Quantum clustering and network analysis of MD simulation trajectories to probe the conformational ensembles of protein-ligand interactions

In this article, we present a novel application of a quantum clustering (QC) technique to objectively cluster the conformations, sampled by molecular dynamics simulations performed on different ligand bound structures of the protein. We further portray each conformational population in terms of dynamically stable network parameters which beautifully capture the ligand induced variations in the ensemble in atomistic detail. The conformational populations thus identified by the QC method and verified by network parameters are evaluated for different ligand bound states of the protein pyrrolysyl-tRNA synthetase (DhPylRS) from D. hafniense. The ligand/environment induced re-distribution of protein conformational ensembles forms the basis for understanding several important biological phenomena such as allostery and enzyme catalysis. The atomistic level characterization of each population in the conformational ensemble in terms of the re-orchestrated networks of amino acids is a challenging problem, especially when the changes are minimal at the backbone level. Here we demonstrate that the QC method is sensitive to such subtle changes and is able to cluster MD snapshots which are similar at the side-chain interaction level. Although we have applied these methods on simulation trajectories of a modest time scale (20 ns each), we emphasize that our methodology provides a general approach towards an objective clustering of large-scale MD simulation data and may be applied to probe multistate equilibria at higher time scales, and to problems related to protein folding for any protein or protein-protein/RNA/DNA complex of interest with a known structure.

Video coding mode decision as a classification problem

In this paper, we show that it is possible to reduce the complexity of Intra MB coding in H.264/AVC based on a novel chance constrained classifier. Using the pairs of simple mean-variances values, our technique is able to reduce the complexity of Intra MB coding process with a negligible loss in PSNR. We present an alternate approach to address the classification problem which is equivalent to machine learning. Implementation results show that the proposed method reduces encoding time to about 20% of the reference implementation with average loss of 0.05 dB in PSNR.

Persistent passive hopping and juggling is possible even with plastic collisions

We describe simple one-dimensional models of passive (no energy input, no control), generally dissipative, vertical hopping and one-ball juggling. The central observation is that internal passive system motions can conspire to eliminate collisions in these systems. For hopping, two point masses are connected by a spring and the lower mass has inelastic collisions with the ground. For juggling, a lower point-mass hand is connected by a spring to the ground and an upper point-mass ball is caught with an inelastic collision and then re-thrown into gravitational free flight. The two systems have identical dynamics. Despite inelastic collisions between non-zero masses, these systems have special symmetric energy-conserving periodic motions where the collision is at zero relative velocity. Additionally, these special periodic motions have a non-zero sized, one-sided region of attraction on the higher-energy side. For either very large or very small mass ratios, the one-sided region of attraction is large. These results persist for mildly non-linear springs and non-constant gravity. Although non-collisional damping destroys the periodic motions, small energy injection makes the periodic motions stable, with a two-sided region of attraction. The existence of such special energy conserving solutions for hopping and juggling points to possibly useful strategies for both animals and robots. The lossless motions are demonstrated with a table-top experiment.

Phase transformation and semiconductor-metal transition in thin films of VO2 deposited by low-pressure metalorganic chemical vapor deposition

Thin films of the semiconducting, monoclinic vanadium dioxide, VO2(M) have been prepared on ordinary glass by two methods: directly by low-pressure metalorganic chemical vapor deposition (MOCVD), and by argon-annealing films of the VO2(B) phase deposited by MOCVD. The composition and microstructure of the films have been examined by x-ray diffraction, scanning electron microscopy, and transmission electron microscopy. Films made predominantly of either the B or the M phase, as deposited, can only be obtained over a narrow range of deposition temperatures. At the lower end of this temperature range, the as-deposited films are strongly oriented, although the substrate is glass. This can be understood from the drive to minimize surface energy. Films of the B phase have a platelet morphology, which leads to an unusual microstructure at the lower-deposition temperatures. Those grown at similar to370 degreesC convert to the metallic, rutile (R) phase when annealed at 550 degreesC, whereas those deposited at 420 degreesC transform to the R phase only at 580 degreesC. (When cooled to room temperature, the annealed films convert reversibly from the R phase to the M phase.) Electron microscopy shows that annealing leads to disintegration of the single crystalline VO2(B) platelets into small crystallites of VO2(R), although the platelet morphology is retained. When the annealing temperature is relatively low, these crystallites are nanometer sized. At a higher-annealing temperature, the transformation leads to well-connected and similarly oriented large grains of VO2(R), enveloped in the original platelet. The semiconductor-metal transition near 68 degreesC leads to a large jump in resistivity in all the VO2(M) films, nearly as large as in epitaxial films on single-crystal substrates. When the annealed films contain well-connected large grains, the transition is very sharp. Even when preferred orientation is present, the transition is not as sharp in as-deposited VO2(M), because the crystallites are not densely packed as in annealed VO2(B). However, the high degree of orientation in these films leads to a narrow temperature hysteresis. (C) 2002 American Institute of Physics.

Pressure-induced phase transitions in alpha-ZrMo2O8

We report high-pressure Raman, infrared (IR), and optical-absorption spectra of alpha-ZrMo2O8 (trigonal) up to 38 GPa at room temperature. The spectroscopic studies are consistent with diffraction results that show that alpha-ZrMo2O8 transforms into delta-ZrMo2O8 (monoclinic) at about 1 GPa and the delta phase converts to the epsilon phase (trielinic) at about 2.0 GPa. Optical-absorption measurements give an estimate of the band gap of about 0.6 eV at the lowest pressure. Band-gap changes with pressure are confirmed with visual observations. ZrMo2O8 changes from transparent at 5 GPa to yellow at 10 GPa, red at 18 GPa, and at about 30 GPa it becomes opaque.

A Passive Hopper With Lossless Collisions

A passive vertical hopping robot is here highly idealised as two vertically arranged masses acted on by gravity and coupled by a linear spring. The lower mass makes dead (e = 0) collisions with the rigid ground. The equations of motion can be reduced to a one dimensional map. Fixed points of the map are found in which case the robot hops incessantly. For these conservative solutions the lower mass collides with the ground with zero impact velocity. The interval of attraction for these conservative fixed points depends on system parameters.

Time Evolution of the Microstructure of VO2(B) Films Deposited on Glass by MOCVD

Thin films of VO2(B), a metastable polymorph of vanadium dioxide, have been grown on glass by low-pressure metalorganic chemical vapor deposition (MOCVD). The films grown for 90 minutes have atypical microstructure, comprising micrometer-sized, island-like entities made up of numerous small, single-crystalline platelets (≅1 μm) emerging orthogonally from larger ones at the center. Microstructure evolution as a function of deposition time has been examined by X-ray diffraction, scanning electron microscopy, and transmission electron microscopy. The metastable VO2(B) transforms to the stable rutile (R) phase at 550°C in inert ambient, which on cooling convert reversibly to M phase. Electron microscopy shows that annealing leads to the disintegration of the VO2(B) platelets into small crystallites of the rutile phase VO2(R), although the platelet morphology is retained. The magnitude of the jump in resistance at the semiconductor-to-metal, VO2(M)→VO2(R) phase transition depends on the arrangement of polycrystalline platelets in the films.

Growth of nanowires of beta-NaxV2O5 by metalorganic chemical vapor deposition

Films comprised of nanowires of beta-NaxV2O5 measuring 20-200 nm in diameter and 10-30 mum in length have been prepared on glass substrates by metalorganic chemical vapor deposition using the beta-diketonate complex, vanadyl acetyl acetonate, as precursor, but without the use of either templates or catalysts. Films consisting of nanowires of monophasic beta-NaxV2O5 with a preferred orientation along (h0l) are formed only at 550 degreesC, whereas those deposited at 540 degreesC comprise a mixture of nanowires (beta-NaxV2O5) and platelets (V2O5). The films deposited at lower temperatures are less crystalline and comprise a mixture of vanadium oxide phases. From the observations that nanowires are formed only in the narrow temperature range of 540-550 degreesC, and from the critical dependence of the formation of nanowires on the balance between the CVD growth rate and the evaporation rate of the film, it is inferred that the formation of nanowires of beta-NaxV2O5 is due to chemical vapor transport.

Rule-based modelling of iron homeostasis in tuberculosis

To establish itself within the host system, Mycobacterium tuberculosis (Mtb) has formulated various means of attacking the host system. One such crucial strategy is the exploitation of the iron resources of the host system. Obtaining and maintaining the required concentration of iron becomes a matter of contest between the host and the pathogen, both trying to achieve this through complex molecular networks. The extent of complexity makes it important to obtain a systems perspective of the interplay between the host and the pathogen with respect to iron homeostasis. We have reconstructed a systems model comprising 92 components and 85 protein-protein or protein-metabolite interactions, which have been captured as a set of 194 rules. Apart from the interactions, these rules also account for protein synthesis and decay, RBC circulation and bacterial production and death rates. We have used a rule-based modelling approach, Kappa, to simulate the system separately under infection and non-infection conditions. Various perturbations including knock-outs and dual perturbation were also carried out to monitor the behavioral change of important proteins and metabolites. From this, key components as well as the required controlling factors in the model that are critical for maintaining iron homeostasis were identified. The model is able to re-establish the importance of iron-dependent regulator (ideR) in Mtb and transferrin (Tf) in the host. Perturbations, where iron storage is increased, appear to enhance nutritional immunity and the analysis indicates how they can be harmful for the host. Instead, decreasing the rate of iron uptake by Tf may prove to be helpful. Simulation and perturbation studies help in identifying Tf as a possible drug target. Regulating the mycobactin (myB) concentration was also identified as a possible strategy to control bacterial growth. The simulations thus provide significant insight into iron homeostasis and also for identifying possible drug targets for tuberculosis.

Re-entrant behavior in dynamics of binary mixtures of soft hybrid nanocolloids and homopolymers

We present results of measurements of temperature and wavevector dependent dynamics in binary mixtures of soft polymer grafted nanoparticles and linear homopolymers. We find evidence of melting of the dynamically arrested state of the soft nanocolloids with addition of linear polymers followed by a re-entrant slowing down of the dynamics with further increase in polymer density, depending on the size ratio, delta, of the polymers and the nanocolloids. For higher delta the re-entrant behavior is not observed, even for the highest added polymer density, explored here. Possible explanation of the observed dynamics in terms of the presence of a double - glass phase is provided. (C) 2011 American Institute of Physics. [doi:10.1063/1.3644930]