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Proceedings of MOL2NET 2018, International Conference on Multidisciplinary Sciences, 4th edition最新文献

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pH effects on PG/PC and PS/PC lipid binary mixtures pH对PG/PC和PS/PC脂质二元混合物的影响
Pedro R. Magalhães, Diogo Vila-Viçosa, Tomás F D Silva, M. Machuqueiro
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引用次数: 0
Optimal Scheduling for Precedence-Constrained Applications on Heterogeneous Machines 异构机器上优先级约束应用的最优调度
A. Santiago, Carlos Soto, H. Fraire, B. Dorronsoro
Graphical Abstract Abstract. High-Performance Computing (HPC) is a growing necessity of our technological society, HPC demands high loads of parallel computing jobs, an optimal scheduling of the parallel applications tasks is a priority to meet the demands of its users on time. Branch-and-bound (BB) Algorithms and Mathematical Programming (MP) solve complex optimization problems in an optimal manner, some MP or BB even have parallel computing capabilities, making them suitable solutions to solve realworld problems. In this paper, we propose two exact algorithms, a BB and an MP Model for scheduling precedence-constrained applications, on heterogeneous computing systems, as far as we known the first ones on his kind presented in the state of the art. One major contribution of the work is the proposed formulations of the objective function in both methods. Experimental results obtained more than twenty optimal values for synthetic applications from the literature.
图形抽象抽象。高性能计算(HPC)是当今技术社会日益增长的需求,高性能计算需要高负载的并行计算任务,优化并行应用任务调度是满足用户需求的首要任务。分支定界算法(BB)和数学规划(MP)以最优的方式解决复杂的优化问题,一些分支定界算法或数学规划(MP)甚至具有并行计算能力,使其成为解决现实问题的合适方法。在本文中,我们提出了两种精确的算法,一个BB和一个MP模型,用于调度优先级约束的应用程序,在异构计算系统上,据我们所知,这是目前最先进的同类算法。这项工作的一个主要贡献是在两种方法中提出了目标函数的公式。实验结果从文献中得到了20多个适合合成应用的最优值。
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引用次数: 2
Application of QM/MM Methods in the Study of PNPOx QM/MM方法在PNPOx研究中的应用
N. Cerqueira, A. Pina, S. Sousa
.
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引用次数: 0
Influence of codon 35 amino acid insertion in HIV-1 protease: insights from molecular dynamics 密码子35氨基酸插入对HIV-1蛋白酶的影响:来自分子动力学的见解
João P. Luís, Ana I Mata, N. Alves, Carlos J. V. Simões, João Pereira-Vaz, Daniela C. Vaz, V. Duque, R. Brito
One of the main challenges facing the development of effective anti HIV-1 medicines relates to the high mutation rate of essential enzymes, such as HIV-1 Protease (HIV1Pr).[1] Pereira Vaz et al. [2] first reported a threonine insertion at position 35 (E35E_T), in the HIV1Pr coding region, among treatment-naive subtype C infected individuals. Undetectable viral loads were attained after antiretroviral therapy in such individuals, with no associated major mutations, implying null contribution of E35E_T to viral resistance. Interestingly, a new study suggests a potential additive effect of position 35 insertions when in presence of major mutations – ultimately leading to resistance to HIV1Pr inhibitors in higher extent. [3] In order to study the role of the E35E_T insertion in the structure and ligand-binding propensity of HIV1Pr, homology models were generated from subtype B and subtype C base sequences, using available X-ray structures corresponding to highest identity sequences as template. Fifty (50)-nanoseconds Molecular Dynamics (MD) simulations were then performed for unbound and bound (HIV1PR:darunavir complex) structures of the wild-type form and a single‑point major mutation variant of HIV1PR – in all cases in presence and absence of E35_T. Combining simple measurements like the root mean square (RMS) deviations and fluctuations, applied to the whole protein and to its two functional flap regions, with principal component analysis (PCA) of the multiple MD trajectories, we herein contrast the behaviour of all systems in attempt to dissect the putative role of E35E_T in the resistance towards HIV1PR inhibitors.
开发有效的抗HIV-1药物面临的主要挑战之一与必需酶(如HIV-1蛋白酶(HIV1Pr))的高突变率有关。[1]Pereira Vaz等人[2]首次报道了在未接受治疗的C亚型感染个体中,在hiv - 1pr编码区35位(E35E_T)插入苏氨酸。在这些个体中,抗逆转录病毒治疗后获得了无法检测到的病毒载量,没有相关的主要突变,这意味着E35E_T对病毒耐药性的贡献为零。有趣的是,一项新的研究表明,当存在主要突变时,35位插入存在潜在的加性效应-最终导致对HIV1Pr抑制剂的更高程度的耐药性。[3]为了研究E35E_T插入在HIV1Pr的结构和配体结合倾向中的作用,以现有的最高同位序列对应的x射线结构为模板,从B亚型和C亚型碱基序列中建立了同源性模型。然后,在存在和不存在E35_T的所有情况下,对未结合和结合(HIV1PR:darunavir复合物)的野生型结构和HIV1PR的单点主要突变变体进行五十(50)纳秒的分子动力学(MD)模拟。结合应用于整个蛋白质及其两个功能性皮瓣区域的均方根(RMS)偏差和波动等简单测量,以及多个MD轨迹的主成分分析(PCA),我们在此对比了所有系统的行为,试图剖析E35E_T在对HIV1PR抑制剂的抗性中的假定作用。
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引用次数: 0
Is the 5,10-methylenetetrahydrofolate cofactor synthesized through a non-enzymatic or enzymatic mechanism? 5,10-亚甲基四氢叶酸辅助因子是通过非酶促还是酶促机制合成的?
N. Cerqueira, Henrique S. Fernandes, S. Sousa
The 5,10-methylenetetrahydrofolate (5,10-mTHF) is a cofactor essential for the synthesis of purines and thymidine, which are crucial for the cell viability.[1] The α-elimination of ʟ-serine, catalyzed by the serine hydroxymethyltransferase (SHMT), is the primary source of 5,10-mTHF in the cell. However, the catalytic mechanism behind the synthesis of 5,10-mTHF was unknown, and two divergent theories were proposed for the mechanism. Some authors suggested that the final steps of the 5,10-mTHF synthesis occur in the cytoplasm whereas other authors showed some evidence that the reaction must occur inside the SHMT. [2] In this study, we addressed the entire catalytic mechanism of the PLP-dependent enzyme SHMT using a QM/MM approach and the mechanism of 5,10-mTHF synthesis in aqueous solution. The calculations were prepared and analyzed using molUP [3] for VMD and run on Gaussian09 and ORCA. This work [4] resulted in the entire e detailed catalytic mechanism of SHMT. The results showed that both hypotheses for the synthesis of 5,10-mTHF shared the two first steps where the -OH group is transferred from the serine to the THF. These reactions occur inside the SHMT and have a ∆G‡ of 18.0 and 2.0 kcal/mol. Then, the reaction can proceed inside the enzyme through 5 sequential steps or in the cytoplasm where only 3 steps are needed. The calculations showed that the mechanism is kinetic and thermodynamically favorable by 0.8 and 24.3 kcal/mol, respectively, when it takes place inside the SHMT. Although the reaction is not impossible in solution, it is very improbable that the THF intermediate might be released to the cytoplasm to overcome a set of reactions that are less favorable when compared to the ones that would occur in the SHMT. Reference [1] Froese, D. S.; et al., Structural basis for the regulation of human 5,10-methylenetetrahydrofolate reductase by phosphorylation and S-adenosylmethionine inhibition. Nature comm 2018, 9 (1), 2261-2261. [2] Schirch, V.; et al, Serine hydroxymethyltransferase revisited. Curr Opin Chem Biol 2005, 9 (5), 482-7. [3] Fernandes, H. S.; et al., molUP: A VMD plugin to handle QM and ONIOM calculations using the Gaussian software. J Comput Chem 2018, 39 (19), 1344-1353. [4] Fernandes, H. S.; et al., Catalytic Mechanism of the Serine Hydroxymethyltransferase: A Computational ONIOM QM/MM Study. ACS Catalysis 2018, 10096-10110. Acknowledgments FCT (SFRH/BD/115396/2016, IF/01310/2013, IF/00052/2014 e PTDC/QUI-QFI/31689/2017)
5,10-亚甲基四氢叶酸(5,10- mthf)是合成嘌呤和胸腺嘧啶所必需的辅助因子,而嘌呤和胸腺嘧啶对细胞存活至关重要由丝氨酸羟甲基转移酶(SHMT)催化的_ -丝氨酸的α-消除是细胞中5,10- mthf的主要来源。然而,5,10- mthf合成的催化机制尚不清楚,对于该机制提出了两种不同的理论。一些作者认为,5,10- mthf合成的最后步骤发生在细胞质中,而另一些作者提出了一些证据,表明该反应必须发生在SHMT内。在这项研究中,我们使用QM/MM方法研究了plp依赖性酶SHMT的整个催化机制,以及5,10- mthf在水溶液中合成的机制。使用molUP[3]对VMD进行了计算和分析,并在Gaussian09和ORCA上运行。这项工作得出了SHMT的完整而详细的催化机理。结果表明,对于5,10- mthf的合成,两种假设都共享了-OH基团从丝氨酸转移到THF的两个第一步。这些反应发生在SHMT内,∆G‡分别为18.0和2.0 kcal/mol。然后,反应可以在酶内通过5个连续步骤进行,或者在细胞质中只需要3个步骤。计算表明,当反应发生在SHMT内部时,动力学和热力学上分别为0.8和24.3 kcal/mol。虽然该反应在溶液中并非不可能发生,但THF中间体被释放到细胞质中以克服一系列与在SHMT中发生的反应相比不太有利的反应是非常不可能的。参考文献[1]Froese, d.s.;磷酸化和s -腺苷蛋氨酸抑制调控人5,10-亚甲基四氢叶酸还原酶的结构基础。自然学报,2018,9(1),2261-2261。[2] Schirch, v;丝氨酸羟甲基转移酶的重新研究。生物化学学报,2005,9(5),482-7。[3]费尔南德斯,h.s.;molUP:一个VMD插件,用于使用高斯软件处理QM和onionm计算。计算化学,2018,39(19),1344-1353。[4]费尔南德斯,h.s.;丝氨酸羟甲基转移酶的催化机制:一个计算的niom QM/MM研究。催化工程学报,2018,10096-10110。FCT (SFRH/BD/115396/2016, IF/01310/2013, IF/00052/2014和PTDC/ qu - qfi /31689/2017)
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引用次数: 0
Use of integrated software, applied to the elaboration of didactic material for students with hearing disability at the basic intercultural education center of deaf 利用集成软件,应用于聋人基础跨文化教育中心的听障学生教材的编写
Viviana Quevedo, Bernabé Ortega-Tenezaca
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引用次数: 0
COMPUTATIONAL STUDY OF HYBRID PLA-PEG NANOPARTICLES AS ANTIPLATELET DRUG CARRIERS 杂化聚乙二醇纳米颗粒作为抗血小板药物载体的计算研究
M. F. Matus, I. Palomo, C. Vilos
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引用次数: 0
Isolation of Erwinia amylovora Bacteriophage from Soil and Pear Trees Plant Tissues 从土壤和梨树植物组织中分离淀粉状欧文菌噬菌体
A. Akremi, Mouna Jlidi, Adel Haj Brahim, M. Ali, L. Daoud, Houda Hmani, S. Bejar, Naser Aliye Feto, Mamdouh Ben Ali
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引用次数: 1
Mini-review on the applications and perspectives of a new simplex machine learning approach in chemistry and biology 一种新的单纯形机器学习方法在化学和生物学中的应用和前景综述
N. Semmar, M. Farman, Asma Hammami, A. Sarraj-Laabidi
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引用次数: 0
LIVER CANCER IN CHILDREN 儿童肝癌
N. Charanraj
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Proceedings of MOL2NET 2018, International Conference on Multidisciplinary Sciences, 4th edition
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