Publications

Enabling tools for high-throughput detection of metabolites: Metabolic engineering and directed evolution applications.

by Lin, JL; Wagner, JM; Alper, HS

Journal of Biotechnology Advances; Jul 16 2017; doi: 10.1016/j.biotechadv.2017.07.005

Within the Design-Build-Test Cycle for strain engineering, rapid product detection and selection strategies remain challenging and limit overall throughput. Here we summarize a wide variety of modalities that transduce chemical concentrations into easily measured absorbance, luminescence, and fluorescence signals. Specifically, we cover protein-based biosensors (including transcription factors), nucleic acid-based biosensors, coupled enzyme reactions, bioorthogonal chemistry, and fluorescent and chromogenic dyes and substrates as modalities for detection. We focus on the use of these methods for strain engineering and enzyme discovery and conclude with remarks on the current and future state of biosensor development for application in the metabolic engineering field.

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Fundamental Understanding of CO2 Capture and Regeneration in Aqueous Amines from First-Principles Studies: Recent Progress and Remaining Challenges

by Stowe, HM; Hwang, GS

Industrial & Engineering Chemistry Research; Jun 21 2017; Volume: 56; Issue: 24; Pages: 6887-6899; DOI: 10.1021/acs.iecr.7b00213

Aqueous amine-based chemical scrubbing has been considered the most promising near-term solution for CO2 capture from flue gas. However, its widespread implementation is hindered by the high cost associated with the parasitic energy consumption during solvent regeneration, along with degradation and corrosion problems. Computer simulations have been widely used to improve our fundamental understanding of CO2 absorption materials and processes in efforts to design and develop high-performance, cost-effective solvents. Here, we review recent progress in first-principles studies on molecular mechanisms underlying CO2 absorption into aqueous amines and solvent regeneration. We also briefly discuss aspects that remain unclear, such as degradation and corrosion mechanisms, and the reaction-diffusion behavior of CO2 at the solvent/gas interface. This review highlights the increasingly significant role of first-principles-based atomistic modeling in exploring the function and properties of candidate materials, as well as the complex physicochemical phenomena underlying CO2 capture, solvent degradation, and corrosion, especially when direct experimental characterization at the atomic level may be difficult.

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A Framework for Integrated Scheduling and Control using Discrete-Time Dynamic Process Models

by Touretzky, CR; Harjunkoski, I; Baldea, M

26TH EUROPEAN SYMPOSIUM ON COMPUTER AIDED PROCESS ENGINEERING (ESCAPE), PT A; 2016; Book Series: Computer Aided Chemical Engineering; Volume: 38; Pages: 601-606; DOI: 10.1016/B978-0-444-63428-3.50105-3

We address the integration of production scheduling and process control using discrete-time, datadriven process models. Our work is based on the scale-bridging model (SBM) framework, with the SBM being a low-order representation of the closed-loop process dynamics over scheduling-relevant time scales. We use autoregressive with exogenous inputs (ARX) SBMs, and formulate the integrated scheduling and control problem using a novel hybrid representation of time, whereby the dynamic process model is presented in discrete time and the scheduling problem uses a continuous time formulation. We introduce a reverse integral criterion to determine transition times between products. A CSTR case study is used to demonstrate our framework.

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SITS Derivatization of Peptides to Enhance 266 nm Ultraviolet Photodissociation (UVPD)

by Quick, MM; Mehaffey, MR; Johns, RW; Parker, WR; Brodbelt, JS

JOURNAL OF THE AMERICAN SOCIETY FOR MASS SPECTROMETRY; Jul 2017; Volume: 28; Issue: 7; Pages: 1462-1472; DOI: 10.1007/s13361-017-1650-y

N-terminal derivatization of peptides with the chromogenic reagent 4acetamido- 4-isothiocyanatostilbene-2,2-disulfonic acid (SITS) is demonstrated to enhance the efficiency of 266 nm ultraviolet photodissociation (UVPD). Attachment of the chromophore results in a mass shift of 454 Da and provides significant gains in the number and abundances of diagnostic fragment ions upon UVPD. Activation of SITS-tagged peptides with 266 nm UVPD leads to many fragment ions akin to the a/b/y ions commonly produced by CID, along with other sequence ions (c, x, and z) typically accessed through higher energy pathways. Extreme bias towards Cterminal fragment ions is observed upon activation of SITS-tagged peptides using multiple 266 nm laser pulses. Due to the high reaction efficiency of the isothiocyanate coupling to the N-terminus of peptides, we demonstrate the ability to adapt this strategy to a high-throughput LCMS/ MS workflow with 266 nm UVPD.

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Imposed Environmental Stresses Facilitate Cell-free Nanoparticle Formation by Deinococcus radiodurans.

by Chen, A; Contreras, LM; Keitz, BK

Applied and Environmental Microbiology; Jul 7 2017; doi: 10.1128/AEM.00798-17

The biological synthesis of metal nanoparticles has been examined in a wide range of organisms due to increased interest in green synthesis and environmental remediation applications involving heavy metal ion contamination. Deinococcus radiodurans is particularly attractive for environmental remediation involving metal reduction due to its high resistance to radiation and other environmental stresses. However, few studies have thoroughly examined the relationship between environmental stresses and their resulting effect on nanoparticle biosynthesis. In this work, we demonstrate cell-free nanoparticle production and study the effect of metal stressor concentration and identity, temperature, pH, and oxygenation on the production of extracellular silver nanoparticles by D. radiodurans R1. We also report the synthesis of bimetallic silver and gold nanoparticles following addition of a metal stressor (silver or gold), highlighting how production of these particles is enabled through application of environmental stresses. Additionally, we found that both the morphology and size of monometallic and bimetallic nanoparticles are dependent on the environmental stresses imposed on the cells. The nanoparticles produced by D. radiodurans exhibit antimicrobial activity comparable to pure silver nanoparticles and display catalytic activity comparable to pure gold nanoparticles. Overall, we demonstrate that biosynthesized nanoparticle properties can be partially controlled through tuning of applied environmental stresses and provide insight into how their application may impact nanoparticle production in D. radiodurans during bioremediation.IMPORTANCE Biosynthetic production of nanoparticles has recently gained prominence as a solution to rising concerns regarding increased bacterial resistance to antibiotics and a desire for environmentally-friendly methods of bioremediation and chemical synthesis. To date, a range of organisms have been utilized for nanoparticle formation. The extremophile D. radiodurans, which can withstand significant environmental stresses and is therefore more robust for metal reduction applications, has yet to be exploited for this purpose. Thus, this work improves our understanding of the impact of environmental stresses on biogenic nanoparticle morphology and composition during metal reduction processes in this organism. This work also contributes towards enhancing the controlled synthesis of nanoparticles with specific attributes and functions using biological systems.

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Controlled co-solvent vapor annealing and the importance of quenching conditions in thin-film block copolymer self-assembly

by Stahl, BC; Kramer, EJ; Hawker, CJ; Lynd, NA

Journal of Polymer Science Part B – Polymer Physics; Aug 1 2017; Volume: 55; Issue: 15; Pages: 1125-1130; DOI: 10.1002/polb.24366

A controlled co-solvent vapor annealing system was designed and constructed to investigate the effects of solvent vapor activity during the rapid ambient quenching process on the morphology of a cylinder-forming poly(styrene)-b-poly (ethylene oxide) (PS-PEO) annealed in toluene and water vapor. A phase transformation from cylinders in the bulk to close-packed spheres in swollen thin films occurred, which was reversed upon quenching with dry nitrogen. Quenching with humidified nitrogen preserved the spherical morphology but could significantly alter domain spacing and reduce long-range order in the dried films under some circumstances. Specifically, long-range order in the quenched films was found to decrease as the quenching humidity decreased from the humidity used during annealing, and the best long-range order was obtained when the humidity remained consistent throughout both annealing and quenching.

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Dopant Mediated Assembly of Cu2ZnSnS4 Nanorods into Atomically Coupled 2D Sheets in Solution

by Singh, A; Singh, A; Ong, GK; Jones, MR; Nordlund, D; Bustillo, K; Ciston, J; Alivisatos, AP; Milliron, DJ

Journal of Nano Letters; Jun 2017; Volume: 17; Issue: 6; Pages: 3421-3428; DOI: 10.1021/acs.nanolett.7b00232

Assembly of anisotropic nanocrystals into ordered superstructures is an area of intense research interest due to its relevance to bring nanocrystal properties to macroscopic length scales and to impart additional collective properties owing to the superstructure. Numerous routes have been explored to assemble such nanocrystal superstructures ranging from self-directed to external field-directed methods. Most of the approaches require sensitive control of experimental parameters that are largely environmental and require extra processing steps, increasing complexity and limiting reproducibility. Here, we demonstrate a simple approach to assemble colloidal nanorods in situ, wherein dopant incorporation during the particle synthesis results in the formation of preassembled 2D sheets of close-packed ordered arrays of vertically oriented nanorods in solution.

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Charge carrier concentration dependence of ultrafast plasmonic relaxation in conducting metal oxide nanocrystals

by Johns, RW; Blemker, MA; Azzaro, MS; Heo, S; Runnerstrom, EL; Milliron, DJ; Roberts, ST

Journal of Materials Chemistry C; Jun 21 2017; Volume: 5; Issue: 23; Pages: 5757-5763; DOI: 10.1039/c7tc00600d

Electronically doped metal oxide nanocrystals exhibit tunable infrared localized surface plasmon resonances (LSPRs). Despite the many benefits of IR resonant LSPRs in solution processable nanocrystals, the ways in which the electronic structure of the host semiconductor material impact metal oxide LSPRs are still being investigated. Semiconductors provide an alternative dielectric environment than metallically bonded solids, such as noble metals, which can impact how these materials undergo electronic relaxation following photoexcitation. Understanding these differences is key to developing applications that take advantage of the unique optical and electronic properties offered by plasmonic metal oxide NCs. Here, we use the two-temperature model in conjunction with femtosecond transient absorption experiments to describe how the internal temperature of two representative metal oxide nanocrystal systems, cubic WO3-x and bixbyite Sn-doped In2O3, change following LSPR excitation. We find that the low free carrier concentrations of metal oxide NCs lead to less efficient heat generation as compared to metallic nanocrystals such as Ag. This suggests that metal oxide NCs may be ideal for applications wherein untoward heat generation may disrupt the application’s overall performance, such as solar energy conversion and photonic gating.

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Generating Large Thermally Stable Marangoni-Driven Topography in Polymer Films by Stabilizing the Surface Energy Gradient

by Jones, AR; Kim, CB; Zhou, SX; Ha, H; Katsumata, R; Blachut, G; Bonnecaze, RT; Ellison, CJ

Journal of Macromolecules; Jun 13 2017; Volume: 50; Issue: 11; Pages: 4588-4596; DOI: 10.1021/acs.macromol.7b00055

Marangoni forces drive a fluid to flow in response to positional differences in surface energy. In thin polymer films, a difference in surface energy between two coincident liquid polymers could offer a useful route to manufacture topographically patterned surfaces via the Marangoni effect. Previously, we have demonstrated a photochemical method using the Marangoni effect for patterning thin polystyrene films. To generalize the approach, a theoretical model that gives the underlying physics of this process was also developed, which further revealed that low viscosities, low diffusivities, and large surface energy gradients favor rapid evolution of large film thickness variations. However, as described by the Stokes Einstein equation or the Rouse model, low viscosity is generally correlated with high diffusivity in a single-component system. Herein, we report a strategy to decouple film viscosity and diffusivity by co-casting a high molecular weight surface energy gradient creating copolymer (low diffusivity) with a low molecular weight majority homopolymer (high diffusivity and low viscosity), which are miscible with each other. Patterned light exposure through a photomask imposes a patterned surface energy gradient between light-exposed and unexposed regions due to photochemical reactions involving only the low diffusivity component. Upon heating the film to the liquid state, the film materials (primarily the low viscosity homopolymer component) flow from the low to high surface energy regions. This strategy either eliminates or greatly slows dissipation of the prepatterned surface energy gradient while maintaining rapid feature formation, resulting in formation of ca. 500 nm high features within only 30 min of thermal annealing. Furthermore, the formed features are stable upon extended thermal annealing for up to one month. It is found that a ratio of Marangoni forces to capillary forces can provide a predictive metric that distinguishes which scenarios produce features that dissipate or persist.

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Supported Cobalt Nanorod Catalysts for Carbon Dioxide Hydrogenation

by Jimenez, J; Bird, A; Santiago, MS; Wen, C; Lauterbach, J

Journal of Energy Technology; Jun 2017; Volume: 5; Issue: 6; Pages: 884-891; Special Issue; DOI: 10.1002/ente.201600575 

To create new CO2 hydrogenation catalysts, we developed a methodology in which the selective surface faceting of nanorods is combined with the practicality of a supported catalyst. The basic Co catalyst with preferential {110} surface faceting was supported with either SiO2, Al-2 O-3, or TiO2. We grafted charged ligands onto the Co nanorods to attract the support precursors to the surface of the Co to allow a large contact area between the Co and the support. The large contact area promoted the chemical interaction between the Co and the support, which was verified by using Raman spectroscopy, XRD, and temperature- programmed reduction. TiO2- and Al2O3- supported Co nanorods showed an increase in activity at low and high reaction temperatures, respectively, whereas the relatively inert SiO2- supported nanorods possessed the same catalytic performance as unsupported rods.

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