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Chemical Engineering Simulation

Ilya G Ryabinkin, Scott N Genin, Artur F Izmaylov
Variational quantum eigensolver (VQE) is an efficient computational method promising chemical accuracy in electronic structure calculations on a universal-gate quantum computer. However, such a simple task as computing the electronic energy of a hydrogen molecular cation, H+2 , is not possible for a general VQE protocol because the calculation will invariably collapse to a lower energy of the corresponding neutral form, H2. The origin of the problem is that VQE effectively performs an unconstrained energy optimization in the Fock space of the original electronic problem...
December 4, 2018: Journal of Chemical Theory and Computation
You Lu, Matthew R Farrow, Pierre Fayon, Andrew J Logsdail, Alexey A Sokol, C Richard A Catlow, Paul Sherwood, Thomas W Keal
ChemShell is a scriptable computational chemistry environment with an emphasis on multiscale simulation of complex systems using combined quantum mechanical and molecular mechanical (QM/MM) methods. Motivated by a scientific need to efficiently and accurately model chemical reactions on surfaces and within microporous solids on massively parallel computing systems, we present a major redevelopment of the ChemShell code, which provides a modern platform for advanced QM/MM embedding models. The new version of ChemShell has been re-engineered from the ground up with a new QM/MM driver module, an improved parallelization framework, new interfaces to high performance QM and MM programs, and a user interface written in the Python programming language...
December 4, 2018: Journal of Chemical Theory and Computation
Guochen Bao, Ka-Leung Wong, Dayong Jin, Peter A Tanner
The optical thermometer has shown great promise for use in the fields of aeronautical engineering, environmental monitoring and medical diagnosis. Self-referencing lanthanide thermo-probes distinguish themselves because of their accuracy, calibration, photostability, and temporal dimension of signal. However, the use of conventional lanthanide-doped materials is limited by their poor reproducibility, random distance between energy transfer pairs and interference by energy migration, thereby restricting their utility...
2018: Light, Science & Applications
Linfeng Fei, Xianglai Gan, Sheung Mei Ng, Hui Wang, Ming Xu, Wei Lu, Yanchun Zhou, Chi Wah Leung, Chee-Leung Mak, Yu Wang
The nucleation of crystals from ubiquitous solid-state reactions impacts a wide range of natural and synthetic processes and is fundamental to physical and chemical synthesis. However, the microscopic organization mechanism of amorphous precursors to nanoscale clusters of ordered atoms (nucleus) in an all-solid environment is inaccessible by common experimental probes. Here, by using in situ transmission electron microscopy in combination with theoretical simulations, we show in the reactive formation of a metal carbide that nucleation actually occurs via a two-step mechanism, in which a spinodal-structured amorphous intermediate reorganizes from an amorphous precursor and precedes the emergence of a crystalline nucleus, rather than direct one-step nucleation from classical consideration...
November 30, 2018: ACS Nano
Alex Alves Bandeira, Karla Oliveira Esquerre, Aline Alves Bandeira, Roxana Cardoso Brasileiro Borges
Environmental pollution analysis should be present in scientific research. The more organized the environmental laws of a particular place, the smaller the risks imputed to the ecosystem. The environmental damages that irregular waste from industrial effluents can cause are notorious. However, Brazil lacks extensive legal regulation, which is an embryonic legal matter. There is no specific law regulating a National Industrial Effluent Policy, dealing with the treatment and final disposal of these chemical compounds...
November 24, 2018: Environmental Science and Pollution Research International
Yingjie Wang, Wei Zhu, Ke Xiao, Zeng Li, Qi Ma, Weifeng Li, Songpo Shen, Xisheng Weng
BACKGROUND: HA modified by bisphosphonate (BP) (HA-BP) was synthesized by chemical reaction and possessed promising properties such as self-healing, injection ability, and strong adhesion. The main aim of this study was to confirm its role in promoting osteogenic differentiation in vitro and bone regeneration in vivo. METHODS: The cell biocompatibility of this material was determined using the CCK-8 assay. Alkaline phosphatase (ALP), osteocalcin (OT), vascular endothelial growth factor (VEGF), and collagen I were assessed by quantitative real-time polymerase chain reaction (Q-PCR) in the treated group...
November 20, 2018: Biochemical and Biophysical Research Communications
Jingyu Liu, Fan Zhang, Andrew J Allen, Aaron C Johnston-Peck, John M Pettibone
Reported reaction kinetics of metal nanoparticles in natural and engineered systems commonly have used proxy measurements to infer chemical transformations, but extension of these methods to complex media has proven difficult. Here, we compare the sulfidation rate of AgNPs using two ion selective electrode (ISE)-based methods, which rely on either (i) direct measurement of free sulfide, or (ii) monitor the free Ag+ available in solution over time in the presence of sulfide species. Most experiments were carried out in moderately hard reconstituted water at pH 7 containing fulvic acid or humic acid, which represented a broad set of known interferences in ISE...
November 22, 2018: Nanoscale
Elyas M Moghaddam, Esmail A Foumeny, Andrzej I Stankiewicz, Johan T Padding
Despite the common use of nonspherical catalyst pellets in chemical engineering applications, the packing structures of such pellets have not been as systematically studied and characterized as spherical packings. We propose a packing algorithm based on rigid body dynamics to simulate packing of nonspherical and possibly nonconvex pellets. The algorithm exerts a hard-body approach to model collision phenomena. The novelty is that the transition between moving and resting particles is controlled by a cutoff on the relative contact velocities, instead of artificially damping linear and angular velocities to stabilize the algorithm...
November 7, 2018: Industrial & Engineering Chemistry Research
Murat Erkurt
The development of form in an embryo is the result of a series of topological and informational symmetry breakings. We introduce the vector-reaction-diffusion-drift (VRDD) system where the limit cycle of spatial dynamics is morphogen concentrations with Dirac delta-type distributions. This is fundamentally different from the Turing reaction-diffusion system, as VRDD generates system-wide broken symmetry. We developed 'fundamental forms' from spherical blastula with a single organizing axis (rotational symmetry), double axis (mirror symmetry) and triple axis (no symmetry operator in three dimensions)...
November 14, 2018: Journal of the Royal Society, Interface
Xingquan Zou, Shuai Wei, Somayesadat Badieyan, McKenna Schroeder, Joshua Jasensky, Charles L Brooks, E Neil G Marsh, Zhan Chen
Immobilization on solid supports provides an effective way to improve enzyme stability and simplify downstream processing for biotechnological applications, which has been widely used in research and in applications. However, surface immobilization may disrupt enzyme structure due to interactions between the enzyme and the supporting substrate, leading to a loss of the enzyme catalytic efficiency and stability. Here, we use a model enzyme, nitroreductase (NfsB), to demonstrate that engineered variants with two strategically positioned surface-tethering sites exhibit improved enzyme stability when covalently immobilized onto a surface...
November 19, 2018: Journal of the American Chemical Society
Bowei Dong, Ting Hu, Xianshu Luo, Yuhua Chang, Xin Guo, Hong Wang, Dim-Lee Kwong, Guo-Qiang Lo, Chengkuo Lee
In this paper, we report a compact wavelength-flattened directional coupler (WFDC) based chemical sensor featuring an incorporated subwavelength grating (SWG) structure for the mid-infrared (MIR). By incorporating a SWG structure into directional coupler (DC), the dispersion in DC can be engineered to allow broadband operation which is advantageous to extract spectroscopic information for MIR sensing analysis. Meanwhile, the Bragg reflection introduced by the SWG structure produces a sharp trough at the Bragg wavelength...
November 1, 2018: Nanomaterials
Jiangang Yang, Yueming Zhu, Ge Qu, Yan Zeng, Chaoyu Tian, Caixia Dong, Yan Men, Longhai Dai, Zhoutong Sun, Yuanxia Sun, Yanhe Ma
Background: Asymmetric aldol-type C-C bond formation with ketones used as electrophilic receptor remains a challenging reaction for aldolases as biocatalysts. To date, only one kind of dihydroxyacetone phosphate (DHAP)-dependent aldolases has been discovered and applied to synthesize branched-chain sugars directly using DHAP and dihydroxyacetone (DHA) as substrate. However, the unstable and high-cost properties of DHAP limit large-scale application. Therefore, biosynthesis of branched-chain sugar from low-cost and abundant carbon sources is essential...
2018: Biotechnology for Biofuels
Abdulhameed Al-Ghabkari, Lori D Moffat, Michael P Walsh, Justin A MacDonald
Zipper-interacting protein kinase (ZIPK) is a Ser/Thr kinase that mediates a variety of cellular functions. Analogue-sensitive kinase technology was applied to the study of ZIPK signaling in coronary artery smooth muscle cells. ZIPK was engineered in the ATP-binding pocket by substitution of a bulky gatekeeper amino acid (Leu93) with glycine. Cell-permeable derivatives of pyrazolo[3,4-d]pyrimidine provided effective inhibition of L93G-ZIPK (1NM-PP1, IC50 , 1.0 μM; 3MB-PP1, IC50 , 2.0 μM; and 1NA-PP1, IC50 , 8...
November 1, 2018: Proteins
Liang Zhu
Despite more than 80 years of animal experiments and clinical practice, efficacy of hypothermia in improving treatment outcomes in patients suffering from cell and tissue damage caused by ischemia is still ongoing. This review will first describe the history of utilizing cooling in medical treatment, followed by chemical and biochemical mechanisms of cooling that can lead to neuroprotection often observed in animal studies and some clinical studies. The next sections will be focused on current cooling approaches/devices, as well as cooling parameters recommended by researchers and clinicians...
2018: Advances in Experimental Medicine and Biology
Dongzheng Yang, Xixi Hu, Daiqian Xie
The rate constants for H2 -HF energy transfer processes, especially for those in vibrationally excited states, are very demanding in astrophysics and chemical laser engineering, especially for those in vibrationally excited states. Based on our recent potential energy surface, we used the coupled-states approximation including the nearest neighboring Coriolis couplings with energy-based local basis set to perform dynamics calculation for the H2 -HF energy transfer system. Rate constants for vibrational transitions (1; 3) → (0; 4), (1; 3) → (2; 2), and (0; 3) → (1; 2) were obtained...
October 11, 2018: Journal of Computational Chemistry
Yuan Li, Marek B Majewski, Saiful M Islam, Shiqiang Hao, Akshay A Murthy, Jennifer G DiStefano, Eve D Hanson, Yaobin Xu, Chris Wolverton, Mercouri G Kanatzidis, Michael R Wasielewski, Xinqi Chen, Vinayak P Dravid
Molybdenum disulfide (MoS2 ) has been recognized as a promising cost-effective catalyst for water-splitting hydrogen production. However, the desired performance of MoS2 is often limited by insufficient edge-terminated active sites, poor electrical conductivity, and inefficient contact to the supporting substrate. To address these limitations, we developed a unique nanoarchitecture (namely, winged Au@MoS2 heterostructures enabled by our discovery of the "seeding effect" of Au nanoparticles for the chemical vapor deposition synthesis of vertically aligned few-layer MoS2 wings)...
November 14, 2018: Nano Letters
Rafael S Costa, Susana Vinga
Over the last years, several genome-scale metabolic models (GEMs) and kinetic models of Escherichia coli were published. Their predictive performance varies according to the evaluation metric considered, the computational simulation methods used, and the type/quality of experimental data available. However, the GEM approach is often not compared with the kinetic modeling framework. Also, the different genome-scale reconstruction versions and simulation methods of mutant phenotypes are usually not validated to predict intracellular fluxes using large experimental datasets...
October 7, 2018: Biotechnology Progress
Dhivyaa Anandan, S Mary Stella, N Arunai Nambiraj, U Vijayalakshmi, Amit Kumar Jaiswal
Cancellous bone region of the human native bone has the potential to bear significant mechanical loads. However, due to the following parameters such as low trabecular volume, more porosity, less thickness and more interconnectivity, cancellous bone is accessible to damage in accidents or when aging. This research led to the effective fabrication and engineering of cancellous region of the bone for its application in reconstruction or filling of bone voids after resection of large tumor mass. Scaffolds containing hydroxyapatite (HAp), polyvinyl alcohol (PVA) and polyvinyl pyrrolidone (PVP) (5% polymer and HAp concentrations) at different HAp: polymer composite ratios (50:50, 70:30 and 80:20), were fabricated by freeze-drying method using only water as solvent and ribose as crosslinker for the scaffolds...
December 2018: Journal of Biomedical Materials Research. Part A
Enming Song, Rui Li, Xin Jin, Haina Du, Yuming Huang, Jize Zhang, Yu Xia, Hui Fang, Yoon Kyeung Lee, Ki Jun Yu, Jan-Kai Chang, Yongfeng Mei, Muhammad A Alam, Yonggang Huang, John A Rogers
Biomedical implants that incorporate active electronics and offer the ability to operate in a safe, stable fashion for long periods of time must incorporate defect-free layers as barriers to biofluid penetration. This paper reports an engineered material approach to this challenge that combines ultrathin, physically transferred films of silicon dioxide (t-SiO2 ) thermally grown on silicon wafers, with layers of hafnium oxide (HfO2 ) formed by atomic layer deposition and coatings of parylene (Parylene C) created by chemical vapor deposition, as a dual-sided encapsulation structure for flexible bioelectronic systems...
October 5, 2018: ACS Nano
William R Smith, Weikai Qi
The molecular simulation of chemical reaction equilibrium (CRE) is a challenging and important problem of broad applicability in chemistry and chemical engineering. The primary molecular-based approach for solving this problem has been the reaction ensemble Monte Carlo (REMC) algorithm [Turner et al. Molec. Simulation2008, 34, (2), 119-146], based on classical force-field methodology. In spite of the vast improvements in computer hardware and software since its original development almost 25 years ago, its more widespread application is impeded by its computational inefficiency...
September 26, 2018: ACS Central Science
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