Accelerating molecular dynamic simulation on graphics processing units

We describe a complete implementation of all‐atom protein molecular dynamics running entirely on a graphics processing unit (GPU), including all standard force field terms, integration, constraints, and implicit solvent. We discuss the design of our algorithms and important optimizations needed to fully take advantage of a GPU. We evaluate its performance, and show that it can be more than 700 times faster than a conventional implementation running on a single CPU core. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2009     

On the solutions of the Wick-Cutkosky model in the instantaneous approximation

By reexamining the analysis of Basu and Biswas, based on the stereographic projection method of Fock and Levy, it is shown that the general solution of the Wick-Cutkosky model in the instantaneous approximation, hitherto unreported, involves only one quantum number; this is contrasted with the well-known solution which involves two quantum numbers, but for which the spectrum is degenerate with respect to one of them. The latter situation is shown to hold under a rather special circumstance.     

Nanofibrous polyaniline thin film prepared by plasma‐induced polymerization technique for detection of NO2 gas

A nanofibrous polyaniline (PANI) thin film was fabricated using plasma‐induced polymerization method and explored its application in the fabrication of NO₂ gas sensor. The effects of substrate position, pressure, and the number of plasma pulses on the PANI film growth rate were monitored and an optimum condition for the PANI thin film preparation was established. The resulting PANI film was characterized with UV–visible spectrophotometer, FTIR, scanning electron microscopy (SEM), and transmission electron microscopy (TEM). The PANI thin film possessed nanofibers with a diameter ranging from 15 to 20 nm. The NO₂ gas sensing behavior was studied by measuring the change in electrical conductivity of PANI film with respect to NO₂ gas concentration and exposure time. The optimized sensor exhibited a sensitivity factor of 206 with a response time of 23 sec. The NO₂ gas sensor using nanofibrous PANI thin film as sensing probe showed a linear current response to the NO₂ gas concentration in the range of 10–100 ppm. Copyright © 2009 John Wiley & Sons, Ltd.     

Efficient nonbonded interactions for molecular dynamics on a graphics processing unit

We describe an algorithm for computing nonbonded interactions with cutoffs on a graphics processing unit. We have incorporated it into OpenMM, a library for performing molecular simulations on high‐performance computer architectures. We benchmark it on a variety of systems including boxes of water molecules, proteins in explicit solvent, a lipid bilayer, and proteins with implicit solvent. The results demonstrate that its performance scales linearly with the number of atoms over a wide range of system sizes, while being significantly faster than other published algorithms. © 2009 Wiley Periodicals, Inc. J Comput Chem, 2010     

PAPER—Accelerating parallel evaluations of ROCS

Modern graphics processing units (GPUs) are flexibly programmable and have peak computational throughput significantly faster than conventional CPUs. Herein, we describe the design and implementation of PAPER, an open‐source implementation of Gaussian molecular shape overlay for NVIDIA GPUs. We demonstrate one to two order‐of‐magnitude speedups on high‐end commodity GPU hardware relative to a reference CPU implementation of the shape overlay algorithm and speedups of over one order of magnitude relative to the commercial OpenEye ROCS package. In addition, we describe errors incurred by approximations used in common implementations of the algorithm. © 2009 Wiley Periodicals, Inc. J Comput Chem 2010     

RF-PACVD of water repellent and protective HMDSO coatings on bell metal surfaces: Correlation between discharge parameters and film properties

Hexamethyldisiloxane (HMDSO) films have been deposited on bell metal using radiofrequency plasma assisted chemical vapor deposition (RF-PACVD) technique. The protective performances of the HMDSO films and their water repellency have been investigated as a function of DC self-bias voltage on the substrates during deposition. Plasma potential measurements during film deposition process are carried out by self-compensated emissive probe. Optical emission spectroscopy (OES) analyses of the plasma during deposition reveal no significant change in the plasma composition within the DC self-bias voltage range of −40 V to −160 V that is used. Raman and X-ray photoelectron spectroscopy (XPS) studies are carried out for film chemistry analysis and indicate that the impinging ion energy on the substrates influences the physio-chemical properties of the HMDSO films. At critical ion energy of 113 qV (corresponding to DC self-bias voltage of −100 V), the deposited HMDSO film exhibits least defective Si-O-Si chemical structure and highest inorganic character and this contributes to its best corrosion resistance behavior. The hardness and elastic modulus of the films are found to be bias dependent and are 1.27 GPa and 5.36 GPa for films deposited at −100 V. The critical load for delamination is also bias dependent and is 11 mN for this film. The water repellency of the HMDSO films is observed to be dependent on the variation in surface roughness. The results of the investigations suggest that HMDSO films deposited by RF-PACVD can be used as protective coatings on bell metal surfaces.     

Modelling of photonic crystal waveguides: a simple and accurate approach

We present an improved variational effective index method for reduction of 2-D Bragg grating problems to 1-D and show significant improvements particularly at smaller wavelengths. The method is based on the optimal variational (Vopt) method, which we have earlier used successfully for conventional waveguides. A 1-D transverse profile along with a longitudinal index variation are reduced to a 1-D longitudinal distribution, reflection and transmission spectra of which have been studied for both the TE and TM modes by transfer matrix methods. An accurate modeling for the out of plane scattering losses has been presented which occur when a guided wave propagating in a conventional waveguide impinges on a photonic crystal waveguide. Taking these losses into account brings the results pretty close to those of a rigorous 2-D Helmholtz solver QUEP, improving them remarkably over the variational EIM (vEIM) results.     

Second order symmetric duality in nondifferentiable multiobjective fractional programming with cone convex functions

In the present paper, we consider Mond-Weir type nondifferentiable second order fractional symmetric dual programs over arbitrary cones and derive duality results under second order K?F-convexity/K?F-pseudoconvexity assumptions. Our results generalize several known results in the literature.     

Exponential type vector variational-like inequalities and vector optimization problems with exponential type invexities

A new class of exponential form of vector variational-like inequality problems is introduced, and then the equivalence among (weakly) efficient solutions, vector critical points of vector optimization problem and the solutions of vector variational-like inequalities under the framework of (p,r)-invexity is established. To the best our knowledge, the presented results are new and highly application oriented to other results based on generalized invexities to the context of optimization problems in the literature.