Design of a grid service-based platform for in silico protein-ligand screenings

Grid computing offers the powerful alternative of sharing resources on a worldwide scale, across different institutions to run computationally intensive, scientific applications without the need for a centralized supercomputer. Much effort has been put into development of software that deploys legacy applications on a grid-based infrastructure and efficiently uses available resources. One field that can benefit greatly from the use of grid resources is that of drug discovery since molecular docking simulations are an integral part of the discovery process. In this paper, we present a scalable, reusable platform to choreograph large virtual screening experiments over a computational grid using the molecular docking simulation software DOCK. Software components are applied on multiple levels to create automated workflows consisting of input data delivery, job scheduling, status query, and collection of output to be displayed in a manageable fashion for further analysis. This was achieved using Opal OP to wrap the DOCK application as a grid service and PERL for data manipulation purposes, alleviating the requirement for extensive knowledge of grid infrastructure. With the platform in place, a screening of the ZINC 2,066,906 compound "drug-like" subset database against an enzyme's catalytic site was successfully performed using the MPI version of DOCK 5.4 on the PRAGMA grid testbed. The screening required 11.56 days laboratory time and utilized 200 processors over 7 clusters.     

Automated process planning method to machine A B-Spline free-form feature on a mill–turn center

In this paper, we present a methodology for automating the process planning and NC code generation for a widely encountered class of free-form features that can be machined on a 3-axis mill–turn center. The free-form feature family that is considered is that of extruded protrusions whose cross-section is a closed, periodic B-Spline curve. In this methodology, for machining a part with B-Spline protrusion located at the free end, the part is first rough turned to the maximum profile diameter of the B-Spline, followed by rough profile cutting and finish profiling with axially mounted end mill tools. The identification and sequencing of machining volumes is completely automated, as is the generation of actual NC code. The approach supports both convex and non-convex profiles. In the case of non-convex profiles, the process planning algorithm ensures that there is no gouging of the work piece by the tool. The algorithm also identifies when sections of the tool path lie outside the work piece and utilizes rapid traverses in these regions to reduce cutting time. This methodology presents an integrated turn–mill process planning where by making the process fully automated from design with no user intervention making the overall process planning efficient. The algorithm was tested on several examples and test parts using the unmodified NC code obtained from the implementation were run on a Moriseiki mill–turn center. The parts that were produced met the dimensional specifications of the desired part.     

Sound isolation by piezoelectric polymer films connected to negative capacitance circuits

Sound isolation has been achieved using a piezoelectric polymer film connected to a negative capacitance feedback circuit. A curved PVDF film was located in the middle of an acoustic tube and the transmission loss of sound through the film was determined in the audio frequency range. At any chosen frequency, the complete isolation of sound was achieved by adjusting the feedback, i.e. the complex capacitance of the circuit was matched precisely to that of the film.     

Nonlinear<Emphasis Type="Italic">I-V</Emphasis> characteristics study of doped SnO<Subscript>2</Subscript>

When tin oxide is doped with Sb₂O₃ and CoO, it shows highly nonlinear current (I)-voltage (V) characteristics. Addition of CoO leads to creation of oxygen vacancies and helps in sintering of SnO₂. Antimony oxide acts as a donor and increases the conductivity. The results are nearly the same when antimony oxide is replaced by tantalum oxide. The observed nonlinear coefficient, α = 30 and the breakdown voltage is 120 V/mm.     

pH Dependent Controlled Release of CTAB Incorporated Dipyridamole Drug from Agar-Based Hydrogel

Highly pH sensitive hydrogels, based on agarose and acrylamide were synthesized and characterized by Fourier transform infrared spectroscopy, thermogravimetric analysis, differential scanning calorimeter, and scanning electron microscopy. The release of dipyridamole from the hydrogel matrix was monitored using fluorescence spectroscopy. Since the solubility of the drug gets enhanced by cationic surfactant, an inclusion complex was prepared using cetyl trimethylammonium bromide and the release of inclusion complex from the polymer matrix was also studied. Swelling behavior of the prepared hydrogels in different pH media were studied at room temperature and maximum swelling was observed at basic pH.     

Analysis of indoor particles and gases and their evolution with natural ventilation

The air composition and reactivity from outdoor and indoor mixing field campaign was conducted to investigate the impacts of natural ventilation (ie, window opening and closing) on indoor air quality. In this study, a thermal desorption aerosol gas chromatograph (TAG) obtained measurements of indoor particle‐ and gas‐phase semi‐ and intermediately volatile organic compounds both inside and outside a single‐family test home. Together with measurements from a suite of instruments, we use TAG data to evaluate changes in indoor particles and gases at three natural ventilation periods. Positive matrix factorization was performed on TAG and adsorbent tube data to explore five distinct chemical and physical processes occurring in the indoor environment. Outdoor‐to‐indoor transport is observed for sulfate, isoprene epoxydiols, polycyclic aromatic hydrocarbons, and heavy alkanes. Dilution of indoor species is observed for volatile, non‐reactive species including methylcyclohexane and decamethylcyclopentasiloxane. Window opening drives enhanced emissions of semi‐ and intermediately volatile species including TXIB, DEET, diethyl phthalate, and carvone from indoor surfaces. Formation via enhanced oxidation was observed for nonanal and 2‐decanone when outdoor oxidants entered the home. Finally, oxidative depletion of gas‐phase terpenes (eg, limonene and α‐pinene) was anticipated but not observed due to limited measurement resolution and dynamically changing conditions.     

Evolution of properties of parts during MIM and sintering of recycled oxide particles

Metal injection moulding (MIM) is an established process for high volume production of complex shaped metallic parts using commercially available feedstocks. The characteristics of parts after moulding, debinding, and sintering cannot be simply predictable from raw materials because the properties get altered with the process parameters and the corresponding levels of porosity during processing steps. In this study, physical properties, microstructure, and mechanical properties of the MIM parts have been characterised to understand the evolution of strength during various steps in MIM processing. Feedstocks with different binder loading show a considerable difference in physical as well as mechanical characteristics. During sintering of parts which have solid loading of grinding sludge, simultaneous in situ reduction and densification takes place, whereas only densification occurs in carbonyl iron parts. It is, therefore, possible to make complex shaped parts of different levels of porosity from downgraded shop floor metallic waste.     

Application of electromagnetic impact technique for welding copper-to-stainless steel sheets

The ability to manufacture a product using different metal combinations greatly increases flexibility in design and production. Joining of dissimilar metal combinations like Copper-to-Stainless Steel (Cu-to-SS) is, however, a challenging task owing to the large differences in physical and chemical properties. The application of electromagnetic (EM) impact technique is demonstrated for welding copper (Cu) to stainless steel (SS) sheets. The welding Cu-to-SS is accomplished by using Al drivers to accelerate Cu and SS work sheets. The tensile shear strength test and the metallographic studies are carried out for Cu-to-SS EM welds.     

Elucidation of accuracy in calibration of MR signal intensity based on transmission amplitude method

To calibrate magnetic resonance (MR) signal intensity that depends on radio frequency (RF) coil loading, the transmission amplitude (TRA) for the excitation in the transmit-receive RF coil has been used as a good index in the so-called TRA method. As this TRA method needs neither an internal reference nor an additional external reference for the calibration, its accuracy is free from reference measurements. This study elucidated the calibration accuracy of MR signal intensities based on the TRA method. A cylindrical gel phantom was used for accuracy measurements with a 1.5-T MRI unit with conventional T1 imaging as a simple pulse sequence for various loading conditions. The brain parenchyma of eight healthy volunteers also showed calibrated MR signal deviations. The error of the phantom calibration measurements was 2.18% (S.D.%). The background noise intensity of images was theoretically derived to correlate with the impedance mismatching of the RF coil, which is inevitable for fixed tuning, even for automatic tuning that is not always exact. Taking into account this noise intensity, the calibration method was modified to reduce its error to 1.50%. The standard deviations of the calibrated values in the thalamus and frontal white matter were 2.9 and 3.8%, respectively. We suggest that the modified TRA method is a practical and reliable technique to obtain clinical numeric evidence.     

Risk-sensitive control for a class of nonlinear systems with multiplicative noise

In this paper, we consider the problem of optimal control for a class of nonlinear stochastic systems with multiplicative noise. The nonlinearity consists of quadratic terms in the state and control variables. The optimality criteria are of a risk-sensitive and generalised risk-sensitive type. The optimal control is found in an explicit closed-form by the completion of squares and the change of measure methods. As applications, we outline two special cases of our results. We show that a subset of the class of models which we consider leads to a generalised quadratic–affine term structure model (QATSM) for interest rates. We also demonstrate how our results lead to generalisation of exponential utility as a criterion in optimal investment.