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Chemical Engineering Simulation

Brian M Bonk, James W Weis, Bruce Tidor
Despite tremendous progress in understanding and engineering enzymes, knowledge of how enzyme structures and their dynamics induce observed catalytic properties is incomplete, and capabilities to engineer enzymes fall far short of industrial needs. Here we investigate the structural and dynamic drivers of enzyme catalysis for the rate-limiting step of the industrially important enzyme ketol-acid reductoisomerase (KARI) and identify a region of the conformational space of the bound enzyme-substrate complex that, when populated, leads to large increases in reactivity...
February 14, 2019: Journal of the American Chemical Society
Ana Sánchez-Grande, Bruno de la Torre, José Santos, Borja Cirera, Koen Lauwaet, Taras Chutora, Shayan Edalatmanesh, Pingo Mutombo, Johanna Rosen, Radek Zboril, Rodolfo Miranda, Jonas Björk, Pavel Jelínek, Nazario Martín, David Ecija
Engineering low band gap π-conjugated polymers is a burgeoning area in basic and applied research. The main synthetic challenge lies in the solubility of the materials during the chemical synthesis which precludes the advance of the field. Here, we report an unprecedented on-surface synthesis protocol to overcome such difficulties, being able to design poly(p-anthracene ethynylene) molecular wires on an Au(111) surface. To this aim, a quinoid anthracene precursor endowed with =CBr2 moieties is deposited and annealed to 400 K resulting in anthracene-based polymers, with a measured electronic bandgap of 1...
February 14, 2019: Angewandte Chemie
Sean M Colby, Dennis G Thomas, Jamie R Nuñez, Douglas J Baxter, Kurt R Glaesemann, Joseph M Brown, Meg A Pirrung, Niranjan Govind, Justin G Teeguarden, Thomas O Metz, Ryan S Renslow
High throughput, comprehensive, and confident identifications of metabolites and other chemicals in biological and environmental samples will revolutionize our understanding of the role these chemically diverse molecules play in biological systems. Despite recent technological advances, metabolomics studies still result in the detection of a disproportionate number of features that cannot be confidently assigned to a chemical structure. This inadequacy is driven by the single most significant limitation in metabolomics: the reliance on reference libraries constructed by analysis of authentic reference materials with limited commercial availability...
February 11, 2019: Analytical Chemistry
John Metzcar, Yafei Wang, Randy Heiland, Paul Macklin
Cancer biology involves complex, dynamic interactions between cancer cells and their tissue microenvironments. Single-cell effects are critical drivers of clinical progression. Chemical and mechanical communication between tumor and stromal cells can co-opt normal physiologic processes to promote growth and invasion. Cancer cell heterogeneity increases cancer's ability to test strategies to adapt to microenvironmental stresses. Hypoxia and treatment can select for cancer stem cells and drive invasion and resistance...
February 2019: JCO Clinical Cancer Informatics
Wayan Wicke, Arman Ahmadzadeh, Vahid Jamali, Harald Unterweger, Christoph Alexiou, Robert Schober
The possibility to guide and control magnetic nanoparticles in a non-invasive manner has spawned various applications in biotechnology such as targeted drug delivery and sensing of biological substances. These applications are facilitated by the engineering of the size, selective chemical reactivity, and general chemical composition of the employed particles. Motivated by their widespread use and favorable properties, in this paper, we provide a theoretical study of the potential benefits of magnetic nanoparticles for the design of molecular communication systems...
January 25, 2019: IEEE Transactions on Nanobioscience
Li Ma, Yilin Liu, Yi Liu, Shuyi Jiang, Ping Li, Yuchen Hao, Pengpeng Shao, Anxiang Yin, Xiao Feng, Bo Wang
Conjugated microporous polymers (CMPs) have full access to the organic synthesis toolbox and feature-rich functionality, structural diversity, and high surface area. We incorporated ferrocene (Fc) into the backbones of CMPs and systematically engineered their optical energy gaps. Compared with the CMPs without Fc units yet adopting similar molecular orbital level, Fc-based CMPs can sufficiently generate reactive oxygen species (ROS) under visible light. The resultant ROS are able to effectively decompose the absorbed pollutants, including organic dyes and chemical warfare agents...
January 29, 2019: Angewandte Chemie
Ryuhei Motokawa, Tohru Kobayashi, Hitoshi Endo, Junju Mu, Christopher D Williams, Andrew J Masters, Mark R Antonio, William T Heller, Michihiro Nagao
Short- and long-range correlations between solutes in solvents can influence the macroscopic chemistry and physical properties of solutions in ways that are not fully understood. The class of liquids known as complex (structured) fluids-containing multiscale aggregates resulting from weak self-assembly-are especially important in energy-relevant systems employed for a variety of chemical- and biological-based purification, separation, and catalytic processes. In these, solute (mass) transfer across liquid-liquid (water, oil) phase boundaries is the core function...
January 23, 2019: ACS Central Science
Erin L Weber, Thomas E Woolley, Chao-Yuan Yeh, Kuang-Ling Ou, Philip K Maini, Cheng-Ming Chuong
Human skin progenitor cells will form new hair follicles, although at a low efficiency, when injected into nude mouse skin. To better study and improve upon this regenerative process, we developed an in vitro system to analyze the morphogenetic cell behavior in detail and modulate physical-chemical parameters to more effectively generate hair primordia. In this three-dimensional culture, dissociated human neonatal foreskin keratinocytes self-assembled into a planar epidermal layer while fetal scalp dermal cells coalesced into stripes, then large clusters, and finally small clusters resembling dermal condensations...
January 25, 2019: Experimental Dermatology
Jingjie Yeo, Gang Seob Jung, Francisco J Martín-Martínez, Jennifer Beem, Zhao Qin, Markus J Buehler
By varying the number of acetylenic linkages connecting aromatic rings, a new family of atomically thin graph-n-yne materials can be designed and synthesized. Generating immense scientific interest due to its structural diversity and excellent physical properties, graph-n-yne has opened new avenues toward numerous promising engineering applications, especially for separation membranes with precise pore sizes. Having these tunable pore sizes in combination with their excellent mechanical strength to withstand high pressures, free-standing graph-n-yne is theoretically posited to be an outstanding membrane material for separating or purifying mixtures of either gases or liquids, rivaling or even dramatically exceeding the capabilities of current, state-of-art separation membranes...
January 15, 2019: Advanced Materials
Hiroki Nishiguchi, Natsuki Hiasa, Kiyoka Uebayashi, James Liao, Hiroshi Shimizu, Fumio Matsuda
In silico kinetic modeling is an essential tool for rationally designing metabolically engineered organisms based on a system-level understanding of their regulatory mechanisms. However, an estimation of enzyme parameters has been a bottleneck in the computer simulation of metabolic dynamics. In this study, the ensemble-modeling approach was integrated with the transomics data to construct kinetic models. Kinetic metabolic models of a photosynthetic bacterium, Synechocystis sp. PCC 6803, were constructed to identify engineering targets for improving ethanol production based on an understanding of metabolic regulatory systems...
January 8, 2019: Metabolic Engineering
Xiong Li, Qinyi Li, Sen Yang, Gang Yang
Clay swelling occurs frequently and is closely relevant to a number of engineering and industrial processes, while the underlying mechanisms remain elusive. In this study, K+-bearing clay systems with different charge amounts and charge locations have been simulated by molecular dynamics, showing that swelling is unfavorable for lower charge amounts (1.00 and 1.25 e uc-1) while it relies on charge locations for higher charge amounts (1.50 and 1.75 e uc-1): inhibited when tetrahedrally charged and favored when octahedrally charged...
January 11, 2019: Physical Chemistry Chemical Physics: PCCP
Annette Kluge, Mike Silbert, Uta S Wiemers, Barbara Frank, Oliver T Wolf
In a simulated process control task, we investigated the effects of refresher training and acute social stress on performing a standard operating procedure (SOP) containing a production and monitoring task and knowledge recall after a retention interval of two weeks. In a 2 × 2 between-group design (Factor 1: induced social stress, Factor 2: refresher training), 76 engineering students performed an SOP at t1 in week 1 and at t2 in week 3. A MANOVA in week three (t2) indicated a main effect of the refresher training for the SOP execution containing a production and a monitoring task and an impairing effect of stress on the monitoring task...
January 10, 2019: Ergonomics
John Tomko, David Hans Olson, Ashutosh Giri, John Thomas Gaskins, Sean M O'Malley, Patrick E Hopkins
Understanding the effects and limitations of solid/liquid interfaces on energy transport is crucial to applications ranging from nano-scale thermal engineering to chemical synthesis. Up to now, the majority of experimental evidence regarding solid/liquid interactions has been limited to macroscale observations and experiments. The lack of experimental works exploring nanoscale solid/liquid interactions has been accentuated as the body of knowledge from theory and simulations at these scales has exploded in recent years...
January 9, 2019: Langmuir: the ACS Journal of Surfaces and Colloids
Qian Zhao, Yingjia Zhang, Wuchuan Sun, Fuquan Deng, Feiyu Yang, Zuohua Huang
As a renewable source of energy, ethanol has been widely used in internal combustion engines as either gasoline alternative fuel or fuel additive. However, as the chemical source term of computational fluid dynamics (CFD) simulation of combustors, it remains disagreement on understanding of chemical kinetic mechanism of ethanol. Reaction mechanism of ethanol + HȮ2 is well known a crucial reaction class in terms of predicting reactivity of ethanol as well as ethylene formation at engine relevant condition. However, the kinetic parameters of the reactions are basically extrapolated by analogy with n-butanol + HȮ2 system calculated by Zhou et al...
January 8, 2019: Journal of Physical Chemistry. A
Farzad Davardoost, Davood Kahforoushan
The presence of chemicals in laboratories and research centers exposes the staff working at such indoor environment to health risks. In this piece of research, a study was performed on the indoor environment of the Center for Environmental Engineering Research at Sahand University of Technology (Tabriz, Iran). For this purpose, the parameters affecting the dispersion of volatile organic compounds (VOCs), including ventilation rate, room temperature, pollution emission time, venting location, air flow regime within the indoor environment, and the number of vents, were simulated via CFD modeling...
January 3, 2019: Environmental Science and Pollution Research International
Roy M Harrison, A Rob MacKenzie, Hongming Xu, Mohammed S Alam, Irina Nikolova, Jian Zhong, Ajit Singh, Soheil Zeraati-Rezaei, Christopher Stark, David C S Beddows, Zhirong Liang, Ruixin Xu, Xiaoming Cai
Diesel engine emissions are by far the largest source of nanoparticles in many urban atmospheres, in which they dominate the particle number count, and may present a significant threat to public health. This paper reviews knowledge of the composition and atmospheric properties of diesel exhaust particles, and exemplifies research in this field through a description of the FASTER project (Fundamental Studies of the Sources, Properties and Environmental Behaviour of Exhaust Nanoparticles from Road Vehicles) which studied the size distribution-and, in unprecedented detail, the chemical composition-of nanoparticles sampled from diesel engine exhaust...
December 2018: Proceedings. Mathematical, Physical, and Engineering Sciences
Anwesha Sarkar, Shuning Zhang, Melvin Holmes, Rammile Ettelaie
Lipid digestion is a bio-interfacial process that is largely governed by the binding of the lipase-colipase-biosurfactant (bile salts) complex onto the surface of emulsified lipid droplets. Therefore, engineering oil-water interfaces that prevent competitive displacement by bile salts and/or delay the transportation of lipase to the lipidoidal substrate can be an effective strategy to modulate lipolysis in human physiology. In this review, we present the mechanistic role of Pickering emulsions i.e. emulsions stabilised by micron-to-nano sized particles in modulating the important fundamental biological process of lipid digestion by virtue of their distinctive stability against coalescence and resilience to desorption by intestinal biosurfactants...
January 2019: Advances in Colloid and Interface Science
Fuyuan Zhang, Bing Liu, Yan Zhang, Junping Wang, Yang Lu, Juan Deng, Shuo Wang
In order to develop a sensitive immunoassay for Aflatoxin B1 (AFB1) monitoring, a hybridoma secreting anti-AFB1 monoclonal antibody with high binding affinity was screened. A new type of CdTe/CdS/ZnS quantum dot was synthesized and conjugated with an artificial antigen for use as a fluorescent probe in a simple one-step fluorescence immunoassay (FLISA). The developed FLISA allowed a sensitive determination of AFB1 in cereal samples in a wide linear range, from 0.08 to 1.97 ng mL-1 , with a detection limit of 0...
January 24, 2019: Analytica Chimica Acta
Rebecca Hanscam, Eric M Shepard, Joan B Broderick, Valérie Copié, Robert K Szilagyi
Peptides coordinated to iron-sulfur clusters, referred to as maquettes, represent a synthetic strategy for constructing biomimetic models of iron-sulfur metalloproteins. These maquettes have been successfully employed as building blocks of engineered heme-containing proteins with electron-transfer functionality; however, they have yet to be explored in reactivity studies. The concept of iron-sulfur nesting in peptides is a leading hypothesis in Origins-of-Life research as a plausible path to bridge the discontinuity between prebiotic chemical transformations and extant enzyme catalysis...
January 15, 2019: Journal of Computational Chemistry
Zahra Shariatinia
Chitosan (CS) is a linear polysaccharide which is achieved by deacetylation of chitin, which is the second most plentiful compound in nature, after cellulose. It is a linear copolymer of β-(1 → 4)-linked 2-acetamido-2-deoxy-β-d-glucopyranose and 2-amino-2-deoxy-β-d-glucopyranose. It has appreciated properties such as biocompatibility, biodegradability, hydrophilicity, nontoxicity, high bioavailability, simplicity of modification, favorable permselectivity of water, outstanding chemical resistance, capability to form films, gels, nanoparticles, microparticles and beads as well as affinity to metals, proteins and dyes...
November 30, 2018: Advances in Colloid and Interface Science
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