Methane activation over Ag-exchanged ZSM-5 zeolites: A theoretical study

Methane activation catalyzed over Ag-exchanged ZSM-5 zeolites was investigated by using the density functional theory (DFT) with a cluster model. Two different pathways were taken into account in this work: the “alkyl” and the “carbenium” pathways. The activation barriers obtained are 34.09 and 66.63 kcal/mol for the “alkyl” and the “carbenium” pathway, respectively. The calculated results show that the activation barrier of the “alkyl” pathway is smaller than that of “carbenium” pathway. Consequently, the “alkyl” pathway is the preferential reaction pathway. A new mechanism of methane conversion in the presence of ethene was proposed. In the catalytic cycle, the initial step of methane activation proceeds with the “alkyl” pathway and the Ag⁺ cation acts as an acceptor of the methyl group, then ethene reacts with the Ag⁺CH₃⁻ group to form propene. In addition, it is found that the Ag⁺ cations play an important role in the methane activation, compared with the reaction of methane activation over H-ZSM-5.     

Optimal Force Mismatch for Fluctuation-Activated Transition in a System of Two Coupled Bistable Oscillators

We study the fluctuation-activated transition process in a system of two coupled forced bistable oscillators with a mismatch σ in the force constants. As the coupling strength μ is increased, the transition pathway undergoes four stages changes from a two-step process with two candidate pathways to a mixture of a two-step pathway and a one-step pathway to a one-step process with also two candidate pathways and then to a one-step process with a single pathway.Interestingly, we find that the total transition rate depends nonmonotonically on σ in the weak coupling: a maximal rate appears in an intermediate magnitude of σ. Moreover, the rate also exhibits an unexpected maximum as a function ofμ. The results are in an excellent agreement with our numerical simulations by forward flux sampling.     

Study of myocardial fiber pathway using magnetic resonance diffusion tensor imaging

The purpose of this study was to investigate myocardial fiber pathway distribution in order to provide supplemental information on myocardial fiber architecture and cardiac mechanics. Diffusion tensor imaging (DTI) with medium diffusion resolution (15 directions) was performed on normal canine heart samples (N=6) fixed in formalin. With the use of diffusion tensor fiber tracking, left ventricle (LV) myocardial fiber pathways and helix angles were computed pixel by pixel at short-axis slices from base to apex. Distribution of DTI-tracked fiber pathway length and number was analyzed quantitatively as a function of fiber helix angle in step of 9 degrees . The long fiber pathways were found to have small helix angles. They are mostly distributed in the middle myocardium and run circumferentially. Fiber pathways tracked at the middle and upper LV are generally longer than those near the apex. Majority of fiber pathways have small helix angles between -20 degrees and 20 degrees , dominating the fiber architecture in myocardium. Likely, such myocardial fiber pathway measurement by DTI may reflect the spatial connectiveness or connectivity of elastic myofiber bundles along their preferential pathway of electromechanical activation. The dominance of the long and circumferentially running fiber pathways found in the study may explain the circumferential predominance in left ventricular contraction.     

Prediction of compounds’ biological function (metabolic pathways) based on functional group composition

Efficient in silico screening approaches may provide valuable hints on biological functions of the compound-candidates, which could help to screen functional compounds either in basic researches on metabolic pathways or drug discovery. Here, we introduce a machine learning method (Nearest Neighbor Algorithm) based on functional group composition of compounds to the analysis of metabolic pathways. This method can quickly map small chemical molecules to the metabolic pathway that they likely belong to. A set of 2,764 compounds from 11 major classes of metabolic pathways were selected for study. The overall prediction rate reached 73.3%, indicating that functional group composition of compounds was really related to their biological metabolic functions.     

Quantum interferences from cross talk in J = 1/2 ↔ J = 1/2 transitions

We consider the possibility of a control field opening up multiple pathways and thereby leading to new interference and coherence effects. We illustrate the idea by considering the J = 1/2 ↔ J = 1/2 transition. As a result of the additional pathways, we show the possibilities of nonzero refractive index without absorption and gain without inversion. We explain these results in terms of the coherence produced by the opening of an extra pathway.     

Rules of engagement promote polarity in RNA trafficking

Many cell biological pathways exhibit overall polarity (net movement of molecules in one direction) even though individual molecular interactions in the pathway are freely reversible. The A2 RNA trafficking pathway exhibits polarity in moving specific RNA molecules from the nucleus to localization sites in the myelin compartment of oligodendrocytes or dendritic spines in neurons. The A2 pathway is mediated by a ubiquitously expressed trans-acting trafficking factor (hnRNP A2) that interacts with a specific 11 nucleotide cis-acting trafficking sequence termed the A2 response element (A2RE) found in several localized RNAs. Five different molecular partners for hnRNP A2 have been identified in the A2 pathway: hnRNP A2 itself, transportin, A2RE RNA, TOG (tumor overexpressed gene) and hnRNP E1, each playing a key role in one particular step of the A2 pathway. Sequential interactions of hnRNP A2 with different molecular partners at each step mediate directed movement of trafficking intermediates along the pathway. Specific "rules of engagement" (both and, either or, only if) govern sequential interactions of hnRNP A2 with each of its molecular partners. Rules of engagement are defined experimentally using three component binding assays to measure differential binding of hnRNP A2 to one partner in the presence of each of the other partners in the pathway. Here we describe rules of engagement for hnRNP A2 binding to each of its molecular partners and discuss how these rules of engagement promote polarity in the A2 RNA trafficking pathway. For molecules with multiple binding partners, specific rules of engagement govern different molecular interactions. Rules of engagement are ultimately determined by structural relationships between binding sites on individual molecules. In the A2 RNA trafficking pathway rules of engagement governing interactions of hnRNP A2 with different binding partners provide the basis for polarity of movement of intermediates along the pathway.     

大数据时代下的化学经验2.0：基于键能的大规模反应途径预测

报道了一个基于键能数据预测反应途径的可编程算法．运用该算法,成功预测了F₂+CH₃Cl气相反应的最优产物(CF₄)和对应的反应途径．提供了一个启示性的化学经验2.0 的例子,并可能开启大数据时代下的大规模反应途径预测的大门．     

二阶量子路径的相干控制

研究了有_N个中间能级连接初态和目标态的情况下量子路径的控制策略．以_N=3的量子体系为例,详细阐述了针对弱的宽频场的4_N分块控制方案,其中分块的边界频率依赖于量子体系的共振频率．此策略利用了路径幅度中共振和非共振项的相干效应,可通过只调节2_N个相位变量实现．     

应用FTIR分析过量表达HPS/PHI转基因与野生型天竺葵叶片在甲醛胁迫下的生理特性差异

6-磷酸己酮糖合成酶(HPS)和6-磷酸果糖异构酶(PHI)是细菌同化甲醛的关键酶。13 C-NMR分析结果说明在天竺葵叶绿体中过量表达HPS/PHI融合蛋白可把RuMP途径整合成卡尔文循环的一个支路,在转基因天竺葵叶绿体中创造一个甲醛光合同化途径。运用FTIR技术分析过量表达HPS/PHI转基因与野生型天竺葵在甲醛胁迫下体内各物质含量的变化规律及光谱表征,考察FTIR能否成为一种鉴定有甲醛光合同化途径的转基因植物与野生型植物表型差异的新方法。分别用4mmol.L-1甲醛处理野生型和转基因植物0,1,2,3,4d,通过对两种植物经甲醛处理不同时间后各光谱特征的比较分析发现,用4mmol.L-1甲醛处理4d后转基因植物中的碳水化合物、蛋白质、脂肪族化合物等的含量明显高于野生型植物。这可能是由于安装HPS/PHI甲醛光合同化途径后使转基因植物同化代谢甲醛的能力更强,能将更多的甲醛固定为6-磷酸果糖,然后进入各种同化途径用于合成细胞内的各种组份所致,说明FTIR可作为一种鉴定有甲醛光合同化途径的转基因天竺葵与野生型天竺葵表型差异的新方法。     

On the deduction of chemical reaction pathways from measurements of time series of concentrations

We discuss the deduction of reaction pathways in complex chemical systems from measurements of time series of chemical concentrations of reacting species. First we review a technique called correlation metric construction (CMC) and show the construction of a reaction pathway from measurements on a part of glycolysis. Then we present two new improved methods for the analysis of time series of concentrations, entropy metric construction (EMC), and entropy reduction method (ERM), and illustrate (EMC) with calculations on a model reaction system. (c) 2001 American Institute of Physics.     

MAPK途径与细胞的辐射应

MAPK信号转导途径在细胞辐射应答中起着重要作用, ERK, JNK, P38 MAPK和大 MAPK 4条不同的 MAPK通路在受辐射细胞中扮演着不同角色, 它们的协调控制作用决定着细胞受辐照后的命运。 描述了辐射应答中的这4条不同的 MAPK途径, 并讨论了这些途径在辐射应答中的作用。MAPK signal transduction pathways play crucial roles in the radiation responses of cells. Four MAPK pathways, ERK, JNK, P38 MAPK and big MAPK pathway induce different effects in the radiation exposed cells. Their corresponding regulations foreordain the cells after exposure. This review describes these four MAPK pathways in radiation responses and discusses their functions in radiation responses respectively.     

Exploring the anti-proliferative activity of <Emphasis Type="BoldItalic">Pelargonium sidoides</Emphasis> DC with in silico target identification and network pharmacology

Pelargonium sidoides DC (Geraniaceae) is a medicinal plant indigenous to Southern Africa that has been widely evaluated for its use in the treatment of upper respiratory tract infections. In recent studies, the anti-proliferative potential of P. sidoides was shown, and several phenolic compounds were identified as the bioactive compounds. Little, however, is known regarding their anti-proliferative protein targets. In this study, the anti-proliferative mechanisms of P. sidoides through in silico target identification and network pharmacology methodologies were evaluated. The protein targets of the 12 phenolic compounds were identified using the target identification server PharmMapper and the server for predicting Drug Repositioning and Adverse Reactions via the Chemical–Protein Interactome (DRAR-CPI). Protein–protein and protein–pathway interaction networks were subsequently constructed with Cytoscape 3.4.0 to evaluate potential mechanisms of action. A total of 142 potential human target proteins were identified with the in silico target identification servers, and 90 of these were found to be related to cancer. The protein interaction network was constructed from 86 proteins involved in 209 interactions with each other, and two protein clusters were observed. A pathway enrichment analysis identified over 80 Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways enriched with the protein targets and included several pathways specifically related to cancer as well as various signaling pathways that have been found to be dysregulated in cancer. These results indicate that the anti-proliferative activity of P. sidoides may be multifactorial and arises from the collective regulation of several interconnected cell signaling pathways.     

Implementing SPAM into STMAS: a net sensitivity improvement in high-resolution NMR of quadrupolar nuclei

Gan and Kwak recently introduced two new tools for high-resolution 2D NMR methods applied to quadrupolar nuclei: double-quantum filtering in STMAS (DQF-STMAS) and the soft-pulse added mixing (SPAM) idea. Double-quantum filtering suppresses all undesired signals in the STMAS method with limited loss in sensitivity. With SPAM, all pathways are added constructively after the second hard-pulse instead of using a single pathway as previously. Here, the sensitivity, advantages and drawbacks of DQF-STMAS are compared to 3QMAS. Additionally, SPAM can be included into DQF-STMAS method, resulting in a net sensitivity gain with respect to 3QMAS of ca. 10-15.     

Size selection of the cooperative ridge-trench formation in heteroepitaxial systems

The cooperative ridge-trench (CRT) formation on heteroepitaxial systems, the process controlling the self-assembly of quantum dot molecules, is investigated by simulating the process and by analyzing the corresponding energy change. The results suggest that the CRT formation is the competition of two exclusive pathways: namely, the growth of the outermost structure and the gradual formation of a new facet structure adjacent to the existing one. The first pathway dictates the process initially, while the second one is more energetically favorable once the size of the outermost structure reaches a critical value. The competition repeats, resulting in the CRT formation.     

Anhydride formation is not a valid mechanism for peptide cleavage by carboxypeptidase-A: a semiempirical reaction pathway study

The mechanism of action of zinc metalloproteinases has been studied by following the direct nucleophilic pathway, which has been frequently suggested but not yet examined by computational methods, and comparing it to other pathways. We computed the reaction enthalpies for the direct nucleophilic attack by Glu270 in the active site model of carboxypeptidase-A on a model substrate's peptide carbonyl and followed this pathway through mixed anhydride formation and subsequent anhydride cleavage by water. The starting molecular coordinates originate in our own high-resolution crystal structure and the computations have been conducted with the minimal neglect of differential overlap (MNDO) Hamiltonian, modified to include the d-orbitals of zinc and the effects of multiple hydrogen bonding, thus labelled MNDO/d/H. Compared to our recent results for two other candidate pathways for this mechanism, both of the General-Acid-General-Base type, we conclude that the direct nucleophilic or ‘anhydride’ pathway has a much higher energy barrier at the rate determining step, which is a proton transfer, than previously calculated paths. We argue that the ‘anhydride’ pathway is thus not a valid one for the cleavage of peptides by carboxypeptidase-A.     

G-SIMS and SMILES: Simulated fragmentation pathways for identification of complex molecules, amino acids and peptides

G-SIMS is a powerful method for the identification of organics and complex molecules at surfaces. We have previously shown that the molecular structure may be reassembled from fragment ions by studying the evolution of G-SIMS intensities as the surface plasma, with effective temperature T_p, is varied, using a method known as G-SIMS-FPM.Here, we develop a novel approach, based on SMILES (Simplified Molecular Input Line Entry Specification), to assist the reassembly process in an automated way through evaluation of the fragmentation pathways for given molecular structures. A computer program takes a parent structure and goes through every possible fragmentation to provide a tree structure of fragmentation products and simulated fragmentation pathways. For any fragment it is then possible to identify the molecular structure, its mass and a pathway to the parent. We find that there is a good correlation with peak evolution in G-SIMS-FPM data and simulated pathways for two amino acids and a simple peptide. This significantly enhances the application of G-SIMS-FPM to unknown materials.     

A measure on the space of RNA folding pathways: towards a new scheme of statistical inference

In this work we define constructively a measure η on the space of sequential folding (SF) pathways for RNA with the aim of making probabilistic inferences on kinetically-controlled folding. This measure will be shown to be adequate for those RNA species known to search for their structure concurrently with their progressive assembling by sequential nucleotide incorporation. We shall validate our approach by showing that the measure is actually concentrated on the SF pathway that has been experimentally confirmed by pulse-chase kinetic probes. The space of SF pathways will be represented as a product of suitably coarse-grained conformation spaces, one for each length of the growing chain. In this context, the measure is induced by a Markovian stochastic process whose specific realizations are precisely the SF pathways. The coarse-graining is necessary to represent only the essential dynamics of SF: We identify rapidly-interconverting structures by regarding the folding dynamics concurrent with chain growth modulo kinetic barriers of order N ( ). Thus, a pathway corresponds to a sequence of clusters of rapidly-equilibrated structures. Within this representation, we show in specific examples that the measure is concentrated solely on the biologically-significant folding pathway whose destination or final structure is functionally-competent, different appreciably from the global free energy minimum.