Assessing the Reproducibility of Clustering of Molecular Dynamics Conformations on Self-Organizing Maps

The goal of most clustering algorithms is to find the optimal number of clusters (i.e. fewest number of clusters). However, analysis of molecular conformations of biological macromolecules obtained from computer simulations may benefit from a larger array of clusters. The Self-Organizing Map (SOM) clustering method has the advantage of generating large numbers of clusters, but often gives ambiguous results. In this work, SOMs have been shown to be reproducible when the same conformational dataset is independently clustered multiple times (~100), with the help of the Cramérs V-index (C_v). The ability of C_v to determine which SOMs are reproduced is generalizable across different SOM source codes. The conformational ensembles produced from MD (molecular dynamics) and REMD (replica exchange molecular dynamics) simulations of the penta peptide Met-enkephalin (MET) and the 34 amino acid protein human Parathyroid Hormone (hPTH) were used to evaluate SOM reproducibility. The training length for the SOM has a huge impact on the reproducibility. Analysis of MET conformational data definitively determined that toroidal SOMs cluster data better than bordered maps due to the fact that toroidal maps do not have an edge effect. For the source code from MATLAB, it was determined that the learning rate function should be LINEAR with an initial learning rate factor of 0.05 and the SOM should be trained by a sequential algorithm. The trained SOMs can be used as a supervised classification for another dataset. The toroidal 10×10 hexagonal SOMs produced from the MATLAB program for hPTH conformational data produced three sets of reproducible clusters (27%, 15%, and 13% of 100 independent runs) which find similar partitionings to those of smaller 6×6 SOMs. The χ^2 values produced as part of the C_v calculation were used to locate clusters with identical conformational memberships on independently trained SOMs, even those with different dimensions. The χ^2 values could relate the different SOM partitionings to each other.

Mesure de probabilité et les jeux fictifs.

Rapport de recherche

Application d'un modèle de microsimulation avec agents partiellement rationnels : le report du fardeau des taxes sur la masse salariale.

Rapport de recherche

Évaluation in vitro de la stérilisation au peroxyde d'hydrogène sur les propriétés biologiques de prothèses utilisées lors de stabilisation du genou chez le chien

Objectif—Comparer les effets de la stérilisation au plasma de gaz de peroxyde d’hydrogène (HPGP) à l’oxyde d’éthylène (EO) et à la vapeur (ST) sur les propriétés physico-chimiques et d’adhésion bactérienne de fils de nylon et de polyéthylène. Design expérimental—Etude in vitro. Matériel—Des brins non stérilisés, stérilisés au HPGP, à l’EO et ST; de fil nylon leader (FNL), de fil de nylon pêche (FNP) et de fil de polyéthylène (PE) ont été utilisés. Méthodes—Une analyse de surface au spectroscope photo-électronique à rayons X (XPS), une mesure de l’angle de contact, une analyse par microscopie à force atomique (AFM) et l’adhésion bactérienne de Staphylococcus intermedius et d’Escherichia Coli ont été testés sur les brins. Résultats—Une oxydation de la surface de tous les échantillons stérilisés a été observée quelque soit la méthode de stérilisation. La stérilisation a augmenté significativement l’angle de contact pour tous les types de fil quelque soit la méthode. La rugosité n’a pas été affectée significativement par la méthode de stérilisation pour le FNL et FNP. L’adhésion bactérienne a été affectée significativement par la méthode de stérilisation. Le PE a un angle de contact, une rugosité et une adhésion bactérienne significativement plus élevée que le FNL et FNP, peu importe la méthode de stérilisation. Conclusion—La stérilisation au HPGP constitue une alternative intéressante à la vapeur et l’EO. Le PE n’est peut être pas un matériel idéal par sa capacité d’adhésion bactérienne. De futures études sont nécessaires pour déterminer la signification clinique de ces trouvailles.

Fabrication and Characterization of Spray Pyrolysed Cadmium Sulphide Homojunction Solar Cells

The study on the fabrication and characterization of spray pyrolysed cadmium sulphide homojunction solar cells. As an alternative to the conventional energy source, the PV technology has to be improved. Study about the factors affecting the performance of the existing solar cells and this will result in the enhancement of efficiency of the cells. At the same time it is equally important to have R&D works on developing new photovoltaic devices and processes which are less expensive for large scale production. CdS is an important binary compound semiconductor, which is very useful in the field of photovoltaics. It is very easy to prepare large area CdS thin films. In order to fabricate thin film homojunction cadmium sulphide cells, prepared and characterized SnO2 thin film as the lower electrode, p-CdS as the active layer and n-CdS as window layer. Cadmium material used for the fabrication of homojunction solar cells is highly toxic. The major damage due to continued exposure to low levels of cadmium are on the kidneys, lungs and bones. The real advantage of spray pyrolysis process is that there is no emission of any toxic gases during the deposition. Very low concentration of the chemicals is needed in this process. The risk involved from this material is very low, though they are toxic. On large scale usage it may become necessary that the cells after their life, should be bought back by the companies to retrieve chemicals like cadmium. This will reduce environmental problem and also the material wastage

Optical emission studies of C2 species in laser-produced plasma from carbon

Optical emission studies of C2 molecules in plasma obtained by Nd:YAG laser ablation of graphite in a helium atmosphere are reported for irradiances in the range (1–9:2/ x 1010 W cm−2. The characteristics of the spectral emission intensity from the C2 (Swan band) species have been investigated as functions of the distance from the target, ambient pressure and laser irradiance. Estimates of vibrational temperatures of C2 species under various irradiance conditions are made. Results of measurements performed under different ambient helium gas pressures are also discussed.

Optical emission studies of C2 species in laser-produced plasma from carbon

Optical emission studies of C2 molecules in plasma obtained by Nd:YAG laser ablation of graphite in a helium atmosphere are reported for irradiances in the range (1–9:2/ x 1010 W cm−2. The characteristics of the spectral emission intensity from the C2 (Swan band) species have been investigated as functions of the distance from the target, ambient pressure and laser irradiance. Estimates of vibrational temperatures of C2 species under various irradiance conditions are made. Results of measurements performed under different ambient helium gas pressures are also discussed.

Studies on the Development and Control of Desiccation cracks in compacted clay liner soils

The present study aimed at critically looking at the current practice of the installation of compacted clay liner using bentonite enhanced sand (BES). The application of bentonite is currently the most accepted practice for lining purposes. The ideal bentonite sand combination, which satisfies the liner requirements is 20% bentonite and 80% sand, was selected as one of the liner materials for the investigation of development of desiccation cracks. Locally available sundried marine clay and its combination with bentonite were also included in the study. The desiccation tests on liner materials were conducted for wet/dry cycles to simulate the seasonal variations. Digital image processing techniques were used to measure the crack intensity factor (CIF), a useful and effective parameter for quantification of desiccation cracking. The repeatability of the tests could be well established, as the variation in CIF values of identical samples had a very narrow range of 0 to 2%. The studies on the development of desiccation cracks showed that the CIF of bentonite enhanced sand mixture (BES) was 18.09%, 39.75% and 21.22% for the first, second and third cycles respectively, while it was only 9.83%, 7.52% and 4.58% respectively for sun dried marine clay (SMC). Thus the locally available, alternate liner material suggested, viz SMC, is far superior to BES, when subjected to alternate wet/dry cycles. Further, the improvement of these liner materials when amended with randomly distributed fibre reinforcements was also investigated. Three types of fibres ,namely nylon fibre, polypropylene monofilament and polypropylene fibre mesh were used for the study of fibre amended BES and SMC.The influence of these amendments on the properties of the above liner materials is also studied. The results showed that there is definite improvement in the properties of the liner materials when it is reinforced with discrete random fibres. The study also proved that the desiccation cracks could be controlled with the help of fibre reinforcement.