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.     

A study of iso- and alio-valent cation doped Ag2SO4 solid electrolyte

2 SO₄. The solid solubility limits up to x≤3 mole% for monovalent, x≤5.27 mole% for divalent and x≤3.63 mole% for trivalent cation doped Ag₂SO₄ are set with XRD, SEM, IR and DSC techniques. A predominant dependence of conductivity on the ionic size of iso- and alio-valent cations is observed. In particular, the conductivity enhances in both α and β phases, despite having a lower ionic-size dopant cation (relative to that of Ag⁺) in the transition element cation doped Ag₂SO₄. Ca²⁺, Ba²⁺, Y³⁺ and Dy³⁺ doped samples show depature from the regular behaviour in the β-phase. The conductivity behaviour is discussed considering ionic size, valence and electronic structure of the guest cations. Received: 3 February 1997/Accepted: 27 May 1997     

Influence of protonation on physico-chemical properties of metal extractants

Summary The protonation constants of several metal extractants, especially hydroxamic acids have been determined by a solvent extraction method. The influence of the acidity on the solubility and the distribution ratio has been studied. A plot correlates the protonation behaviour of these metal extractants with the Hammett Acidity Function, H_o. The protonation constant is useful to explain the acid catalysed hydrolysis rate of these metal extractants and to determine the extraction coefficients of their metal chelates.     

Preliminary design studies of a 100 MeV H−/H+ LINAC as injector for SNS synchrotron/ADS LINAC

It is proposed to construct a spallation neutron source (SNS) at Centre for Advanced Technology (CAT) based on a 1 GeV proton synchrotron with 100 MeV H⁻ LINAC as injector. Additionally, the LINAC can form the first 100 MeV part of a 1 GeV proton LINAC to be built in future for accelerator driven system (ADS) applications. We are exploring a configuration of the 100 MeV LINAC which will consist of an H⁻ ion source, a 4–6 MeV RFQ followed either by a 20 MeV drift tube LINAC (DTL) and 100 MeV separated function drift tube LINAC (SDTL) or a coupled cavity drift tube LINAC (CCDTL) structure. In this paper, we present the results of our preliminary physics design studies of the RFQ-SDTL, RFQ-CCDTL and RFQ-DTL-SDTL configurations. The design of the 4.5 MeV RFQ is discussed along with the matching sections between the RFQ-SDTL/DTL and RFQ-CCDTL. The choice of the accelerator configuration and that of various parameters of the individual accelerator structures under consideration are discussed. The design objectives are to arrive at a configuration which eases heat removal for CW operation and which is less prone to halo formation in order to reduce the beam loss at higher energies.     

Analysis of poly(amidoamine) dendrimer structure by UV-vis spectroscopy

We report a UV-vis spectroscopic study of four different types of poly(amidoamine) dendrimers. The results indicate that the degree of protonation of the interior tertiary amines of these dendrimers correlates directly to an absorption band with λ(max) in the range of 280-285 nm. Specifically, at low pH, the tertiary amines are protonated and the 280-285 nm band is absent. However, at elevated pH, when these groups are deprotonated, this band appears. Similar results were obtained for a simple model compound. The dependence of the 280-285 nm band on the chemical state of the tertiary amines of the dendrimers was confirmed by complexing them with Pd(2+) and Pt(2+). In this case the band disappears, and it only reappears when the metal ions are decomplexed following reduction with BH(4)(-). Finally, filtration experiments showed that the absorption band between 280-285 nm arises exclusively from intact, or nearly intact, dendrimers rather than low-molecular-weight fragments.     

Optimal use of data in parallel tempering simulations for the construction of discrete-state Markov models of biomolecular dynamics

Parallel tempering (PT) molecular dynamics simulations have been extensively investigated as a means of efficient sampling of the configurations of biomolecular systems. Recent work has demonstrated how the short physical trajectories generated in PT simulations of biomolecules can be used to construct the Markov models describing biomolecular dynamics at each simulated temperature. While this approach describes the temperature-dependent kinetics, it does not make optimal use of all available PT data, instead estimating the rates at a given temperature using only data from that temperature. This can be problematic, as some relevant transitions or states may not be sufficiently sampled at the temperature of interest, but might be readily sampled at nearby temperatures. Further, the comparison of temperature-dependent properties can suffer from the false assumption that data collected from different temperatures are uncorrelated. We propose here a strategy in which, by a simple modification of the PT protocol, the harvested trajectories can be reweighted, permitting data from all temperatures to contribute to the estimated kinetic model. The method reduces the statistical uncertainty in the kinetic model relative to the single temperature approach and provides estimates of transition probabilities even for transitions not observed at the temperature of interest. Further, the method allows the kinetics to be estimated at temperatures other than those at which simulations were run. We illustrate this method by applying it to the generation of a Markov model of the conformational dynamics of the solvated terminally blocked alanine peptide.     

Mass spectrometry of halo-pyrazolium salts

Eleven halogen substituted 1-methyl-2-phenylpyrazolium bromides or chlorides were investigated by field desorption, field ionization, and electron impact mass spectrometry. Dealkylation was found to be the predominant thermal decomposition. An exchange between covalent and ionic halogen prior to dealkylation was observed and is discussed in detail.