The sequence-dependent morphology of self-assembly peptides after binding with organophosphorus nerve agent VX

VX is a highly toxic organophosphorus nerve agent that the Chemical Weapons Convention classifies as a Schedule 1. In our previous study, we developed a method for detecting organophosphorus compounds using peptide self-assembly. Nevertheless, the self-assembly mechanisms of peptides that bind organophosphorus and the roles of each peptide residue remain elusive, restricting the design and application of peptide materials. Here, we use a multi-scale computational combined with experimental approach to illustrate the self-assembly mechanism of peptide-bound VX and the roles played by residues in different peptide sequences. We calculated that the self-assembly of peptides was accelerated after adding VX, and the final size of assembled nanofibers was larger than the original one, aligning with experimental findings. The atomic scale details offered by our approach enabled us to clarify the connection between the peptide sequences and nanostructures formation, as well as the contribution of various residues in binding VX and assembly process. Our investigation revealed a tight correlation between the number of Tyrosine residues and morphology of the assembly. These results indicate a self-assembly mechanism of peptide and VX, which can be used to design functional peptides for binding and hydrolyzing other organophosphorus nerve agents for detoxification and biomedical applications.

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.

Nanostructured Columns from Self-assemblyof Complementary Molecular Components

Nanostructured columns with a length about several tens of micrometer and a diameter of about 80 nm were obtained by molecular recognition directed self-assembly of a pair of comple- mentary molecular components, 4-amino-2 , 6-didodecylamino-1 , 3, 5-triazine(M) and 5- (4-dode- cyloxybenzylidene )-(1H, 3H)-2, 4, 6-pyrimidinetrione (B) in chloroform. In this system, with positive cooperativity, π-aromatic stacking and van der Waals interactions as well as hydrogen bonds cause the formation of the nanocolumns.

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.

Factors resisting protein adsorption on hydrophilic/hydrophobic self-assembled monolayers terminated with hydrophilic hydroxyl groups

The hydroxyl-terminated self-assembled monolayer(OH-SAM),as a surface resistant to protein adsorption,exhibits substantial potential in applications such as ship navigation and medical implants,and the appropriate strategies for designing anti-fouling surfaces are crucial.Here,we employ molecular dynamics simulations and alchemical free energy calculations to systematically analyze the factors influencing resistance to protein adsorption on the SAMs terminated with single or double OH groups at three packing densities(∑=2.0 nm^(-2),4.5 nm^(-2),and 6.5 nm^(-2)),respectively.For the first time,we observed that the compactness and order of interfacial water enhance its physical barrier effect,subsequently enhancing the resistance of SAM to protein adsorption.Notably,the spatial hindrance effect of SAM leads to the embedding of protein into SAM,resulting in a lack of resistance of SAM towards protein.Furthermore,the number of hydroxyl groups per unit area of double OH-terminated SAM at ∑=6.5 nm^(-2) is approximately 2 to 3 times that of single OH-terminated SAM at ∑=6.5 nm^(-2) and 4.5 nm^(-2),consequently yielding a weaker resistance of double OH-terminated SAM towards protein.Meanwhile,due to the structure of SAM itself,i.e.,the formation of a nearly perfect ice-like hydrogen bond structure,the SAM exhibits the weakest resistance towards protein.This study will complement and improve the mechanism of OH-SAM resistance to protein adsorption,especially the traditional barrier effect of interfacial water.

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.

Fabrication of Au/SiO_(2) Nanocomposite Films by Self-Assembly Multilayer Method

Gold colloid was prepared by chemical reduction of hydrogen tetrachloroaurate, polyelectrolyte/gold nanoparticle/silica nanoparticie composite films were fabricated via an electrostatic self-assembly multilayer method, and composite films of gold nanoparticle dispersed in silica matrix were formed by heat-treating the polyelectrolyte/gold nanoparticle/silica nanoparticle composite films to eliminate the polyelectrolyte. The obtained composite films were investigated with UV-vis, TEM, AFM and XRD. The results show that the self-assembly multilayer method is a promising process to produce composite films of gold nanoparticle-dispersed in organic and/or inorganic matrixes.

Differentiated self-assembly through orthogonal noncovalent interactions towards the synthesis of two-dimensional woven supramolecular polymers

Molecular weaving is a powerful approach to make molecularly woven materials that have showed unprecedented characteristics and properties intrinsically distinct to those of non-woven materials.We here report a facile and efficient approach for the synthesis of 2D woven supramolecular polymers by differentiated self-assembly through orthogonal noncovalent interactions.Importantly,the difference in binding strength of two orthogonal noncovalent interactions can be used to control the process of molecular weaving.Consequently,single-layered 2D woven supramolecular polymers were synthesized and fully characterized by various techniques.This study demonstrates a controllable method for molecular weaving,and will significantly hasten the development of molecularly woven materials.

Preparation of PVA/GO/h-BN Janus Film with High Thermal Conductivity and Excellent Flexibility via a Density Deposition Self-assembly Method

Janus films with asymmetric physical/chemical properties have attracted con siderable attention due to their promising applications in personal thermal management,electronic skin s,sensors,actuators,etc.However,traditional methods for fabricating Janus films conventionally need the assistance of an interface or auxiliary equipment,which are usually complex and time-consuming.Herein,flexible poly(vinyl alcohol)(PVA)/graphene oxide(GO)/h-BN(recorded as PVA/GO/h-BN)Janus films with thermally,optically,and electrically anisotropic properties are fabricated by a simple density deposition self-assem bly method,which just utilizes the density difference between GO and h-BN during water evaporation.Experimental results show that the two sides of the acquired Janus films have obvious asymmetric characteristics.In the original state of the PVA/GO/h-BN Janus films,the thermal conductivity of the GO side(10.06 W·m^(-1)·K^(-1))is generally lower than that of the h-BN side(10.48W·m^(-1)·K^(-1)).But after GO is reduced,the thermal conductivity of the rGO side reaches 12.17 W·m^(-1)·K^(-1),surpassing that of the h-BN side.In addition,the relative reflectance of the h-BN side of Janus film is also significantly higher than that of the rGO side,and the su rface resistance difference between the two sides is about 4 orders of magnitude.The prepared PVA/GO/h-BN Janus films show great application potential in human thermal management,light conversion switches,and electronic skins.This study provides a simple and versatile strategy for fabricating Janus films with multifunctional(such as thermal,optical,and electrical)anisotropies.

A Facile Self-assembly Synthesis of Hexagonal ZnO Nanosheet Films and Their Photoelectrochemical Properties

Here, large-scale and uniform hexagonal zinc oxide(ZnO) nanosheet films were deposited onto indium tin oxide(ITO)-coated transparent conducting glass substrates via a facile galvanic displacement deposition process. Compared with other commonly used solution methods, this process avoids high temperature and electric power as well as supporting agents to make it simple and cost-effective. The as-fabricated ZnO nanosheet films have uniform hexagonal wurtzite structure. The photoelectrochemical(PEC) cell based on ZnO nanosheet film/ITO photoelectrode was also fabricated and its performance was improved by optimizing the solution concentration. A higher photocurrent density of*500 l A cm^(-2)under AM 1.5 G simulated illumination of 100 m W cm^(-2)with zero bias potential(vs. Ag/AgCl electrode) was obtained, which may ascribe to the increased surface-to-volume ratio of disordered Zn O nanosheet arrays. Our developed method may be used to deposit other oxide semiconductors, and the Zn O nanosheet film/ITO PEC cell can be used to design low-cost optoelectronic and photoelectrochemical devices.

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

Molecular Component Structures MediatedFormation of Self-assemblies

Molecular recognition directed self-assemblies from complementary molecular components, melamine and barbituric acid derivatives were studied by means of NMR, fluorescence, and TEM. It was found that both the process of the self-assembly and the morphologies of the result- ed self-assemblies could be mediated by modifying the structures of the molecular components used. The effect of the structures of the molecular components on the formation of the self-as- semblies was discussed in terms of intermolecular interactions.

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.

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,