scholarly journals An accurate and robust algorithm for solvent-excluded surface computation

2018 ◽  
Author(s):  
Lincong Wang
Keyword(s):  
Protein Interaction ◽  
Large Scale ◽  
Geometrical Property ◽  
Membrane Lipid ◽  
Solvent Interaction ◽  
Geometrical Properties ◽  
Different Types ◽  
Small Molecule Compound ◽  
Numerical Precision

AbstractThe solvent-excluded surface (SES1) of a molecule is an important geometrical property relevant to its solvation in aqueous solution and its interactions with other molecules. In this paper we present an accurate and robust analytic algorithm suitable for a large-scale SES analysis. The accuracy and robustness of our algorithm are made possible by an iterative strategy for the treatments of probe-probe intersections, probe-probe overlaps and limited numerical precision. The accuracy and robustness of our algorithm in turn make it possible to analyze on a large-scale the SESs for different types of proteins and various sets of ligand-protein interaction interfaces. The results illustrate the usefulness of SES and SES-defined physical and geometrical properties for the characterization of protein-solvent interaction and ligand-protein interaction where ligand could be either small molecule compound, or membrane lipid, or DNA or protein.

scholarly journals An entropic characterization of protein interaction networks and cellular robustness

2006 ◽  
Vol 3 (11) ◽  
pp. 843-850 ◽  
Author(s):  
Thomas Manke ◽  
Lloyd Demetrius ◽  
Martin Vingron
Keyword(s):  
Protein Interaction ◽  
Large Scale ◽  
Global Network ◽  
Molecular Networks ◽  
Local Network ◽  
Large Contribution ◽  
Fundamental Relation ◽  
Cellular Behaviour ◽  
Network Entropy

The structure of molecular networks is believed to determine important aspects of their cellular function, such as the organismal resilience against random perturbations. Ultimately, however, cellular behaviour is determined by the dynamical processes, which are constrained by network topology. The present work is based on a fundamental relation from dynamical systems theory, which states that the macroscopic resilience of a steady state is correlated with the uncertainty in the underlying microscopic processes, a property that can be measured by entropy. Here, we use recent network data from large-scale protein interaction screens to characterize the diversity of possible pathways in terms of network entropy. This measure has its origin in statistical mechanics and amounts to a global characterization of both structural and dynamical resilience in terms of microscopic elements. We demonstrate how this approach can be used to rank network elements according to their contribution to network entropy and also investigate how this suggested ranking reflects on the functional data provided by gene knockouts and RNAi experiments in yeast and Caenorhabditis elegans . Our analysis shows that knockouts of proteins with large contribution to network entropy are preferentially lethal. This observation is robust with respect to several possible errors and biases in the experimental data. It underscores the significance of entropy as a fundamental invariant of the dynamical system, and as a measure of structural and dynamical properties of networks. Our analytical approach goes beyond the phenomenological studies of cellular robustness based on local network observables, such as connectivity. One of its principal achievements is to provide a rationale to study proxies of cellular resilience and rank proteins according to their importance within the global network context.

scholarly journals Characterization of the in-flight properties of the Planck telescope

2019 ◽  
Vol 622 ◽  
pp. A55
Author(s):  
J. A. Tauber ◽  
P. H. Nielsen ◽  
A. Martín-Polegre ◽  
B. Crill ◽  
F. Cuttaia ◽  
...  
Keyword(s):  
Optical System ◽  
Large Scale ◽  
Geometric Model ◽  
Honeycomb Structure ◽  
Main Beam ◽  
New Model ◽  
Geometrical Properties ◽  
Scientific Analysis ◽  
Flight Measurements

The European Space Agency’s Planck satellite was launched on 14 May 2009, and surveyed the sky stably and continuously between August 2009 and October 2013. The scientific analysis of the Planck data requires understanding the optical response of its detectors, which originates partly from a physical model of the optical system. In this paper, we use in-flight measurements of planets within ∼1° of boresight to estimate the geometrical properties of the telescope and focal plane. First, we use observed grating lobes to measure the amplitude of mechanical dimpling of the reflectors, which is caused by the hexagonal honeycomb structure of the carbon fibre reflectors. We find that the dimpling amplitude on the two reflectors is larger than expected from the ground, by 20% on the secondary and at least a factor of 2 on the primary. Second, we use the main beam shapes of 26 detectors to investigate the alignment of the various elements of the optical system, as well as the large-scale deformations of the reflectors. We develop a metric to guide an iterative fitting scheme, and are able to determine a new geometric model that fits the in-flight measurements better than the pre-flight prediction according to this metric. The new alignment model is within the mechanical tolerances expected from the ground, with some specific but minor exceptions. We find that the reflectors contain large-scale sinusoidal deformations most probably related to the mechanical supports. In spite of the better overall fit, the new model still does not fit the beam measurements at a level compatible with the needs of cosmological analysis. Nonetheless, future analysis of the Planck data would benefit from taking into account some of the features of the new model. The analysis described here exemplifies some of the limitations of in-flight retrieval of the geometry of an optical system similar to that of Planck, and provides useful information for similar efforts in future experiments.

scholarly journals DoE Analysis of Approaches for Hydrogel Microbeads’ Preparation by Millifluidic Methods

Micromachines ◽  
2020 ◽  
Vol 11 (11) ◽  
pp. 1007
Author(s):  
Anna Nastruzzi ◽  
Gabriele Pitingolo ◽  
Giovanni Luca ◽  
Claudio Nastruzzi
Keyword(s):  
Mass Production ◽  
Large Scale ◽  
Single Cells ◽  
Great Promise ◽  
Scale Production ◽  
Large Scale Production ◽  
Different Types ◽  
Cell Transplants

Hydrogel microbeads hold great promise for immune-protective cell transplants and in vitro studies. Millifluidic generation of hydrogel microbeads is a highly efficient and reproducible approach enabling a mass production. This paper illustrates the preparation and characterization of highly controlled and reproducible microbeads made by different types of hydrogel using millifluidic approaches. The optimization of the process was made by a design of experiments (DoE) approach. The microbeads’ large-scale production can be potentially used for single cells or clusters encapsulation.

scholarly journals Synthesis and characterization of nanocrystalline tungsten oxide nanosheets in large scale

2009 ◽  
Vol 24 (1) ◽  
pp. 187-191 ◽  
Author(s):  
Rong Hu ◽  
Huasheng Wu ◽  
Kunquan Hong
Keyword(s):  
Tungsten Oxide ◽  
Growth Mechanism ◽  
Large Scale ◽  
Synthesis And Characterization ◽  
Geometrical Properties ◽  
And Tungsten

A high quantity of tungsten oxide nanosheets were synthesized by oxidizing tungsten plates with potassium hydrate as the catalyst and tungsten plate as the substrate. The structural and geometrical properties were characterized by various techniques. It was found that the crystalline nanosheets have a WO3 structure with thicknesses of 30–50 nm and widths up to tens of micrometers. There exist two characteristic acute angles of about 37° or 51° on the nanosheet plane. The formation of these angles and the growth mechanism were discussed.

Some applications of electron beam microanalysis techniques in VLSI process evaluation

1983 ◽  
Vol 41 ◽  
pp. 160-161
Author(s):  
Simon Thomas
Keyword(s):  
Integrated Circuits ◽  
Process Evaluation ◽  
Large Scale ◽  
Technology Development ◽  
Analytical Techniques ◽  
Successful Implementation ◽  
Analysis Of Failures ◽  
Characterization Of Materials ◽  
Circuits Vlsi

Trends in the technology development of very large scale integrated circuits (VLSI) have been in the direction of higher density of components with smaller dimensions. The scaling down of device dimensions has been not only laterally but also in depth. Such efforts in miniaturization bring with them new developments in materials and processing. Successful implementation of these efforts is, to a large extent, dependent on the proper understanding of the material properties, process technologies and reliability issues, through adequate analytical studies. The analytical instrumentation technology has, fortunately, kept pace with the basic requirements of devices with lateral dimensions in the micron/ submicron range and depths of the order of nonometers. Often, newer analytical techniques have emerged or the more conventional techniques have been adapted to meet the more stringent requirements. As such, a variety of analytical techniques are available today to aid an analyst in the efforts of VLSI process evaluation. Generally such analytical efforts are divided into the characterization of materials, evaluation of processing steps and the analysis of failures.

Electron microscopic characterization of diamond thin films and substrates for diamond heteroepitaxial growth

1989 ◽  
Vol 47 ◽  
pp. 592-593
Author(s):  
J.B. Posthill ◽  
R.P. Burns ◽  
R.A. Rudder ◽  
Y.H. Lee ◽  
R.J. Markunas ◽  
...  
Keyword(s):  
Thin Films ◽  
Wide Band ◽  
Deposition Process ◽  
Heteroepitaxial Growth ◽  
Electron Microscopic ◽  
Wide Band Gap ◽  
Lattice Matching ◽  
Different Types ◽  
Diamond Thin Films

Because of diamond’s wide band gap, high thermal conductivity, high breakdown voltage and high radiation resistance, there is a growing interest in developing diamond-based devices for several new and demanding electronic applications. In developing this technology, there are several new challenges to be overcome. Much of our effort has been directed at developing a diamond deposition process that will permit controlled, epitaxial growth. Also, because of cost and size considerations, it is mandatory that a non-native substrate be developed for heteroepitaxial nucleation and growth of diamond thin films. To this end, we are currently investigating the use of Ni single crystals on which different types of epitaxial metals are grown by molecular beam epitaxy (MBE) for lattice matching to diamond as well as surface chemistry modification. This contribution reports briefly on our microscopic observations that are integral to these endeavors.

Characterization of seawater reverse osmosis fouled membranes from large scale commercial desalination plant

2019 ◽  
Author(s):  
Chem Int
Keyword(s):  
Reverse Osmosis ◽  
Large Scale ◽  
Retention Rate ◽  
Local Level ◽  
Microscopic Analysis ◽  
Transmembrane Pressure ◽  
Hydraulic Permeability ◽  
Seawater Reverse Osmosis ◽  
A Chain

The objective of this work is to study the ageing state of a used reverse osmosis (RO) membrane taken in Algeria from the Benisaf Water Company seawater desalination unit. The study consists of an autopsy procedure used to perform a chain of analyses on a membrane sheet. Wear of the membrane is characterized by a degradation of its performance due to a significant increase in hydraulic permeability (25%) and pressure drop as well as a decrease in salt retention (10% to 30%). In most cases the effects of ageing are little or poorly known at the local level and global measurements such as (flux, transmembrane pressure, permeate flow, retention rate, etc.) do not allow characterization. Therefore, a used RO (reverse osmosis) membrane was selected at the site to perform the membrane autopsy tests. These tests make it possible to analyze and identify the cause as well as to understand the links between performance degradation observed at the macroscopic scale and at the scale at which ageing takes place. External and internal visual observations allow seeing the state of degradation. Microscopic analysis of the used membranes surface shows the importance of fouling. In addition, quantification and identification analyses determine a high fouling rate in the used membrane whose foulants is of inorganic and organic nature. Moreover, the analyses proved the presence of a biofilm composed of protein.

Characterization of Interconnect Defects Using Scanning Thermal Conductivity Microscopy

2004 ◽  
Author(s):  
H.W. Ho ◽  
J.C.H. Phang ◽  
A. Altes ◽  
L.J. Balk
Keyword(s):  
Thermal Conductivity ◽  
Integrated Circuits ◽  
Large Scale

Abstract In this paper, scanning thermal conductivity microscopy is used to characterize interconnect defects due to electromigration. Similar features are observed both in the temperature and thermal conductivity micrographs. The key advantage of the thermal conductivity mode is that specimen bias is not required. This is an important advantage for the characterization of defects in large scale integrated circuits. The thermal conductivity micrographs of extrusion, exposed and subsurface voids are presented and compared with the corresponding topography and temperature micrographs.

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