Abstract: Protein-protein interactions (PPI) play a crucial role in many biological processes such as cell signalling, transcription, translation, replication, signal transduction, and drug targeting, etc. Structural information about protein-protein interaction is essential for understanding the molecular mechanisms of these processes. Structures of protein-protein complexes are still difficult to obtain by biophysical methods such as NMR and X-ray crystallography, and therefore protein-protein docking computation is considered an important approach for understanding protein-protein interactions. However, reliable prediction of the protein-protein complexes is still under way. In the past decades, several grid-based docking algorithms based on the Katchalski-Katzir scoring scheme were developed, e.g., FTDock, ZDOCK, HADDOCK, RosettaDock, HEX, etc. However, the success rate of protein-protein docking prediction is still far from ideal. In this work, we first propose a more practical measure for evaluating the success of protein-protein docking predictions,the rate of first success (RFS), which is similar to the concept of mean first passage time (MFPT). Accordingly, we have assessed the ZDOCK bound and unbound benchmarks 2.0 and 3.0. We also createda new benchmark set for protein-protein docking predictions, in which the complexes have experimentally determined binding affinity data. We performed free energy calculation based on the solution of non-linear Poisson-Boltzmann equation (nlPBE) to improve the binding mode prediction. We used the well-studied thebarnase-barstarsystem to validate the parameters for free energy calculations. Besides,thenlPBE-based free energy calculations were conducted for the badly predicted cases by ZDOCK and ZRANK. We found that direct molecular mechanics energetics cannot be used to discriminate the native binding pose from the decoys.Our results indicate that nlPBE-based calculations appeared to be one of the promising approaches for improving the success rate of binding pose predictions.
Abstract: This paper presents a new study on the applications of
optimization and regression analysis techniques for optimal
calculation of partial ratios of four-step helical gearboxes for getting
minimal gearbox length. In the paper, basing on the moment
equilibrium condition of a mechanic system including four gear units
and their regular resistance condition, models for determination of the
partial ratios of the gearboxes are proposed. In particular, explicit
models for calculation of the partial ratios are proposed by using
regression analysis. Using these models, the determination of the
partial ratios is accurate and simple.
Abstract: In contrast to existing methods which do not take into account multiconnectivity in a broad sense of this term, we develop mathematical models and highly effective combination (BIEM and FDM) numerical methods of calculation of stationary and quasistationary temperature field of a profile part of a blade with convective cooling (from the point of view of realization on PC). The theoretical substantiation of these methods is proved by appropriate theorems. For it, converging quadrature processes have been developed and the estimations of errors in the terms of A.Ziqmound continuity modules have been received. For visualization of profiles are used: the method of the least squares with automatic conjecture, device spline, smooth replenishment and neural nets. Boundary conditions of heat exchange are determined from the solution of the corresponding integral equations and empirical relationships. The reliability of designed methods is proved by calculation and experimental investigations heat and hydraulic characteristics of the gas turbine first stage nozzle blade.
Abstract: This work presents a comparison between the Annual
Energy Output (AEO) of two commercial vertical-axis wind turbines
(VAWTs) for a low-wind urban site: both a drag-driven and a liftdriven
concepts are examined in order to be installed on top of the
new Via dei Giustinelli building, Trieste (Italy). The power-curves,
taken from the product specification sheets, have been matched to the
wind characteristics of the selected installation site. The influence of
rotor swept area and rated power on the performance of the two
proposed wind turbines have been examined in detail, achieving a
correlation between rotor swept area, electrical generator size and
wind distribution, to be used as a guideline for the calculation of the
AEO.
Abstract: Aggressive scaling of MOS devices requires use of ultra-thin gate oxides to maintain a reasonable short channel effect and to take the advantage of higher density, high speed, lower cost etc. Such thin oxides give rise to high electric fields, resulting in considerable gate tunneling current through gate oxide in nano regime. Consequently, accurate analysis of gate tunneling current is very important especially in context of low power application. In this paper, a simple and efficient analytical model has been developed for channel and source/drain overlap region gate tunneling current through ultra thin gate oxide n-channel MOSFET with inevitable deep submicron effect (DSME).The results obtained have been verified with simulated and reported experimental results for the purpose of validation. It is shown that the calculated tunnel current is well fitted to the measured one over the entire oxide thickness range. The proposed model is suitable enough to be used in circuit simulator due to its simplicity. It is observed that neglecting deep sub-micron effect may lead to large error in the calculated gate tunneling current. It is found that temperature has almost negligible effect on gate tunneling current. It is also reported that gate tunneling current reduces with the increase of gate oxide thickness. The impact of source/drain overlap length is also assessed on gate tunneling current.
Abstract: An effort has been taken to simulate the combustion
and performance characteristics of biodiesel fuel in direct injection
(D.I) low heat rejection (LHR) diesel engine. Comprehensive
analyses on combustion characteristics such as cylinder pressure,
peak cylinder pressure, heat release and performance characteristics
such as specific fuel consumption and brake thermal efficiency are
carried out. Compression ignition (C.I) engine cycle simulation was
developed and modified in to LHR engine for both diesel and
biodiesel fuel. On the basis of first law of thermodynamics the
properties at each degree crank angle was calculated. Preparation and
reaction rate model was used to calculate the instantaneous heat
release rate. A gas-wall heat transfer calculations are based on the
ANNAND-s combined heat transfer model with instantaneous wall
temperature to analyze the effect of coating on heat transfer. The
simulated results are validated by conducting the experiments on the
test engine under identical operating condition on a turbocharged D.I
diesel engine. In this analysis 20% of biodiesel (derived from
Jatropha oil) blended with diesel and used in both conventional and
LHR engine. The simulated combustion and performance
characteristics results are found satisfactory with the experimental
value.
Abstract: Numerical parametric study is conducted to study the effects of ampoule rotation on the flows and the dopant segregation in vertical bridgman (vb) crystal growth. Calculations were performed in unsteady state. The extended darcy model, which includes the time derivative and coriolis terms, has been employed in the momentum equation. It’s found that the convection, and dopant segregation can be affected significantly by ampoule rotation, and the effect is similar to that by an axial magnetic field. Ampoule rotation decreases the intensity of convection and stretches the flow cell axially. When the convection is weak, the flow can be suppressed almost completely by moderate ampoule rotation and the dopant segregation becomes diffusion-controlled. For stronger convection, the elongated flow cell by ampoule rotation may bring dopant mixing into the bulk melt reducing axial segregation at the early stage of the growth. However, if the cellular flow cannot be suppressed completely, ampoule rotation may induce larger radial segregation due to poor mixing.
Abstract: The indoor airflow with a mixed natural/forced convection
was numerically calculated using the laminar and turbulent
approach. The Boussinesq approximation was considered for a simplification
of the mathematical model and calculations. The results
obtained, such as mean velocity fields, were successfully compared
with experimental PIV flow visualizations. The effect of the distance
between the cooled wall and the heat exchanger on the temperature
and velocity distributions was calculated. In a room with a simple
shape, the computational code OpenFOAM demonstrated an ability to
numerically predict flow patterns. Furthermore, numerical techniques,
boundary type conditions and the computational grid quality were
examined. Calculations using the turbulence model k-omega had a
significant effect on the results influencing temperature and velocity
distributions.
Abstract: This paper describes an efficient and practical method
for economic dispatch problem in one and two area electrical power
systems with considering the constraint of the tie transmission line
capacity constraint. Direct search method (DSM) is used with some
equality and inequality constraints of the production units with any
kind of fuel cost function. By this method, it is possible to use several
inequality constraints without having difficulty for complex cost
functions or in the case of unavailability of the cost function
derivative. To minimize the number of total iterations in searching,
process multi-level convergence is incorporated in the DSM.
Enhanced direct search method (EDSM) for two area power system
will be investigated. The initial calculation step size that causes less
iterations and then less calculation time is presented. Effect of the
transmission tie line capacity, between areas, on economic dispatch
problem and on total generation cost will be studied; line
compensation and active power with reactive power dispatch are
proposed to overcome the high generation costs for this multi-area
system.
Abstract: An appropriate project delivery system (PDS) is crucial
to the success of a construction projects. Case-based Reasoning (CBR)
is a useful support for PDS selection. However, the traditional CBR
approach represents cases as attribute-value vectors without taking
relations among attributes into consideration, and could not calculate
the similarity when the structures of cases are not strictly same.
Therefore, this paper solves this problem by adopting the Relational
Case-based Reasoning (RCBR) approach for PDS selection,
considering both the structural similarity and feature similarity. To
develop the feature terms of the construction projects, the criteria and
factors governing PDS selection process are first identified. Then
feature terms for the construction projects are developed. Finally, the
mechanism of similarity calculation and a case study indicate how
RCBR works for PDS selection. The adoption of RCBR in PDS
selection expands the scope of application of traditional CBR method
and improves the accuracy of the PDS selection system.
Abstract: A simple and easy algorithm is presented for a fast calculation of kernel functions which required in fluid simulations using the Smoothed Particle Hydrodynamic (SPH) method. Present proposed algorithm improves the Linked-list algorithm and adopts the Pair-Wise Interaction technique, which are widely used for evaluating kernel functions in fluid simulations using the SPH method. The algorithm is easy to be implemented without any complexities in programming. Some benchmark examples are used to show the simulation time saved by using the proposed algorithm. Parametric studies on the number of divisions for sub-domains, smoothing length and total amount of particles are conducted to show the effectiveness of the present technique. A compact formulation is proposed for practical usage.
Abstract: In this paper, we analyze the rotor eddy currents losses provoqued by the stator slot harmonics developed in the permanent magnets or pole pieces of synchronous machines. An analytical approach is presented to evaluate the effect of slot ripples on rotor field and losses calculation. This analysis is then tested on a model by 2D/3D finite element (FE) calculation. The results show a good agreement on loss calculations when skin effect is negligible and the magnet is considered.
Abstract: One of the essential components of much of DSP
application is noise cancellation. Changes in real time signals are
quite rapid and swift. In noise cancellation, a reference signal which
is an approximation of noise signal (that corrupts the original
information signal) is obtained and then subtracted from the noise
bearing signal to obtain a noise free signal. This approximation of
noise signal is obtained through adaptive filters which are self
adjusting. As the changes in real time signals are abrupt, this needs
adaptive algorithm that converges fast and is stable. Least mean
square (LMS) and normalized LMS (NLMS) are two widely used
algorithms because of their plainness in calculations and
implementation. But their convergence rates are small. Adaptive
averaging filters (AFA) are also used because they have high
convergence, but they are less stable. This paper provides the
comparative study of LMS and Normalized NLMS, AFA and new
enhanced average adaptive (Average NLMS-ANLMS) filters for noise
cancelling application using speech signals.
Abstract: Three dimensional nanostructure materials have attracted the attention of many researches because the possibility to apply them for near future devices in sensors, catalysis and energy related. Tin dioxide is the most used material for gas sensing because its three-dimensional nanostructures and properties are related to the large surface exposed to gas adsorption. We propose the use of branch SnO2 nanowhiskers in interaction with ethanol. All Sn atoms are symmetric. The total energy, potential energy and Kinetic energy calculated for interaction between SnO2 and ethanol in different distances and temperatures. The calculations achieved by methods of Langevin Dynamic and Mont Carlo simulation. The total energy increased with addition ethanol molecules and temperature so interactions between them are endothermic.
Abstract: Fundamental motivation of this paper is how gaze estimation can be utilized effectively regarding an application to games. In games, precise estimation is not always important in aiming targets but an ability to move a cursor to an aiming target accurately is also significant. Incidentally, from a game producing point of view, a separate expression of a head movement and gaze movement sometimes becomes advantageous to expressing sense of presence. A case that panning a background image associated with a head movement and moving a cursor according to gaze movement can be a representative example. On the other hand, widely used technique of POG estimation is based on a relative position between a center of corneal reflection of infrared light sources and a center of pupil. However, a calculation of a center of pupil requires relatively complicated image processing, and therefore, a calculation delay is a concern, since to minimize a delay of inputting data is one of the most significant requirements in games. In this paper, a method to estimate a head movement by only using corneal reflections of two infrared light sources in different locations is proposed. Furthermore, a method to control a cursor using gaze movement as well as a head movement is proposed. By using game-like-applications, proposed methods are evaluated and, as a result, a similar performance to conventional methods is confirmed and an aiming control with lower computation power and stressless intuitive operation is obtained.
Abstract: the intension in this work is to investigate the effect of
different bending manifold pipes on engine performance for different
engine speed. Power, Torque, and BSFC were calculated and
presented to show the effect of varying bending pipes angles on them
for all cases considered. A special program used to carry out the
calculations. A simulation model for 4-cylinders spark ignition
engine with turbocharger has been built and calculated. The analysis
of the results shows that for 120o angle the torque increases about
40% at 3000 rpm and 25% at 4000 rpm without changing in fuel
consumption. For 90o angle the increment in torque is about 10 %.
For the same bending angle the increment in brake power is around
40% at 3000 rpm and 25% at 4000 rpm. The increment in fuel
consumption is about 12% for 60o and 30% for 90o between (6000-
7000) rpm.
Abstract: The aim of this study is to analyze influence of
differences of heat insulation methods on indoor thermal environment and comfort of apartment buildings.
This study analyzes indoor thermal environment and comfort on units of apartment buildings using calculation software "THERB" and
compares three different kinds of heat insulation methods. Those are
outside insulation on outside walls, inside insulation on outside walls and interior insulation. In terms of indoor thermal environment, outside insulation is the best to stabilize room temperature. In winter, room temperature on
outside insulation after heating is higher than other and it is kept 3-5 degrees higher through all night. But the surface temperature with
outside insulation did not dramatically increase when heating was used, which was 3 to 5oC lower than the temperature with other
insulation. The PMV of interior insulation fall nearly range of comfort when the heating and cooling was use.
Abstract: The purpose of the present study is the calculation of Gutenber-Richter parameters (a, b) and analyze the mean annual rate of exceedance of earthquake magnitude (Om ) of southern segment of the Sagaing fault and its associate components. The study area is situated about 200 km radius centered at Yangon. Earthquake data file is using from 1975 to 2006 August 31. The bounded Gutenberg- Richter recurrence law for 0 M is 4.0 and max M is 7.5.
Abstract: Knowledge about the magnetic quantities in a magnetic circuit is always of great interest. On the one hand, this information is needed for the simulation of a transformer. On the other hand, parameter studies are more reliable, if the magnetic quantities are derived from a well established model. One possibility to model the 3-phase transformer is by using a magnetic equivalent circuit (MEC). Though this is a well known system, it is often not an easy task to set up such a model for a large number of lumped elements which additionally includes the nonlinear characteristic of the magnetic material. Here we show the setup of a solver for a MEC and the results of the calculation in comparison to measurements taken. The equations of the MEC are based on a rearranged system of the nodal analysis. Thus it is possible to achieve a minimum number of equations, and a clear and simple structure. Hence, it is uncomplicated in its handling and it supports the iteration process. Additional helpful tasks are implemented within the solver to enhance the performance. The electric circuit is described by an electric equivalent circuit (EEC). Our results for the 3-phase transformer demonstrate the computational efficiency of the solver, and show the benefit of the application of a MEC.
Abstract: In this paper, He-s amplitude frequency formulation is used to obtain a periodic solution for a nonlinear oscillator with fractional potential. By calculation and computer simulations, compared with the exact solution shows that the result obtained is of high accuracy.