Message passing interface and multithreading hybrid for parallel molecular docking of large databases on petascale high performance computing machines

A mixed parallel scheme that combines message passing interface (MPI) and multithreading was implemented in the AutoDock Vina molecular docking program. The resulting program, named VinaLC, was tested on the petascale high performance computing (HPC) machines at Lawrence Livermore National Laboratory. To exploit the typical cluster‐type supercomputers, thousands of docking calculations were dispatched by the master process to run simultaneously on thousands of slave processes, where each docking calculation takes one slave process on one node, and within the node each docking calculation runs via multithreading on multiple CPU cores and shared memory. Input and output of the program and the data handling within the program were carefully designed to deal with large databases and ultimately achieve HPC on a large number of CPU cores. Parallel performance analysis of the VinaLC program shows that the code scales up to more than 15K CPUs with a very low overhead cost of 3.94%. One million flexible compound docking calculations took only 1.4 h to finish on about 15K CPUs. The docking accuracy of VinaLC has been validated against the DUD data set by the re‐docking of X‐ray ligands and an enrichment study, 64.4% of the top scoring poses have RMSD values under 2.0 Å. The program has been demonstrated to have good enrichment performance on 70% of the targets in the DUD data set. An analysis of the enrichment factors calculated at various percentages of the screening database indicates VinaLC has very good early recovery of actives. © 2013 Wiley Periodicals, Inc.     

Mass spectrometry and non-covalent protein-ligand complexes: confirmation of binding sites and changes in tertiary structure

An experimental approach is described for determining protein-small molecule non-covalent ligand binding sites and protein conformational changes induced by ligand binding. The methodology utilizes time resolved limited proteolysis and the high throughput analysis capability of MALDI TOF MS to determine the binding site in a tetanus toxin C-fragment (51 kDa)-doxorubicin (543 Da) non-covalent complex. Comparing relative ion abundances of peptides released from the time resolved limited proteolysis of tetanus toxin C-fragment (TetC) and the TetC-doxorubicin complex every 10 min from 10 to 120 min of digestion revealed that the binding of doxorubicin induced a significant change in surface topology of TetC. Four of the twenty-nine peptides observed by MALDI MS, including amino acids 351-360, 299-304, 305-311 and 312-316, had a lower abundance in the TetC-doxorubicin complex relative to TetC from 10 to 100 min of digestion. A decrease in ion abundance suggests doxorubicin obstructs the access of the protease to one or both termini of these peptides, identifying doxorubicin binding site(s). Conversely, five peptide ions, including amino acids 335-350, 364-375, 364-376, 281-298, and 316-328, all had a greater abundance in the digest of the complex, indicating an increase in accessibility to these sites. These five peptides flank regions of decreased ion abundance, suggesting that doxorubicin not only binds to the surface, but also induces a conformational change in TetC.     

A convenient field-installable antireflection coating for optical fiber connectors and other components

Disc-shaped pellicles 15 microns thick are antireflection coated and cemented to the polished ends of optical fiber connectors. Excess loss due to increased fiber separation is a maximum of 10% (.46 dB), typically 3.8% (.16 dB) in graded index fibers; Fresnel back-reflections are reduced by a factor of more than 10.     

Gas-phase interaction of thiophene with the Ti(8)C(12)(+) and Ti(8)C(12) met-car clusters

The reactivity of the Ti(8)C(12)(+) met-car cation toward thiophene was investigated using density functional theory (DFT) and mass selective ion chemistry. It is shown that the experimentally observed mass spectrum can be well described by the DFT calculations. In contrast to the weak bonding interactions seen for thiophene on a TiC(001) surface, the Ti(8)C(12)(+) met-car cation is able to interact strongly with up to four thiophene molecules with the cluster staying intact. In the most stable conformation, the thiophene molecules bond to the four low-coordinated Ti(0) sites of Ti(8)C(12)(+) via a eta(5)-C,S coordination. The stability and the activity of the Ti(8)C(12)(+) met-car is observed to increase with an increasing number of attached thiophene molecules at the Ti(0) sites, which is associated with a significant transfer of electron density from thiophene to the cluster. The additional electron density on the Ti(8)C(12)(+) cation cluster, however, is not sufficient to cleave the C-S bonds of thiophene and the dissociation reaction of thiophene is predicted to be a highly activated process. By contrast, DFT calculations for the neutral Ti(8)C(12) met-car predict that the dissociation reaction leading to adsorbed S and C(4)H(4) fragments is energetically favorable for the first thiophene molecule. The binding behavior for subsequent addition of thiophene molecules to the neutral met-car is also presented and compared to that of the cation.     

First principles and classical molecular dynamics simulations of solvated benzene

We have performed extensive ab initio and classical molecular dynamics (MD) simulations of benzene in water in order to examine the unique solvation structures that are formed. Qualitative differences between classical and ab initio MD simulations are found and the importance of various technical simulation parameters is examined. Our comparison indicates that nonpolarizable classical models are not capable of describing the solute-water interface correctly if local interactions become energetically comparable to water hydrogen bonds. In addition, a comparison is made between a rigid water model and fully flexible water within ab initio MD simulations which shows that both models agree qualitatively for this challenging system.     

Self-consistency and the use of correlated stochastic separated flow models for prediction of particle-laden flows

Computational fluid dynamics (CFD) is being used increasingly in the design and analysis of particle-laden flows. A significant challenge of this work is in correctly predicting the interaction of the fluid turbulence with the particulate phase. Typically, Lagrangian tracking is used to calculate the particle trajectories with stochastic treatments used to provide an instantaneous turbulent flow field. The stochastic calculations are based on the mean velocities and turbulence quantities calculated by the CFD solver. The current work examines the correlated stochastic separated flow (SSF) model used to synthesize the instantaneous fluid velocity field. Two functional forms of the Eulerian spatial correlation are considered: exponential, and Frenkiel with loop parameter m equal to unity. It is well known that the use of a Frenkiel function is incorrect due to the Markovian nature of the model. Nonetheless, a literature review indicates that the Frenkiel function is still being used in the CFD community. In order to illustrate the implications of this, numerical predictions are compared to Taylor's analytical result for fluid particle dispersion in homogeneous isotropic turbulence. Excellent predictions are obtained with the exponential correlation and recommendations on timestep requirements are made. In contrast, predictions from the Frenkiel model are in poor agreement with Taylor's solution. This poor agreement results from an inconsistency between the effective correlation of fluid velocities arising from the model and the original intended correlation.     

Magnetic structure variation in manganese-oxide clusters

Negative-ion photoelectron spectroscopy and ab initio simulations are used to study the variation in magnetic structure in Mn(x)O(y) (x = 3, 4[semicolon] y = 1, 2) clusters. The ferrimagnetic and antiferromagnetic ground-state structures of Mn(x)O(y) are 0.16-1.20 eV lower in energy than their ferromagnetic isomers. The presence of oxygen thus stabilizes low-spin isomers relative to the preferred high-spin ordering of bare Mn(3) and Mn(4). Each cluster has a preferred overall magnetic moment, and no evidence is seen of competing states with different spin multiplicities. However, non-degenerate isomags, which possess the same spin multiplicity but different arrangements of local moments, do contribute additional features and peak broadening in the photoelectron spectra. Proper accounting for all possible isomags is shown to be critical for accurate computational prediction of the spectra.     

Host-guest interactions at self-assembled monolayers of cyclodextrins on gold

We have developed synthesis routes for the introduction of short and long dialkylsulfides onto the primary side of alpha-, beta-, and gamma-cyclodextrins. Monolayers of these cyclodextrin adsorbates were characterized by electrochemistry, wettability studies, X-ray photoelectron spectroscopy (XPS), time-of-flight secondary ion mass spectrometry (TOF-SIMS), and atomic force microscopy (AFM). The differences in thickness and polarity of the outerface of the monolayers were measured by electro-chemistry and wettability studies. On average about 70% of the sulfide moieties were used for binding to the gold, as measured by XPS. Tof-SIMS measurements showed that the cyclodextrin adsorbates adsorb without any bond breakage. AFM measurements revealed for beta-cyclodextrin monolayers a quasi-hexagonal lattice with a lattice constant of 20.6 A, which matches the geometrical size of the adsorbate. The alpha-cyclodextrin and gamma-cyclodextrin monolayers are less ordered. Interactions of the anionic guests 1-anilinonaphthalene-8-sulfonic acid (1,8-ANS) and 2-(p-toluidinyl)naphthalene-6-sulfonic acid (2,6-TNS) and the highly ordered monolayers of heptapodant beta-cyclodextrin adsorbates were studied by surface plasmon resonance (SPR) and electrochemical impedance spectroscopy. The SPR measurements clearly showed interactions between a beta-cyclodextrin monolayer and 1,8-ANS. Electrochemical impedance spectroscopy measurements gave high responses even at low guest concentrations (< or = 5 microM). The association constant for the binding of 1,8-ANS (K = 289,000 +/- 13,000M-1) is considerably higher than the corresponding value in solution. (Partial) methylation of the secondary side of the beta-cyclodextrin strongly decreases the binding.     

Dynamics in physisorbed monolayers of 5-alkoxy-isophthalic acid derivatives at the liquid/solid interface investigated by scanning tunneling microscopy

Monolayers of isophthalic acid derivatives at the liquid/solid interface have been studied with scanning tunneling microscopy (STM). We have investigated the dynamics related to the phenomenon of solvent co-deposition, which was previously observed by our research group when using octan-1-ol or undecan-1-ol as solvents for 5-alkoxy-isophthalic acid derivatives. This solvent co-deposition has now been visualized in real-time (two frames per second) for the first time. Dynamics of individual molecules were investigated in mixtures of semi-fluorinated molecules with video-STM. The specific contrast arising from fluorine atoms in STM images allows us to use this functionality as a probe to analyze the data obtained for the mixtures under investigation. Upon imaging the same region of a monolayer for a period of time we observed that non-fluorinated molecules progressively substitute the fluorinated molecules. These findings illustrate the metastable equilibrium that exists at the liquid/solid interface, between the physisorbed molecules and the supernatant solution.