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Molecular dynamic simulation on the conformation of mouse muscle type nAChR

Shengai SUN, Rilei YU, Yanhui ZHANG, Yanni LI,

《化学科学与工程前沿（英文）》 2010年 第4卷 第3期   页码 348-352 doi: 10.1007/s11705-009-0284-4

摘要： A mouse muscle type nAChR model ((α1)βδγ) was built based on the cryoelectron microscopic structure of intact nAChR and the high resolution crystal structure of nAChR-α1 subunit. The conformation of the pentameric nAChR model was investigated by molecular dynamic simulation. The function of water molecule in the hydrophilic interior was clarified. The reason for Tyr127 showing two alternative conformations was discussed in detail.

关键词： pentameric     hydrophilic     Tyr127     cryoelectron microscopic     conformation    

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Molecular network-based intervention brings us closer to ending the HIV pandemic

Xiaoxu Han, Bin Zhao, Minghui An, Ping Zhong, Hong Shang

《医学前沿（英文）》 2020年 第14卷 第2期   页码 136-148 doi: 10.1007/s11684-020-0756-y

摘要： Precise identification of HIV transmission among populations is a key step in public health responses. However, the HIV transmission network is usually difficult to determine. HIV molecular networks can be determined by phylogenetic approach, genetic distance-based approach, and a combination of both approaches. These approaches are increasingly used to identify transmission networks among populations, reconstruct the history of HIV spread, monitor the dynamics of HIV transmission, guide targeted intervention on key subpopulations, and assess the effects of interventions. Simulation and retrospective studies have demonstrated that these molecular network-based interventions are more cost-effective than random or traditional interventions. However, we still need to address several challenges to improve the practice of molecular network-guided targeting interventions to finally end the HIV epidemic. The data remain limited or difficult to obtain, and more automatic real-time tools are required. In addition, molecular and social networks must be combined, and technical parameters and ethnic issues warrant further studies.

关键词： human immunodeficiency virus type 1     molecular cluster     transmission cluster     risk network     targeted intervention     evaluation    

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Molecular epidemiology of Cryptococcus neoformans species complex isolates from HIV-positive and HIV-negative

Min CHEN MM, Wei-Hua PAN MD, Wan-Qing LIAO MM, Xiao-Ran LI BS, Bi-Wei FENG BS, Zhe-Xue QUAN PhD, Shao-Xi WU MD, Xiao-Ping TANG MD, Zhi-Rong YAO MD,

《医学前沿（英文）》 2010年 第4卷 第1期   页码 117-126 doi: 10.1007/s11684-010-0011-z

摘要： This study investigated the molecular types of the species complex isolates and their clinical manifestations among human immunodeficiency virus (HIV)-positive and HIV-negative patients in southeast China in the past 15 years. The molecular types of 109 isolates from 108 patients were analyzed by the PCR fingerprinting method, sequences of internal transcribed spacers of rDNA (ITS region), and sequences of the capsule-associated gene (). In HIV-positive patients, clinical isolates were grouped into molecular types VNI (75%, 15/20), VNII (15%, 3/20), and VNIII (10%, 2/20). In HIV-negative patients, the majority of the clinical isolates were grouped into molecular types VNI (72%, 64/89), VNII (13%, 12/89), VGI (12%, 11/89), VNIII (1%, 1/89), and VGII (1%, 1/89). In reference to the mating type of the isolates, 97% (106/109) were of the α, 2% (2/109) were of the α/- and 1% (1/109) were of theα/. As for the clinical manifestations of the molecular types among the patients, the average cerebrospinal fluid (CSF) pressure of the patients infected by the was higher than that of the patients infected by the . These results suggest that both HIV-positive and HIV-negative cryptococcal patients in the southeast of China are mostly infected by the strains. No strains were found in HIV-positive patients.

关键词： Cryptococcus neoformans     Cryptococcus gattii     cryptococcosis     molecular epidemiology     molecular type     mating type    

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New practice in semaglutide on type-2 diabetes and obesity: clinical evidence and expectation

《医学前沿（英文）》 2022年 第16卷 第1期   页码 17-24 doi: 10.1007/s11684-021-0873-2

摘要： Obesity is an important risk factor of type 2 diabetes (T2D), which has become an important factor threatening human health. However, no perfect drug choice for obesity exists. Semaglutide is a kind of human glucagon-like peptide-1 (GLP-1) analog that promotes insulin secretion while inhibiting glucagon secretion through a glucose concentration-dependent mechanism. GLP-1 can also delay stomach emptying and suppress appetite to help lose weight. This review summarizes clinical evidence of the semaglutide effect on T2D and obesity and establishes expectations on future clinical trials for obesity treatment.

关键词： semaglutide     type 2 diabetes     obesity    

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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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Catalytic oxidation of carbon monoxide, toluene, and ethyl acetate over the

Zhidan Fu, Lisha Liu, Yong Song, Qing Ye, Shuiyuan Cheng, Tianfang Kang, Hongxing Dai

《化学科学与工程前沿（英文）》 2017年 第11卷 第2期   页码 185-196 doi: 10.1007/s11705-017-1631-5

摘要： The Pd catalyst supported on cryptomelane-type manganese oxide octahedral molecular sieve (OMS-2) were prepared. The effect of Pd loading on the catalytic oxidation of carbon monoxide, toluene, and ethyl acetate over Pd/OMS-2 has been investigated. The results show that the Pd loading plays an important role on the physicochemical properties of the Pd/OMS-2 catalysts which outperform the Pd-free counterpart with the 0.5Pd/OMS-2 catalyst being the best. The temperature for 50% conversion was 25, 240 and 160 °C, and the temperature for 90% conversion was 55, 285 and 200 °C for oxidation of CO, toluene, and ethyl acetate, respectively. The low-temperature reducibility and high oxygen mobility of Pd/OMS-2 are the factors contributable to the excellent catalytic performance of 0.5Pd/OMS-2.

关键词： cryptomelane-type manganese oxide octahedral molecular sieve     oxygen mobility     reducibility     carbon monoxide oxidation     volatile organic compound combustion    

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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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Personalized medicine of type 2 diabetes

null

《医学前沿（英文）》 2013年 第7卷 第1期   页码 1-3 doi: 10.1007/s11684-013-0241-y

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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    

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标题 作者 时间 类型 操作

Molecular dynamic simulation on the conformation of mouse muscle type nAChR

Shengai SUN, Rilei YU, Yanhui ZHANG, Yanni LI,

期刊论文

Molecular network-based intervention brings us closer to ending the HIV pandemic

Xiaoxu Han, Bin Zhao, Minghui An, Ping Zhong, Hong Shang

期刊论文

Molecular epidemiology of Cryptococcus neoformans species complex isolates from HIV-positive and HIV-negative

Min CHEN MM, Wei-Hua PAN MD, Wan-Qing LIAO MM, Xiao-Ran LI BS, Bi-Wei FENG BS, Zhe-Xue QUAN PhD, Shao-Xi WU MD, Xiao-Ping TANG MD, Zhi-Rong YAO MD,

期刊论文

New practice in semaglutide on type-2 diabetes and obesity: clinical evidence and expectation

期刊论文

Special issue on “Molecular Sensors and Molecular Logic Gates”

Luling Wu , Tony D. James

期刊论文

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

期刊论文

Progress on molecular biomarkers and classification of malignant gliomas

null

期刊论文

Molecular classification and molecular targeted therapy of cancer

null

期刊论文

Catalytic oxidation of carbon monoxide, toluene, and ethyl acetate over the

Zhidan Fu, Lisha Liu, Yong Song, Qing Ye, Shuiyuan Cheng, Tianfang Kang, Hongxing Dai

期刊论文

分子电子学的发展

Paven Thomas Mathew, 房丰洲

期刊论文

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

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

期刊论文

Personalized medicine of type 2 diabetes

null

期刊论文

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

期刊论文

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

期刊论文

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

Lin ZHANG, Yan SUN

期刊论文