Molecular dynamics simulation of a model oligomer for poly(N-isopropylamide) in water

Molecular dynamics (MD) has been used to simulate a dilute aqueous solution of a 50-units oligomer model for the thermoresponsive polymer poly(N-isopropylacrylamide) at 300 and 310 K, i.e., below and above its lower critical solution temperature (LCST) in water. Statistical analyses of the system trajectories show that at 310 K the oligomer exhibits a more compact conformation than at 300 K, in qualitative agreement with experiments, and that it is surrounded by a smaller number of first-hydrationshell water molecules

Molecular dynamics of electrosprayed water nanodroplets containing sodium bis(2-ethylhexyl)sulfosuccinate

The behavior of aqueous solutions of sodium bis(2-ethylhexyl)sulfosuccinate (AOTNa) subject to electrospray ionization (ESI) has been investigated by molecular dynamics (MD) simulations at three temperatures (350, 500 and 800 K). We consider several types of water nanodroplets containing AOTNa molecules and composed of a fixed number of water molecules (1000), N0 AOT AOT anions (N0 AOT = 0, 5, 10) and N0 Na sodium ions (N0 Na = 0, 5, 10, 15, 20): in a short time scale (less than 1 ns), the AOTNa molecules, initially forming direct micelles in the interior of the water nanodroplets, are observed in all cases to diffuse nearby the nanodroplet surface, so that the hydrophilic heads and sodium ions become surrounded by water molecules, whereas the alkyl chains lay at the droplet surface. Meanwhile, evaporation of water molecules and of solvated sodium ions occurs, leading to a decrease of the droplet size and charge. At 350 K, no ejection of neutral or charged surfactant molecules is observed, whereas at 500 K, some fragmentation occurs, and at 800 K, this event becomes more frequent. The interplay of all these processes, which depend on the values of temperature, N0 AOT and N0 Na eventually leads to anhydrous charged surfactant aggregates with prevalence of monocharged ones, in agreement with experimental results of ESI mass spectrometry. The quantitative analysis of theMD trajectories allows to evidencemolecular details potentially useful in designing future ESI experimental conditions

Mosaic DNA imports with interspersions of recipient sequence after natural transformation of Helicobacter pylori

Helicobacter pylori colonizes the gastric mucosa of half of the human population, causing gastritis, ulcers, and cancer. H. pylori is naturally competent for transformation by exogenous DNA, and recombination during mixed infections of one stomach with multiple H. pylori strains generates extensive allelic diversity. We developed an in vitro transformation protocol to study genomic imports after natural transformation of H. pylori. The mean length of imported fragments was dependent on the combination of donor and recipient strain and varied between 1294 bp and 3853 bp. In about 10% of recombinant clones, the imported fragments of donor DNA were interrupted by short interspersed sequences of the recipient (ISR) with a mean length of 82 bp. 18 candidate genes were inactivated in order to identify genes involved in the control of import length and generation of ISR. Inactivation of the antimutator glycosylase MutY increased the length of imports, but did not have a significant effect on ISR frequency. Overexpression of mutY strongly increased the frequency of ISR, indicating that MutY, while not indispensable for ISR formation, is part of at least one ISR-generating pathway. The formation of ISR in H. pylori increases allelic diversity, and contributes to the uniquely low linkage disequilibrium characteristic of this pathogen

Natural Transformation of Helicobacter pylori Involves the Integration of Short DNA Fragments Interrupted by Gaps of Variable Size

Helicobacter pylori are gram-negative bacteria notable for their high level of genetic diversity and plasticity, features that may play a key role in the organism's ability to colonize the human stomach. Homeologous natural transformation, a key contributor to genomic diversification, has been well-described for H. pylori. To examine the mechanisms involved, we performed restriction analysis and sequencing of recombination products to characterize the length, fragmentation, and position of DNA imported via natural transformation. Our analysis revealed DNA imports of small size (1,300 bp, 95% confidence limits 950–1850 bp) with instances of substantial asymmetry in relation to selectable antibiotic-resistance markers. We also observed clustering of imported DNA endpoints, suggesting a possible role for restriction endonucleases in limiting recombination length. Additionally, we observed gaps in integrated DNA and found evidence suggesting that these gaps are the result of two or more separate strand invasions. Taken together, these observations support a system of highly efficient short-fragment recombination involving multiple recombination events within a single locus

Molecular dynamics simulation of small water-binding cavitands

Analyses of 20-ns simulations of aqueous solutions of the recently synthesized cavitand benzotriborneol (BTB) show that this molecule binds a single water molecule within its hydrophilic cavity for an average time interval of ca. 750 ps, that is 370 times longer than the permanence time of water around borneol. Moreover, this time becomes three times longer in a 99.8% (V/V) chloroform\u2013water solution, while it decreases for BTB methylether derivatives in water, becoming 279, 36 or 119 ps when one, two or all three hydroxyl hydrogen atoms are replaced by methyl groups, respectively

TRANSPUTER-BASED PARALLEL SYSTEM FOR ACQUISITION AND ONLINE ANALYSIS OF SINGLE-FIBER ELECTROMYOGRAPHIC SIGNALS

We describe a transputer-based system suitable for accurate measurements of single-fiber electromyographic jitter. It consists of a conventional electromyograph, a home-made interface and a commercially available transputer-based board installed within a PC/AT compatible. Taking advantage of the concurrent operation of two transputer modules, the system features simultaneous data acquisition and statistical signal processing: while data are acquired and analyzed, a real-time visualization of the signal latency and its variability is provided. In the present configuration, the system can acquire and analyze up to 40,000 consecutive action potentials, which can be grouped into up to eight sets at different stimulation rates programmable up to 16 Hz. Since the determination of the electromyographic signal latency relies on least-squares smoothing and interpolation of the acquired data rather than on amplitude-threshold triggering, a low value (0.7 μs) of so called technical jitter is achieved. Computing power and memory can be easily extended by addition of transputer-based modules. Typical results of data acquisition and on-line analysis are reported

A Molecular Dynamics study of structure, stability and fragmentation patterns of Sodium bis(2-ethylhexyl)sulfosuccinate positively charged aggregates in vacuo

Positively charged supramolecular aggregates formed in vacuo by n AOTNa (sodium bis(2-ethylhexyl)sulfosuccinate) molecules and nc additional sodium ions, i.e. [AOTnNan+nc ]nc, have been investigated by molecular dynamics (MD) simulations for n = 1–20 and nc = 0–5. Statistical analysis of physical quantities like gyration radii, atomic B-factors and moment of inertia tensors provides detailed information on their structural and dynamical properties. Even for nc = 5, all stable aggregates show a reverse micelle-like structure with an internal solid-like core including sodium counterions and surfactant polar heads surrounded by an external layer consisting of the surfactant alkyl chains. Moreover, the aggregate shapes may be approximated by rather flat and elongated ellipsoids whose longer axis increases with n and nc. The fragmentation patterns of a number of these aggregates have also been examined and have been found to markedly depend on the aggregate charge state. In one particular case, for which experimental findings are available in the literature, a good agreement is found with the present fragmentation data