MOLECULAR CLOSE-PACKING METHOD AND ITS APPLICATION TO CRYSTAL STRUCTURE DETERMINATION OF DESHEXAPEPTIDE (B25--B30) INSULIN

Based on the molecule-packing theory, we defined a molecule-packing function express-ing the compatibility of packing among the symmetry-related molecules in a unit cell. Acomputer program imitating the close-packing of molecules in the objective crystal latticeand giving the function value of each rotation and translation of the molecule in the unitcell was performed, and it therefore made the close-packing of molecules expressquantitatively. This method not only could judge a correct solution from several peaks ofthe rotation or translation function but it may also independently, quantitatively and quicklysolve some specific problems of rotation and translation. Using known structure of despenta-peptide (B26--B30) insulin as an example, the effectiveness of this method and its programwas inspected, and this method was successfully applied to solving the translation problem ofthe unknown structure of deshexapeptide (B25--B30) insulin. The molecular close-packingmethod proved by the results of R--search and electron density maps is relatively independ-ent of the molecular replacement method, though an effective complement of it.

Comparative study of nudged elastic band and molecular dynamics methods for diffusion kinetics in solid-state electrolytes

Considerable efforts are being made to transition current lithium-ion and sodium-ion batteries towards the use of solid-state electrolytes.Computational methods,specifically nudged elastic band(NEB)and molecular dynamics(MD)methods,provide powerful tools for the design of solid-state electrolytes.The MD method is usually the choice for studying the materials involving complex multiple diffusion paths or having disordered structures.However,it relies on simulations at temperatures much higher than working temperature.This paper studies the reliability of the MD method using the system of Na diffusion in MgO as a benchmark.We carefully study the convergence behavior of the MD method and demonstrate that total effective simulation time of 12 ns can converge the calculated diffusion barrier to about 0.01 eV.The calculated diffusion barrier is 0.31 eV from both methods.The diffusion coefficients at room temperature are 4.3×10^(-9) cm^(2)⋅s^(−1) and 2.2×10^(-9) cm^(2)⋅s^(−1),respectively,from the NEB and MD methods.Our results justify the reliability of the MD method,even though high temperature simulations have to be employed to overcome the limitation on simulation time.

COMPUTERIZED SIMULATION OF MOLTEN SALT SOLUTION OF Li,KF,Cl SYSTEM BY MOLECULAR DYNAMIC METHOD

The structure and properties of molten salt solution o J Li,K|F,Cl system have been investiged by computerized simulation of molecular dynamic method.The partial RDF,the partial molar energy of mixing and the diffusion coeffients of Li^+,K^+,F^- and Cl^- have been calculated. The results are in agreement with the experimental values.The regularities of the distribution of ions and mieroscopic holes are discussed based on the results of computerized simulation.

Adaptive hp finite element method for fluorescence molecular tomography with simplified spherical harmonics approximation

Recently,the simplified spherical harmonics equations(SP)model has at tracted much att entionin modeling the light propagation in small tissue ggeometriesat visible and near-infrared wave-leng ths.In this paper,we report an eficient numerical method for fluorescence moleeular tom-ography(FMT)that combines the advantage of SP model and adaptive hp finite elementmethod(hp-FEM).For purposes of comparison,hp-FEM and h-FEM are,respectively applied tothe reconstruction pro cess with diffusion approximation and SPs model.Simulation experiments on a 3D digital mouse atlas and physical experiments on a phantom are designed to evaluate thereconstruction methods in terms of the location and the reconstructed fluorescent yield.Theexperimental results demonstrate that hp-FEM with SPy model,yield more accurate results thanh-FEM with difusion approximation model does.The phantom experiments show the potentialand feasibility of the proposed approach in FMT applications.

Clinical Observation on Treatment of 78 Patients of B-Thalassemla with Bushen Ylsul (补肾益髓) Method and Study on Its Molecular Mechanism

Objective: To study the treatment of B-Thalas-semia (ThE) with Chinese herbal medicine for Bushen Yisui (BSYS), its theoretical base and molecular mechanism. Methods: Seventy-eight patients with ThE were treated with BSYS recipe (consisted of 11 Chinese herbal drugs as Dogwood fruit, Fleeceflower root, prepared Rehmannia root and turtle shell, etc.) orally taken, 3 times per day, 10 g/time, 3 months as one therapeutic course. Hemoglobin (Hb), red blood cell (RBC), reticulocyte (Ret) and hemoglobin F (HbF) were checked every month. At the same time, PAGE, PVR, PCR-SSCP, RT-PCR, DNA series analysis, mRNA gene expression analysis techniques were used to conduct the systematic gene analysis in patients to study the molecular mechanism of TCM treatment from aspects of gene mutation, gene expression and control-regulation. Results: All the blood criteria in patients after BSYS treatment were improved significantly with clinical symptoms

A Modified Molecular Structural Mechanics Method for Analysis of Carbon Nanotubes

A modified molecular structural mechanics method, based on molecular mechanics and similar to the finite element method, was developed. The energy of a system was expressed by the force field functions of the molecular mechanics. Under the small deformation assumption and by the principle of minimum potential energy, the system function was established. The properties of tension and bending of single-walled carbon nanotubes were analyzed. The Young＇s modulus is about 0.36 TPa nm, which agrees perfectly with the results of previous analysis by other researchers. It is found, for the first time, that the Young＇s moduli, for Zigzag nanotubes, are different from each other when the system energy was expressed as the sum of two or three individual energy terms in molecular mechanics. Whereas, the Young＇s moduli were the same for the Armchair nanotubes. It is found, when simulating the bending, that the deflections are closer to the theoretical ones, of the classical elasticity, when the diameter of the carbon nanotube increases.

The LBFGS quasi-Newtonian method for molecular modeling prion AGAAAAGA amyloid fibrils

Experimental X-ray crystallography, NMR (Nuclear Magnetic Resonance) spectroscopy, dual polarization interferometry, etc. are indeed very powerful tools to determine the 3-Dimensional structure of a protein (including the membrane protein);theoretical mathematical and physical computational approaches can also allow us to obtain a description of the protein 3D structure at a submicroscopic level for some unstable, noncrystalline and insoluble proteins. X-ray crystallography finds the X-ray final structure of a protein, which usually need refinements using theoretical protocols in order to produce a better structure. This means theoretical methods are also important in determinations of protein structures. Optimization is always needed in the computer-aided drug design, structure-based drug design, molecular dynamics, and quantum and molecular mechanics. This paper introduces some optimization algorithms used in these research fields and presents a new theoretical computational method—an improved LBFGS Quasi-Newtonian mathematical optimization method—to produce 3D structures of prion AGAAAAGA amyloid fibrils (which are unstable, noncrystalline and insoluble), from the potential energy minimization point of view. Because the NMR or X-ray structure of the hydrophobic region AGAAAAGA of prion proteins has not yet been determined, the model constructed by this paper can be used as a reference for experimental studies on this region, and may be useful in furthering the goals of medicinal chemistry in this field.

Evaluation of gases'molecular abundance ratio by fiber-optic laser-induced breakdown spectroscopy with a metal-assisted method

A metal-assisted method is proposed for the evaluation of gases’molecular abundance ratio in fiber-optic laser-induced breakdown spectroscopy(FO-LIBS).This method can reduce the laser ablation energy and make gas composition identification possible.The principle comes from the collision between the detected gases and the plasma produced by the laser ablation of the metal substrate.The interparticle collision in the plasma plume leads to gas molecules dissociating and sparking,which can be used to determine the gas composition.The quantitative relationship between spectral line intensity and molecular abundance ratio was developed over a large molecular abundance ratio range.The influence of laser ablation energy and substrate material on gas quantitative calibration measurement is also analyzed.The proposed metal-assisted method makes the measurement of gases’molecular abundance ratios possible with an FO-LIBS system.

Establishment of Molecular Biological Method for Identification of Bacteria by 16S rDNA and gyrB Gene

[Objectives]The paper was to establish a molecular biological method for identification of bacterial strains.[Methods]The thalli of standard bacterial strains existing in the laboratory were collected and genomic DNA was extracted for amplification of 16S rDNA and gyrB gene.The 16S rDNA and gyrB gene sequences were obtained after sequencing.Sequences were aligned and analyzed via EzBioCloud and NCBI database,and phylogenetic trees were constructed to determine the species relationship of strains.Meantime,they were compared with known strains.[Results]This method could identify 5 standard strains accurately to the species level.The 16S rDNA and gyrB gene sequences were aligned and analyzed in EzBioCloud database and NCBI database.The strain with the max score was consistent with the known strain.And the query cover and ident were both above 99%.[Conclusions]The established molecular biological method for identification of bacterial strains by 16S rDNA and gyrB gene has good accuracy,which effectively solves the problem that the laboratory identification of bacteria relies on traditional methods and the accuracy can not be guaranteed,and further improves the identification ability of laboratory bacterial strains.

Molecular methods for detection of pathogenic viruses of respiratory tract——A review

Human respiratory system is harbored by a vast array of transient and normal microbial flora.A number of pathogenic viruses were diagnosed from samples in different occasions from mild to severe infections of respiratory tract.Molecular methods were developed for detection of these viruses during last two decades.Nucleic acid amplification methods were introduced for rapid and accurate diagnosis of pathogenic viruses.Multiplex detection systems were employed to identify a panel of pathogenic viruses,which requires specialized kits and instruments in some cases.This review summarizes different types of molecular approaches which were developed with time and applied for the detection of pathogenic viruses associated with infections of the respiratory system.

GALERKIN METHOD FOR COMPRESSIBLE FLOW OF CONTAMINATION FROM NUCLEAR WASTE WITH MOLECULAR DIFFUSION AND DISPERSION

Abstract A system of quasilinear coupled equations which arise from simulation of contamination of geologic nulear waste in porous media is studied. We’ll discuss Galerkin method for the model of compressible flow with molecular diffusion and dispersion. Some new techniques are introcued to error analysis. Only one dimensional case is considered. The optimal error estimate in both L^2 and H^1 is proved. A contribution of this paper is how the dispersion term can be handled,

An efficient method for mapping the 12C+12C molecular resonances at low energies

The 12C+12C fusion reaction is famous because of its complication of molecular resonances,and it plays an important role in both nuclear structural research and astrophysics. It is extremely difficult to measure the cross sections of 12C+12C fusions at energies of astrophysical relevance because of the very low reaction yields. To measure the complicated resonant structure that exists in this important reaction, an efficient thick target method has been developed and applied for the first time at energies Ec.m.<5.3 MeV. A scan of the cross sections over a relatively wide range of energies can be carried out using only a single beam energy. The result of measurement at Ec.m.=4.1 MeV is compared with results from previous work.This method will be useful for searching for potentially existing resonances of 12C+12C in the energy range 1 MeV<Ec.m.<3 MeV.

Identification of key residues in protein functional movements by using molecular dynamics simulations combined with a perturbation-response scanning method

The realization of protein functional movement is usually accompanied by specific conformational changes,and there exist some key residues that mediate and control the functional motions of proteins in the allosteric process.In the present work,the perturbation-response scanning method developed by our group was combined with the molecular dynamics(MD)simulation to identify the key residues controlling the functional movement of proteins.In our method,a physical quantity that is directly related to protein specific function was introduced,and then based on the MD simulation trajectories,the perturbation-response scanning method was used to identify the key residues for functional motions,in which the residues that highly correlated with the fluctuation of the function-related quantity were identified as the key residues controlling the specific functional motions of the protein.Two protein systems,i.e.,the heat shock protein 70 and glutamine binding protein,were selected as case studies to validate the effectiveness of our method.Our calculated results are in good agreement with the experimental results.The location of the key residues in the two proteins are similar,indicating the similar mechanisms behind the performance of their biological functions.

Evaluation of Quantum Chemical Methods and Basis Sets Applied in the Molecular Modeling of Artemisinin

In this paper, we evaluate semiempirical methods (AM1, PM3, and ZINDO), HF and DFT (B3LYP) in different basis sets to determine which method best describes the sign and magnitude of the geometrical parameters of artemisinin in the region of the endoperoxide ring compared to crystallographic data. We also classify these methods using statistical analysis. The results of PCA were based on three main components, explaining 98.0539% of the total variance, for the geometrical parameters C3O13, O1O2C3, O13C12C12a, and O2C3O13C12. The DFT method (B3LYP) corresponded well with the experimental data in the hierarchical cluster analysis (HCA). The experimental and theoretical angles were analyzed by simple linear regression, and statistical parameters (correlation coefficients, significance, and predictability) were evaluated to determine the accuracy of the calculations. The statistical analysis exhibited a good correlation and high predictive power for the DFT (B3LYP) method in the 6-31G** basis set.

Clinical Value of Molecular Biological Methods in Respiratory Tuberculosis in Children

The pattern of clinical forms of respiratory tuberculosis in children shows a preponderance of intrathoracic lymph node tuberculosis （89.4%） that is characterized by a complicated process in every third child under present-day conditions. Positive result of PCR closely correlates with the severity and extent of the specific process in children. Real-time PCR （RT-PCR） was ascertain to exhibit the highest sensitivity in detecting Mycobacterium tuberculosis DNA in children with primary generalized tuberculosis （62.5%） and in those with a disseminated specific process （55.6%）, which was much higher than conventional bacteriological study of diagnostic materials. By taking into account the findings, the RT-PCR detection of M. tuberculosis was considered as a substantial criterion for evaluating the magnitude of specific changes and the degree of tuberculosis infection activity in children.

Probing the electric double layer structure at nitrogen-doped graphite electrodes by constant-potential molecular dynamics simulations

Electric double layer(EDL)is a critical topic in electrochemistry and largely determines the working performance of lithium batteries.However,atomic insights into the EDL structures on heteroatom-modified graphite anodes and EDL evolution with electrode potential are very lacking.Herein,a constant-potential molecular dynamics(CPMD)method is proposed to probe the EDL structure under working conditions,taking N-doped graphite electrodes and carbonate electrolytes as an example.An interface model was developed,incorporating the electrode potential and atom electronegativities.As a result,an insightful atomic scenario for the EDL structure under varied electrode potentials has been established,which unveils the important role of doping sites in regulating both the EDL structures and the following electrochemical reactions at the atomic level.Specifically,the negatively charged N atoms repel the anions and adsorb Li~+at high and low potentials,respectively.Such preferential adsorption suggests that Ndoped graphite can promote Li~+desolvation and regulate the location of Li~+deposition.This CPMD method not only unveils the mysterious function of N-doping from the viewpoint of EDL at the atomic level but also applies to probe the interfacial structure on other complicated electrodes.

A Real-time Prediction System for Molecular-level Information of Heavy Oil Based on Machine Learning

Acquiring accurate molecular-level information about petroleum is crucial for refining and chemical enterprises to implement the“selection of the optimal processing route”strategy.With the development of data prediction systems represented by machine learning,it has become possible for real-time prediction systems of petroleum fraction molecular information to replace analyses such as gas chromatography and mass spectrometry.However,the biggest difficulty lies in acquiring the data required for training the neural network.To address these issues,this work proposes an innovative method that utilizes the Aspen HYSYS and full two-dimensional gas chromatography-time-of-flight mass spectrometry to establish a comprehensive training database.Subsequently,a deep neural network prediction model is developed for heavy distillate oil to predict its composition in terms of molecular structure.After training,the model accurately predicts the molecular composition of catalytically cracked raw oil in a refinery.The validation and test sets exhibit R2 values of 0.99769 and 0.99807,respectively,and the average relative error of molecular composition prediction for raw materials of the catalytic cracking unit is less than 7%.Finally,the SHAP(SHapley Additive ExPlanation)interpretation method is used to disclose the relationship among different variables by performing global and local weight comparisons and correlation analyses.

GALERKIN METHOD FOR COMPLETELY COMPRESSIBLE DISPLACEMENT WITH MOLECULAR DIFFUSION AND DISPERSION

In this paper, the numerical approximation by Galerkin method for completely compressible miscible displacement with molecular diffusion and dispersion in porous media is considered. Continuous time procedure is introduced and analysed. Some new techniques are applied to the analysis. Optimal error estimates in L ∞(J;H 1(Ω)) are proved, which implies an essential improvement to existed results. MR Subject Classification: 65N15,65N30.

Comparison of Genomic DNA Extraction Methods for Chenopodium quinoa Willd

To rapidly obtain high-quality genomic DNA from Chenopodium quinoa Willd, the genomic DAN in different tissues （leaves, stems and roots） of Chenopodi- um quinoa Willd was extracted by modified CTAB method, SDS method and high- salt Iow-pH method, respectively. The quality and yield of extracted DNA was deter- mined using agarose gel electrophoresis and UV spectrophotometry. At the same time, the PCR-SSR and SSCP molecular detection was also performed. The results showed that the gel test strips, without obvious decomposition, of all the extraction methods were relatively obvious; the genomic DNA yield extracted by modified CTAB method was highest, followed by that by SDS method, and the genomic DNA extracted by high-salt Iow-pH method was lowest： the genomic DNA yields extracted by different methods from Chenopodium quinoa Wiltd leaves were all high- er than those from roots and stems; the quality of Chenopodium quinoa Willd ge- nomic DNA extracted by modified CTAB method and high-salt Iow-pH method was better, and polyphenols, polysaccharides and other impurities were removed more completely. The PCR-SSR and SSCP detection results showed that the genomic DNA extracted by different methods from different tissues of Chenopodium quinoa Willd all could be better amplified, and high-quality strips could be obtained. So the Chenopodium quinoa Willd genomic DNA extracted by the three methods all can be used for subsequent molecular biology research.

多光谱法研究二氢杨梅素对胰脂肪酶的抑制作用

藤茶中主要黄酮类物质——二氢杨梅素(DMY)具有多种生物活性,而其降血脂机理鲜有报道。采用紫外光谱研究了DMY对胰脂肪酶(PL)的抑制作用,结合荧光光谱、同步荧光光谱、三维荧光光谱及分子对接模拟法研究了二者之间的相互作用及机理。紫外光谱测得DMY对PL的半抑制浓度为2.6×10^(-4)mol·L^(-1),表明其对PL具有较好的抑制作用,采用Lineweaver-Burk方程得出该抑制剂为竞争性作用,其抑制常数为6×10^(-4)mol·L^(-1);通过Stern-Volmer方程和静态猝灭双对数公式对293和310 K两者互作的荧光光谱计算,结果表明DMY能猝灭PL的自发荧光,荧光猝灭方式为静态猝灭,猝灭常数K_(SV)与温度负相关;结合常数K a与温度正相关,结合位点数n约为1,说明DMY与PL结合并形成稳定的配位复合物;采用Van't Hoff方程求出结合过程中的热力学参数ΔS=0.2014 J·mol^(-1)·K^(-1),ΔH=32.311 kJ·mol^(-1),ΔG小于0,表明两者通过疏水作用力自发结合且放热;由F rster非辐射能量转移理论计算出结合距离r=1.475 nm,说明DMY与PL结合生成复合物时发生了非辐射能量转移;同步荧光光谱结果表明,DMY与PL的相互作用对PL的二级构象发生了明显改变,主要作用于色氨酸(Tyr)附近。紫外光谱进一步揭示DMY可使PL发生π→π跃迁,导致其氨基酸残基的微环境变化;三维荧光光谱显示DMY可使PL两个特征峰(peak1,peak2)分别红移10和5 nm,荧光强度分别下降51.38%和41.93%,证实两者发生疏水作用后PL的微环境极性增大,构象改变;分子对接模拟结果表明,DMY结合位点位于PL中由PHE77、PHE215、TYR114、ILE209、PRO180氨基酸形成的疏水口袋内,其A环C5、B环C4′、C环C3、C环C O的-OH分别与氨基酸HIS263、TYR114、SER152、PHE215形成氢键,与氨基酸LRU213、GLU179、ALA178、THR78产生范德华力。实验数据有助于深入解DMY的降血脂分子作用机制,其独特的结构为天然抑制剂的药物合成和筛选提供了理论依据。