Probing potential energy surfaces in confined systems: behavior of mean-square displacement in zeolites

Time evolution of mean-squared displacement based on molecular dynamics for a variety of adsorbate-zeolite systems is reported. Transition from ballistic to diffusive behavior is observed for all the systems. The transition times are found to be system dependent and show different types of dependence on temperature. Model calculations on a one-dimensional system are carried out which show that the characteristic length and transition times are dependent on the distance between the barriers, their heights, and temperature. In light of these findings, it is shown that it is possible to obtain valuable information about the average potential energy surface sampled under specific external conditions.

Combining Bayes Classification and Point Group Symmetry under Boolean Framework for Enhanced Protein Quaternary Structure Inference

Our ability to infer the protein quaternary structure automatically from atom and lattice information is inadequate, especially for weak complexes, and heteromeric quaternary structures. Several approaches exist, but they have limited performance. Here, we present a new scheme to infer protein quaternary structure from lattice and protein information, with all-around coverage for strong, weak and very weak affinity homomeric and heteromeric complexes. The scheme combines naive Bayes classifier and point group symmetry under Boolean framework to detect quaternary structures in crystal lattice. It consistently produces >= 90% coverage across diverse benchmarking data sets, including a notably superior 95% coverage for recognition heteromeric complexes, compared with 53% on the same data set by current state-of-the-art method. The detailed study of a limited number of prediction-failed cases offers interesting insights into the intriguing nature of protein contacts in lattice. The findings have implications for accurate inference of quaternary states of proteins, especially weak affinity complexes.

Using Correlated Parameters for Improved Ranking of Protein-Protein Docking Decoys

A successful protein-protein docking study culminates in identification of decoys at top ranks with near-native quaternary structures. However, this task remains enigmatic because no generalized scoring functions exist that effectively infer decoys according to the similarity to near-native quaternary structures. Difficulties arise because of the highly irregular nature of the protein surface and the significant variation of the nonbonding and solvation energies based on the chemical composition of the protein-protein interface. In this work, we describe a novel method combining an interface-size filter, a regression model for geometric compatibility (based on two correlated surface and packing parameters), and normalized interaction energy (calculated from correlated nonbonded and solvation energies), to effectively rank decoys from a set of 10,000 decoys. Tests on 30 unbound binary protein-protein complexes show that in 16 cases we can identify at least one decoy in top three ranks having <= 10 angstrom backbone root mean square deviation from true binding geometry. Comparisons with other state-of-art methods confirm the improved ranking power of our method without the use of any experiment-guided restraints, evolutionary information, statistical propensities, or modified interaction energy equations. Tests on 118 less-difficult bound binary protein-protein complexes with <= 35% sequence redundancy at the interface showed that in 77% cases, at least 1 in 10,000 decoys were identified with <= 5 angstrom backbone root mean square deviation from true geometry at first rank. The work will promote the use of new concepts where correlations among parameters provide more robust scoring models. It will facilitate studies involving molecular interactions, including modeling of large macromolecular assemblies and protein structure prediction. (C) 2010 Wiley Periodicals, Inc. J Comput Chem 32: 787-796, 2011.

Sorbate properties of xenon in cloverite: A molecular dynamics study

Molecular dynamics calculations on xenon adsorbed in the cubic cavity of cloverite, a gallophosphate, is presented. Guest-host radial distribution functions, guest-host energy distribution functions, power spectra, and diffusion coefficients for xenon are reported at 397, 494, and 716 K. Results suggest that xenon is highly mobile at 700 K. A shift in the peak position of the power spectra toward lower frequency is observed with increase in temperature. (C) 1994 Academic Press, Inc.

Stabilizing trench's algorithm to invert symmetric toeplitz matrices

Presented here is a stable algorithm that uses Zohar's formulation of Trench's algorithm and computes the inverse of a symmetric Toeplitz matrix including those with vanishing or nearvanishing leading minors. The algorithm is based on a diagonal modification of the matrix, and exploits symmetry and persymmetry properties of the inverse matrix.

Molecular dynamics investigation of sorption of argon in NaCaA zeolite

A molecular dynamics calculation of argon in NaCaA zeolite at 393 K and 1 atom per cage is reported. Equilibrium properties such as guest-host interaction energy, guest-guest dimerization and bonding energy, various guest-host and guest-guest radial distribution functions and dynamical properties such as the mean-square displacement, power spectra and diffusion coefficient have been obtained.

Pipelined ring algorithm for matrix multiplication on transputer networks: performance analysis and estimation

A parallel matrix multiplication algorithm is presented, and studies of its performance and estimation are discussed. The algorithm is implemented on a network of transputers connected in a ring topology. An efficient scheme for partitioning the input matrices is introduced which enables overlapping computation with communication. This makes the algorithm achieve near-ideal speed-up for reasonably large matrices. Analytical expressions for the execution time of the algorithm have been derived by analysing its computation and communication characteristics. These expressions are validated by comparing the theoretical results of the performance with the experimental values obtained on a four-transputer network for both square and irregular matrices. The analytical model is also used to estimate the performance of the algorithm for a varying number of transputers and varying problem sizes. Although the algorithm is implemented on transputers, the methodology and the partitioning scheme presented in this paper are quite general and can be implemented on other processors which have the capability of overlapping computation with communication. The equations for performance prediction can also be extended to other multiprocessor systems.

DockYard-a repository to assist modeling of protein-protein docking

In the absence of interlogs, building docking models is a time intensive task, involving generation of a large pool of docking decoys followed by refinement and screening to identify near native docking solutions. This limits the researcher interested in building docking methods with the choice of benchmarking only a limited number of protein complexes. We have created a repository called dockYard (http://pallab.serc.iisc.ernet.in/dockYard), that allows modelers interested in protein-protein interaction to access large volume of information on protein dimers and their interlogs, and also download decoys for their work if they are interested in building modeling methods. dockYard currently offers four categories of docking decoys derived from: Bound (native dimer co-crystallized), Unbound (individual subunits are crystallized, as well as the target dimer), Variants (match the previous two categories in at least one subunit with 100% sequence identity), and Interlogs (match the previous categories in at least one subunit with >= 90% or >= 50% sequence identity). The web service offers options for full or selective download based on search parameters. Our portal also serves as a repository to modelers who may want to share their decoy sets with the community.

Design and implementation of a PC-based FPGA tester

A new range of programmable logic devices are revolutionizing the way complex digital hardware is designed and built all over the world. Being able to test these devices in order to validate and dynamically improve on the design is crucial. This paper describes a low-cost FPGA tester that can test SRAM based FPGAs in the laboratory.

Design and realization of high-performance wave-pipelined 8×8 b multiplier in CMOS technology

Wave pipelining is a design technique for increasing the throughput of a digital circuit or system without introducing pipelining registers between adjacent combinational logic blocks in the circuit/system. However, this requires balancing of the delays along all the paths from the input to the output which comes the way of its implementation. Static CMOS is inherently susceptible to delay variation with input data, and hence, receives a low priority for wave pipelined digital design. On the other hand, ECL and CML, which are amenable to wave pipelining, lack the compactness and low power attributes of CMOS. In this paper we attempt to exploit wave pipelining in CMOS technology. We use a single generic building block in Normal Process Complementary Pass Transistor Logic (NPCPL), modeled after CPL, to achieve equal delay along all the propagation paths in the logic structure. An 8×8 b multiplier is designed using this logic in a 0.8 ?m technology. The carry-save multiplier architecture is modified suitably to support wave pipelining, viz., the logic depth of all the paths are made identical. The 1 mm×0.6 mm multiplier core supports a throughput of 400 MHz and dissipates a total power of 0.6 W. We develop simple enhancements to the NPCPL building blocks that allow the multiplier to sustain throughputs in excess of 600 MHz. The methodology can be extended to introduce wave pipelining in other circuits as well

Diffusion Anomaly in Silicalite and VPI-5 from Molecular Dynamics Simulations

Molecular dynamics (MD) simulations on rigid and flexible framework models of silicalite and a rigid framework model of the aluminophosphate VPI-5 for different sorbate diameters are reported. The sorbate-host interactions are modeled in terms of simple atom-atom Lennard-Jones interactions. The results suggest that the diffusion coefficient exhibits an anomaly as gamma approaches unity. The MD results confirm the existence of a linear regime for sorbate diameters significantly smaller than the channel diameter and an anomalous regime observed for sorbate diameters comparable to the channel diameter. The power spectra obtained by Fourier transformation of the velocity autocorrelation function indicate that there is an increase in the intensity of the low-frequency component for the velocity component parallel to the direction of motion for the sorbate diameter in the anomalous regime. The present results suggest that the diffusion anomaly is observed irrespective of (1) the geometry and topology of the pore structure and (2) the nature of the host material. The results are compared with the work of Derouane and co-workers, who have suggested the existence of ''floating molecules'' on the basis of earlier theoretical and computational approaches.

Structure-potential relationship and nature of disorder in liquids and glassy solids

A method based on the minimal-spanning tree is extended to a collection of points in three dimensions. Two parameters, the average edge length and its standard deviation characterize the disorder. The structural phase diagram for a monatomic system of particles and the characteristic values for the uniform random distribution of points have been obtained. The method is applied to hard spheres and Lennard-Jones systems. These systems occupy distinct regions in the structural phase diagram. The structure of the Lennard-Jones system approaches that of the defective close-packed arrangements at low temperatures whereas in the liquid regime, it deviates from the close-packed configuration.

Link Conditions for Simplifying Meshes with Embedded Structures

Interactive visualization applications benefit from simplification techniques that generate good-quality coarse meshes from high-resolution meshes that represent the domain. These meshes often contain interesting substructures, called embedded structures, and it is desirable to preserve the topology of the embedded structures during simplification, in addition to preserving the topology of the domain. This paper describes a proof that link conditions, proposed earlier, are sufficient to ensure that edge contractions preserve the topology of the embedded structures and the domain. Excluding two specific configurations, the link conditions are also shown to be necessary for topology preservation. Repeated application of edge contraction on an extended complex produces a coarser representation of the domain and the embedded structures. An extension of the quadric error metric is used to schedule edge contractions, resulting in a good-quality coarse mesh that closely approximates the input domain and the embedded structures.

Symmetrizing a Hessenberg matrix: Designs for VLSI parallel processor arrays

A symmetrizer of a nonsymmetric matrix A is the symmetric matrix X that satisfies the equation XA = A(t)X, where t indicates the transpose. A symmetrizer is useful in converting a nonsymmetric eigenvalue problem into a symmetric one which is relatively easy to solve and finds applications in stability problems in control theory and in the study of general matrices. Three designs based on VLSI parallel processor arrays are presented to compute a symmetrizer of a lower Hessenberg matrix. Their scope is discussed. The first one is the Leiserson systolic design while the remaining two, viz., the double pipe design and the fitted diagonal design are the derived versions of the first design with improved performance.