A novel approach for large-scale polypeptide folding based on elastic networks using continuous optimization

We present a new computationally efficient method for large-scale polypeptide folding using coarse-grained elastic networks and gradient-based continuous optimization techniques. The folding is governed by minimization of energy based on Miyazawa–Jernigan contact potentials. Using this method we are able to substantially reduce the computation time on ordinary desktop computers for simulation of polypeptide folding starting from a fully unfolded state. We compare our results with available native state structures from Protein Data Bank (PDB) for a few de-novo proteins and two natural proteins, Ubiquitin and Lysozyme. Based on our simulations we are able to draw the energy landscape for a small de-novo protein, Chignolin. We also use two well known protein structure prediction software, MODELLER and GROMACS to compare our results. In the end, we show how a modification of normal elastic network model can lead to higher accuracy and lower time required for simulation.

Large-scale structures in turbulent and reverse-transitional sink flow boundary layers

Aspects of large-scale organized structures in sink flow turbulent and reverse-transitional boundary layers are studied experimentally using hot-wire anemometry. Each of the present sink flow boundary layers is in a state of 'perfect equilibrium' or 'exact self-preservation' in the sense of Townsend (The Structure of Turbulent Shear Flow, 1st and 2nd edns, 1956, 1976, Cambridge University Press) and Rotta (Progr. Aeronaut. Sci., vol. 2, 1962, pp. 1-220) and conforms to the notion of 'pure wall-flow' (Coles, J. Aerosp. Sci., vol. 24, 1957, pp. 495-506), at least for the turbulent cases. It is found that the characteristic inclination angle of the structure undergoes a systematic decrease with the increase in strength of the streamwise favourable pressure gradient. Detectable wall-normal extent of the structure is found to be typically half of the boundary layer thickness. Streamwise extent of the structure shows marked increase as the favourable pressure gradient is made progressively severe. Proposals for the typical eddy forms in sink flow turbulent and reverse-transitional flows are presented, and the possibility of structural self-organization (i.e. individual hairpin vortices forming streamwise coherent hairpin packets) in these flows is also discussed. It is further indicated that these structural ideas may be used to explain, from a structural viewpoint, the phenomenon of soft relaminarization or reverse transition of turbulent boundary layers when subjected to strong streamwise favourable pressure gradients. Taylor's 'frozen turbulence' hypothesis is experimentally shown to be valid for flows in the present study even though large streamwise accelerations are involved, the flow being even reverse transitional in some cases. Possible conditions, which are required to be satisfied for the safe use of Taylor's hypothesis in pressure-gradient-driven flows, are also outlined. Measured convection velocities are found to be fairly close to the local mean velocities (typically 90% or more) suggesting that the structure gets convected downstream almost along with the mean flow.

Meridional propagation of large-scale monsoon convective zones

Observational studies indicate that the convective activity of the monsoon systems undergo intraseasonal variations with multi-week time scales. The zone of maximum monsoon convection exhibits substantial transient behavior with successive propagating from the North Indian Ocean to the heated continent. Over South Asia the zone achieves its maximum intensity. These propagations may extend over 3000 km in latitude and perhaps twice the distance in longitude and remain as coherent entities for periods greater than 2-3 weeks. Attempts to explain this phenomena using simple ocean-atmosphere models of the monsoon system had concluded that the interactive ground hydrology so modifies the total heating of the atmosphere that a steady state solution is not possible, thus promoting lateral propagation. That is, the ground hydrology forces the total heating of the atmosphere and the vertical velocity to be slightly out of phase, causing a migration of the convection towards the region of maximum heating. Whereas the lateral scale of the variations produced by the Webster (1983) model were essentially correct, they occurred at twice the frequency of the observed events and were formed near the coastal margin, rather than over the ocean. Webster's (1983) model used to pose the theories was deficient in a number of aspects. Particularly, both the ground moisture content and the thermal inertia of the model were severely underestimated. At the same time, the sea surface temperatures produced by the model between the equator and the model's land-sea boundary were far too cool. Both the atmosphere and the ocean model were modified to include a better hydrological cycle and ocean structure. The convective events produced by the modified model possessed the observed frequency and were generated well south of the coastline. The improved simulation of monsoon variability allowed the hydrological cycle feedback to be generalized. It was found that monsoon variability was constrained to lie within the bounds of a positive gradient of a convective intensity potential (I). The function depends primarily on the surface temperature, the availability of moisture and the stability of the lower atmosphere which varies very slowly on the time scale of months. The oscillations of the monsoon perturb the mean convective intensity potential causing local enhancements of the gradient. These perturbations are caused by the hydrological feedbacks, discussed above, or by the modification of the air-sea fluxes caused by variations of the low level wind during convective events. The final result is the slow northward propagation of convection within an even slower convective regime. The ECMWF analyses show very similar behavior of the convective intensity potential. Although it is considered premature to use the model to conduct simulations of the African monsoon system, the ECMWF analysis indicates similar behavior in the convective intensity potential suggesting, at least, that the same processes control the low frequency structure of the African monsoon. The implications of the hypotheses on numerical weather prediction of monsoon phenomenon are discussed.

Mapping of large scale 158 mu m [CII] line emission: Orion A

We present the first results of an observational programme undertaken to map the fine structure line emission of singly ionized carbon ([ CII] 157 : 7409 mum) over extended regions using a Fabry Perot spectrometer newly installed at the focal plane of a 100 cm balloon- borne far- infrared telescope. This new combination of instruments has a velocity resolution of similar to 200 km s(-1) and an angular resolution of 1.'5. During the first flight, an area of 30' x 15' in Orion A was mapped. These observations extend over a larger area than previous observations, the map is fully sampled and the spectral scanning method used enables reliable estimation of the continuum emission at frequencies adjacent to the [ CII] line. The total [ CII] line luminosity, calculated by considering up to 20% of the maximum line intensity is 0.04% of the luminosity of the far- infrared continuum. We have compared the [ CII] intensity distribution with the velocity- integrated intensity distributions of (CO)-C-13(1- 0), CI(1- 0) and CO( 3- 2) from the literature. Comparison of the [ CII], [ CI] and the radio continuum intensity distributions indicates that the largescale [ CII] emission originates mainly from the neutral gas, except at the position of M 43, where no [ CI] emission corresponding to the [ CII] emission is seen. Substantial part of the [ CII] emission from here originates from the ionized gas. The observed line intensities and ratios have been analyzed using the PDR models by Kaufman et al. ( 1999) to derive the incident UV flux and volume density at a few selected positions. The models reproduce the observations reasonably well at most positions excepting the [ CII] peak ( which coincides with the position of theta(1) Ori C). Possible reason for the failure could be the simplifying assumption of a homogeneous plane parallel slab in place of a more complicated geometry.

An improvement on the theoretical model for the large-scale coherent structures in the outer region of a turbulent boundary layer

According to the experimental results, there exist large-scale coherent structures in the outer region of a turbulent boundary layer, which have been studied by many authors.As experimental results, Antonia (1990) showed the phase- aver aged streamlines and isovorticity lines of the large-scale coherent structures in a turbulent boundary layer for different Reynolds numbers. Based on the hydrodynamic stability theory, the 2-D theoretical model for the large-scale structures was proposed by Luo and Zhou, in which the eddy viscosity was defined as a complex function of the position in the normal direction. The theoretical results showed in ref. were in agreement with those in ref. However, there were two problems in the results. One is that in the experimental results, there were divergent focuses between two saddle points in the streamlines, but in the theoretical results, there were centers. The other is that the stretched parts of the isovorticity lines appear at the location of centers in the theoretical results, while in the experimental results they located somewhere between the focuses and saddle points. The reason is that the computations were based on a 2-D model.

Nanoelectromechanical DRAM for ultra-large-scale integration (ULSI)

A Nanoelectromechanical (NEM) device developed for dynamic random access memory (DRAM) is reported. A vertical nanotube structure is employed to form the electromechanical switch and capacitor structure. The mechanical movement of the nanotube defines 'On' and 'OFF' states and the electrical signals which result lead to charge storage in a vertical capacitor structure as in a traditional DRAM. The vertical structure contributes greatly to a decrease in cell dimension. The main concept of the NEM switch and capacitor can be applied to other memory devices as well. © 2005 IEEE.

Observation of large-scale features on graphite by scanning tunnelling microscopy

Superlattice structures and rippling fringes were imaged on two separate pieces of graphite (HOPG) by scanning tunnelling microscopy (STM). We observed the corrugation conservation phenomenon on one of the superlattice structures where an overlayer does not attenuate the corrugation amplitude of the superlattice. Such a phenomenon may illustrate an implication that nanoscale defects a few layers underneath the surface may propagate through many layers without decay and form the superlattice structure on the topmost surface. Some rippling fringes with periodicities of 20 nm and 30 nm and corrugations of 0.1 nm and 0.15nm were observed in the superlattice area and in nearby regions. Such fringes are believed to be due to physical buckling of the surface. The stress required to generate such structures is estimated, and a possible cause is discussed. An equation relating the attenuation factor to the number of overlayers is proposed. © 2005 The Japan Society of Applied Physics.

Large-scale synthesis of single-phase, high-quality GaN nanocrystallites

Large-scale synthesis of high-quality GaN nano-crystallites has been achieved by direct reaction of a 4:1 molar Ga/Ga2O3 mixture with ammonia at 950degreesC. X-ray diffraction, transmission electron microscopy, selected-area electron diffraction and high-resolution transmission electron microscopy revealed that the produced GaN nanocrystallites were single hexagonal wurtzite structure with an average particle size around 45 nm. A sharp near band edge emission peak and a blue light emission peak were observed in photoluminescence spectroscopy. The synthesis approach is simple and easy to be commercialized.

Blue-violet photoluminescence from large-scale highly aligned boron carbonitride nanofibers

We report on the strong blue-violet photoluminescence (PL) at room temperature from the large-scale highly aligned boron carbonitride (BCN) nanofibers synthesized by bias-assisted hot filament chemical vapor deposition. The photoluminescence peak wavelength shifts in the range of 470-390 nm by changing the chemical composition of the BCN nanofibers, which shows an interesting blue and violet-light-emitting material with adjustable optical properties. The mechanism for the shift of the PL peaks at room temperature is also discussed. (C) 2000 American Institute of Physics. [S0003-6951(00)04427-2].

The Kiloparsec-scale structure of 3C 286

We present radio images of the compact steep spectrum (CSS) quasar 3C 286 acquired with the Very Large Array (VLA) at 8.4 and 22.5 GHz. The source exhibits a two-sided core-jet structure with a bright central component and two extended components one to the east (P.A. 100degrees) and another to the southwest (P.A. -116degrees). From the compact core, an extension runs towards the southwest component up to similar to 0.7 arcsecond. The emission between the primary central component and the southwest component exhibits a knotty structure. A gradual change of the jet position angles from -135degrees to -120degrees in the inner southwest jet suggests a local bend. The position angle changes of the major eastern components E2 and E1 suggest that the eastern jet likely follows a curved trace. The bends in the jet trace may be associated with a relativistic precession or some interaction between the jet and the ambient matter. A mean spectral index of alpha(8.4)(22.5) similar to -0.76 (S-nu proportional to nu(alpha)) is estimated for the core component. Steep spectra are also obtained for the extended southwest component (2.6", P.A. -116degrees) and eastern component (0.8", P.A. 100degrees), with alpha(8.4)(22.5) similar to -0.88 and alpha(8.4)(22.5) similar to -1.79, respectively. The radio morphologies and spectral index distributions suggest that the core seen in our images is likely to be the beamed inner jet while the real nucleus is dimmed by it beaming away from us.

Lithography-independent and large scale fabrication of a metal electrode nanogap

A lithography-independent and wafer scale method to fabricate a metal nanogap structure is demon-strated. Polysilicon was first dry etched using photoresist (PR) as the etch mask patterned by photolithography.Then, by depositing conformal SiO_2 on the polysilicon pattern, etching back SiO_2 anisotropically in the perpendic-ular direction and removing the polysilicon with KOH, a sacrificial SiO_2 spacer was obtained. Finally, after metal evaporation and lifting-off of the SiO_2 spacer, an 82 nm metal-gap structure was achieved. The size of the nanogap is not determined by the photolithography, but by the thickness of the SiO_2. The method reported in this paper is compatible with modern semiconductor technology and can be used in mass production.

Monodisperse raspberry-like gold submicrometer spheres: Large-scale synthesis and interface assembling for colloid sphere array

We first suggested a one-pot method to synthesize monodisperse raspberry-like submicrometer gold spheres (MRSGS) with high yield. The resulting gold spheres were characterized by scanning electron microscopy, transmission electron microscopy, energy-dispersed X-ray spectroscopy, X-ray photoelectron spectroscopy, X-ray diffraction, and electrochemical technology. It was found that the rough structure provided by raspberry-like gold spheres led to a tremendous electrochemical active area, which was very important because these novel hierarchical gold spheres will probably find important applications in biosensors, electrocatalysis, and others.

Representing Knowledge of Large-Scale Space

This dissertation presents a model of the knowledge a person has about the spatial structure of a large-scale environment: the "cognitive map". The functions of the cognitive map are to assimilate new information about the environment, to represent the current position, and to answer route-finding and relative-position problems. This model (called the TOUR model) analyzes the cognitive map in terms of symbolic descriptions of the environment and operations on those descriptions. Knowledge about a particular environment is represented in terms of route descriptions, a topological network of paths and places, multiple frames of reference for relative positions, dividing boundaries, and a structure of containing regions. The current position is described by the "You Are Here" pointer, which acts as a working memory and a focus of attention. Operations on the cognitive map are performed by inference rules which act to transfer information among different descriptions and the "You Are Here" pointer. The TOUR model shows how the particular descriptions chosen to represent spatial knowledge support assimilation of new information from local observations into the cognitive map, and how the cognitive map solves route-finding and relative-position problems. A central theme of this research is that the states of partial knowledge supported by a representation are responsible for its ability to function with limited information of computational resources. The representations in the TOUR model provide a rich collection of states of partial knowledge, and therefore exhibit flexible, "common-sense" behavior.

Large-Scale Neural Systems for Vision and Cognition

— Consideration of how people respond to the question What is this? has suggested new problem frontiers for pattern recognition and information fusion, as well as neural systems that embody the cognitive transformation of declarative information into relational knowledge. In contrast to traditional classification methods, which aim to find the single correct label for each exemplar (This is a car), the new approach discovers rules that embody coherent relationships among labels which would otherwise appear contradictory to a learning system (This is a car, that is a vehicle, over there is a sedan). This talk will describe how an individual who experiences exemplars in real time, with each exemplar trained on at most one category label, can autonomously discover a hierarchy of cognitive rules, thereby converting local information into global knowledge. Computational examples are based on the observation that sensors working at different times, locations, and spatial scales, and experts with different goals, languages, and situations, may produce apparently inconsistent image labels, which are reconciled by implicit underlying relationships that the network’s learning process discovers. The ARTMAP information fusion system can, moreover, integrate multiple separate knowledge hierarchies, by fusing independent domains into a unified structure. In the process, the system discovers cross-domain rules, inferring multilevel relationships among groups of output classes, without any supervised labeling of these relationships. In order to self-organize its expert system, the ARTMAP information fusion network features distributed code representations which exploit the model’s intrinsic capacity for one-to-many learning (This is a car and a vehicle and a sedan) as well as many-to-one learning (Each of those vehicles is a car). Fusion system software, testbed datasets, and articles are available from http://cns.bu.edu/techlab.

Anatomical identification of extracellularly recorded cells in large-scale multielectrode recordings.

This study combines for the first time two major approaches to understanding the function and structure of neural circuits: large-scale multielectrode recordings, and confocal imaging of labeled neurons. To achieve this end, we develop a novel approach to the central problem of anatomically identifying recorded cells, based on the electrical image: the spatiotemporal pattern of voltage deflections induced by spikes on a large-scale, high-density multielectrode array. Recordings were performed from identified ganglion cell types in the macaque retina. Anatomical images of cells in the same preparation were obtained using virally transfected fluorescent labeling or by immunolabeling after fixation. The electrical image was then used to locate recorded cell somas, axon initial segments, and axon trajectories, and these signatures were used to identify recorded cells. Comparison of anatomical and physiological measurements permitted visualization and physiological characterization of numerically dominant ganglion cell types with high efficiency in a single preparation.