The impact of the number of layers of the graphene nanopores and the electrical field on ssDNA translocation

Graphene-based nanopore devices hold great promise for the next generation DNA sequencing because graphene is atomically thin which is extremely important for single base recognition. To understand the fundamental details of DNA translocation through a graphene nanopore, in this work, molecular dynamics simulations of ssDNA translocation through the nanopore were performed to trace the nucleobase trajectories and to investigate the impact of the number of layers of the graphene membrane and the electrical field on ssDNA translocation. We found that the velocity of ssDNA translocation was speeded up with the higher bias voltage, and the two-layered and five-layered graphene membrane with 1.0-nm diameter circular nanopore could discern different DNA strand by the translocation time.     

Conidial water affinity is an important characteristic for thermotolerance in entomopathogenic fungi

The interspecific thermotolerance of several species of entomopathogenic fungi was evaluated based on the conidial water affinity. The species were divided between hydrophilic and hydrophobic conidia. The species with hydrophobic conidia were Beauveria bassiana (ARSEF 252), Metarhizium brunneum (ARSEF 1187), Metarhizium robertsii (ARSEF 2575), Isaria fumosorosea (ARSEF 3889) and Metarhizium anisopliae s.l. (ARSEF 5749). The species with hydrophilic conidia were Tolypocladium cylindrosporum (ARSEF 3392), Tolypocladium inflatum (ARSEF 4877), Simplicillium lanosoniveum (ARSEF 6430), Lecanicillium aphanocladii (ARSEF 6433), S. lanosoniveum (ARSEF 6651), Aschersonia placenta (ARSEF 7637) and Aschersonia aleyrodis (ARSEF 10276). The conidial surface tension of each isolate was also studied. Conidial suspensions were exposed to 38, 41 or 45 °C. After exposure, the suspensions were inoculated on media and conidial germination was evaluated. Considerable differences in thermotolerance were found among the 12 entomopathogenic fungal species. Species with hydrophobic conidia were generally more thermotolerant than species with hydrophilic conidia. All isolates with hydrophobic conidia showed higher conidial surface tension than the isolates with hydrophilic conidia.     

Protein folding and association: insights from the interfacial and thermodynamic properties of hydrocarbons.

We demonstrate in this work that the surface tension, water-organic solvent, transfer-free energies and the thermodynamics of melting of linear alkanes provide fundamental insights into the nonpolar driving forces for protein folding and protein binding reactions. We first develop a model for the curvature dependence of the hydrophobic effect and find that the macroscopic concept of interfacial free energy is applicable at the molecular level. Application of a well-known relationship involving surface tension and adhesion energies reveals that dispersion forces play little or no net role in hydrophobic interactions; rather, the standard model of disruption of water structure (entropically driven at 25 degrees C) is correct. The hydrophobic interaction is found, in agreement with the classical picture, to provide a major driving force for protein folding. Analysis of the melting behavior of hydrocarbons reveals that close packing of the protein interior makes only a small free energy contribution to folding because the enthalpic gain resulting from increased dispersion interactions (relative to the liquid) is countered by the freezing of side chain motion. The identical effect should occur in association reactions, which may provide an enormous simplification in the evaluation of binding energies. Protein binding reactions, even between nearly planar or concave/convex interfaces, are found to have effective hydrophobicities considerably smaller than the prediction based on macroscopic surface tension. This is due to the formation of a concave collar region that usually accompanies complex formation. This effect may preclude the formation of complexes between convex surfaces.     

Zwitterionic polymers functionalised nanoporous graphene for water desalination: a molecular dynamics study

In this paper, one nanoporous graphene grafting several zwitterionic polymer chains was designed as the osmosis membrane for seawater desalination. Using molecular dynamics simulation, the efficiency and mechanism of salt rejection were discussed. The simulated results showed that the zwitterionic polymer chains on nanoporous graphene can form the charge channel to block Na⁺ and Cl^? ions pass through, and the slat rejection efficiency of functionalised graphene can reach to about 90%. In the simulation, the steric hindrance and electrostatic interaction are the main factors for the salt rejection. With time evolution, the charge channel formed by the soft polymer chains can decrease the effective pore area of membrane, leading to the increase of steric hindrance; the positive and negative centres of polymer chains can adsorb Na⁺ and Cl^? ions under electrostatic interaction in the solution, contributing into the increase of charge density above the membrane. These conclusions are consistent with experimental report. Our designed osmosis membrane about the graphene is helpful for improving the potential application of defect graphene in water desalination and reducing the trouble of obtaining appropriate graphene sheet with small aperture.     

Do β-lactam antibiotics permeabilize the outer membrane of gram-negative bacteria? An electrochemical investigation

Abstract The extent of short-term adhesion of various suspension-cultured plant cell species to polymer substrates exhibiting a wide range of surface tensions was examined. Adhesion of cells with a relatively low surface tension, suspended in distilled water, to the polymers fluorinated ethylenepropylene (FEP), polystyrene (PS), polyethylene terephthalate (PET), and sulphonated polystyrene (SPS) increased with decreasing substrate surface tension following the sequence SPS < PET < PS < FEP. These results are in agreement with the predictions of a thermodynamic model of particle adhesion which considers the role of the substrate, suspending-liquid, and cellular surface tensions. In contrast, little adhesion of relatively high surface tension cells to any of the polymer substrates was observed. Electrostatic repulsive forces between these cells and the polymer surface prevent adhesion because the magnitude of the attractive van der Waals force is small. A correlation was observed between the general adhesiveness of the various cultured plant cell species, especially to the low surface tension substrates, and the cellular surface tension determined by measuring the water contact angle on smooth layers of the cells. The cellular surface tensions ranged from approximately 42 mJ/m² for Digitalis purpurea cells to approximately 70mJ/m² for Papaver somniferum cells. Adhesion of cells to the polymer substrates increased with decreasing cellular surface tension under otherwise identical conditions. These results are also consistent with thermodynamic model predictions.     

Uptake modes of octadecane by Pseudomonas sp. DG17 and synthesis of biosurfactant

Aims: In order to gain more insight into the uptake modes of octadecane by bacteria. Methods and Results: A strain that could utilize octadecane well was isolated from crude oil contaminated soil, and named as Pseudomonas sp. DG17 by 16S rDNA analysis. Culture growth result showed that Pseudomonas sp. DG17 grew well in the addition of 200 and 400 mg l^?1 of octadecane, which showed that physical contact between substrate and bacteria was important in the substrate biodegradation. Meanwhile, Pseudomonas sp. DG17 produced rhamnolipids biosurfactant that contains 10 congeners, thus causing the surface tension of the culture medium decline and facilitating the contact between hydrocarbon and bacteria. Scanning‐electron‐microscopy results showed that a disruption of the surface membranes in certain zones was observed in some of the cells grown in 400 mg l^?1 octadecane at 176 h compared with the cells in exponential phase at 72 h due to the production of biosurfactant‐rhamnolipid. Conclusions: These results indicated the possibility that the direct contact with insoluble octadecane droplets occurred before the contact with pseudosolubilization smaller oil droplets. Significance: This report throws more light on the uptake mechanisms of octadecane by bacteria, and proposes the possibility that role of biosurfactant is to increase the contact between hydrocarbon and bacteria by changing the cell membrane structure which needs studied in depth. Impact of Study: Results of this study are useful in the bioremediation of petroleum polluted soil.     

The transport of Mycobacterium avium subsp. paratuberculosis through saturated aquifer materials

Aims:  To investigate the processes controlling the transport of Mycobacterium avium subsp. paratuberculosis ( Map ) through aquifer materials.
Methods and Results:  We measured two important surface characteristics known to affect bacterial attachment to sediment surfaces: surface charge and hydrophobicity. We then measured the transport of Map through laboratory columns packed with aquifer sand with varying ionic strength solutions and sediment surface charge. We found that Map has a strong negative charge and is highly hydrophobic and that the transport of Map through positively charged Fe-coated sands was reduced compared with transport through negatively charged clean quartz sand, although Map transport for all treatments was low compared with the transport behaviour reported in the literature for other bacteria.
Conclusions:  Our results suggest that the potential for groundwater contamination by Map is low; however, the organism may remain bound to the soil near the surface where it can be ingested by grazing animals or be released during run off events.
Significance and Impact of the Study:  This is the first study looking at the surface characteristics and transport behaviour of Map through aquifer materials and therefore provides important information for understanding the movement of Map in the environment.     

不同初始含水率下粘质土壤的入渗过程

土壤入渗是降雨渗入土体形成土壤水的基本水文过程,土壤渗透能力影响着地表径流和土壤侵蚀强度。土壤初始含水量决定了入渗初期的土水势,是影响土壤入渗过程的重要因素。利用环刀法,观测了三峡库区林地和草地的土壤入渗过程,对比分析了不同初始含水率下土壤入渗率和常用入渗模型的适宜性。结果表明,随土壤初始含水率的增大,林地和草地下土壤初始入渗率减小,入渗趋于稳定所需时间缩短,累积入渗量和稳定入渗率增大。土壤含水率为12%的林地初始入渗率为8.95 mm/min,是含水率40%林地初始入渗率的4倍,但1h累积入渗量仅是含水率40%林地的2/3。有机质含量丰富的草地土壤入渗过程对初始含水率的敏感性较弱,干湿草地相比较入渗参数的差异不如林地明显。随时间的延长,土壤入渗率逐渐降低,入渗曲线渐趋平缓,最小二乘法拟合结果显示Horton模型对林地和草地下土壤入渗过程的拟合效果较好,且模型参数具有物理意义,是分析和预测三峡库区林草覆盖下土壤入渗过程的适宜模型。     

Surface hydrophobicity and water transport of the toad urinary bladder: Effects of vasopressin

Summary The present study investigated whether the hydrophobic properties (wettability) of the luminal surface of the toad urinary bladder might play a role in modulating water transport across this epithelium. In the absence of vasopressin (ADH), water transport across the tissue was low, while luminal surface hydrophobicity (water contact angle) was relatively high. Following stimulation by ADH, water transport increased and surface hydrophobicity decreased. The addition of indomethacin to inhibit ADH-induced prostaglandin synthesis did not reduce these actions of ADH. In an attempt to alter water transport in this tissue, a liposomal suspension of surface-active phospholipids was administered to the luminal surface. This addition had no detectable influence on the low basal rates of water transport, but blocked the ADH-induced stimulation of water transport. We suggest that surface-active phospholipids on the toad bladder luminal membrane may contribute to the hydrophobic characteristics of this tissue. ADH may act to decrease surface hydrophobicity, facilitating the movement of water molecules across an otherwise impermeable epithelium. This surface alteration may be associated with the appearance of water channels in the apical membrane.     

Nonspecific cleavage of proteins using graphene oxide

In this article, we report the intrinsic catalytic activity of graphene oxide (GO) for the nonspecific cleavage of proteins. We used bovine serum albumin (BSA) and a recombinant esterase (rEstKp) from the cold-adapted bacterium Pseudomonas mandelii as test proteins. Cleavage of BSA and rEstKp was nonspecific regarding amino acid sequence, but it exhibited dependence on temperature, time, and the amount of GO. However, cleavage of the proteins did not result in complete hydrolysis into their constituent amino acids. GO also invoked hydrolysis of p-nitrophenyl esters at moderate temperatures lower than those required for peptide hydrolysis regardless of chain length of the fatty acyl esters. Based on the results, the functional groups of GO, including alcohols, phenols, and carboxylates, can be considered as crucial roles in the GO-mediated hydrolysis of peptides and esters via general acid–base catalysis. Our findings provide novel insights into the role of GO as a carbocatalyst with nonspecific endopeptidase activity in biochemical reactions.     

Mechanism of pressure-induced water flow across plant roots

Summary Pressure-induced non-linear water flow across plant roots was analyzed theoretically. The double-canal model of radial water transport shown lately explained accurately the observed non-linear water flow in maize roots. The driving force rather than the hydraulic permeability caused the non-linear flow of water. The conclusion was drawn that non-linearity in pressure-induced water flow was an inherent property of the apoplast canal system in roots. Net solute transport plays a primary part for water transport.     

Experimental methodology to quantify Candida albicans cell surface hydrophobicity

A new method of formation of yeast cell lawns for contact angle measurement (with water, formamide and 1-bromonaphthalene) is described. The cell lawns were formed on agar layers avoiding liquid penetration. The method was validated by comparing the hydrophobicity of Candida albicans grown at different temperatures and the hydrophobicity of bacterial cell lawns built on agar layers and obtained by the usual filtration method.     

Mechanical properties of pristine and nanoporous graphene

We present molecular dynamics simulations of monolayer graphene under uniaxial tensile loading. The Morse, bending angle, torsion and Lennard-Jones potential functions are adopted within the mdFOAM library in the OpenFOAM software, to describe the molecular interactions in graphene. A well-validated graphene model using these set of potentials is not yet available. In this work, we investigate the accuracy of the mechanical properties of graphene when derived using these simpler potentials, compared to the more commonly used complex potentials such as the Tersoff-Brenner and AIREBO potentials. The computational speed up of our approach, which scales O(1.5N), where N is the number of carbon atoms, enabled us to vary a larger number of system parameters, including graphene sheet orientation, size, temperature and concentration of nanopores. The resultant effect on the elastic modulus, fracture stress and fracture strain is investigated. Our simulations show that graphene is anisotropic, and its mechanical properties are dependant on the sheet size. An increase in system temperature results in a significant reduction in the fracture stress and strain. Simulations of nanoporous graphene were created by distributing vacancy defects, both randomly and uniformly, across the lattice. We find that the fracture stress decreases substantially with increasing defect density. The elastic modulus was found to be constant up to around 5% vacancy defects, and decreases for higher defect densities.     

Molecular dynamics simulation of water confined in a nanopore of amorphous silica

Molecular dynamics simulations are performed to study the transport and structural properties of water confined in a cylindrical silica nanopore. The pore wall is amorphous and mimics a typical mesoporous silica material. The diameters of silica pores studied are 4.75, 9.51, 20 and 25 Å. The self-diffusion of water calculated decreases with pore size and indicates much slower transport compared to the bulk phase. Strong adsorption of water to the silica wall is observed in the density profiles, indicating the hydrophilic nature of the wall. The hydrogen-bonding network is strongly affected by water–silica wall interaction. The average number of hydrogen bonds per water decreased with decreasing pore diameter.     

Growth Conditions Influence Expression of Cell Surface Hydrophobicity of Staphylococci and Other Wound Infection Pathogens

The initial adhesion of microbes to tissue and solid surfaces can be mediated by hydrophobic interaction. Expression of microbial cell surface hydrophobicity (CSH) is influenced by growth conditions, and often best expressed after growth under nutrient-poor conditions, or “starvation.” In the present study, the CSH of 133 strains of Enterobacteriaceae, Staphylococcus aureus, coagulase-negative staphylococci, Enterococcus faecalis, group A streptococcus, Pseudomonas aeruginosa, Clostridium perfringens, Bacteroides fragilis, Peptococcus magnus, and of 8 Candida albicans strains was measured by the salt aggregation test after growth on hematin agar in a 5% CO₂ atmosphere, or under anaerobiosis. Cells of all but 8 strains expressed pronounced or moderate CSH, i.e., they aggregated in 0.01-2 M ammonium sulfate. When the agar surface was covered by human serum (diluted 1:5) to mimic growth conditions in a wound, 94 strains expressed higher CSH, and 44 strains the same CSH as after growth without serum. The CSH of 12 strains of different species was measured after growth on blood, hematin and PDM agar, with or without serum, and in an aerobic or a 5% CO₂ atmosphere. The highest CSH was expressed after growth in 5% CO₂ with serum, and the lowest growth after on blood agar in aerobic atmosphere. Identical results were obtained with native and heat-inactivated (56 C, 20 min) serum. The reduced surface tension obtained in 5% CO₂, as well as yet unidentified serum factors, promotes expression of CSH.     

Molecular simulation for separation of ethylene and ethane by functionalised graphene membrane

ABSTRACT

Graphene is an excellent adsorbent and a membrane material for separation which has attracted wide attention in recent years. Moreover, compared with typical polymer materials, porous graphene has exhibited superior performance. In this paper, molecular dynamics and quantum mechanics were used to explore the appropriate pore size and separation mechanism of graphene. The 2N-Pore-13 (modified by N and H atom) membrane can prevent the penetration of ethane while maintaining high ethylene flux. The permeation rate of ethylene reached 3.7×10⁶ GPU in 5N-Pore-13 membrane, while the one of ethane was only 227 GPU. The mechanism is based on the fact that molecular structure of ethylene is two-dimensional, so that ethylene can get closer to membrane surface when it is adsorbed. When passing through the pores, ethylene has lower enthalpy and entropy barrier.     

Local description of surface tension through thermodynamic and mechanical definitions

For a half century, the calculation of local pressure components and surface tension along the normal to the surface have been carried out using mechanical definitions. This has led to three principal definitions: Irving and Kirkwood, Harasima and Kirkwood–Buff. Recently, thermodynamic definitions based on the energy calculation have been introduced to compute the local properties. We propose here to compare both definitions for Lennard–Jones particles interacting through a truncated and shifted potential. For this, two locations of the pairwise interaction involved in the calculation of the local pressure components and surface tension within the thermodynamic routes are investigated. For the first time, we show that the thermodynamic definition suffers, to one least degree with respect to the mechanical definition, from the same ambiguity. From a numerical standpoint, thermodynamic definition is more simple and less computationally expensive. Therefore, with the complicated potential, the thermodynamic approach appears to be most interesting to compute macroscopic and local pressure and surface tension.     

Influence of constant magnetic fields on certain physiochemical properties of water

There has been considerable recent interest in the question of effects of constant magnetic fields (CMF) on living organisms. The possible alteration of the physiochemical properties of water appears to be one example of such an influence. The dielectric constant, pH, and surface tension of water exposed to CMF action were studied. The results fail to confirm the changes observed by some authors. Controversial opinions on this problem are also summarized and discussed.     

The influence of electrostatic interactions on partition in aqueous polyethylene glycol/dextran biphasic systems: Part II

In aqueous polyethylene glycol/dextran two-phase systems, the hydrophobicity, free volume, surface tension, and interfacial tension of the phases in equilibrium were measured as a function of pH and ionic strength. These parameters were found to change with pH, but the pattern and magnitude cannot explain the unusual partition of charged macromolecules, observed previously. The electrostatic potential difference was determined by a new experimental approach based on the measurement of the pH difference between the phases at equilibrium. In polyethylene glycol/dextran systems containing sodium chloride as ionized species, the electrostatic potential is not constant in the pH range 2 to 11. The partition behavior of charged macromolecules and its dependence on pH can be explained by the combined action of charge and phase potential. This conclusion was tested with poly-L-glutamate, which partitioned as predicted and in a pattern opposite to positively charged macro- molecules. (c) 1995 John Wiley & Sons, Inc.