relationship to determine the amount of solute (and solvent adsorbed, as only the bulk liquid reservoir can be probed directly, molecular simulations are used to provide a relationship between solute and solvent adsorption for input to the experimental bulk measurements. The combination of bulk experimental measurements and simulated solute-solvent relationship yields solvent and solute loadings that are self-consistent with simulation alone, and allow for an assessment of the various assumptions made in literature. Read More

AIChE J 2018 Aug 23;64(8):2927-2933. Epub 2018 Feb 23.

Division of Chemistry and Chemical Engineering, California Institute of Technology, Pasadena, CA 91125.

Ultrasound and hyperpolarized magnetic resonance imaging enable the visualization of biological processes in deep tissues. However, few molecular contrast agents are available to connect these modalities to specific aspects of biological function. We recently discovered that a unique class of gas-filled protein nanostructures known as gas vesicles could serve as nanoscale molecular reporters for these modalities. Read More

AIChE J 2018 Aug 7;64(8):3011-3022. Epub 2017 Dec 7.

Dept. of Haematology Imperial College London Harrow London HA1 3UJ U. K.

As breakthrough cellular therapy discoveries are translated into reliable, commercializable applications, effective stem cell biomanufacturing requires systematically developing and optimizing bioprocess design and operation. This article proposes a rigorous computational framework for stem cell biomanufacturing under uncertainty. Our mathematical tool kit incorporates: high-fidelity modeling, single variate and multivariate sensitivity analysis, global topological superstructure optimization, and robust optimization. Read More

AIChE J 2018 May 1;64(5):1859-1873. Epub 2018 Feb 1.

Shtern Research and Consulting Houston TX 77096.

The hydrodynamics of secondary flow phenomena in a disc-shaped gas vortex unit (GVU) is investigated using experimentally validated numerical simulations. The simulation using ANSYS FLUENT v.14a reveals the development of a backflow region along the core of the central gas exhaust, and of a counterflow multivortex region in the bulk of the disc part of the unit. Read More

AIChE J 2018 May 6;64(5):1573-1590. Epub 2018 Feb 6.

Dept. of Chemical Engineering & Chemistry, Multiphase Reactors Group Eindhoven University of Technology 5600 MB Eindhoven The Netherlands.

Fluidization is widely used in industries and has been extensively studied, both experimentally and theoretically, in the past. However, most of these studies focus on spherical particles while in practice granules are rarely spherical. Particle shape can have a significant effect on fluidization characteristics. Read More

AIChE J 2017 Dec 18;63(12):5335-5342. Epub 2017 Jul 18.

Process & Energy Dept., Intensified Reaction and Separation Systems group Delft University of Technology 2628 CB Delft The Netherlands.

In granular flow operations, often particles are nonspherical. This has inspired a vast amount of research in understanding the behavior of these particles. Various models are being developed to study the hydrodynamics involving nonspherical particles. Read More

AIChE J 2017 Apr 5;63(4):1263-1271. Epub 2016 Oct 5.

Dept. of Mechanical and Process Engineering ETH Zurich Zurich 8092 Switzerland.

Thermochemical splitting of CO via a ceria-based redox cycle was performed in a solar-driven thermogravimetric analyzer. Overall reaction rates, including heat and mass transport, were determined under concentrated irradiation mimicking realistic operation of solar reactors. Reticulated porous ceramic (RPC) structures and fibers made of undoped and Zr-doped CeO, were endothermally reduced under radiative fluxes of 1280 suns in the temperature range 1200-1950 K and subsequently re-oxidized with CO at 950-1400 K. Read More

AIChE J 2016 03 8;62(3):956-964. Epub 2016 Jan 8.

Dept. of Chemical Engineering, Center for Bioelectronics and Biosensors, Biodesign Institute and Fulton School of Engineering Matter, Transport, and Energy, Arizona State University, Tempe, AZ 85287.

The development and performance characterization of a new differential pressure-based flow meter for human breath measurements is presented in this article. The device, called a "Confined Pitot Tube," is comprised of a pipe with an elliptically shaped expansion cavity located in the pipe center, and an elliptical disk inside the expansion cavity. The elliptical disk, named Pitot Tube, is exchangeable, and has different diameters, which are smaller than the diameter of the elliptical cavity. Read More

AIChE J 2016 Oct 6;62(10):3575-3584. Epub 2016 May 6.

Laboratory for Chemical Technology Faculty of Engineering and Architecture, Ghent University Ghent Belgium.

Coincident (simultaneous) three-component particle velocity measurements performed using two laser Doppler anemometry probes at the outlet section of a 9 m high cylindrical riser are for the first time presented for dilute flow conditions. Near the blinded extension of the T-outlet a solids vortex is formed. Particle downflow along the riser wall opposite the outlet tube is observed, which is restricted to higher riser heights at higher gas flow rates. Read More