A two-tier model of polymyxin B resistance in Burkholderia cenocepacia

P>Burkholderia cenocepacia is an environmental bacterium causing serious human opportunistic infections and is extremely resistant to multiple antibiotics including antimicrobial peptides, such as polymyxin B (PmB). Extreme antibiotic resistance is attributed to outer membrane impermeability ('intrinsic' resistance). Previous work showed that production of full-length lipopolysaccharide (LPS) prevents surface binding of PmB. We hypothesized that two tiers of resistance mechanisms rendering different thresholds of PmB resistance exist in B. cenocepacia. To test this notion, candidate genes were mutated in two isogenic strains expressing full-length LPS or truncated LPS devoid of heptose ('heptoseless LPS') respectively. We uncovered various proteins required for PmB resistance only in the strain with heptoseless LPS. These proteins are not involved in preventing PmB binding to whole cells or permeabilization of the outer membrane. Our results support a two-tier model of PmB resistance in B. cenocepacia. One tier sets a very high threshold mediated by the LPS and the outer membrane permeability barrier. The second tier sets a lower threshold that may play a role in PmB resistance only when outer membrane permeability is compromised. This model may be of general applicability to understanding the high antimicrobial peptide resistance of environmental opportunistic pathogens.

Better understanding of mechanochemical reactions: Raman monitoring reveals surprisingly simple 'pseudo-fluid' model for a ball milling reaction

Quantitative monitoring of a mechanochemical reaction by Raman spectroscopy leads to a surprisingly straightforward second-order kinetic model in which the rate is determined simply by the frequency of reactive collisions between reactant particles.

Ion-acoustic waves in a plasma consisting of adiabatic warm ions, non-isothermal electrons and a weakly relativistic electron beam: linear and higher-order nonlinear effects

The nonlinear propagation of finite amplitude ion acoustic solitary waves in a plasma consisting of adiabatic warm ions, nonisothermal electrons, and a weakly relativistic electron beam is studied via a two-fluid model. A multiple scales technique is employed to investigate the nonlinear regime. The existence of the electron beam gives rise to four linear ion acoustic modes, which propagate at different phase speeds. The numerical analysis shows that the propagation speed of two of these modes may become complex-valued (i.e., waves cannot occur) under conditions which depend on values of the beam-to-background-electron density ratio , the ion-to-free-electron temperature ratio , and the electron beam velocity v0; the remaining two modes remain real in all cases. The basic set of fluid equations are reduced to a Schamel-type equation and a linear inhomogeneous equation for the first and second-order potential perturbations, respectively. Stationary solutions of the coupled equations are derived using a renormalization method. Higher-order nonlinearity is thus shown to modify the solitary wave amplitude and may also deform its shape, even possibly transforming a simple pulse into a W-type curve for one of the modes. The dependence of the excitation amplitude and of the higher-order nonlinearity potential correction on the parameters , , and v0 is numerically investigated.

Relativistic theory for localized electrostatic excitations in degenerate electron-ion plasmas

A self-consistent relativistic two-fluid model is proposed for electron-ion plasma dynamics. A one-dimensional geometry is adopted. Electrons are treated as a relativistically degenerate fluid, governed by an appropriate equation of state. The ion fluid is also allowed to be relativistic, but is cold, nondegenerate, and subject only to an electrostatic potential. Exact stationary-profile solutions are sought, at the ionic scale, via the Sagdeev pseudopotential method. The analysis provides the pulse existence region, in terms of characteristic relativistic parameters, associated with the (ultrahigh) particle density.

Ion-acoustic envelope modes in a degenerate relativistic electron-ion plasma

A self-consistent relativistic two-fluid model is proposed for one-dimensional electron-ion plasma dynamics. A multiple scales perturbation technique is employed, leading to an evolution equation for the wave envelope, in the form of a nonlinear Schrödinger type equation (NLSE). The inclusion of relativistic effects is shown to introduce density-dependent factors, not present in the non-relativistic case - in the conditions for modulational instability. The role of relativistic effects on the linear dispersion laws and on envelope soliton solutions of the NLSE is discussed.

Kinetics of phase transformations in a model with metastable fluid-fluid separation: A molecular dynamics study

By molecular dynamics (MD) simulations we study the crystallization process in a model system whose particles interact by a spherical pair potential with a narrow and deep attractive well adjacent to a hard repulsive core. The phase diagram of the model displays a solid-fluid equilibrium, with a metastable fluid-fluid separation. Our computations are restricted to fairly small systems (from 2592 to 10368 particles) and cover long simulation times, with constant energy trajectories extending up to 76x10(6) MD steps. By progressively reducing the system temperature below the solid-fluid line, we first observe the metastable fluid-fluid separation, occurring readily and almost reversibly upon crossing the corresponding line in the phase diagram. The nucleation of the crystal phase takes place when the system is in the two-fluid metastable region. Analysis of the temperature dependence of the nucleation time allows us to estimate directly the nucleation free energy barrier. The results are compared with the predictions of classical nucleation theory. The critical nucleus is identified, and its structure is found to be predominantly fcc. Following nucleation, the solid phase grows steadily across the system, incorporating a large number of localized and extended defects. We discuss the relaxation processes taking place both during and after the crystallization stage. The relevance of our simulation for the kinetics of protein crystallization under normal experimental conditions is discussed. (C) 2002 American Institute of Physics.

Investigation of tanpura string vibrations using a two-dimensional time-domain model incorporating coupling and bridge friction

Tanpura string vibrations have been investigated previously using numerical models based on energy conserving schemes derived from a Hamiltonian description in one-dimensional form. Such time-domain models have the property that, for the lossless case, the numerical Hamiltonian (representing total energy of the system) can be proven to be constant from one time step
to the next, irrespective of any of the system parameters; in practice the Hamiltonian can be shown to be conserved within machine precision. Models of this kind can reproduce a jvari effect, which results from the bridge-string interaction. However the one-dimensional formulation has recently been shown to fail to replicate the jvaris strong dependence on the thread placement. As a first step towards simulations which accurately emulate this sensitivity to the thread placement, a twodimensional model is proposed, incorporating coupling of controllable level between the two string polarisations at the string termination opposite from the barrier. In addition, a friction force acting when the string slides across the bridge in horizontal direction is introduced, thus effecting a further damping mechanism. In this preliminary study, the string is terminated at the position of the thread. As in the one-dimensional model, an implicit scheme has to be used to solve the system, employing Newton's method to calculate the updated positions and momentums of each string segment. The two-dimensional model is proven to be energy conserving when the loss parameters are set to zero, irrespective of the coupling constant. Both frequency-dependent and independent losses are then added to the string, so that the model can be compared to analogous instruments. The influence of coupling and the bridge friction are investigated.

Analytical calculation of far infrared spectra of ice in terms of a molecular model

Wideband far infrared (FIR) spectra of complex permittivity e(p) of ice are calculated in terms of a simple analytical theory based on the method of dipolar autocorrelation functions. The molecular model represents a revision of the model recently presented for liquid water in Adv. Chem. Phys. 127 (2003) 65. A composite two-fractional model is proposed. The model is characterised by three phenomenological potential wells corresponding to the three FIR bands observed in ice. The first fraction comprises dipoles reorienting in a rather narrow and deep hat-like well; these dipoles generate the librational band centred at the frequency approximate to 880 cm(-1). The second fraction comprises elastically interacting particles; they generate two nearby bands placed around frequency 200 cm(-1). For description of one of these bands the harmonic oscillator (HO) model is used, in which translational oscillations of two charged molecules along the H-bond are considered. The other band is produced by the H-bond stretch, which governs hindered rotation of a rigid dipole. Such a motion and its dielectric response are described in terms of a new cut parabolic (CP) model applicable for any vibration amplitude. The composite hat-HO-CP model results in a smooth epsilon(nu) ice spectrum, which does not resemble the noise-like spectra of ice met in the known literature. The proposed theory satisfactorily agrees with the experimental ice spectrum measured at - 7 degrees C. The calculated longitudinal optic-transverse optic (LO-TO) splitting occurring at approximate to 250 cm(-1) qualitatively agrees with the measured data. (c) 2004 Elsevier B.V. All rights reserved.

Laser pulse compression and amplification via Raman backscattering in plasma

A simple theoretical model is proposed for the interaction between two counter-propagating laser pulses (a pump and a seed pulse) in unmagnetized plasma. Pulse compression and amplification are observed via numerical simulation. A one dimensional fluid model for stimulated Raman backscattering is proposed to investigate the pulse compression and pulse amplification mechanisms. To accomplish this, energy is transferred from the long pump pulse to a seed pulse, with a Langmuir plasma wave mediating the transfer. The study focuses on the intensity profile of the pump laser pulse. A Gaussian and a ring intensity profile are, separately, considered for the pump laser pulse.

Diagnostic-based modeling on a micro-scale atmospheric-pressure plasma jet

Diagnostic-based modeling (DBM) actively combines complementary advantages of numerical plasma simulations and relatively simple optical emission spectroscopy (OES). DBM is applied to determine spatial absolute atomic oxygen ground-state density profiles in a micro atmospheric-pressure plasma jet operated in He–O2. A 1D fluid model with semi-kinetic treatment of the electrons yields detailed information on the electron dynamics and the corresponding spatio-temporal electron energy distribution function. Benchmarking this time- and space-resolved simulation with phase-resolved OES (PROES) allows subsequent derivation of effective excitation rates as the basis for DBM. The population dynamics of the upper O(3p3P) oxygen state (? = 844 nm) is governed by direct electron impact excitation, dissociative excitation, radiation losses, and collisional induced quenching. Absolute values for atomic oxygen densities are obtained through tracer comparison with the upper Ar(2p1) state (? = 750.4 nm). The resulting spatial profile for the absolute atomic oxygen density shows an excellent quantitative agreement to a density profile obtained by two-photon absorption laser-induced fluorescence spectroscopy.

Modulated electrostatic modes in pair plasmas: Modulational stability profile and envelope excitations

A pair plasma consisting of two types of ions, possessing equal masses and opposite charges, is considered. The nonlinear propagation of modulated electrostatic wave packets is studied by employing a two-fluid plasma model. Considering propagation parallel to the external magnetic field, two distinct electrostatic modes are obtained, namely a quasiacoustic lower moddfe and a Langmuir-like, as optic-type upper one, in agreement with experimental observations and theoretical predictions. Considering small yet weakly nonlinear deviations from equilibrium, and adopting a multiple-scale technique, the basic set of model equations is reduced to a nonlinear Schrodinger equation for the slowly varying electric field perturbation amplitude. The analysis reveals that the lower (acoustic) mode is stable and may propagate in the form of a dark-type envelope soliton (a void) modulating a carrier wave packet, while the upper linear mode is intrinsically unstable, and may favor the formation of bright-type envelope soliton (pulse) modulated wave packets. These results are relevant to recent observations of electrostatic waves in pair-ion (fullerene) plasmas, and also with respect to electron-positron plasma emission in pulsar magnetospheres. (c) 2006 American Institute of Physics.

Electrostatic mode envelope excitations in e-p-i plasmas - application in warm pair ion plasmas with a small fraction of stationary ions

The nonlinear propagation of amplitude-modulated electrostatic wavepackets in an electron-positron-ion (e-p-i) plasma is considered, by employing a two-fluid plasma model. Considering propagation parallel to the external magnetic field, two distinct electrostatic modes are obtained, namely a quasi-thermal acoustic-like lower mode and a Langmuir-like optic-type upper one. These results equally apply in warm pair ion ( e. g. fullerene) plasmas contaminated by a small fraction of stationary ions ( or dust), in agreement with experimental observations and theoretical predictions in pair plasmas. Considering small yet weakly nonlinear deviations from equilibrium, and adopting a multiple-scales perturbation technique, the basic set of model equations is reduced to a nonlinear Schrodinger (NLS) equation for the slowly varying electric field perturbation amplitude. The analysis reveals that the lower ( acoustic) mode is mostly stable for large wavelengths, and may propagate in the form of a dark-type envelope soliton ( a void) modulating a carrier wavepacket, while the upper linear mode is intrinsically unstable, and thus favours the formation of bright-type envelope soliton ( pulse) modulated wavepackets. The stability ( instability) range for the acoustic ( Langmuir-like optic) mode shifts to larger wavenumbers as the positive-to-negative ion temperature ( density) ratio increases. These results may be of relevance in astrophysical contexts, where e-p-i plasmas are encountered, and may also serve as prediction of the behaviour of doped ( or dust-contaminated) fullerene plasmas, in the laboratory.

Nonlinear Dynamics of Rotating Multi-Component Pair Plasmas and e-p-i Plasmas

The propagation of small amplitude stationary profile nonlinear electrostatic excitations in a pair plasma is investigated, mainly drawing inspiration from experiments on fullerene pair-ion plasmas. Two distinct pair ion species are considered of opposite polarity and same mass, in addition to a massive charged background species, which is assumed to be stationary, given the frequency scale of interest. In the pair-ion context, the third species is thought of as a background defect (e.g. charged dust) component. On the other hand, the model also applies formally to electron-positron-ion (e-p-i) plasmas, if one neglects electron-positron annihilation. A two-fluid plasma model is employed, incorporating both Lorentz and Coriolis forces, thus taking into account the interplay between the gyroscopic (Larmor) frequency ?c and the (intrinsic) plasma rotation frequency O0. By employing a multi-dimensional reductive perturbation technique, a Zakharov-Kuznetsov (ZK) type equation is derived for the evolution of the electric potential perturbation. Assuming an arbitrary direction of propagation, with respect to the magnetic field, we derive the exact form of nonlinear solutions, and study their characteristics. A parametric analysis is carried out, as regards the effect of the dusty plasma composition (background number density), species temperature(s) and the relative strength of rotation to Larmor frequencies. It is shown that the Larmor and mechanical rotation affect the pulse dynamics via a parallel-to-transverse mode coupling diffusion term, which in fact diverges at ?c ? ±2O0. Pulses collapse at this limit, as nonlinearity fails to balance dispersion. The analysis is complemented by investigating critical plasma compositions, in fact near-symmetric (T- ˜ T+) “pure” (n- ˜ n+) pair plasmas, i.e. when the concentration of the 3rd background species is negligible, case in which the (quadratic) nonlinearity vanishes, so one needs to resort to higher order nonlinear theory. A modified ZK equation is derived and analyzed. Our results are of relevance in pair-ion (fullerene) experiments and also potentially in astrophysical environments, e.g. in pulsars.

Interaction of spatially overlapping standing electromagnetic solitons in plasmas

Numerical investigations on mutual interactions between two spatially overlapping standing electromagnetic solitons in a cold unmagnetized plasma are reported. It is found that an initial state comprising of two overlapping standing solitons evolves into different end states, depending on the amplitudes of the two solitons and the phase difference between them. For small amplitude solitons with zero phase difference, we observe the formation of an oscillating bound state whose period depends on their initial separation. These results suggest the existence of a bound state made of two solitons in the relativistic cold plasma fluid model. (C) 2012 Elsevier B.V. All rights reserved.