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A computational toolbox for molecular property prediction based on quantum mechanics and quantitativestructure-property relationship

《化学科学与工程前沿（英文）》 2022年第16卷第2期页码 152-167 doi: 10.1007/s11705-021-2060-z

摘要： Chemical industry is always seeking opportunities to efficiently and economically convert raw materials to commodity chemicals and higher value-added chemical-based products. The life cycles of chemical products involve the procedures of conceptual product designs, experimental investigations, sustainable manufactures through appropriate chemical processes and waste disposals. During these periods, one of the most important keys is the molecular property prediction models associating molecular structures with product properties. In this paper, a framework combining quantum mechanics and quantitative structure-property relationship is established for fast molecular property predictions, such as activity coefficient, and so forth. The workflow of framework consists of three steps. In the first step, a database is created for collections of basic molecular information; in the second step, quantum mechanics-based calculations are performed to predict quantum mechanics-based/derived molecular properties (pseudo experimental data), which are stored in a database and further provided for the developments of quantitative structure-property relationship methods for fast predictions of properties in the third step. The whole framework has been carried out within a molecular property prediction toolbox. Two case studies highlighting different aspects of the toolbox involving the predictions of heats of reaction and solid-liquid phase equilibriums are presented.

关键词： molecular property quantum mechanics quantitative structure-property relationship heat of reaction solid-liquid phase equilibrium

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Effect of / molecular structures on pyrolysis performance and heat sink of decalin isomers

《化学科学与工程前沿（英文）》 2023年第18卷第1期 doi: 10.1007/s11705-023-2375-z

摘要： Decalin is considered as an important compound of high-energy-density endothermic fuel, which is an ideal on-board coolant for thermal management of advanced aircraft. However, decalin contains two isomers with a tunable composition, and their effects on the pyrolysis performance, such as the heat sink and coking tendency have not been demonstrated. Herein, we investigated the pyrolysis of decalin isomers, i.e., cis-decalin, trans-decalin and their mixtures (denoted as mix-decalin), in order to clarify the effects of the cis-/trans-structures on the pyrolysis performance of decalin fuels. The pyrolysis results confirmed that conversion of the tested fuels (600–725 °C, 4 MPa) decreased in the order cis-decalin > mix-decalin > trans-decalin. Detailed analyses of the pyrolysis products were used to compare the product distributions from cis-decalin, mix-decalin and trans-decalin, and the yields of some typical components (such as cyclohexene, 1-methylcyclohexene, benzene and toluene) showed significant differences, which could be ascribed to deeper cracking of cis-decalin. Additionally, the heat sinks and coking tendencies of the decalins decreased in the order cis-decalin > mix-decalin > trans-decalin. This work demonstrates the relationship between the cis/trans structures and the pyrolysis performance of decalin, which provides a better understanding of the structure-activity relationships of endothermic hydrocarbon fuels.

关键词： endothermic fuel decalin pyrolysis heat sink molecular structure

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关于浮选药剂的梦想 ——浮选药剂结构-性能关系和分子设计

王淀佐,姚国成

《中国工程科学》 2011年第13卷第3期页码 4-11

摘要：

泡沫浮选技术从20世纪初开始规模工业应用，是矿产资源高效利用的重要手段。浮选药剂是这一技术的科学基础和关键。文章介绍并讨论了浮选药剂的结构-性能定量关系及药剂分子设计的研究历程和新进展。

关键词：选矿浮选药剂结构性能分子设计

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饲料的分子结构与动物营养物质利用率和有效性的关系——一种新方法

俞培强, Luciana L. Prates

《工程（英文）》 2017年第3卷第5期页码 726-730 doi: 10.1016/J.ENG.2017.03.007

摘要：

新的研究思路、研究方法和生物分析技术的创造和发展对动物科学（包括饲料和营养科学）的进步是必不可少的。本文介绍了以同步加速器为基础的先进生物分析技术作为一项崭新的研究工具，在研究由多种处理（如基因修饰、基因沉默、饲料的热加工处理、生物燃料加工等）诱导的饲料分子结构变化与动物消化吸收饲料营养物质的关系方面的潜在应用。以同步辐射为基础的先进技术[如同步辐射红外显微光谱技术（synchrotron radiation infrared microspectroscopy，SR-IMS）和同步辐射X射线技术]作为一种快速、无损的生物分析技术被开发利用。与传统的湿化学法不同，同步辐射技术不会破坏饲料内在的分子结构。尖端和先进的同步加速器光源（是日光的上百万倍）能够以超高分辨率在细胞和分子水平上探测生物组织的内在结构。总的来说，最近开发的基于同步辐射的生物分析技术结合常用的研究技术将带来动物饲料和营养研究的巨大进步。

关键词：内部分子结构同步辐射应用分子营养饲料科学技术分子成像养分消化与吸收

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Effect of ambient polycyclic aromatic hydrocarbons and nicotine on the structure of Aβ protein

《环境科学与工程前沿（英文）》 2023年第17卷第2期 doi: 10.1007/s11783-023-1615-2

摘要：

● B[a]P, nicotine and phenanthrene molecules altered the secondary structure of Aβ₄₂.

关键词： Polycyclic aromatic hydrocarbons Nicotine toxicology Aβ₄₂ peptide Alzheimer’s disease Molecular dynamics simulations Environmental pollution

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Crk-associated substrate, vascular smooth muscle and hypertension

TANG Dale

《医学前沿（英文）》 2008年第2卷第4期页码 323-331 doi: 10.1007/s11684-008-0062-6

摘要： Hypertension is characterized by vascular smooth muscle constriction and vascular remodeling involving cell migration, hypertrophy and growth. Crk-associated substrate (CAS), the first discovered member of the adapter protein CAS family, has been shown to be a critical cellular component that regulates various smooth muscle functions. In this review, the molecular structure and protein interactions of the CAS family members are summarized. Evidence for the role of CAS in the regulation of vascular smooth muscle contractility is presented. Contraction stimulation induces CAS phosphorylation on Tyr-410 in arterial smooth muscle, creating the binding site for the Src homology (SH) 2/SH3 protein CrkII, which activates neuronal Wiskott-Aldrich syndrome protein (N-WASP)-mediated actin assembly and force development. The functions of CAS in cell migration, hypertrophy and growth are also summarized. Abelson tyrosine kinase (Abl), c-Src, focal adhesion kinase (FAK), proline-rich tyrosine kinase 2 (PYK2), protein tyrosine phosphatase-proline, glutamate, serine and threonine sequence protein (PTP-PEST) and SHP-2 have been documented to coordinate the phosphorylation and dephosphorylation of CAS. The downstream signaling partners of CAS in the context of cell motility, hypertrophy, survival and growth are also discussed. These new findings establish the important role of CAS in the modulation of vascular smooth muscle functions. Furthermore, the upstream regulators of CAS may be new biologic targets for the development of more effective and specific treatment of cardiovascular diseases such as hypertension.

关键词： Contraction stimulation phosphatase-proline molecular structure discovered hypertension

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Study on the gas permeabilities in styrene-butadiene rubber by molecular dynamics simulation

Hailu LIU, Xuejia DING, Jun YI, Liqun ZHANG, Sizhu WU,

《化学科学与工程前沿（英文）》 2010年第4卷第3期页码 257-262 doi: 10.1007/s11705-009-0270-x

摘要： In this research, molecular dynamics (MD)simulations were used to study the transport properties of small gas molecules in the butadiene-styrene copolymer(SBR). The condensed-phase optimized molecular potentials for atomistic simulation studies (COMPASS) force field was applied. The diffusion coefficients were obtained from MD (NVT ensemble) and the relationship between gas permeability; the chemical structure and free volume of butadiene-styrene copolymer were investigated. The results indicated that the diffusion coefficient of oxygen declined with increasing styrene content. The fraction of free volume (FFV) in butadiene-styrene copolymer was calculated. It was concluded that diffusion coefficient increased as the FFV increases, which is in accordance with the analysis of the small molecular hop through the free volume in polymer matrix. Subsequently, the glass transition temperatures of these copolymers were calculated by MD. The result showed that the glass transition temperature increased with increasing styrene content in polymer.

关键词： diffusion atomistic simulation permeability chemical structure relationship

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Special issue on “Molecular Sensors and Molecular Logic Gates”

Luling Wu , Tony D. James

《化学科学与工程前沿（英文）》 2022年第16卷第1期页码 1-3 doi: 10.1007/s11705-021-2134-y

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Design of bio-oil additives via molecular signature descriptors using a multi-stage computer-aided molecular

《化学科学与工程前沿（英文）》 2022年第16卷第2期页码 168-182 doi: 10.1007/s11705-021-2056-8

摘要： Direct application of bio-oil from fast pyrolysis as a fuel has remained a challenge due to its undesirable attributes such as low heating value, high viscosity, high corrosiveness and storage instability. Solvent addition is a simple method for circumventing these disadvantages to allow further processing and storage. In this work, computer-aided molecular design tools were developed to design optimal solvents to upgrade bio-oil whilst having low environmental impact. Firstly, target solvent requirements were translated into measurable physical properties. As different property prediction models consist different levels of structural information, molecular signature descriptor was used as a common platform to formulate the design problem. Because of the differences in the required structural information of different property prediction models, signatures of different heights were needed in formulating the design problem. Due to the combinatorial nature of higher-order signatures, the complexity of a computer-aided molecular design problem increases with the height of signatures. Thus, a multi-stage framework was developed by developing consistency rules that restrict the number of higher-order signatures. Finally, phase stability analysis was conducted to evaluate the stability of the solvent-oil blend. As a result, optimal solvents that improve the solvent-oil blend properties while displaying low environmental impact were identified.

关键词： computer-aided molecular design bio-oil additives molecular signature descriptor

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Progress on molecular biomarkers and classification of malignant gliomas

null

《医学前沿（英文）》 2013年第7卷第2期页码 150-156 doi: 10.1007/s11684-013-0267-1

摘要：

Gliomas are the most common primary intracranial tumors in adults. Anaplastic gliomas (WHO grade III) and glioblastomas (WHO grade IV) represent the major groups of malignant gliomas in the brain. Several diagnostic, predictive, and prognostic biomarkers for malignant gliomas have been reported over the last few decades, and these markers have made great contributions to the accuracy of diagnosis, therapeutic decision making, and prognosis of patients. However, heterogeneity in patient outcomes may still be observed, which highlights the insufficiency of a classification system based purely on histopathology. Great efforts have been made to incorporate new information about the molecular landscape of gliomas into novel classifications that may potentially guide treatment. In this review, we summarize three distinctive biomarkers, three most commonly altered pathways, and three classifications based on microarray data in malignant gliomas.

关键词： malignant glioma molecular biomarker IDH1 MGMT molecular classification

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Molecular classification and molecular targeted therapy of cancer

null

《医学前沿（英文）》 2013年第7卷第2期页码 147-149 doi: 10.1007/s11684-013-0274-2

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分子电子学的发展 Review

Paven Thomas Mathew, 房丰洲

《工程（英文）》 2018年第4卷第6期页码 760-771 doi: 10.1016/j.eng.2018.11.001

摘要：

分子电子学（moletronics）是用分子作为单元对分子电子学器件进行装配。这是一个包含物理、化学、材料科学及工程等学科的多学科交叉领域。分子电子学致力于使硅元件尺寸进一步减小。科学家已经在等效分子器件方面进行了诸多探索性研究。分子电子学在电子以及光子应用中逐渐产生影响，如导电聚合物、光色材料、有机超导体、电致变色材料等。为了满足减小硅片尺寸的需求，研究人员有必要将这种新型技术引入到分子层面。虽然分子层面仪器的实验验证和建模分析是一项艰巨的任务，但分子电子学领域依然出现了突破性进展。本文将对不同分子器件和潜在的适用于不同器件的分子应用结合起来进行讨论，如分子晶体管、分子二极管、分子电容、分子导线和分子绝缘体等。本文简要讨论未来的发展趋势以及介绍各种基于石墨烯已取得一定研究成果的分子仪器。

关键词：分子电子学分子晶体管分子二极管分子电容器分子导线石墨烯

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Molecular size characterization of heavy oil fractions in vacuum and solution by molecular dynamic simulation

Wenpo REN, Honggang CHEN, Chaohe YANG, Honghong SHAN,

《化学科学与工程前沿（英文）》 2010年第4卷第3期页码 250-256 doi: 10.1007/s11705-009-0281-7

摘要： Two kinds of heavy oils were fractionated into eight fractions by Liquid-Solid Adsorption Chromatography, respectively, and samples were collected to measure properties. According to the elemental analysis, molecular weight and H-NMR data, average molecular structures of polycyclic aromatic and heavy resin were constructed with improved Brown-Ladner (B-L) method and several corrections. And then, the most stable conformations of polycyclic aromatic and heavy resin in vacuum and toluene solution were obtained by molecular dynamic simulation, and the molecular size was gotten via the radius of gyration analysis. The results showed that the radius of gyration of polycyclic aromatic and heavy resin was 0.55–0.70 nm in vacuum and 0.60–0.90 nm in toluene solution. With molecular weight increasing, the molecular size in vacuum and toluene solution also increased. Due to the swelling behavior of solvent, the alkyl side chains of heavy oil molecule in solution were more stretched. Thus, the molecular size in toluene solution was larger than that in vacuum.

关键词： dynamic simulation molecular dynamic behavior molecule Adsorption Chromatography

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Enhanced separation of tetrafluoropropanol from water via carbon nanotubes membranes: insights from molecular

《环境科学与工程前沿（英文）》 2023年第17卷第11期 doi: 10.1007/s11783-023-1740-y

摘要：

● MD simulations unveil the transport mechanism for TFP-water mixture through CNTs.

关键词： Fluorinated alcohol Carbon nanotube Molecular simulation Fluorine modified

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Effect of ligand chain length on hydrophobic charge induction chromatography revealed by molecular dynamics

Lin ZHANG, Yan SUN

《化学科学与工程前沿（英文）》 2013年第7卷第4期页码 456-463 doi: 10.1007/s11705-013-1357-y

摘要： Hydrophobic charge induction chromatography (HCIC) is a mixed-mode chromatography which is advantageous for high adsorption capacity and facile elution. The effect of the ligand chain length on protein behavior in HCIC was studied. A coarse-grain adsorbent pore model established in an earlier work was modified to construct adsorbents with different chain lengths, including one with shorter ligands (CL2) and one with longer ligands (CL4). The adsorption, desorption, and conformational transition of the proteins with CL2 and CL4 were examined using molecular dynamics simulations. The ligand chain length has a significant effect on both the probability and the irreversibility of the adsorption/desorption. Longer ligands reduced the energy barrier of adsorption, leading to stronger and more irreversible adsorption, as well as a little more unfolding of the protein. The simulation results elucidated the effect of the ligand chain length, which is beneficial for the rational design of adsorbents and parameter optimization for high-performance HCIC.

关键词： adsorption desorption irreversibility protein conformational transition molecular dynamics simulation