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Chemical Engineering Simulation

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https://www.readbyqxmd.com/read/30113814/minimizing-context-dependency-of-gene-networks-using-artificial-cells
#1
Yunfeng Ding, Luis Eduardo Contreras-Llano, Eliza Morris, Michelle Mao, Cheemeng Tan
The functioning of synthetic gene circuits depends on their local chemical context defined by the types and concentrations of biomolecules in the surrounding milieu that influence gene transcription and translation. This chemical-context dependence of synthetic gene circuits arises from significant yet unknown crosstalk between engineered components, host cells, and environmental factors, and has been a persistent challenge for synthetic biology. Here, we show that the sensitivity of synthetic gene networks to their chemical contexts can be minimized and their designed functions rendered robust using artificial cells, which are synthetic biomolecular compartments engineered from the bottom-up using liposomes that encapsulate the gene networks...
August 16, 2018: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/30110436/molecular-mechanism-of-viscoelastic-polymer-enhanced-oil-recovery-in-nanopores
#2
Jing Cun Fan, Feng Chao Wang, Jie Chen, Yin Bo Zhu, De Tang Lu, He Liu, Heng An Wu
Polymer flooding is a promising chemical enhanced oil recovery (EOR) method, which realizes more efficient extraction in porous formations characterized with nanoscale porosity and complicated interfaces. Understanding the molecular mechanism of viscoelastic polymer EOR in nanopores is of great significance for the advancement of oil exploitation. Using molecular dynamics simulations, we investigated the detailed process of a viscoelastic polymer displacing oil at the atomic scale. We found that the interactions between polymer chains and oil provide an additional pulling effect on extracting the residual oil trapped in dead-end nanopores, which plays a key role in increasing the oil displacement efficiency...
June 2018: Royal Society Open Science
https://www.readbyqxmd.com/read/30109934/long-range-modulations-of-the-electric-fields-in-proteins
#3
Hernan Biava, Toni Schreiber, Sagie Katz, Jan-Stefan Völler, Michael Stolarski, Claudia Schulz, Norbert Michael, Nediljko Budisa, Jacek Arthur Kozuch, Tillmann Utesch, Peter Hildebrandt
Electrostatic interactions are essential for controlling protein structure and function. Whereas so far experimental and theoretical efforts focused on the effect of local electrostatics, this work aims at elucidating the long-range modulation of electric fields in proteins upon binding to charged surfaces. The study is based on cytochrome c (Cytc) variants carrying nitrile reporters for the vibrational Stark effect that are incorporated into the protein via genetic engineering and chemical modification. The Cytc variants were thoroughly characterized with respect to possible structural perturbations due to labeling...
August 15, 2018: Journal of Physical Chemistry. B
https://www.readbyqxmd.com/read/30105348/multiscale-prediction-of-functional-self-assembled-materials-using-machine-learning-high-performance-surfactant-molecules
#4
Takuya Inokuchi, Na Li, Kei Morohoshi, Noriyoshi Arai
Various physical properties of functional materials can be induced by controlling their chemical molecular structures. Therefore, molecular design is crucial in the fields of engineering and materials science. With its remarkable development in various fields, machine learning combined with molecular simulation has recently been found to be effective at predicting the electronic structure of materials (Nat. Commun., 2017, 8, 872 and Nat. Commun., 2017, 8, 13890). However, previous studies have used similar microscale information as input and output data for machine learning, i...
August 14, 2018: Nanoscale
https://www.readbyqxmd.com/read/30102539/sparsity-facilitates-chemical-reaction-selection-for-engine-simulations
#5
Gina M Magnotti, Zihan Wang, Wei Liu, Raghu Sivaramakrishnan, Sibendu Som, Michael J Davis
Analysis of large-scale, realistic models incorporating detailed chemistry can be challenging because each simulation is computationally expensive, and a complete analysis may require many simulations. This paper addresses one such problem of this type, chemical-reaction selection in engine simulations. In this computationally challenging case, it is demonstrated how the important concept of sparsity can facilitate chemical reaction selection, which is the process of finding the most important chemical reactions for modeling a chemical process...
August 13, 2018: Journal of Physical Chemistry. A
https://www.readbyqxmd.com/read/30096230/metabolic-engineering-of-escherichia-coli-for-efficient-production-of-2-pyrone-4-6-dicarboxylic-acid-from-glucose
#6
Zi Wei Luo, Won Jun Kim, Sang Yup Lee
2-Pyrone-4,6-dicarboxylic acid (PDC) is a pseudo-aromatic dicarboxylic acid and is a promising bio-based building block chemical that can be used to make diverse polyesters with novel functionalities. In this study, Escherichia coli was metabolically engineered to produce PDC from glucose. First, an efficient biosynthetic pathway for PDC production from glucose was suggested by in silico metabolic flux simulation. This best pathway employs a single-step biosynthetic route to protocatechuic acid (PCA), a metabolic precursor for PDC biosynthesis...
August 10, 2018: ACS Synthetic Biology
https://www.readbyqxmd.com/read/30094961/evaluation-of-continuous-nonaffinity-capture-chromatography-for-a-recombinant-enzyme-optimization-for-a-changing-perfusion-feedstream-and-comparison-to-batch-processing
#7
Christopher Thompson, Kelly Wilson, Christopher Larkin, Jeong Lee, William K Wang, Michaela Wendeler
This work presents the optimization and critical evaluation of continuous capture chromatography in the downstream process of a recombinant enzyme. For the upstream manufacturing of this molecule, a perfusion process was implemented due to benefits for product quality and productivity. This process is, however, characterized by low titer and significant changes over the course of the harvest duration in terms of active enzyme concentration and impurity content. We evaluated the feasibility and benefits of a continuous capture operation...
August 9, 2018: Biotechnology Progress
https://www.readbyqxmd.com/read/30091904/the-influence-of-rock-mineralogy-on-reactive-fracture-evolution-in-carbonate-rich-caprocks
#8
Kasparas Spokas, Catherine A Peters, Laura Pyrak-Nolte
Fractures present environmental risks for subsurface engineering activities, such as geologic storage of greenhouse gases, because of the possibility of unwanted upward fluid migration. The risks of fluid leakage may be exacerbated if fractures are subjected to physical and chemical perturbations that alter their geometry. This study investigated this by constructing a 2D fracture model to numerically simulate fluid flow, acid-driven reactions, and mechanical deformation. Three rock mineralogies were simulated: a limestone with 100% calcite, a limestone with 68% calcite, and a banded shale with 34% calcite...
August 9, 2018: Environmental Science & Technology
https://www.readbyqxmd.com/read/30039704/engineering-atrazine-loaded-poly-lactic-co-glycolic-acid-nanoparticles-to-ameliorate-environmental-challenges
#9
Brian Schnoor, Ahmad Elhendawy, Suzanna Joseph, Mark Putman, Randall Chacón-Cerdas, Dora Flores-Mora, Felipe Bravo-Moraga, Fernando Gonzalez-Nilo, Carolina Salvador-Morales
The use of herbicides plays a vital role in controlling weeds and conserving crops; however, its usage generates both environmental and economic problems. For example, herbicides pose a financial issue as farmers must apply large quantities to protect crops due to absorption rates of less than 0.1%. Therefore, there is a great need for the development of new methods to mitigate these issues. Here, we report for the first time the synthesis of poly(lactic- co-glycolic-acid) (PLGA) nanoherbicides loaded with atrazine as an active ingredient...
August 1, 2018: Journal of Agricultural and Food Chemistry
https://www.readbyqxmd.com/read/30038792/effect-of-divalent-ions-and-a-polyphosphate-on-composition-structure-and-stiffness-of-simulated-drinking-water-biofilms
#10
Yun Shen, Pin Chieh Huang, Conghui Huang, Peng Sun, Guillermo L Monroy, Wenjing Wu, Jie Lin, Rosa M Espinosa-Marzal, Stephen A Boppart, Wen-Tso Liu, Thanh H Nguyen
The biofilm chemical and physical properties in engineered systems play an important role in governing pathogen transmission, fouling facilities, and corroding metal surfaces. Here, we investigated how simulated drinking water biofilm chemical composition, structure, and stiffness responded to the common scale control practice of adjusting divalent ions and adding polyphosphate. Magnetomotive optical coherence elastography (MM-OCE), a tool developed for diagnosing diseased tissues, was used to determine biofilm stiffness in this study...
2018: NPJ Biofilms and Microbiomes
https://www.readbyqxmd.com/read/30038028/computational-discovery-of-chemically-patterned-surfaces-that-effect-unique-hydration-water-dynamics
#11
Jacob I Monroe, M Scott Shell
The interactions of water with solid surfaces govern their apparent hydrophobicity/hydrophilicity, influenced at the molecular scale by surface coverage of chemical groups of varied nonpolar/polar character. Recently, it has become clear that the precise patterning of surface groups, and not simply average surface coverage, has a significant impact on the structure and thermodynamics of hydration layer water, and, in turn, on macroscopic interfacial properties. Here we show that patterning also controls the dynamics of hydration water, a behavior frequently thought to be leveraged by biomolecules to influence functional dynamics, but yet to be generalized...
August 7, 2018: Proceedings of the National Academy of Sciences of the United States of America
https://www.readbyqxmd.com/read/30023726/role-of-cys-i-cys-iii-disulfide-bond-on-the-structure-and-activity-of-%C3%AE-conotoxins-at-human-neuronal-nicotinic-acetylcholine-receptors
#12
Nargis Tabassum, Han-Shen Tae, Xinying Jia, Quentin Kaas, Tao Jiang, David J Adams, Rilei Yu
α-Conotoxins preferentially antagonize muscle and neuronal nicotinic acetylcholine receptors (nAChRs). Native α-conotoxins have two disulfide links, CI -CIII and CII -CIV , and owing to the inherent properties of disulfide bonds, α-conotoxins have been systematically engineered to improve their chemical and biological properties. In this study, we explored the possibility of simplifying the disulfide framework of α-conotoxins Vc1.1, BuIA, ImI, and AuIB, by introducing [C2H,C8F] modification to the CI -CIII bond...
August 31, 2017: ACS Omega
https://www.readbyqxmd.com/read/30008502/mathematical-modelling-of-expanded-bed-adsorption-a-perspective-on-in-silico-process-design
#13
Victor Koppejan, Guilherme Ferreira, Dong-Qiang Lin, Marcel Ottens
Expanded bed adsorption (EBA) emerged in the early 1990s in an attempt to integrate the clarification, capture and initial product concentration/purification process. Several mathematical models have been put forward to describe its operation. However, none of the models developed specifically for EBA allows simultaneous prediction of bed hydrodynamics, mass transfer/adsorption and (unwanted) interactions and fouling. This currently limits the development and early optimization of EBA-based separation processes...
July 2018: Journal of Chemical Technology and Biotechnology
https://www.readbyqxmd.com/read/30006550/influence-of-atomic-site-specific-strain-on-catalytic-activity-of-supported-nanoparticles
#14
Torben Nilsson Pingel, Mikkel Jørgensen, Andrew B Yankovich, Henrik Grönbeck, Eva Olsson
Heterogeneous catalysis is an enabling technology that utilises transition metal nanoparticles (NPs) supported on oxides to promote chemical reactions. Structural mismatch at the NP-support interface generates lattice strain that could affect catalytic properties. However, detailed knowledge about strain in supported NPs remains elusive. We experimentally measure the strain at interfaces, surfaces and defects in Pt NPs supported on alumina and ceria with atomic resolution using high-precision scanning transmission electron microscopy...
July 13, 2018: Nature Communications
https://www.readbyqxmd.com/read/29994771/computational-models-for-trapping-ebola-virus-using-engineered-bacteria
#15
Daniel Perez Martins, Michael Barros, Massimiliano Pierobon, Meenakshisundaram Kandhavelu, Pietro Lio, Sasitharan Balasubramaniam
The outbreak of Ebola virus in recent years has resulted in numerous research initiatives to seek new solutions to contain the virus. A number of approaches that have been investigated include new vaccines to boost the immune system. An alternative post-exposure treatment is presented in this paper. The proposed approach for clearing Ebola virus can be developed through a microfluidic attenuator, which contains the engineered bacteria that traps Ebola flowing through the blood onto its membrane. The paper presents the analysis of the chemical binding force between the virus and a genetically engineered bacterium considering the opposing forces acting on the attachment point, including hydrodynamic tension and drag force...
May 15, 2018: IEEE/ACM Transactions on Computational Biology and Bioinformatics
https://www.readbyqxmd.com/read/29944342/laser-ablation-as-a-versatile-tool-to-mimic-polyethylene-terephthalate-nanoplastic-pollutants-characterization-and-toxicology-assessment
#16
Davide Magrì, Paola Sánchez-Moreno, Gianvito Caputo, Francesca Gatto, Marina Veronesi, Giuseppe Bardi, Tiziano Catelani, Daniela Guarnieri, Athanassia Athanassiou, Pier Paolo Pompa, Despina Fragouli
The presence of micro- and nanoplastics in the marine environment is raising strong concerns since they can possibly have a negative impact on human health. In particular, the lack of appropriate methodologies to collect the nanoplastics from water systems imposes the use of engineered model nanoparticles to explore their interactions with biological systems, with results not easily correlated with the real case conditions. In this work, we propose a reliable top-down approach based on laser ablation of polymers to form polyethylene terephthalate (PET) nanoplastics, which mimic real environmental nanopollutants, unlike synthetic samples obtained by colloidal chemistry...
June 26, 2018: ACS Nano
https://www.readbyqxmd.com/read/29939009/engineering-the-slow-photon-effect-in-photoactive-nanoporous-anodic-alumina-gradient-index-filters-for-photocatalysis
#17
Siew Yee Lim, Cheryl Suwen Law, Marijana Markovic, Jason K Kirby, Andrew D Abell, Abel Santos
In this study, we explore for the first time the capabilities of nanoporous anodic alumina gradient-index filters (NAA-GIFs) functionalized with titanium dioxide (TiO2 ) photoactive layers to enhance photon-to-electron conversion rates and improve the efficiency of photocatalytic reactions by "slow photon" effect. A set of NAA-GIFs was fabricated by sinusoidal pulse anodization, in which a systematic modification of various anodization parameters (i.e., pore widening time, anodization period, and anodization time) enables the fine-tuning of the photonic stopband (PSB) of these nanoporous photonic crystals (PCs) across the spectral regions...
July 18, 2018: ACS Applied Materials & Interfaces
https://www.readbyqxmd.com/read/29922773/the-confined-bmim-bf-4-ionic-liquid-flow-through-graphene-oxide-nanochannels-a-molecular-dynamics-study
#18
Yanlei Wang, Feng Huo, Hongyan He, Suojiang Zhang
Ionic liquid (IL) flow in graphene oxide (GO) nanochannels plays a key role in the performance of IL- and GO-based fluidics devices and other chemical separator techniques. Here, we investigate the flow behavior of ILs in GO nanochannels via molecular dynamics simulations. The quantitative relation between slip velocity and shear stress has been identified, showing that the interfacial friction coefficient can be enhanced by almost sixty times, while the slip length is reduced by about three orders of magnitude, with the fraction of hydroxylation in graphene ranging from 0% to 15%...
July 4, 2018: Physical Chemistry Chemical Physics: PCCP
https://www.readbyqxmd.com/read/29908501/review-of-modelling-air-pollution-from-traffic-at-street-level-the-state-of-the-science
#19
REVIEW
H Forehead, N Huynh
Traffic emissions are a complex and variable cocktail of toxic chemicals. They are the major source of atmospheric pollution in the parts of cities where people live, commute and work. Reducing exposure requires information about the distribution and nature of emissions. Spatially and temporally detailed data are required, because both the rate of production and the composition of emissions vary significantly with time of day and with local changes in wind, traffic composition and flow. Increasing computer processing power means that models can accept highly detailed inputs of fleet, fuels and road networks...
October 2018: Environmental Pollution
https://www.readbyqxmd.com/read/29891310/comparison-of-nanocrystals-and-nanofibers-produced-from-shrimp-shell-%C3%AE-chitin-from-energy-production-to-material-cytotoxicity-and-pickering-emulsion-properties
#20
Fatma Larbi, Araceli García, Luis J Del Valle, Ahmed Hamou, Jordi Puiggalí, Naceur Belgacem, Julien Bras
Chitin nanocrystals (ChNCs) and chitin nanofibers (ChNFs) are nanomaterials with great innovative potential for sustainable applications in academic and industrial fields. The research related to their isolation and production, characterization, and utilization is still new. The aim of this study is to investigate the effects of the production process on the morphology and properties of ChNFs and ChNCs produced from the same source of chitin. ChNCs were prepared by acid hydrolysis of commercial shrimp shell α-chitin, and ChNFs were prepared by mechanical defibrillation using closed loop supermass colloidal grinding...
September 15, 2018: Carbohydrate Polymers
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