The role of disulfide bridges in the 3-D structures of the antimicrobial peptides gomesin and protegrin-1: a molecular dynamics study

Some antimicrobial peptides have a broad spectrum of action against many different kinds of microorganisms. Gomesin and protegrin-1 are examples of such antimicrobial peptides, and they were studied by molecular dynamics in this research. Both have a beta-hairpin conformation stabilized by two disulfide bridges and are active against Gram-positive and Gram-negative bacteria, as well as fungi. In this study, the role of the disulfide bridge in the maintenance of the tertiary peptide structure of protegrin-1 and gomesin is analyzed by the structural characteristics of these peptides and two of their respective variants, gomy4 and proty4, in which the four cysteines are replaced by four tyrosine residues. The absence of disulfide bridges in gomy4 and proty4 is compensated by overall reinforcement of the original hydrogen bonds and extra attractive interactions between the aromatic rings of the tyrosine residues. The net effects on the variants with respect to the corresponding natural peptides are: i) maintenance of the original beta-hairpin conformation, with great structural similarities between the mutant and the corresponding natural peptide; ii) combination of positive F and. Ramachandran angles within the hairpin head region with a qualitative change to a combination of positive (F) and negative (.) angles, and iii) significant increase in structural flexibility. Experimental facts about the antimicrobial activity of the gomesin and protegrin-1 variants have also been established here, in the hope that the detailed data provided in the present study may be useful for understanding the mechanism of action of these peptides.

Hydrogen bond interactions between acetone and supercritical water

Hydrogen bond interactions between acetone and supercritical water are investigated using a combined and sequential Monte Carlo/quantum mechanics (S-MC/QM) approach. Simulation results show a dominant presence of con. gurations with one hydrogen bond for different supercritical states, indicating that this specific interaction plays an important role on the solvation properties of acetone in supercritical water. Using QM MP2/aug-cc-pVDZ the calculated average interaction energy reveals that the hydrogen-bonded acetone-water complex is energetically more stable under supercritical conditions than ambient conditions and its stability is little affected by variations of temperature and/or pressure. All average results reported here are statistically converged.

Dynamic polarizability, Cauchy moments, and the optical absorption spectrum of liquid water: A sequential molecular dynamics/quantum mechanical approach

The dynamic polarizability and optical absorption spectrum of liquid water in the 6-15 eV energy range are investigated by a sequential molecular dynamics (MD)/quantum mechanical approach. The MD simulations are based on a polarizable model for liquid water. Calculation of electronic properties relies on time-dependent density functional and equation-of-motion coupled-cluster theories. Results for the dynamic polarizability, Cauchy moments, S(-2), S(-4), S(-6), and dielectric properties of liquid water are reported. The theoretical predictions for the optical absorption spectrum of liquid water are in good agreement with experimental information.

Impact on HDPE and PVC plates - Experimental tests and numerical simulations

This paper presents first material tests on HDPE and PVC, and subsequently impact tests on plates made of the same materials. Finally, numerical simulations of the plate impact tests are compared with the experimental results. A rather comprehensive series of mechanical material tests were performed to disclose the behaviour of PVC and HDPE in tension and compression. Quasi-static tests were carried out at three rates in compression and two in tension. Digital image correlation. DIC, was used to measure the in-plane strains, revealing true stress-strain curves and allowing to analyze strain-rate sensitivity and isotropy of Poisson`s ratio. In addition, dynamic compression tests were carried out in a split-Hopkinson pressure bar. Quasi-static and dynamic tests were also performed on clamped plates made of the same PVC and HDPE materials, using an optical technique to measure the full-field out-of-plane deformations. These tests, together with the material data, were used for comparative purposes of a finite element analysis. A reasonable agreement between experimental and numerical results was achieved. (C) 2010 Elsevier Ltd. All rights reserved.

Molecular modeling as a promising tool to study dendrimer prodrugs delivery

Molecular modeling methodologies were applied to perform preliminary studies concerning the release of active agents from potentially antichagasic and antileishmanial dendrimer prodrugs. The dendrimer was designed having myo-inositol as a core, L-malic acid as a spacer group, and hydroxymethylnitrofurazone (NFOH), 3-hydroxyflavone or quercetin, as active compounds. Each dendrimer presented a particular behavior concerning to the following investigated properties: spatial hindrance, map of electrostatic potential (MEP), and the lowest unoccupied molecular orbital energy (E(LUMO)). Additionally, the findings suggested that the carbonyl group next to the active agent seems to be the most promising ester breaking point. (C) 2009 Elsevier B.V. All rights reserved.

Quantum trajectory simulations of the fluorescence intensity from a two-level atom driven by a multichromatic field

The quantum trajectories method is illustrated for the resonance fluorescence of a two-level atom driven by a multichromatic field. We discuss the method for the time evolution of the fluorescence intensity in the presence of bichromatic and trichromatic driving fields. We consider the special case wherein one multichromatic field component is strong and resonant with the atomic transition whereas the other components are much weaker and arbitrarily detuned from the atomic resonance. We find that the phase-dependent modulations of the Rabi oscillations, recently observed experimentally [Q. Wu, D. J. Gauthier, and T. W. Mossberg, Phys. Rev. A 49, R1519 (1994)] for the special case when the weaker component of a bichromatic driving field is detuned from the atomic resonance by the strong-field Rabi frequency, appear also for detunings close to the subharmonics of the Rabi frequency. Furthermore, we show that for the atom initially prepared in one of the dressed states of the strong field component the modulations are not sensitive to the phase. We extend the calculations to the case of a trichromatic driving field and find that apart from the modulations of the amplitude there is a modulation of the frequency of the Rabi oscillations. Moreover, the time evolution of the fluorescence intensity depends on the phase regardless of the initial conditions and a phase-dependent suppression of the Rabi oscillations can be observed when the sideband fields are tuned to the subharmonics of the strong-field Rabi frequency. [S1050-2947(98)03501-X].

Disagreement between correlations of quantum mechanics and stochastic electrodynamics in the damped parametric oscillator

Intracavity and external third order correlations in the damped nondegenerate parametric oscillator are calculated for quantum mechanics and stochastic electrodynamics (SED), a semiclassical theory. The two theories yield greatly different results, with the correlations of quantum mechanics being cubic in the system's nonlinear coupling constant and those of SED being linear in the same constant. In particular, differences between the two theories are present in at least a mesoscopic regime. They also exist when realistic damping is included. Such differences illustrate distinctions between quantum mechanics and a hidden variable theory for continuous variables.

Energy and averages in the mechanics of granular materials

We derive a general thermo-mechanical theory for particulate materials consisting of granules of arbitrary whose material points possess three translational and three independent rotational degrees of freedom. Additional field variables are the translational and rotational granular temperatures, the kinetic energies shape and size. The kinematics of granulate is described within the framework of a polar continuum theory of the velocity and spin fluctuations respectively and the usual thermodynamic temperature. We distinguish between averages over particle categories (averages in mass/velocity and moment of inertia/spin space, respectively) and particle phases where the average extends over distinct subsets of particle categories (multi phase flows). The relationship between the thermal energy in the granular system and phonon energy in a molecular system is briefly discussed in the main body of the paper and discussed in detail in the Appendix A. (C) 2001 Elsevier Science B.V. All rights reserved.

Computer simulations of coupled problems in geological and geochemical systems

The finite element method is used to simulate coupled problems, which describe the related physical and chemical processes of ore body formation and mineralization, in geological and geochemical systems. The main purpose of this paper is to illustrate some simulation results for different types of modelling problems in pore-fluid saturated rock masses. The aims of the simulation results presented in this paper are: (1) getting a better understanding of the processes and mechanisms of ore body formation and mineralization in the upper crust of the Earth; (2) demonstrating the usefulness and applicability of the finite element method in dealing with a wide range of coupled problems in geological and geochemical systems; (3) qualitatively establishing a set of showcase problems, against which any numerical method and computer package can be reasonably validated. (C) 2002 Published by Elsevier Science B.V.

Longevity and stability of cratonic lithosphere: Insights from numerical simulations of coupled mantle convection and continental tectonics

[1] The physical conditions required to provide for the tectonic stability of cratonic crust and for the relative longevity of deep cratonic lithosphere within a dynamic, convecting mantle are explored through a suite of numerical simulations. The simulations allow chemically distinct continents to reside within the upper thermal boundary layer of a thermally convecting mantle layer. A rheologic formulation, which models both brittle and ductile behavior, is incorporated to allow for plate-like behavior and the associated subduction of oceanic lithosphere. Several mechanisms that may stabilize cratons are considered. The two most often invoked mechanisms, chemical buoyancy and/or high viscosity of cratonic root material, are found to be relatively ineffective if cratons come into contact with subduction zones. High root viscosity can provide for stability and longevity but only within a thick root limit in which the thickness of chemically distinct, high-viscosity cratonic lithosphere exceeds the thickness of old oceanic lithosphere by at least a factor of 2. This end-member implies a very thick mechanical lithosphere for cratons. A high brittle yield stress for cratonic lithosphere as a whole, relative to oceanic lithosphere, is found to be an effective and robust means for providing stability and lithospheric longevity. This mode does not require exceedingly deep strength within cratons. A high yield stress for only the crustal or mantle component of the cratonic lithosphere is found to be less effective as detachment zones can then form at the crust-mantle interface which decreases the longevity potential of cratonic roots. The degree of yield stress variations between cratonic and oceanic lithosphere required for stability and longevity can be decreased if cratons are bordered by continental lithosphere that has a relatively low yield stress, i.e., mobile belts. Simulations that combine all the mechanisms can lead to crustal stability and deep root longevity for model cratons over several mantle overturn times, but the dominant stabilizing factor remains a relatively high brittle yield stress for cratonic lithosphere.

Semiquantum versus semiclassical mechanics for simple nonlinear systems

Quantum mechanics has been formulated in phase space, with the Wigner function as the representative of the quantum density operator, and classical mechanics has been formulated in Hilbert space, with the Groenewold operator as the representative of the classical Liouville density function. Semiclassical approximations to the quantum evolution of the Wigner function have been defined, enabling the quantum evolution to be approached from a classical starting point. Now analogous semiquantum approximations to the classical evolution of the Groenewold operator are defined, enabling the classical evolution to be approached from a quantum starting point. Simple nonlinear systems with one degree of freedom are considered, whose Hamiltonians are polynomials in the Hamiltonian of the simple harmonic oscillator. The behavior of expectation values of simple observables and of eigenvalues of the Groenewold operator are calculated numerically and compared for the various semiclassical and semiquantum approximations.

Macroscopic test of quantum mechanics versus stochastic electrodynamics

We identify a test of quantum mechanics versus macroscopic local realism in the form of stochastic electrodynamics. The test uses the steady-state triple quadrature correlations of a parametric oscillator below threshold.

Effects of chronic L-NAME treatment lung tissue mechanics, eosinophilic and extracellular matrix responses induced by chronic pulmonary inflammation

The importance of lung tissue in asthma pathophysiology has been recently recognized. Although nitric oxide mediates smooth muscle tonus control in airways, its effects on lung tissue responsiveness have not been investigated previously. We hypothesized that chronic nitric oxide synthase (NOS) inhibition by N-omega-nitro-L-arginine methyl ester (L-NAME) may modulate lung tissue mechanics and eosinophil and extracellular matrix remodeling in guinea pigs with chronic pulmonary inflammation. Animals were submitted to seven saline or ovalbumin exposures with increasing doses (1 similar to 5 mg/ml for 4 wk) and treated or not with L-NAME in drinking water. After the seventh inhalation (72 h), animals were anesthetized and exsanguinated, and oscillatory mechanics of lung tissue strips were performed in baseline condition and after ovalbumin challenge (0.1%). Using morphometry, we assessed the density of eosinophils, neuronal NOS (nNOS)- and inducible NOS (iNOS)-positive distal lung cells, smooth muscle cells, as well as collagen and elastic fibers in lung tissue. Ovalbumin-exposed animals had an increase in baseline and maximal tissue resistance and elastance, eosinophil density, nNOS- and iNOS-positive cells, the amount of collagen and elastic fibers, and isoprostane-8-PGF(2 alpha) expression in the alveolar septa compared with controls (P < 0.05). L-NAME treatment in ovalbumin-exposed animals attenuated lung tissue mechanical responses (P < 0.01), nNOS- and iNOS-positive cells, elastic fiber content (P < 0.001), and isoprostane-8-PGF(2 alpha) in the alveolar septa (P < 0.001). However, this treatment did not affect the total number of eosinophils and collagen deposition. These data suggest that NO contributes to distal lung parenchyma constriction and to elastic fiber deposition in this model. One possibility may be related to the effects of NO activating the oxidative stress pathway.

Structure optimization combining soft-core interaction functions, the diffusion equation method, and molecular dynamics

Smoothing the potential energy surface for structure optimization is a general and commonly applied strategy. We propose a combination of soft-core potential energy functions and a variation of the diffusion equation method to smooth potential energy surfaces, which is applicable to complex systems such as protein structures; The performance of the method was demonstrated by comparison with simulated annealing using the refinement of the undecapeptide Cyclosporin A as a test case. Simulations were repeated many times using different initial conditions and structures since the methods are heuristic and results are only meaningful in a statistical sense.

Characterizing mixing and measurement in quantum mechanics

What fundamental constraints characterize the relationship between a mixture rho = Sigma (i)p(i)rho (i) of quantum states, the states rho (i) being mixed, and the probabilities p(i)? What fundamental constraints characterize the relationship between prior and posterior states in a quantum measurement? In this paper we show that then are many surprisingly strong constraints on these mixing and measurement processes that can be expressed simply in terms of the eigenvalues of the quantum states involved. These constraints capture in a succinct fashion what it means to say that a quantum measurement acquires information about the system being measured, and considerably simplify the proofs of many results about entanglement transformation.