2,233 research outputs found
A web/grid portal implementation of BioSimGrid: a biomolecular simulation database
Get PDFThe overall aim of the BioSimGrid project (www.biosimgrid.org) is to exploit the Grid infrastructure to enable comparative analysis of the distributed results of biomolecular simulations. In particular this paper presents the implementation of the current BioSimGrid Web Portal. The portal has a SOA (Service Oriented Architecture) framework built on the layer of OGSA (Open Grid Services Architecture) and OGSA-DAI (Open Grid Services Architecture Data Access and Integration) middleware. The PortalLib has been developed to allow RAD (Rapid Application Development) of portal applications. The portal also integrates PKI (Public Key Infrastructure) and supports two levels of distributed SSO (Single Sign On): Grid certificate-based SSO for high security, and user/password based SSO for maximal flexibility
BioSimGrid: grid-enabled biomolecular simulation data storage and analysis
Get PDFIn computational biomolecular research, large amounts of simulation data are generated to capture the motion of proteins. These massive simulation data can be analysed in a number of ways to reveal the biochemical properties of the proteins. However, the legacy way of storing these data (usually in the laboratory where the simulations have been run) often hinders a wider sharing and easier cross-comparison of simulation results. The data is commonly encoded in a way specific to the simulation package that produced the data and can only be analysed with tools developed specifically for that simulation package. The BioSimGrid platform seeks to provide a solution to these challenges by exploiting the potential of the Grid in facilitating data sharing. By using BioSimGrid either in a scripting or web environment, users can deposit their data and reuse it for analysis. BioSimGrid tools manage the multiple storage locations transparently to the users and provide a set of retrieval and analysis tools for processing the data in a convenient and efficient manner. This paper details the usage and implementation of BioSimGrid usinga combination of commercial databases, the Storage Resource Broker and Python scripts, gluing the building blocks together. It introduces a case study of how BioSimGrid can be used for better storage, retrieval and analysis of biomolecular simulation data
Implicit large-eddy simulation of the stratocumulus-topped boundary layer: A grid sensitivity study
No full textA range of implicit large-eddy simulations of the stratocumulus-topped boundary layer is performed to study the influence of grid resolution on selected parameters including liquid water path and second and third moments of vertical velocity fluctuations. The simulations are based on two sets of aircraft measurements, which are also used to evaluate the results of the simulations. The specific case presented here indicates that simulations with a grid aspect ratio accounting for the anisotropic nature of the turbulence near the surface and at the top of the boundary layer lead to better agreement with measurements than simulations with an isotropic grid
Entrainment and detrainment rates from the piv measurements at the top of laboratory analogs of stratocumulus and cumulus clouds
No full textWe analyze mixing at the top of laboratory analogs of convective clouds: stratocumulus and cumulus to investigate entrainment of environmental air into the cloud. We retrieve two components of air velocity using Particle Image Velocimetry technique. Suitable image processing allows to determine cloud–clear air interface. Using velocity differences between cloudy and clear sides of the interface we calculate entrainment / detrainment rates
Quality assurance for biomolecular simulations
No full textContemporary structural biology has an increased emphasis on high- throughput methods. Biomolecular simulations can add value to structural biology via the provision of dynamic information. However, at present there are no agreed measures for the quality of biomolecular simulation data. In this Letter, we suggest suitable measures for the quality assurance of molecular dynamics simulations of biomolecules. These measures are designed to be simple, fast, and general. Reporting of these measures in simulation papers should become an expected practice, analogous to the reporting of comparable quality measures in protein crystallography. We wish to solicit views and suggestions from the simulation community on methods to obtain reliability measures from molecular- dynamics trajectories. In a database which provides access to previously obtained simulations-for example BioSimGrid (http://www.biosimgrid.org/)-the user needs to be confident that the simulation trajectory is suitable for further investigation. This can be provided by the simulation quality measures which a user would examine prior to more extensive analyses
Prof. S.P. Fedorov — founder of urology in Russia (150th anniversary of the birthday)
Get PDFThis article presents the important scientific achievements of S.P. Fedorov as a urologist. S.P. Fedorov is the author of over 120 scientific papers. It was noted that in 1892 he was the first in Russia to prepare and use cholera antitoxin for the treatment of patients, then tetanus toxin and antitoxin, found that antitoxin protects against tetanus if it is administered simultaneously with the toxin. Abroad S.P. Fedorov studied the system of aseptic mode of operation from K. Schimmelbush, and L. Casper studied the method of cystoscopy and catheterization of the ureters and other endoscopic methods that appeared at that time. It was shown that S.P. Fedorov developed new surgeries — in situ pyelotomy, subcapsular nephrectomy, and new surgical instruments were proposed. He is rightly called the father of Russian urology. The circumstance is analyzed that the main direction of S.P. Fedorov's scientific activity was the problems of surgery of the urinary and biliary tracts. He summarized the extensive experience of the surgeon in the Atlas of Cystoscopy and Rectoscopy (1911), the Surgery of the Kidneys and Ureters (1923-1925), and others. Galpernom edition of the surgical journal «New Surgical Archive», essentially the first Soviet surgical journal, created in the difficult years of the Civil War and post-war devastation. He was the editor of the 1st edition of the BME, together with S.S. Girgolavom and A.V. Martynov was the editor of the multivolume Guide to Practical Surgery. S.P. Fedorov created a major domestic surgical school, from which dozens of specialists, heads of surgical departments of medical universities in various cities of the USSR graduated. The name of S.P. Fedorov was given to the department of hospital surgery of the Military Medical Academy. S.M. Kirov. It is noted that he was the first of the Soviet surgeons to be awarded the Order of Lenin (1933)
Optical signal degradation study in fixed human skin using confocal microscopy and higher-harmonic optical microscopy
No full textMeasurements of turbulence at stratocumulus top
No full textUsing 1m resolution airborne data from research flights we divide stratocumulus top region into sublayers and characterize properties of turbulence in each sublayer. Results indicate, that there are no clear differences of turbulence properties between thermodynamically different "calassical" and "non-classical" stratocumulus regimes, but there are clear signs of turbulence ainsotropy in stably stratified sublayers in the cloud top region
BioSimGrid: towards a worldwide repository for biomolecular simulations
No full textBioSimGrid is a database for biomolecular simulations, or, a 'Protein Data Bank extended in time' for molecular dynamics trajectories. We describe the implementation details: architecture, data schema, deposition, and analysis modules. We encourage the simulation community to explore BioSimGrid and work towards a common trajectory exchange format
Kinematic and electromyographic analysis of the push movement in Tai chi
No full textBackground: Tai chi is a form of exercise derived from the martial art folk traditions of China. The force used in tai chi includes different principles of mechanical advantage. No studies on the kinematic features of tai chi exercise have been published.
Objective: To analyse the kinematics and electromyographic characteristics of tai chi.
Methods: An experienced tai chi master was asked to perform a sequence of basic movements: ward off, roll back, press, and push. The movements were videotaped and digitised using a motion analysis system. Electromyographic activities of the lumbar erector spinae, rectus femoris, medial hamstrings, and medial head of gastrocnemius were recorded by surface electrodes. The push movement data were analysed.
Results: The medial hamstrings and medial head of gastrocnemius muscle groups maintained low activity, with higher electromyographic values in the lumbar erector spinae and substantially higher ones in the rectus femoris during the push movement. Both concentric and eccentric contractions occurred in muscles of the lower limbs, with eccentric contraction occurring mainly in the anti-gravity muscles such as the rectus femoris and the medial head of gastrocnemius. The forward and backward shifts in centre of gravity (CG) were mainly accomplished by increasing and decreasing respectively the joint angles of the bilateral lower limbs rather than by adopting a forward or backward postural lean. The path of the CG in the anteroposterior and mediolateral component was unique, and the sway or deviation from the path was small. The master maintained an upright posture and maintained a low CG (hips, knees, and ankles bent) while travelling slowly and steadily from one position to another.
Conclusion: The eccentric muscle contraction of the lower limbs in the push movement of tai chi may help to strengthen the muscles
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