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In numerous realizations of complex plasmas, dust-dust interactions are characterized by two screening lengths and are thus better described by a combination of Yukawa potentials. The present work investigates the static correlations and the thermodynamics of repulsive dense bi-Yukawa fluids based on the fact that such strongly coupled systems exhibit isomorph invariance. The strong virial-potential energy correlations are demonstrated with the aid of molecular dynamics simulations, an accurate analytical expression for the isomorph family of curves is obtained, and an empirical expression for the fluid-solid phase-coexistence line is proposed. The isomorph-based empirically modified hypernetted-chain approach, grounded on the ansatz of isomorph invariant bridge functions, is then extended to such systems and the resulting structural properties show an excellent agreement with the results of computer simulations. A simple and accurate closed-form expression is obtained for the excess internal energy of dense bi-Yukawa fluids by capitalizing on the compact parameterization offered by the Rosenfeld-Tarazona decomposition in combination with the Rosenfeld scaling, which opens up the energy route to thermodynamics., QC 20190620

We investigate vortex merging at low Reynolds numbers from a topological point of view. We identify vortices as local extremal points of vorticity and follow the motion and bifurcation of these points as time progresses. We consider both two-dimensional simulations of the vorticity transport equation and an analytical study of the core growth model. The merging process of identical vortices is shown to occur through a pitchfork bifurcation and for asymmetric vortices one vortex merges with a saddle through a cusp (perturbed pitchfork) bifurcation. Excellent agreement between the core growth model and the numerical simulations is observed. For higher Reynolds numbers, filamentation becomes dominant hence limiting the predictive value of the core growth model. A complete investigation of merging in the core growth model is conducted for all possible vortex strengths. Simple, analytical expressions are derived for bifurcation curves, merging time, and vortex positions depending on systems parameters.

This is a practical, step-by-step guide that will help you to quickly become a proficient Octave user. The book is packed with clear examples, screenshots, and code to carry out your data analysis without any problems. This book is intended for anyone interested in scientific computing and data analysis. The reader should have a good level of mathematics and a basic understanding of programming will be useful, although it is not a prerequisite.

Black lipid membrane (BLM) formation across apertures in an ethylene tetra-fluoroethylene (ETFE) partition separating two aqueous compartments is an established technique for the creation of biomimetic membranes. Recently multi-aperture BLM arrays have attracted interest and in order to increase BLM array stability we studied the effect of covalently modifying the partition substrate using surface plasma polymerization with hydrophobic n-hexene, 1-decene and hexamethyldisiloxane (HMDSO) as modification groups. Average lifetimes across singlesided HMDSO modified partitions or using 1-decene modified partitions were similar and significantly lower than for arrays formed using untreated ETFE partitions. For single side n-hexene modification average membrane array lifetimes were not significantly changed compared to untreated ETFE. Double-sided n-hexene modification greatly improved average membrane array lifetimes compared to membrane arrays formed across untreated ETFE partitions. n-hexene modifications resulted in BLM membrane arrays which over time developed significantly lower conductance (Gm) and higher capacitance (Cm) values compared to the other membranes with the strongest effect for double sided modification. n-hexene modification is evident as a change in surface energy whereas the surface roughness does not change significantly. The concomitant low Gm and high Cm values for BLM arrays formed using double-sided n-hexene modification enable transmembrane ionic current recordings with a high signal-to-noise (s/n) ratio. We demonstratesd this by reconstituting gA and α-hemolysin (α-HL) into BLM arrays. The improvement in membrane array lifetime and s/n ratio demonstrates that surface plasma polymerization of the supporting partition can be used to increase the stability of biomimetic membrane arrays.

We show by nonequilibrium molecular dynamics simulations that the Navier-Stokes equation does not correctly describe water flow in a nanoscale geometry. It is argued that this failure reflects the fact that the coupling between the intrinsic rotational and translational degrees of freedom becomes important for nanoflows. The coupling is correctly accounted for by the extended Navier-Stokes equations that include the intrinsic angular momentum as an independent hydrodynamic degree of freedom. © 2011 American Physical Society.

This study describes the interaction between sodium dodecyl sulfate (SDS) and membrane proteins reconstituted into large unilamellar lipid vesicles and detergent micelles studied by circular dichroism (CD) and polarity sensitive probe labeling. Specifically, we carried out a comparative study of two aquaporins with high structural homology SoPIP2;1 and AqpZ using identical reconstitution conditions. Our CD results indicate that SDS, when added to membrane-reconstituted aquaporins in concentrations below the SDS critical micelle concentration (CMC, ~8mM), causes helical rearrangements of both aquaporins. However, we do not find compelling evidence for unfolding. In contrast when SDS is added to detergent stabilized aquaporins, SoPIP2;1 partly unfolds, while AqpZ secondary structure is unaffected. Using a fluorescent polarity sensitive probe (Badan) we show that SDS action on membrane reconstituted SoPIP2;1 as well as AqpZ is associated with initial increased hydrophobic interactions in protein transmembrane (TM) spanning regions up to a concentration of 0.1× CMC. At higher SDS concentrations TM hydrophobic interactions, as reported by Badan, decrease and reach a plateau from SDS CMC up to 12.5× CMC. Combined, our results show that SDS does not unfold neither SoPIP2;1 nor AqpZ during transition from a membrane reconstituted form to a detergent stabilized state albeit the native folds are changed.

In this paper, the dynamical equation for polarization is derived. From this the dielectric response to a spatially varying electric field is analyzed showing a reduced response due to flux of polarization in the material. This flux is modeled as a diffusive process through linear constitutive relations between the flux and the gradient of the polarization. Comparison between the theory and molecular dynamics simulations confirms this effect. The effect is significant for small length scale electric field variations and the inclusion of the flux is thus important in nanoscale modeling of dielectric response

We show by nonequilibrium molecular dynamics simulations that the Navier-Stokes equation does not correctly describe water flow in a nanoscale geometry. It is argued that this failure reflects the fact that the coupling between the intrinsic rotational and translational degrees of freedom becomes important for nanoflows. The coupling is correctly accounted for by the extended Navier-Stokes equations that include the intrinsic angular momentum as an independent hydrodynamic degree of freedom.

We show by nonequilibrium molecular dynamics simulations that the Navier-Stokes equation does not correctly describe water flow in a nanoscale geometry. It is argued that this failure reflects the fact that the coupling between the intrinsic rotational and translational degrees of freedom becomes important for nanoflows. The coupling is correctly accounted for by the extended Navier-Stokes equations that include the intrinsic angular momentum as an independent hydrodynamic degree of freedom.

We show by nonequilibrium molecular dynamics simulations that the Navier-Stokes equation does not correctly describe water flow in a nanoscale geometry. It is argued that this failure reflects the fact that the coupling between the intrinsic rotational and translational degrees of freedom becomes important for nanoflows. The coupling is correctly accounted for by the extended Navier-Stokes equations that include the intrinsic angular momentum as an independent hydrodynamic degree of freedom.

We show by nonequilibrium molecular dynamics simulations that the Navier-Stokes equation does not correctly describe water flow in a nanoscale geometry. It is argued that this failure reflects the fact that the coupling between the intrinsic rotational and translational degrees of freedom becomes important for nanoflows. The coupling is correctly accounted for by the extended Navier-Stokes equations that include the intrinsic angular momentum as an independent hydrodynamic degree of freedom.

The extended Navier-Stokes theory accounts for the coupling between the translational and rotational molecular degrees of freedom. In this paper, we generalize this theory to non-zero frequencies and wavevectors, which enables a new study of spatio-temporal correlation phenomena present in molecular fluids. To discuss these phenomena in detail, molecular dynamics simulations of molecular chlorine are performed for three different state points. In general, the theory captures the behavior for small wavevector and frequencies as expected. For example, in the hydrodynamic regime and for molecular fluids with small moment of inertia like chlorine, the theory predicts that the longitudinal and transverse intrinsic angular velocity correlation functions are almost identical, which is also seen in the molecular dynamics simulations. However, the theory fails at large wavevector and frequencies. To account for the correlations at these scales, we derive a phenomenological expression for the frequency dependent rotational viscosity and wavevector and frequency dependent longitudinal spin viscosity. From this we observe a significant coupling enhancement between the molecular angular velocity and translational velocity for large frequencies in the gas phase; this is not observed for the supercritical fluid and liquid state points.