Multiscale dynamics of the cell envelope of Shewanella putrefaciens as a response to pH change

The bacterial surface properties of gram-negative Shewanella putrefaciens were characterized by microbial adhesion to hydrocarbons (MATH), adhesion to polystyrene dishes, and electrophoresis at different values of pH and ionic strength. The bacterial adhesion to these two apolar substrates shows significant variations according to pH and ionic strength. Such behavior could be partly explained by electrostatic repulsions between bacteria and the solid or liquid interface. However, a similar trend was also observed at rather high ionic strength where electrostatic interactions are supposed to be screened. The nanomechanical properties at pH 4 and 10 and at high ionic strength were investigated by using atomic force microscopy (AFM). The indentation curves revealed the presence of a polymeric external layer that swells and softens up with increasing pH. This suggests a concomitant increase of the water permeability and so did of the hydrophilicity of the bacterial surface. Such evolution of the bacterial envelope in response to changes in pH brings new insight to the pH dependence in the bacterial adhesion tests. It especially demonstrates the necessity to consider the hydrophobic/hydrophilic surface properties of bacteria as not univocal for the various experimental conditions investigated.     

Probing the modifications of polystyrene surface properties after incubation with the Shewanella putrefaciens bacteria at two pH values (4, 10) by atomic force microscopy

The local surface properties of polystyrene (PS) dishes incubated for 14 h with gram‐negative cells (Shewanella putrefaciens) were investigated by atomic force microscopy (AFM) in aqueous solutions at two pH values (4 and 10). The AFM images and force curves revealed the presence of a polymeric layer adsorbed onto the PS surfaces in acid media. In contrast, no evolution was observed in the case of basic media. Copyright © 2007 John Wiley & Sons, Ltd.     

On the electrophoretic mobility of a cylindrical soft particle

A previous theory for the electrophoresis of a cylindrical soft particle (that is, a cylindrical hard particle covered with a layer of polyelectrolytes) [7], which makes use of the condition that the electrical force acting on the polymer segments is balanced with a frictional force exerted by the liquid flow, is modified by replacing this condition with an alternative and more appropriate boundary condition that pressure is continuous at the boundary between the surface layer and the surrounding electrolyte solution. The general mobility expression thus obtained is found to reproduce all of the approximate analytic mobility expressions derived previously. Received: 20 July 2000/Accepted: 21 August 2000     

Conserving the linear momentum in stochastic dynamics: Dissipative particle dynamics as a general strategy to achieve local thermostatization in molecular dynamics simulations

Stochastic dynamics is a widely employed strategy to achieve local thermostatization in molecular dynamics simulation studies; however, it suffers from an inherent violation of momentum conservation. Although this short‐coming has little impact on structural and short‐time dynamic properties, it can be shown that dynamics in the long‐time limit such as diffusion is strongly dependent on the respective thermostat setting. Application of the methodically similar dissipative particle dynamics (DPD) provides a simple, effective strategy to ensure the advantages of local, stochastic thermostatization while at the same time the linear momentum of the system remains conserved. In this work, the key parameters to employ the DPD thermostats in the framework of periodic boundary conditions are investigated, in particular the dependence of the system properties on the size of the DPD‐region as well as the treatment of forces near the cutoff. Structural and dynamical data for light and heavy water as well as a Lennard–Jones fluid have been compared to simulations executed via stochastic dynamics as well as via use of the widely employed Nose–Hoover chain and Berendsen thermostats. It is demonstrated that a small size of the DPD region is sufficient to achieve local thermalization, while at the same time artifacts in the self‐diffusion characteristic for stochastic dynamics are eliminated. © 2016 Wiley Periodicals, Inc.     

Changes in charge density and softness of a poly(l-lactide) microcapsule surface in the hydrolytic degradation process

The changes in surface properties of poly(l-lactide) microcapsules caused by hydrolytic degradation have been studied with electrophoretic mobility measurements. An electrokinetic model has been applied to examine the electrophoretic mobility data, which were previously analyzed with a model that does not take into account the liquid flow inside the microcapsule membrane [K. Makino, H. Ohshima and T. Kondo, J. Microencapsulation, 4 (1987) 47]. The present new model involves two parameters, the charge density in the microcapsule membrane and a softness parameter, the latter of which characterizes the reciprocal of the frictional coefficient of the polymer exerted on the liquid flow. Information about the changes in charge density and in the softness of the poly(l-lactide) microcapsule surface have been newly obtained. The surface charge density increases by the cleavage of ester bonds in the polymer chain in the initial stage of the degradation process. It then gradually decreases down to the value for intact poly(l-lactide) microcapsules as a result of the release of degraded polymer segments from the microcapsule surface. Also, as the degradation proceeds, the softness parameter value increases, suggesting that the surface of the microcapsules becomes softer, probably because the surface becomes porous. The above change in the softness and the decrease in charge density at the later stage of the degradation both imply liberation of charged polymer segments. The degradation of poly(l-lactide) microcapsules proceeds by alternate repetition of cleavage of the ester bonds in the polymer chains and liberation of the degraded polymer segments from the surface.     

Molecular dynamics simulation as a complement to diffraction in the study of disorder in crystals

Summary It is not uncommon that a crystal structure contains a minority component which does not share the overall space-group of the remainder of the structure, but has a lower (or no) effective space-group symmetry. A conventional diffraction treatment will inevitably be made within the space-group of the majority of the system, and will therefore result in an average structure also with this symmetry. We here indicate the value of molecular dynamics (MD) simulation within a supercell of the structure as a complementary tool in providing information concerning the local structure for the minority component. Such information, though illusive, is often the most interesting and the physically most significant aspect of the structure. It can also be crucial information for the testing of new theory, and in the design of new materials. The approach is illustrated for the case of the Na⁺ ion distribution in Na⁺ '-alumina, and for the experimentally more inaccessible mixed-ion system Na⁺/Ba²⁺ '-alumina.On leave of absence from Departamento de Fisica, Universidad Autonoma Metropolitana, Unidad Iztapalapa, Mexico D.F., Mexico.     

泛函数迭代法求解反胶束内双电层电势

用泛函数分析理论中的迭代法求解了反胶束内关于双电层势的Poisson- Boltzmann（PB）方程，导出了泛电位下的第一、二次迭代的解析表达式。与 Debye-Huckel（DH）线性近似及计算机的数值解进行对比表明，迭代解不仅在低电 位条件下能与两者相符合，而且在高电位下与数值解在相吻合。     

Impact of ionic strength of growth on the physiochemical properties, structure, and adhesion of Listeriamonocytogenes polyelectrolyte brushes to a silicon nitride surface in water

The adhesion energies between pathogenic Listeriamonocytogenes EGDe to a model surface of silicon nitride were quantified using atomic force microscopy (AFM) in water for cells grown in pure media (as the control) and in media of four different ionic strengths of added NaCl (IS of 0.05 M, 0.1 M, 0.3 M and 0.5 M NaCl). The physiochemical properties of L. monocytogenes EGDe surface brushes were shown to have a strong influence on the adhesion of the microbe to the silicon nitride surface. The transitions in the adhesion energies, physiochemical properties, and the structure of bacterial surface polyelectrolyte brushes were observed for the cells grown in the media of 0.1 M added NaCl. Our results suggested that the highest long-range electrostatic repulsion which was partially balanced by the Liftshitz-van der Waals attraction for the cells grown at 0.1 M was responsible for the highest energy barrier to adhesion for these cells as predicted by the soft-particle analysis of DLVO theory and the lower adhesion measured by AFM.     

Calcium as a factor influencing the response of Serratia marcescens strain SMG40 to growth surfaces

Serratia marcescens, like several other bacterial species, is able to adhere to and swarm on growth surfaces, and this property is correlated with changes in the structures and functions of cells which pass from broth to solid media. In the case of the pigmented form of S. marcescens strain SMG40, the response to the contact with agar was influenced by the presence of Ca²⁺ ions as follows. (1) In the swimming phase, i.e. in soft 0.35% agar media, expansion was not modified upon the addition of 5–35 mM Ca²⁺ ions. (2) On growth surfaces inducing swarming, i.e. on media containing 0.75% agar (low agar), Ca²⁺ ions used at low concentrations (e.g. 0.5mM) enhanced both growth and expansion. (3) At higher concentrations (from 3 mM). the Ca²⁺ ions inhibited expansion but not growth. Correlatively, the cell density per unit of the surface occupied by bacteria inhibited from swarming was increased: expansion rates of swarms at successive periods were lower and showed less fluctuation than normal. In a non-pigmented but still good swarmer mutant, found to be more sensitive to calcium, expansion was reduced to 50% with at most 0.5 mM Ca²⁺ ions. One-step revenants recovered pigmentation and the initial response to Ca²⁺ ions described in points (2) and (3) above. The inhibitory activity of CaCl₂ was partly antagonized by NaCl. Other properties implied in the interactions of Serratia cells with agar, i.e. pigmentation, adherence to solid surfaces and the production of an extracellular surfactant were not inhibited by Ca²⁺ ions.     

Solid-liquid-liquid extraction as an approach to the sensitive detection of a hydrophobic pollutant through surface-enhanced Raman spectroscopy

Surface-enhanced Raman scattering (SERS) spectra of thiram (tetramethylthiuram disulfide), a dimethyl dithiocarbamate fungicide, were recorded after the adsorption on plasmonic silver nanowires from a system of water, organic solvent and nanoparticles. As organic solvents dichloromethane and 1-octanol were involved. A method for measuring the adsorption constant of thiram as a model molecule to the silver surface by studying its partition phenomena in a binary solvent system is presented. The method is based on the extraction of a hydrophobic molecule from an organic solvent by an aqueous suspension of silver anisotropic nanoparticles. The obtained results demonstrate the effectiveness of SERS methodology for the sensitive analysis of compounds with low aqueous solubility, and a reliable SERS spectrum of thiram was obtained with excellent signal/noise ratio at low concentrations. In addition, for vibrational assignments, Density Functional Theory (DFT) was used for the simulation of the Raman and SERS spectra of thiram and its complexes with silver considering the following two models: a single silver atom and an Ag₂₀ cluster.     

Topological analysis of the charge density response of a Ni4 cluster to a probe H2 molecule

Local density self-consistent field (SCF) discrete variationalX calculations are performed on a Ni₄ tetrahedron interacting with a probe H₂ molecule in special geometries. Optimized basis functions generated from the spherically averaged SCF potential are used. Topological charge-density analyses and binding energy calculations are used to study a portion of the energy surface for the approach of the H₂ molecule toward the Ni₄ tetrahedron. The effect of the H₂ molecule on Ni-Ni, Ni-H bonds and changes in the H-H covalent bond are investigated with the help of the field and various data at its critical points. The qualitative relationship between these data and the calculated binding energies is exploited.     

Application of the Doehlert experimental design to molecularly imprinted polymers: surface response optimization of specific template recognition as a function of the type and degree of cross-linking

We propose the use of Doehlert’s experimental design, a second-order uniform shell design, for the optimization of molecularly imprinted polymers (MIPs). We have chosen a simple model system where the influence of kind and degree of cross-linking on template recognition was studied using S-propranolol as the template. We found that Doehlert’s design allows—with very few experiments—one to screen the evolution of the binding capacity of a MIP as a function the different parameters, and thus appears to be a powerful means to screen for the best composition and synthesis method for MIPs. We believe that this chemometric tool can significantly accelerate the development of new MIPs as synthetic recognition elements, particularly in the context of a given application, and will be a versatile complement or alternative to first-order designs to fit complex processes. Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Low‐pressure barrier discharge ion source using air as a carrier gas and its application to the analysis of drugs and explosives

In this work, a low‐pressure air dielectric‐barrier discharge (DBD) ion source using a capillary with the inner diameter of 0.115 and 12 mm long applicable to miniaturized mass spectrometers was developed. The analytes, trinitrotoluene (TNT), 1,3,5‐trinitroperhydro‐1,3,5‐triazine (RDX), 1,3,5,7‐tetranitroperhydro‐1,3,5,7‐tetrazocine (HMX), pentaerythritol tetranitrate (PETN), nitroglycerine (NG), hexamethylene triperoxide diamine (HMTD), caffeine, cocaine and morphine, introduced through the capillary, were ionized by a low‐pressure air DBD. The ion source pressures were changed by using various sizes of the ion sampling orifice. The signal intensities of those analytes showed marked pressure dependence. TNT was detected with higher sensitivity at lower pressure but vice versa for other analytes. For all analytes, a marked signal enhancement was observed when a grounded cylindrical mesh electrode was installed in the DBD ion source. Among nine analytes, RDX, HMX, NG and PETN could be detected as cluster ions [analyte + NO₃]^? even at low pressure and high temperature up to 180 °C. The detection indicates that these cluster ions are stable enough to survive under present experimental conditions. The unexpectedly high stabilities of these cluster ions were verified by density functional theory calculation. Copyright © 2016 John Wiley & Sons, Ltd.     

Formation of a four-electron donor carbonyl group in the decarbonylation of the unsaturated H2C2Fe2(CO)6 tetrahedrane as an alternative to an iron-iron triple bond

The unsaturated Fe₂C₂ tetrahedrane derivatives R₂C₂Fe₂(CO)₆ (R = Ph, ^tBu) are among the many products obtained from reactions of the alkynes RCCR with iron carbonyls. In this connection theoretical studies have been performed on the simplest such compounds H₂C₂Fe₂(CO)_n (n = 6, 5) for comparison with the experimentally known structure of the t-butyl derivative t-Bu₂C₂Fe₂(CO)₆ and in order to predict the decarbonylation pathways for such (alkyne)Fe₂(CO)₆ derivatives. These theoretical studies predict an Fe₂C₂ tetrahedrane structure for H₂C₂Fe₂(CO)₆ with a formal FeFe double bond very similar to the experimental structure for t-Bu₂C₂Fe₂(CO)₆. Decarbonylation of H₂C₂Fe₂(CO)₆ is predicted to give an H₂C₂Fe₂(CO)₅ isomer retaining the Fe₂C₂ tetrahedrane structure, with an FeFe double bond but with the unprecedented feature of a four-electron donor bridging carbonyl group in an M₂C₂ tetrahedrane structure. The formation of formal FeFe triple bonds appears to be avoided in even the higher energy H₂C₂Fe₂(CO)₅ structures. These include three triplet Fe₂C₂ tetrahedrane structures with formal FeFe double bonds as well as a coordinately unsaturated singlet structure, still with an FeFe double bond.