Application of combined Monte Carlo and molecular dynamics method to simulation of dipalmitoyl phosphatidylcholine lipid bilayer

We describe a new equilibration procedure for the atomic level simulation of a hydrated lipid bilayer. The procedure consists of alternating molecular dynamics trajectory calculations in a constant surface tension and temperature ensemble with configurational bias Monte Carlo moves to different regions of the configuration space of the bilayer, in a constant volume and temperature ensemble. The procedure is described in detail and is applied to a bilayer of 100 molecules of dipalmitoyl phosphatidylcholine (DPPC) and 3205 water molecules. We find that the hybrid simulation procedure enhances the equilibration of the bilayer as measured by the convergence of the area per molecule and the segmental order parameters, as compared with a simulation using only molecular dynamics (MD). Progress toward equilibration is almost three times as fast in CPU time, compared with a purely MD simulation. Equilibration is complete, as judged by the lack of energy drift in three separate 200-ps runs of continuous MD started from different initial states. Results of the simulation are presented and compared with experimental data and with other recent simulations of DPPC. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 1153–1164, 1999     

Radial basis function (RBF)‐based parametric models for closed and open curves within the method of regularized stokeslets

The method of regularized Stokeslets (MRS) is a numerical approach using regularized fundamental solutions to compute the flow due to an object in a viscous fluid where inertial effects can be neglected. The elastic object is represented as a Lagrangian structure, exerting point forces on the fluid. The forces on the structure are often determined by a bending or tension model, previously calculated using finite difference approximations. In this paper, we study spherical basis function (SBF), radial basis function (RBF), and Lagrange–Chebyshev parametric models to represent and calculate forces on elastic structures that can be represented by an open curve, motivated by the study of cilia and flagella. The evaluation error for static open curves for the different interpolants, as well as errors for calculating normals and second derivatives using different types of clustered parametric nodes, is given for the case of an open planar curve. We determine that SBF and RBF interpolants built on clustered nodes are competitive with Lagrange–Chebyshev interpolants for modeling twice‐differentiable open planar curves. We propose using SBF and RBF parametric models within the MRS for evaluating and updating the elastic structure. Results for open and closed elastic structures immersed in a 2D fluid are presented, showing the efficacy of the RBF–Stokeslets method. Copyright © 2015 John Wiley & Sons, Ltd.     

Influence of sol-gel precursors on the electrochemical performance of NaMn<Subscript>0.33</Subscript>Ni<Subscript>0.33</Subscript>Co<Subscript>0.33</Subscript>O<Subscript>2</Subscript> positive electrode for sodium-ion battery

Among the various cathode materials explored for sodium-ion batteries (SIBs), NaMn_0.33Ni_0.33Co_0.33O₂, with a layered oxide structure, is a promising material due to its high theoretical capacity (240 mAhg^?1). We have synthesized NaMn_0.33Ni_0.33Co_0.33O₂ using two different types of precursors, namely metal acetates and metal nitrates by the sol-gel method. XRD patterns confirm the formation of a stable phase of the material at 900 °C. Coupled TGA-FTIR analysis was used to optimize the calcination conditions and to understand the hydrolysis and condensation mechanism of the sol-gel precursors. FTIR spectra extracted at different temperatures reveal the polymer network-forming tendency of the acetate ligands whereas the polymerization is inhibited in the nitrate precursors. SEM analysis shows spherical and platelet morphologies of samples synthesized from nitrate and acetate precursors, respectively. Using in situ impedance and galvanostatic charge/discharge studies, we observed that the precursors used to synthesize the cathode material influence the electrochemical properties of the material, as in this case, where we observe a 20 % improvement in terms of capacity by using acetate precursors instead of nitrate precursors.     

Low-loss amorphous silicon-on-insulator technology for photonic integrated circuitry

We report the fabrication of low-loss amorphous silicon photonic wires deposited by plasma enhanced chemical vapor deposition. Single mode photonic wires were fabricated by 193 nm optical lithography and dry etching. Propagation loss measurements show a loss of 3.46 dB/cm for photonic wires and 1.34 dB/cm for ridge waveguides.     

Improved approximation algorithms for metric maximum ATSP and maximum 3-cycle cover problems

We consider an -hard variant (Δ-Max-ATSP) and an -hard relaxation (Max-3-DCC) of the classical traveling salesman problem. We present a -approximation algorithm for Δ-Max-ATSP and a -approximation algorithm for Max-3-DCC with polynomial running time. The results are obtained via a new way of applying techniques for computing undirected cycle covers to directed problems.     

Time dependent stretching of aging dynamics in a generalized hydrodynamic model for supercooled liquids

The nonequilibrium dynamics and aging behavior of a supercooled liquid is investigated from an analysis of the correlation of density fluctuations at two different times. The dynamic correlation functions are computed by solving numerically the equations of nonlinear fluctuating hydrodynamics. The aging time dependence follows a modified stretched exponential form with a relaxation time which is dependent on the aging time. This is similar to the behavior seen in the aging data of dielectric response functions of a typical glass forming liquid.     

Strategies for the synthesis of fluorescently labelled PNA

A simple and effective strategy for preparing fluorophore-labelled PNA is described. A C-terminal S-t-butylmercaptocysteine-derivatized PNA was prepared on solid-phase using Fmoc chemistry. Selective deprotection of the S-t-butylmercapto group on-bead, allowed the free thiol to be reacted with a fluorophore derivatized via an iodoacetamido or maleimido linker. Subsequent cleavage and sidechain deprotection yielded C-terminal labelled PNA in good yield and purity. Dual labelled PNA was also prepared by using both C-terminal (-SH) and N-terminal (-NH(2)) labelling chemistries.     

Radiationless transitions in trivalent lanthanide ions embedded in solids

Radiationless transitions in lanthanide ions embedded in glassy and crystalline hosts have been briefly reviewed. The correlations of multiphonon relaxation rates with energy gaps, vibrational frequencies, temperatures and electronic symmetries have been discussed. The essence of various theories, such as Nth order methods, non-adiabatic Hamiltonian method, dynamic coupling model has also been presented.