Molecular dynamics analysis on tensile properties of carbon nanotubes with different cracks

Molecular dynamics simulation is employed for the axial tension of single-walled carbon nanotubes (SWCNTs) with different cracks. The cracks of SWCNTs in this study actually are the crack-like defects. AIREBO potential is used to simulate the interactions among carbon atoms. The effects of the crack length, temperature, strain rate and tube diameter on the mechanical properties of SWCNTs are studied. It is found that the failure stress and failure strain decrease with the increase of crack length. And the results show that the failure stress and failure strain are related to the applied strain rate and affected by temperature especially by lower temperature. It is also revealed that the failure stress increases with the increase in tube diameter. The deformation behaviours of SWCNTs are also obtained.     

Fracture analysis of single-layer graphene sheets with edge crack under tension

In this study, the fracture of single-layered graphene sheets (SLGSs) with edge crack under simple tension is investigated using molecular dynamics simulations, and the variations in fracture strength of SLGSs with crack length, strain rate and temperature are analysed. It is found that the existing edge crack weakens mechanical properties of SLGSs. Fracture strength and strain decrease with the increase in crack length and temperature, but increase with the increase in strain rate. It is also shown that shorter initial cracks propagate faster than longer initial cracks, but shorter initial cracks begin propagating at higher axial strain at a certain temperature and strain rate. And cracks are found to propagate faster in higher strain rates.     

A molecular dynamics investigation on the compression of cross-linked epoxy resins

Molecular dynamics method is employed to simulate the compression deformation of the polymer materials for electronic packaging. The effects of moisture content, conversion degree, strain rate and temperature on the mechanical properties of epoxy resin are investigated. The stress–strain curves, Young's modulus and Poisson ratio are compared with existing experimental data. The results show that mechanical properties of epoxy resin decrease obviously with increasing moisture content and temperature. However, the high cross-linking conversion and strain rate enhance the mechanical properties of resin.     

Conceptual comparison of metabolic pathways with electronic circuits

1 Introduction Based on the review of the previous work on genecircuits [1–7] , this paper discusses an electronic circuitwhich has been designed to mimic glycolysis, the CitricAcid (TCA) cycle and the electron transport chain. En-zymes play a vital role in metabolic pathways. Thespecificity of enzymic action is explained in terms of theprecise fitting of enzyme and substrate [8–9] . Enzymes areusually very specific…     

一株产碱性蛋白酶菌株的筛选鉴定及酶学特性研究

【目的】从丝茅草中筛选得到产蛋白酶菌株并研究驯化过程中微生物群落结构,以及探究该菌株的生长特性和蛋白酶的酶学特性。【方法】通过高通量测序探究来源于丝茅草的菌株在不同培养条件下细菌种类及丰度,通过选择性培养基来筛选能够分解酪素并产生蛋白酶的菌株,通过单因素试验方法确定环境因子对菌株生长和蛋白酶活性的影响。【结果】微生物群落结构在基础培养基和牛肉膏蛋白胨培养基中不同。通过含酪素的选择性培养基里筛选到1株产蛋白酶菌株H-16,经生理生化试验和16S r DNA鉴定知该菌株属于Escherichia marmotae,菌株H-16能产生分子量为70 k Da左右的单亚基蛋白酶。胰蛋白胨、蔗糖、30°C或35°C、p H 7分别为菌株生长的最适氮源、碳源、温度和p H。菌株H-16分泌的蛋白酶最适p H为6–8,在50°C及6%盐度以下酶活性几乎不受影响。此外,Cu(II)和Ag(I)等金属离子能够抑制蛋白酶的活性。【结论】该菌株H-16为嗜中温菌株,能够产生碱性蛋白酶。     

Study on thermomechanical properties of cross-linked epoxy resin

In this paper, molecular dynamics simulation was carried out to investigate the thermomechanical properties of cross-linked epoxy resin. The glass transition temperature, coefficients of thermal and moisture expansion, mechanical property parameters and so on are studied with the influence of temperature, water concentration and polymer conversion taken into account. The simulation results were in good agreement with existing experimental data.     

Mechanical response and deformation mechanics of Type IV pili investigated using steered coarse-grained molecular dynamics simulation

Type IV pili are long filamentous structures on the surface of bacteria, which can be rapidly assembled or disassembled with pilin subunits by molecular motors. They can generate force during retraction and are involved in many bacterial functions. Steered molecular dynamics simulations with coarse-grained MARTINI models are carried out to investigate the mechanical behaviors of pili under tension. Our study is the first to report a Young's modulus of 0.80 ± 0.07 GPa and a spring constant of 1294.6 ± 116.5 kJ mol⁻¹ nm⁻² for pilus. Our results show the mechanical responses of pili are different from those described by the worm-like chain model and the van der Waal's interactions play a critical role in the mechanical responses. Moreover, the effects of pulling rates and virtual spring constants of pilus on Young's modulus are studied and two distinct morphological stages with the conformational changes appear during the extension of pilus are observed. This work provide insight into the mechanics and the deformation mechanism of pilus assembly.     

Understanding interaction and dynamics of water molecules in the epoxy via molecular dynamics simulation

The robust structural integrity of the epoxy plays an important role in ensuring the long-term service life of its applications, which is affected by the absorbed moisture. In order to understand the mechanism of the moisture effect, the knowledge of the interaction and dynamics of the water molecules inside the epoxy is of great interest. Molecular dynamics simulation is used in this work to investigate the structure and bonding behaviour of the water molecules in the highly cross-linked epoxy network. When the moisture concentration is low, the water molecules are well dispersed in the cross-linked structure and located in the vicinity of the epoxy functional groups, which predominantly form the hydrogen bond (H-bond) with the epoxy network, resulting in the low water mobility in the epoxy. At the high concentration, the water favourably forms the large cluster due to the predominant water–water H-bond interaction, and the water molecules diffuse primarily inside the cluster, which leads to the high water mobility and the accelerated H-bond dynamics. The variation of the bonding behaviour and dynamics of the water molecules reported here could be exploited to understand the material change and predict the long-term performance of the epoxy-based products during the intended service life.     

Self-diffusivity,hydrogen bonding and density of different water models in carbon nanotubes

In this paper, the density, hydrogen bonding and self-diffusivity of water confined in carbon nanotubes are investigated. Molecular dynamics is used to simulate a large variety of nanotubes with various water models. Our results produce, for the first time, the complete trend of these properties from narrow nanotubes, where water shows particularly anomalous behaviour, to large ones where its characteristics are similar to those of bulk.     

Scaling of Folding Properties in Go Models of Proteins

Insights about scaling of folding properties of proteins are obtained bystudying folding in heteropolymers described by Go-like Hamiltonians. Bothlattice and continuum space models are considered. In the latter case, themonomer-monomer interactions correspond to the Lennard-Jones potential.Several statistical ensembles of the two- and three-dimensional targetnative conformations are considered. Among them are maximally compactconformations which are confined to a lattice and those which are obtainedeither through quenching or annealing of homopolymers to their compactlocal energy minima. Characteristic folding times are found to grow aspower laws with the system size. The corresponding exponents are notuniversal. The size related deterioration of foldability is found to beconsistent with the scaling behavior of the characteristic temperatures:asymptotically, the folding temperature becomes much lower than thetemperature at which glassy kinetics become important. The helicalconformations are found to have the lowest overall scaling exponent andthe best foldability among the classes of conformations studied. Thescaling properties of the Go-like models of the protein conformationsstored in the Protein Data Bank suggest that proteins are not optimizedkinetically.     

Structural insights on identification of potential lead compounds targeting WbpP in Vibrio vulnificus through structure-based approaches

WbpP encoding UDP-GlcNAC C4 epimerase is responsible for the activation of virulence factor in marine pathogen Vibrio vulnificus (V. vulnificus) and it is linked to many aquatic diseases, thus making it a potential therapeutic target. There are few reported compounds that include several natural products and synthetic compounds targeting Vibrio sp, but specific inhibitor targeting WbpP are unavailable. Here, we performed structure-based virtual screening using chemical libraries such as Binding, TOSLab and Maybridge to identify small molecule inhibitors of WbpP with better drug-like properties. Deficient structural information forced to model the structure and the stable protein structure was obtained through 30?ns of MD simulations. Druggability regions are focused for new lead compounds and our screening protocol provides fast docking of entire small molecule library with screening criteria of ADME/Lipinski filter/Docking followed by re-docking of top hits using a method that incorporates both ligand and protein flexibility. Docking conformations of lead molecules interface displays strong H-bond interactions with the key residues Gly101, Ser102, Val195, Tyr165, Arg298, Val209, Ser142, Arg233 and Gln200. Subsequently, the top-ranking compounds were prioritized using the molecular dynamics simulation-based conformation and stability studies. Our study suggests that the proposed compounds may aid as a starting point for the rational design of novel therapeutic agents.     

Fluctuation Simulations and the Calculation of Mechanical Partial Molar Properties

Abstract

A method for the direct calculation of partial molar volumes, energies, and enthalpies in multicomponent mixtures in which all species have finite concentrations is presented. The approach, which is based on fluctuation theory, allows the simultaneous determination of the properties of all components in the mixture. The advantages and limitations of the method are illustrated through the (N, U, V) molecular dynamics calculation of the mechanical partial molar properties of two binary Lennard-Jones mixtures.     

Laying out ground rules for protein-aided nanofabrication: ZnO synthesis at 70°C as a case study

Designer proteins that incorporate solid-binding peptides hold promise to control the nucleation, growth, morphology, and assembly of inorganic phases under mild conditions of temperature and pressure. However, protein-aided nanofabrication remains more art than science and some materials can only be synthesized at temperatures that cause most mesophilic proteins to unfold. Using zinc oxide (ZnO) synthesis at 70°C as case study, we show here that seemingly unimportant variables, such as the carry-over concentration of Tris buffer and the \"empty\" host protein scaffold can exert a significant influence on materials morphology. We also show that, once well-controlled conditions are established, thermodynamic predictions and adsorption isotherms are powerful tools to understand how various ZnO-binding sequence inserted within the thermostable framework of Escherichia coli thioredoxin A (TrxA) affect inorganic morphogenesis.     

Molecular dynamics simulations showing 1-palmitoyl-2-oleoyl-phosphatidylcholine (POPC) membrane mechanoporation damage under different strain paths

Continuum finite element material models used for traumatic brain injury lack local injury parameters necessitating nanoscale mechanical injury mechanisms be incorporated. One such mechanism is membrane mechanoporation, which can occur during physical insults and can be devastating to cells, depending on the level of disruption. The current study investigates the strain state dependence of phospholipid bilayer mechanoporation and failure. Using molecular dynamics, a simplified membrane, consisting of 72 1-palmitoyl-2-oleoyl-phosphatidylcholine (POPC) phospholipids, was subjected to equibiaxial, 2:1 non-equibiaxial, 4:1 non-equibiaxial, strip biaxial, and uniaxial tensile deformations at a von Mises strain rate of 5.45 × 10⁸ s^?1, resulting in velocities in the range of 1 to 4.6 m·s^?1. A water bridge forming through both phospholipid bilayer leaflets was used to determine structural failure. The stress magnitude, failure strain, headgroup clustering, and damage responses were found to be strain state-dependent. The strain state order of detrimentality in descending order was equibiaxial, 2:1 non-equibiaxial, 4:1 non-equibiaxial, strip biaxial, and uniaxial. The phospholipid bilayer failed at von Mises strains of .46, .47, .53, .77, and 1.67 during these respective strain path simulations. Additionally, a Membrane Failure Limit Diagram (MFLD) was created using the pore nucleation, growth, and failure strains to demonstrate safe and unsafe membrane deformation regions. This MFLD allowed representative equations to be derived to predict membrane failure from in-plane strains. These results provide the basis to implement a more accurate mechano-physiological internal state variable continuum model that captures lower length scale damage and will aid in developing higher fidelity injury models.     

氧化石墨烯对红细胞功能的影响

纳米材料的生物相容性是人们关注的热点。氧化石墨烯是一种被广泛应用于生物医学的纳米材料,但其毒性不容忽视。本文从溶血率、红细胞脆性、乙酰胆碱酯酶活性三方面研究了氧化石墨烯对血液系统的毒性。结果表明,红细胞的溶血率在氧化石墨烯浓度低于100 μg/mL时均低于8% (P<0.01);低浓度氧化石墨烯 (<5 μg/mL) 对红细胞的脆性没有显著影响,高浓度氧化石墨烯 (如10 μg/mL) 会提高红细胞的脆性 (P=0.01);氧化石墨烯能增加红细胞上乙酰胆碱酯酶的活性,浓度为20 μg/mL的直径>5 μm的氧化石墨烯 (LGO) 可将乙酰胆碱酯酶的活性提高42.67% (P<0.05)。之后利用分子动力学模拟研究氧化石墨烯与乙酰胆碱酯酶相互作用并提高其活性的机理,推测氧化石墨烯会附着在细胞膜上并提供一个电负性环境,帮助水解产物更快地从活性位点脱离,从而提高乙酰胆碱酯酶的活性。