Long Range Corrections for Inhomogeneous Simulations of Mie n-m Potential.

The long-range correction scheme for dispersion interactions in inhomogeneous simulations is generalized to Mie n-m potential. The influence of the cutoff distance and lateral dimensions of the simulation box are studied for 8-6, 12-6, and 20-6 Mie fluids at two different temperatures (close and far from the critical point). For sufficiently large systems (2400 particles, Rc = 3.5σ) equilibrium properties are simulated over the whole vapor-liquid coexistence using the inhomogeneous Monte Carlo simulations, and the results are compared with the Gibbs Ensemble technique and with the square gradient theory combined with the SAFT Mie equation of state.

Morphological and proteomic analysis of early stage air-liquid interface biofilm formation in Mycobacterium smegmatis.

We studied the early stages of pellicle formation by Mycobacterium smegmatis on the surface of a liquid medium [air-liquid interface (A-L)]. Using optical and scanning electron microscopy, we showed the formation of a compact biofilm pellicle from micro-colonies over a period of 8-30 h. The cells in the pellicle changed size and cell division pattern during this period. Based on our findings, we created a model of M. smegmatis A-L early pellicle formation showing the coordinate growth of cells in the micro-colonies and in the homogeneous film between them, where the accessibility to oxygen and nutrients is different. A proteomic approach utilizing high-resolution two-dimensional gel electrophoresis, in combination with mass spectrometry-based protein identification, was used to analyse the protein expression profiles of the different morphological stages of the pellicle. The proteins identified formed four expression groups; the most interesting of these groups contained the proteins with highest expression in the biofilm development phase, when the floating micro-colonies containing long and more robust cells associate into flocs and start to form a compact pellicle. The majority of these proteins, including GroEL1, are involved in cell wall synthesis or modification, mostly through the involvement of mycolic acid biosynthesis, and their expression maxima correlated with the changes in cell size and the rigidity of the bacterial cell wall observed by scanning electron microscopy.

Influence of hydrogen bonding on the structure of the (001) corundum-water interface. Density functional theory calculations and Monte Carlo simulations.

Density functional theory calculations and classical Monte Carlo simulations are applied to study the behavior of water in contact with a hydroxylated corundum (001) surface. Using DFT with periodic boundary conditions at T = 0 K, we systematically study the influence of the number of water molecules on the surface geometry and on the structure of the contact water layer. Only little effect of the thickness of the water layer on the geometry of the surface hydroxyl groups is observed. On the other hand, the molecules in the second layer have strong influence on the arrangement of water molecules in direct contact with the solid surface. In order to mimic macroscopic systems at room temperature, we perform inhomogeneous MC simulations of model corundum surface in contact with the water phase modeled by SPC/E model. The water molecules are classified according to their hydrogen-bonded partners into several groups. It is found that the preferential orientation of interfacial water molecules is primarily determined by the type of their hydrogen bonding. The hydroxyl groups at the corundum surface can serve as hydrogen bond donor or acceptor, depending on their orientation. No surface hydroxyls are found to coordinate two water molecules at the same time. On the other hand, water molecules coordinated by two different surface groups appear in MC simulations.

Size distribution of associated clusters in liquid alcohols: interpretation of simulation results in the frame of SAFT approach.

The size distribution and topology of associated clusters for primary alcohols is studied using molecular dynamics simulations. Liquid ethanol, propanol, butanol, hexanol, and octanol are simulated at pressure P = 1 bar and temperatures T = 300 K, T = 350 K, and T = 400 K. The fractions of molecules with different sets of hydrogen bonded partners, the size of associated cluster and the site-site distribution functions between atoms participating on hydrogen bonding are extracted from simulated trajectories. For all alcohols longer than ethanol, the length of the alkyl chain has only a marginal effect on the association. Consequently, related properties like coordination numbers of hydroxyl group, size distribution of associates, or fractions of differently coordinated alcohol molecules are independent on the molecular size. Although we employed a force-field without involved polarizability, we observe a positive cooperativity of hydrogen bonding simply as a consequence of steric and electrostatic interactions. The size and topology of associates is analyzed within the frame of 3B model of statistical association fluid theory. Although this approach enables good thermodynamic description of systems containing associating compounds, several insufficiencies appear in the description at molecular level.

Analysis of evoked deep brain connectivity.

Establishing dependencies and connectivity among different structures in the human brain is an extremely complex issue. Methods that are often used for connectivity analysis are based on correlation mechanisms. Correlation methods can analyze changes in signal shape or instantaneous power level. Although recent studies imply that observation of results from both groups of methods together can disclose some of the basic functions and behavior of the human brain during mental activity and decision-making, there is no technique covering changes in the shape of signals along with changes in their power levels. We present a method using a time evaluation of the correlation along with a comparison of power levels in every available contact pair from intracranial electrodes placed in deep brain structures. Observing shape changes in signals after stimulation together with their power levels provides us with new information about signal character between different structures in the brain during task-related events - visual stimulation with motor response. The results for a subject with 95 intracerebral contacts used in this paper demonstrate a clear methodology capable of spatially analyzing connectivity among deep brain structures.

Fitness and proteome changes accompanying the development of erythromycin resistance in a population of Escherichia coli grown in continuous culture.

We studied the impact of a sublethal concentration of erythromycin on the fitness and proteome of a continuously cultivated population of Escherichia coli. The development of resistance to erythromycin in the population was followed over time by the gradient plate method and minimum inhibitory concentration (MIC) measurements. We measured the growth rate, standardized efficiency of synthesis of radiolabeled proteins, and translation accuracy of the system. The proteome changes were followed over time in two parallel experiments that differed in the presence or absence of erythromycin. A comparison of the proteomes at each time point (43, 68, and 103 h) revealed a group of unique proteins differing in expression. From all 35 proteins differing throughout the cultivation, only three were common to more than one time point. In the final population, a significant proportion of upregulated proteins was localized to the outer or inner cytoplasmic membranes or to the periplasmic space. In a population growing for more than 100 generations in the presence of antibiotic, erythromycin-resistant bacterial clones with improved fitness in comparison to early resistant culture predominated. This phenomenon was accompanied by distinct changes in protein expression during a stepwise, population-based development of erythromycin resistance.

Influence of cyclic dimer formation on the phase behavior of carboxylic acids. II. Cross-associating systems.

The doubly bonded dimer association scheme (DBD) proposed by Sear and Jackson is extended to mixtures exhibiting both self- and cross-associations. The PC-SAFT equation of state is combined with the new DBD association contribution to describe the vapor-liquid equilibria of binary mixtures of carboxylic acids + associating compounds (water, alcohols, and carboxylic acids). The effect of doubly bonded dimers on the phase behavior in such systems is less important than in mixtures of carboxylic acids with nonassociating compounds, due to the cross-associations that compete with the formation of DBDs. Nevertheless, a clear improvement in the description of vapor-liquid coexistence curves is achieved over the classical 2B association model, particularly for the dew point curves.

On the time course of synchronization patterns of neuronal discharges in the human brain during cognitive tasks.

Using intracerebral EEG recordings in a large cohort of human subjects, we investigate the time course of neural cross-talk during a simple cognitive task. Our results show that human brain dynamics undergo a characteristic sequence of synchronization patterns across different frequency bands following a visual oddball stimulus. In particular, an initial global reorganization in the delta and theta bands (2-8 Hz) is followed by gamma (20-95 Hz) and then beta band (12-20 Hz) synchrony.

Surface hydrophobicity and roughness influences the morphology and biochemistry of streptomycetes during attached growth and differentiation.

Streptomycetes, soil-dwelling mycelial bacteria, can colonise surface of organic soil debris and soil particles. We analysed the effects of two different inert surfaces, glass and zirconia/silica, on the growth and antibiotic production in Streptomyces granaticolor. The surfaces used were in the form of microbeads and were surrounded by liquid growth media. Following the production of the antibiotic granaticin, more biomass was formed as well as a greater amount of antibiotic per milligram of protein on the glass beads than on the zirconia/silica beads. Comparison of young mycelium (6 h) proteomes, obtained from the cultures attached to the glass and zirconia/silica beads, revealed three proteins with altered expression levels (dihydrolipoamide dehydrogenase, amidophosphoribosyltransferase and cystathionine beta-synthase) and one unique protein (glyceraldehyde-3-phosphate dehydrogenase) that was present only in cells grown on glass beads. All of the identified proteins function primarily as cytoplasmic enzymes involved in different parts of metabolism; however, in several microorganisms, they are exposed on the cell surface and have been shown to be involved in adhesion or biofilm formation.

Influence of cyclic dimer formation on the phase behavior of carboxylic acids.

A new thermodynamic approach based on the Sear and Jackson association theory for doubly bonded dimers [Mol. Phys.1994, 82, 1033] is proposed to describe the thermodynamic properties of carboxylic acids. The new model is able to simultaneously represent the vapor pressures, saturated densities, and vaporization enthalpies of the shortest acids and is in a much better agreement with experimental data than other approaches that do no consider the formation of cyclic dimers. The new model is applied to mixtures of carboxylic acids with nonassociating compounds, and a very good description of the vapor-liquid equilibria in mixtures of alkanes + carboxylic acids is obtained.

Effect of the interfacial area on the equilibrium properties of Lennard-Jones fluid.

The influence of the system size on the interfacial and equilibrium properties of the Lennard-Jones fluid obtained using the inhomogeneous Monte Carlo simulations is studied for temperatures covering the vapor-liquid coexistence region. The values of the surface tension, coexistence densities, as well as the pressure of saturated vapor are affected by the varying area of the interface. Moreover the loss of isotropy of the fluid structure is observed as a consequence of using the periodic boundary conditions in molecular simulations. The equilibrium properties are evaluated also in simulation boxes of the shape of hexangular prism and compared to the results of simulations performed in the commonly used quadrangular parallelepiped. Both sets seem to be affected by the finite-size effects in similar extent.

Effective screening length and quasiuniversality for the restricted primitive model of an electrolyte solution.

Monte Carlo simulations for the restricted primitive model of an electrolyte solution above the critical temperature are performed at a wide range of concentrations and temperatures. Thermodynamic properties such as internal energy, osmotic coefficient, activity coefficient, as well as spatial correlation functions are determined. These observables are used to investigate whether quasiuniversality in terms of an effective screening length exists, similar to the role played by the effective electron mass in solid-state physics. To that end, an effective screening length is extracted from the asymptotic behavior of the Fourier-transformed charge-correlation function and plugged into the Debye-Huckel limiting expressions for various thermodynamic properties. Comparison with numerical results is favorable, suggesting that correlation and other effects not captured on the Debye-Huckel limiting level can be successfully incorporated by a single effective parameter while keeping the functional form of Debye-Huckel expressions. We also compare different methods to determine mean ionic activity coefficient in molecular simulations and check the internal consistency of the numerical data.

Water at polar and nonpolar solid walls.

Recent progress in simulating the properties of interfacial water at hard hydrophobic and hydrophilic surfaces is reviewed and compared to results for the air/water interface. The authors discuss static properties such as the equilibrium contact angle, the depletion layer thickness, and the orientation of interfacial water molecules. Relations between these properties, e.g., the relation between the contact angle and the thickness of the depletion layer which is experimentally observed on hydrophobic surfaces, are emphasized. For a hydrophilic sapphire surface, the authors discuss the influence of geometry and density of polar surface groups on the interfacial water structure. They discuss nonequilibrium effects arising in laminar shear flows, where the classic no-slip hydrodynamic boundary condition is violated at hydrophobic interfaces. They discuss the arising slip and relate it to static properties of the solid hydrophobic/water interface.

Interfacial water at hydrophobic and hydrophilic surfaces: depletion versus adsorption.

The structure of the water-solid interface for widely varying surface properties is investigated with Monte Carlo simulations using the SPC/E water model. Of particular interest is the relation between the wetting coefficient as a measure of the hydrophobicity of the substrate and the density depletion close to the solid surface. The substrates are modeled as rigid ordered lattices of sites that interact with water molecules through an orientation-independent Lennard-Jones potential of varying strength. Hydrophilic character is obtained by addition of polar hydroxyl groups on the substrate surface, and the influence of density, spatial distribution, and angular orientation of the polar groups on the interfacial water structure is studied.

Interfacial properties of cyclic hydrocarbons: a Monte Carlo study.

The Monte Carlo technique is used to study the vapor-liquid interface of cyclopentane, cyclohexane, and benzene. The OPLS and TraPPE potential fields are compared in the temperature range from 298.15 to 348.15 K (273.15-298.15 K for C5H10). A new method for the treatment of the long-range interactions in inhomogeneous simulations is used. When this new method is employed, the obtained values of saturated liquid density and of enthalpy of vaporization are equal to those obtained using the bulk isothermal-isobaric Monte Carlo technique. The values of surface tension become independent of the cutoff distance and they are significantly larger than those when only simple spherical truncation of intermolecular interactions is used.

Long range corrections in inhomogeneous simulations.

An improved method for the treatment of the long range corrections in molecular simulations of inhomogeneous systems with planar interfaces is presented. To evaluate the quality of this approach, Monte Carlo simulations of the Lennard-Jones fluid are performed in the temperature range T* is an element of <0.7, 1.25>. The attention is focused especially on the values of the surface tension, which represents a property significantly sensitive to the truncation of the intermolecular interactions. When the presented approach is employed, the values of coexisting densities and surface tensions obtained with the cutoff distance R(c) = 2.5sigma are within experimental errors identical with those obtained for cutoff distance R(c) = 5.5sigma.

Characterization of a eukaryotic type serine/threonine protein kinase and protein phosphatase of Streptococcus pneumoniae and identification of kinase substrates.

Searching the genome sequence of Streptococcus pneumoniae revealed the presence of a single Ser/Thr protein kinase gene stkP linked to protein phosphatase phpP. Biochemical studies performed with recombinant StkP suggest that this protein is a functional eukaryotic-type Ser/Thr protein kinase. In vitro kinase assays and Western blots of S. pneumoniae subcellular fractions revealed that StkP is a membrane protein. PhpP is a soluble protein with manganese-dependent phosphatase activity in vitro against a synthetic substrate RRA(pT)VA. Mutations in the invariant aspartate residues implicated in the metal binding completely abolished PhpP activity. Autophosphorylated form of StkP was shown to be a substrate for PhpP. These results suggest that StkP and PhpP could operate as a functional pair in vivo. Analysis of phosphoproteome maps of both wild-type and stkP null mutant strains labeled in vivo and subsequent phosphoprotein identification by peptide mass fingerprinting revealed two possible substrates for StkP. The evidence is presented that StkP can phosphorylate in vitro phosphoglucosamine mutase GlmM which catalyzes the first step in the biosynthetic pathway leading to the formation of UDP-N-acetylglucosamine, an essential common precursor to cell envelope components.