Synchrotron X-ray diffraction study of microtubules buckling and bundling under osmotic stress: a probe of interprotofilament interactions

Microtubules are hollow cylinders composed of tubulin heterodimers that stack into linear protofilaments that interact laterally to form the microtubule wall. Synchrotron x-ray diffraction of microtubules under increasing osmotic stress shows they transition to rectangular bundles with noncircular buckled cross sections, followed by hexagonally packed bundles. This new technique probes the strength of interprotofilamen bonds, yielding insight into the mechanism by which associated proteins and the chemotherapy drug taxol stabilize microtubules.     

Coupling the lattice‐Boltzmann and spectrin‐link methods for the direct numerical simulation of cellular blood flow

The implementation of a spectrin‐link (SL) red blood cell (RBC) membrane method coupled with a lattice‐Boltzmann (LB) fluid solver is discussed. Details of the methodology are included along with subtleties associated with its integration into a massively parallel hybrid LB finite element (FE) suspension flow solver. A comparison of the computational performance of the coupled LB–SL method with that of the previously implemented LB–FE is given for an isolated RBC and for a dense suspension in Hagen–Poiseuille flow. Validating results for RBCs isolated in shear and parachuting in microvessel flow are also presented. Copyright © 2011 John Wiley & Sons, Ltd.     

Extension of the Lattice-Boltzmann Method for Direct Simulation of Suspended Particles Near Contact

Computational methods based on the solution of the lattice-Boltzmann equation have been demonstrated to be effective for modeling a variety of fluid flow systems including direct simulation of particles suspended in fluid. Applications to suspended particles, however, have been limited to cases where the gap width between solid particles is much larger than the size of the lattice unit. The present extension of the method removes this limitation and improves the accuracy of the results even when two solid surfaces are near contact. With this extension, the forces on two moving solid particles, suspended in a fluid and almost in contact with each other, are calculated. Results are compared with classical lubrication theory. The accuracy and robustness of this computational method are demonstrated with several test problems.     

Thermodynamic modeling of hydrogen sulfide solubility in ionic liquids using modified SAFT-VR and PC-SAFT equations of state

Equations of state based on the statistical associating fluid theory for potentials of variable range (SAFT-VR) and the perturbed chain statistical associating fluid theory (PC-SAFT) have been used to model the PVT behavior of ionic liquids and the solubility of H₂S in six imidazolium-based ionic liquids. The studied systems included [bmim][PF6], [hmim][PF6], [bmim][BF4], [hmim][BF4], [bmim][NTF2] and [hmim][NTF2] at various temperatures and pressures.For pure components, parameters of the models have been obtained by fitting the models to experimental data on liquid densities; the average relative deviation between the calculated and experimental densities for ionic liquids is less than 2.42% in the PC-SAFT model and 5.44% in the SAFT-VR approach, the latter which incorporates the square-well potential for short-range interactions. In both models an additional term has been added to account for dipole-dipole interactions between solute molecules resulting from the permanent charges on the chain molecules of the solvents. The model parameters have also been correlated as functions of the molecular weight of the solvents. For binary mixtures of ionic liquids and H₂S, the association interactions between H₂S molecules and between the ionic liquids and H₂S molecules have also been taken into account in both approaches, using binary interaction coefficients. The results show an average deviation of less than 5% in the calculation of the mole fraction of H₂S in the ionic liquids. The effect of inclusion of the polar term has been studied for binary systems in both models.     

Nanogyroids incorporating multivalent lipids: enhanced membrane charge density and pore forming ability for gene silencing

The self-assembly of a custom-synthesized pentavalent cationic lipid (MVL5) and glycerol monooleate (GMO) with small interfering RNA (siRNA) results in the formation of a double-gyroid bicontinuous inverted cubic phase with colocalized lipid/siRNA domains as shown by synchrotron X-ray scattering and fluorescence microscopy. The high charge density (due to MVL5) and positive Gaussian modulus of the GMO-containing membranes confer optimal electrostatic and elastic properties for endosomal escape, enabling efficient siRNA delivery and effective, specific gene silencing.     

Optimization of the operational parameters in a fast axial flow CW CO2 laser using artificial neural networks and genetic algorithms

This paper presents an artificial intelligence approach for optimization of the operational parameters such as gas pressure ratio and discharge current in a fast-axial-flow CW CO₂ laser by coupling artificial neural networks and genetic algorithm. First, a series of experiments were used as the learning data for artificial neural networks. The best-trained network was connected to genetic algorithm as a fitness function to find the optimum parameters. After the optimization, the calculated laser power increases by 33% and the measured value increases by 21% in an experiment as compared to a non-optimized case.     

Role of hydrogen bonding in cellulose deformation: the leverage effect analyzed by molecular modeling

The axial modulus of the cellulose Iβ crystal is as high as 120–160 GPa. The importance of hydrogen bonds is often emphasized in this context, although intrinsic stiffness of the hydrogen bonds is relatively low. Here, hydrogen bond–covalent bond synergies are investigated quantitatively using molecular mechanics and molecular dynamics simulations for the so-called leverage effect, a model introduced recently in which strains for intra-molecular hydrogen bonds are higher than for the cellulose chain as a whole, thereby amplifying their contribution to the total stiffness. The present work also includes simulation of the hydrogen bonding band shifts in vibrational spectra during cellulose deformation, which are compared with FT-IR data. The leverage effect hypothesis was supported by the results, although the total contribution to cellulose stiffness is only 12 %. Hydrogen bonding is still critically important and would lower the modulus much more than 12 %, if “artificially” removed in the model. The reason is that intra-molecular hydrogen bonding preserves the crystal structure and directs axial deformation mechanisms towards higher energy deformation and high stiffness.     

New technique for finding needles in haystacks: geometric approach to distinguishing between a new source and random fluctuations

We propose a new test statistic based on a score process for determining the statistical significance of a putative signal that may be a small perturbation to a noisy experimental background. We derive the reference distribution for this score test statistic; it has an elegant geometrical interpretation as well as broad applicability. We illustrate the technique in the context of a model problem from high-energy particle physics. Monte Carlo experimental results confirm that the score test results in a significantly improved rate of signal detection.