Scalable and portable visualization of large atomistic datasets

A scalable and portable code named Atomsviewer has been developed to interactively visualize a large atomistic dataset consisting of up to a billion atoms. The code uses a hierarchical view frustum-culling algorithm based on the octree data structure to efficiently remove atoms outside of the user's field-of-view. Probabilistic and depth-based occlusion-culling algorithms then select atoms, which have a high probability of being visible. Finally a multiresolution algorithm is used to render the selected subset of visible atoms at varying levels of detail. Atomsviewer is written in C++ and OpenGL, and it has been tested on a number of architectures including Windows, Macintosh, and SGI. Atomsviewer has been used to visualize tens of millions of atoms on a standard desktop computer and, in its parallel version, up to a billion atoms.

Program summary

Title of program: AtomsviewerCatalogue identifier: ADUMProgram summary URL:http://cpc.cs.qub.ac.uk/summaries/ADUMProgram obtainable from: CPC Program Library, Queen's University of Belfast, N. IrelandComputer for which the program is designed and others on which it has been tested: 2.4 GHz Pentium 4/Xeon processor, professional graphics card; Apple G4 (867 MHz)/G5, professional graphics cardOperating systems under which the program has been tested: Windows 2000/XP, Mac OS 10.2/10.3, SGI IRIX 6.5Programming languages used: C++, C and OpenGLMemory required to execute with typical data: 1 gigabyte of RAMHigh speed storage required: 60 gigabytesNo. of lines in the distributed program including test data, etc.: 550 241No. of bytes in the distributed program including test data, etc.: 6 258 245Number of bits in a word: ArbitraryNumber of processors used: 1Has the code been vectorized or parallelized: NoDistribution format: tar gzip fileNature of physical problem: Scientific visualization of atomic systemsMethod of solution: Rendering of atoms using computer graphic techniques, culling algorithms for data minimization, and levels-of-detail for minimal renderingRestrictions on the complexity of the problem: NoneTypical running time: The program is interactive in its executionUnusual features of the program: NoneReferences: The conceptual foundation and subsequent implementation of the algorithms are found in [A. Sharma, A. Nakano, R.K. Kalia, P. Vashishta, S. Kodiyalam, P. Miller, W. Zhao, X.L. Liu, T.J. Campbell, A. Haas, Presence—Teleoperators and Virtual Environments 12 (1) (2003)].     

Development of skin barrier function in premature infants

ANCA directed against PR3 are highly specific for Wegener's granulomatosis and microscopic polyangiitis, and have been implicated in the pathogenesis of small vessel vasculitis. Most PR3-ANCA are directed against conformational epitopes on PR3. This study was designed to determine whether the cleavage of the N-terminal activation dipeptide of PR3 is required for the binding of PR3-ANCA. Recombinant PR3 (rPR3) variants were expressed in the epithelial cell line, 293. As confirmed by radiosequencing, the rPR3 secreted into the 293 cell culture supernatant is N-terminally unprocessed. Two enzymatically inactive rPR3 mutants were expressed in 293 cells: rPR3-S176A and delta-rPR3-S176A. rPR3-S176A contains the N-propetide Ala-2-Glu-1, delta-rPR3-S176A does not. Culture supernatants of rPR3-S176A and delta-rPR3-S176A expressing 293 cells were used as sources of target antigen for PR3-ANCA testing by capture ELISA. Forty unselected consecutive PR3-ANCA+ sera were tested. With delta-rPR3-S176A as antigen all 40 were recognized, compared with only 34 of 40 when rPR3-S176A served as target antigen. The majority of the serum samples contained a mixture of antibodies reacting with epitopes accessible on the mature and on the proform of PR3. In conclusion, the cleavage of the N-terminal activation dipeptide of PR3 is not an absolute requirement for recognition by all PR3-ANCA. However, a substantial proportion of PR3-ANCA recognize (a) target antigen(s) exposed only after the conformational change of PR3 associated with the N-terminal processing. In 15% of sera this PR3-ANCA subset occurred exclusively. PR3-ANCA subtypes can be differentiated using specifically designed rPR3 variants as target antigens, and non-haematopoietic mammalian cells without regulated secretory pathway can be used for their expression.     

Silica under very large positive and negative pressures: Molecular dynamics simulations on parallel computers

A highly efficient multiresolution algorithm has been developed to carry out large-scale molecular dynamics (MD) simulations for systems with long-range Coulomb and three-body covalent interactions. The algorithm combines the reduced cell and fast multipole methods and multiple time-step approach. Pressure-induced structural transformation, loss of intermediate range order, and dynamcal correlations in SiO₂, glass are investigated with the moleculardynamics method. At twice the normal density, the Si-O bond length increases, the Si O coordination changes from 4 to 6, and the O-Si-O band-angle changes from 109 to 90°. This is a tetrahedral-to-octahedral transformation, which was reported by Meade, Hemley, and Mao. Results for phonon density of states also reveal significant changes at high pressures. The multiresolution MD approach has been used to investigate the structural properties and mechanical failure in microporous silica. Structural correlations are characterized by the fractal dimension, internal surface area, and pore surface-tovolume ratio. Critical behavior at fracture is analyzed in terms of pore percolation, and kinetic roughening of fractured surface is also investigated.Paper presented at the Twelfth Symposium on Thermophysical Properties, June 19–24, 1994, Boulder, Colorado, U.S.A.     

Hybrid quantum mechanical/molecular dynamics simulation on parallel computers: density functional theory on real-space multigrids

A hybrid quantum mechanical/molecular dynamics simulation scheme is developed, in which a quantum mechanical system described by the density functional theory on real-space multigrids is embedded in a classical system of atoms interacting via an empirical interatomic potential. Handshake atoms coupling the quantum and the classical systems are treated by a novel scaled position method. The scheme is implemented on parallel computers using both task and spatial decompositions. An application to oxidation of Si (100) surface demonstrates seamless coupling of the quantum and the classical systems.     

Anodic oxidation of p-anisidines at the tubular graphite electrode

Anodic voltammetric behaviour of anisidines has been studied at the tubular graprhite electrode in hydrodynamic conditions. While only one oxidation wave is obtained in the case of ortho and meta isomers, two distinct oxidation waves are obtained in the case of the para-isomer, the total limiting current remaining the same in all the three cases. A probable mechanism for the above voltammetric behaviour has been suggested.     

Transdermal delivery of peptides by iontophoresis

Transdermal administration by iontophoresis (enhanced transport via the skin using the driving force of an applied electric field) has been successfully demonstrated but no formal relationship between peptide sequence/structure and efficiency of delivery has been established. There are notable examples, such as the lipophilic leutinizing hormone releasing hormone (LHRH) analogs, Nafarelin and Leuprolide, that exhibit down-regulation of their own transport across the skin under the influence of an iontophoretic current. The hypothesis that this phenomenon is due to neutralization of the skin's net negative charge by these cationic peptides was examined with LHRH oligopeptides. The impact of these compounds on the electroosmotic flow of solvent into the skin, which is induced by iontophoresis and which contributes significantly to the electrotransport of large, positively charged ions, was examined and quantified. Close juxtaposition of cationic and lipophilic residues profoundly inhibited electroosmosis and, presumably, peptide flux. The results indicate that the lipophilicity of the oligopeptides facilitates van der Waals interactions with hydrophobic patches along the transport route, thereby permitting the positively charged oligopeptide to interact with carboxylate side chains that give the skin its net negative charge at neutral pH. The lipophilic, cationic oligopeptide, therefore, becomes anchored in the transport path, neutralizing the original charge of the membrane, and completely altering the permselective properties of the skin.     

Fluidic Flow Assisted Deterministic Folding of Van der Waals Materials

Origami offers a distinct approach for designing and engineering new material structures and properties. The folding and stacking of atomically thin van der Waals (vdW) materials, for example, can lead to intriguing new physical properties including bandgap tuning, Van Hove singularity, and superconductivity. On the other hand, achieving well‐controlled folding of vdW materials with high spatial precision has been extremely challenging and difficult to scale toward large areas. Here, a deterministic technique is reported to fold vdW materials at a defined position and direction using microfluidic forces. Electron beam lithography (EBL) is utilized to define the folding area, which allows precise control of the folding geometry, direction, and position beyond 100 nm resolution. Using this technique, single‐atomic‐layer vdW materials or their heterostructures can be folded without the need for any external supporting layers in the final folded structure. In addition, arrays of patterns can be folded across a large area using this technique and electronic devices that can reconfigure device functionalities through folding are also demonstrated. Such scalable formation of folded vdW material structures with high precision can lead to the creation of new atomic‐scale materials and superlattices as well as opening the door to realizing foldable and reconfigurable electronics.     

Analysis of scalable data-privatization threading algorithms for hybrid MPI/OpenMP parallelization of molecular dynamics

We propose and analyze threading algorithms for hybrid MPI/OpenMP parallelization of a molecular-dynamics simulation, which are scalable on large multicore clusters. Two data-privatization thread scheduling algorithms via nucleation-growth allocation are introduced: (1) compact-volume allocation scheduling (CVAS); and (2) breadth-first allocation scheduling (BFAS). The algorithms combine fine-grain dynamic load balancing and minimal memory-footprint data privatization threading. We show that the computational costs of CVAS and BFAS are bounded by Θ(n ^5/3 p ^?2/3) and Θ(n), respectively, for p threads working on n particles on a multicore compute node. Memory consumption per node of both algorithms scales as O(n+n ^2/3 p ^1/3), but CVAS has smaller prefactors due to a geometric effect. Based on these analyses, we derive the selection criterion between the two algorithms in terms of the granularity, n/p. We observe that memory consumption is reduced by 75 % for p=16 and n=8,192 compared to a naïve data privatization, while maintaining thread imbalance below 5 %. We obtain a strong-scaling speedup of 14.4 with 16-way threading on a four quad-core AMD Opteron node. In addition, our MPI/OpenMP code achieves 2.58× and 2.16× speedups over the MPI-only implementation on 32,768 cores of BlueGene/P for 0.84 and 1.68 million particle systems, respectively.     

Novel Insights into Guide RNA 5′-Nucleoside/Tide Binding by Human Argonaute 2

The human Argonaute 2 (hAgo2) protein is a key player of RNA interference (RNAi). Upon complex formation with small non-coding RNAs, the protein initially interacts with the 5′-end of a given guide RNA through multiple interactions within the MID domain. This interaction has been reported to show a strong bias for U and A over C and G at the 5′-position. Performing molecular dynamics simulations of binary hAgo2/OH–guide–RNA complexes, we show that hAgo2 is a highly flexible protein capable of binding to guide strands with all four possible 5′-bases. Especially, in the case of C and G this is associated with rather large individual conformational rearrangements affecting the MID, PAZ and even the N-terminal domains to different degrees. Moreover, a 5′-G induces domain motions in the protein, which trigger a previously unreported interaction between the 5′-base and the L2 linker domain. Combining our in silico analyses with biochemical studies of recombinant hAgo2, we find that, contrary to previous observations, hAgo2 is capable of functionally accommodating guide strands regardless of the 5′-base.