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Molecular simulation of the interaction mechanism between CodY protein and DNA in

Linchen Yuan, Hao Wu, Yue Zhao, Xiaoyu Qin, Yanni Li

《化学科学与工程前沿（英文）》 2019年第13卷第1期页码 133-139 doi: 10.1007/s11705-018-1737-4

摘要： In , the global transcriptional regulatory factor CodY can interact with the promoter DNA to regulate the growth, metabolism, environmental adaptation and other biological activities of the strains. In order to study the mechanism of interaction between CodY and its target DNA, molecular docking and molecular dynamics simulations were used to explore the binding process at molecular level. Through the calculations of the free energy of binding, hydrogen bonding and energy decomposition, nine key residues of CodY were identified, corresponding to SER184, SER186, SER208, THR217, ARG218, SER219, ASN223, LYS242 and GLY243, among which SER186, ARG218 and LYS242 play a vital role in DNA binding. Our research results provide important theoretical guidance for using wet-lab methods to study and optimize the metabolic network regulated by CodY.

关键词： CodY DNA molecular docking molecular dynamics

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Synthesis, molecular docking and antibacterial evaluation of 2-(4-(4-aminophenylsulfonyl)phenylamino)

Palanisamy RAVICHANDIRAN, Dhanaraj PREMNATH, Samuel VASANTHKUMAR

《化学科学与工程前沿（英文）》 2015年第9卷第1期页码 46-56 doi: 10.1007/s11705-015-1506-6

摘要： A new series of 2-(4-(4-aminophenylsulfonyl)phenylamino)-3-(thiophen-2-ylthio)naphthalene-1,4-dione derivatives ( 3a-3n) were synthesized and characterized by spectral techniques. To understand the interaction of binding sites with bacterial protein receptor, the docking study was performed by the GLIDE program and compound -(4-(4-(1,4-dioxo-3-(thiophen-2-ylthio)-1,4-dihydronaphthalen-2-ylamino)phenylsulfonyl)phenyl)-3-methylbenzamide ( 3b) exhibited good glide and E model scores of ?5.89 and ?94.90, respectively. Moreover among all the molecules studied including the standards used, namely Sparfloxacin (4.8 μg/mL) and Norfloxacin (no inhibition observed) for their antibacterial property, compound -(4-(4-(1,4-dioxo-3-(thiophen-2-ylthio)-1,4-dihydronaphthalen-2-ylamino)phenylsulfonyl)phenyl)-4-nitrobenzamide ( 3e) exhibited the lowest minimum inhibitory concentration (MIC) value of 1.3 μg/mL against .

关键词： MIC 2-thiophene thiol water as solvent acid chlorides sulfone

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一种新型葡激酶分子的设计基因构建表达纯化及性质研究

宋钢,于敏,莫炜,宋后燕

《中国工程科学》 2000年第2卷第11期页码 68-72

摘要：

在葡激酶构效关系的研究过程中发现，葡激酶易形成二聚体，甚至多聚体，不利于葡激酶的临床应用。为了探究聚合体的形成机制以研制不易聚合的新型葡激酶分子，在葡激酶X射线晶体衍射结构模型的基础上，采用分子对接软件GRAMM V1.03，以高分辨率整体对接方式预测了葡激酶二聚体可能的结合区。结合区主要有两种可能的形成方式，通过强疏水相互作用及氢键结合。根据模型设计了旨在降低聚合能力的葡激酶突变体RGD-Sak,将Fill置换为D111，并且改变K109为R109，恰好使分子中形成RGD结构，使新型分子还可能具有抑制血小板聚集作用。利用定点突变及DNA重组技术，构建了RGD-Sak基因，并利用大肠杆菌原核表达系统进行了高效表达。RGD-Sak以包涵体形式存在，包涵体经洗涤，8 mol/L尿素溶解，稀释复性，离子交换色谱一步分离得到电泳纯的RGD-Sak,纯度达95%以上，分子量与理论值相符，比活性5×10⁴HU/mg。RGD-Sak与纤溶酶形成的复合物催化纤溶酶原的Km、Kcat值分别为12.40 μmol/L、0.81 s^-1。RGD-Sak显示了很弱的聚合能力。此研究为研制防止二聚体形成的新型葡激酶分子打下了基础。

关键词：葡激酶二聚体分子对接分子设计定点突变

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Triggering the biocontrol of

Kandasamy SARAVANAKUMAR, Zhixiang LU, Hai XIA, Meng WANG, Jianan SUN, Shaoqing WANG, Qiang-qiang WANG, Yaqian LI, Jie CHEN

《农业科学与工程前沿（英文）》 2018年第5卷第2期页码 271-279 doi: 10.15302/J-FASE-2018214

摘要： This study reports a strain of CCTCC-SBW0162 with potential to enhance biocontrol activity against gray mold pathogen, , and with a pivotal role in tomato ( ) plant growth enhancement. A total of 254 isolates were screened by antagonistic assay. Of these, 10 were selected for greenhouse experiments based on their greater inhibition of . The antagonistic assay and greenhouse experiments indicated that CCTCC-SBW0162 gave the highest inhibition rate (90.6%) and disease reduction (80.7%). Also, to study the possible mechanism associated with antifungal activity of CCTCC-SBW0162 against , molecular docking was used to assess the interactions between CCTCC-SBW0162-derived metabolites, and pathogencity and virulence related proteins of . The molecular docking results indicated that the combination of harzianopyridone, harzianolide and anthraquinone C derived from CCTCC-SBW0162 could synergistically improve antifungal activity against through the inhibition/modification of pathogenicity and virulence related proteins. However, this computerized modeling work emphasized the need for further study in the laboratory to confirm the effect derived metabolites against the proteins of and their interactions.

关键词： anthraquinone Botrytis cinerea harzianolide harzianopyridone molecular docking Trichoderma harzianum

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含硫醚和砜亚结构的新型芳香酰胺类衍生物的设计、合成及生物活性 Article

华学文, 刘南南, 周沙, 张蕾蕾, 殷昊, 王桂清, 范志金, 马翼

《工程（英文）》 2020年第6卷第5期页码 553-559 doi: 10.1016/j.eng.2019.09.011

摘要：

近年来，土壤线虫危害日趋严重，然而市场上应用的杀线虫剂品种匮乏且结构单一。氟吡菌酰胺（fluopyram）是德国拜耳公司开发的琥珀酸脱氢酶抑制剂（SDHI）类杀菌剂，因其高效和作用机制新颖被广泛用于土壤线虫的防治。本文以杀菌、杀线虫剂氟吡菌酰胺为分子骨架，通过引入硫醚和砜亚结构，设计合成了两个系列的结构新颖的目标化合物，并经核磁共振氢谱（¹H NMR）、核磁共振碳谱（¹³C NMR）和高分辨质谱（HRMS）表征新结构。经生物活性测试发现，与对照药氟吡菌酰胺相比，大多数目标化合物在200 μg·mL⁻¹浓度下显示出优异的杀线虫活性，而当浓度降低为100 μg·mL⁻¹时，线虫死亡率大大降低，其中，化合物I-11、II-6除外。在杀菌活性方面，化合物I-9具有优异的抑菌率，其分子对接结果将为高活性杀菌先导化合物的设计和探索提供重要的理论指导。

关键词：合成杀线虫活性杀菌活性分子对接

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停留交会应用中减少邻居发现延迟 Research Articles

Shuai-zhao JIN, Zi-xiao WANG, Ya-bo DONG, Dong-ming LU

《信息与电子工程前沿（英文）》 2019年第20卷第8期页码 1147-1164 doi: 10.1631/FITEE.1800412

摘要：邻居发现在停留交会应用中十分重要。在停留交会应用中移动传感器节点与部署在不同交会点的固定传感器节点进行通信。在现有邻居发现协议中，概率性邻居发现协议在一般情况下表现良好，但存在非周期性、不可预测性和无限发现延迟。确定性邻居发现协议可牺牲平均邻居发现性能以提供最差情况下的邻居发现延迟。本文提出一种基于移动信息辅助的时槽同步技术，通过时槽同步提升确定性邻居发现协议的平均性能，同时不增加额外传感器节点能量开销。针对邻居发现中的信标帧冲突可能导致的邻居发现失败情况，提出一种优化的信标帧发送策略。通过理论分析和基于莫高窟游客追踪系统积累的实际数据，验证该基于移动信息辅助时槽同步技术的性能。实验结果表明，所提时槽同步技术最高可将目前最优的确定性邻居发现协议平均性能提升两个数量级。

关键词：邻居发现；停留交会应用；时槽同步；基于移动信息辅助的时槽同步

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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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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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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