Extracting Three Dimensional Surface Model of Human Kidney from the Visible Human Data Set using Free Software

Three dimensional digital model of a representative human kidney is needed for a surgical simulator that is capable of simulating a laparoscopic surgery involving kidney. Buying a three dimensional computer model of a representative human kidney, or reconstructing a human kidney from an image sequence using commercial software, both involve (sometimes significant amount of) money. In this paper, author has shown that one can obtain a three dimensional surface model of human kidney by making use of images from the Visible Human Data Set and a few free software packages (ImageJ, ITK-SNAP, and MeshLab in particular). Images from the Visible Human Data Set, and the software packages used here, both do not cost anything. Hence, the practice of extracting the geometry of a representative human kidney for free, as illustrated in the present work, could be a free alternative to the use of expensive commercial software or to the purchase of a digital model.

A Procedure for the 3D Reconstruction of Biological Organs from 2D Image Sequences

In this work, a procedure is presented for the reconstruction of biological organs from image sequences obtained through CT-scan. Although commercial software, which can accomplish this task, are readily available, the procedure presented here needs only free software. The procedure has been applied to reconstruct a liver from the scan data available in literature. 3D biological organs obtained this way can be used for the finite element analysis of biological organs and this has been demonstrated by carrying out an FE analysis on the reconstructed liver.

Demonstrating the Usefulness of CAELinux for Computer Aided Engineering using an Example of the Three Dimensional Reconstruction of a Pig Liver

CAELinux is a Linux distribution which is bundled with free software packages related to Computer Aided Engineering (CAE). The free software packages include software that can build a three dimensional solid model, programs that can mesh a geometry, software for carrying out Finite Element Analysis (FEA), programs that can carry out image processing etc. Present work has two goals: 1) To give a brief description of CAELinux 2) To demonstrate that CAELinux could be useful for Computer Aided Engineering, using an example of the three dimensional reconstruction of a pig liver from a stack of CT-scan images. One can note that instead of using CAELinux, using commercial software for reconstructing the liver would cost a lot of money. One can also note that CAELinux is a free and open source operating system and all software packages that are included in the operating system are also free. Hence one can conclude that CAELinux could be a very useful tool in application areas like surgical simulation which require three dimensional reconstructions of biological organs. Also, one can see that CAELinux could be a very useful tool for Computer Aided Engineering, in general.

Effect of resonator length and working fluid on the performance of twin thermoacoustic heat engine - experimental and simulation studies

Success in the advancement of thermoacoustic field led the researchers to develop the thermoacoustic engines which found its applications in various fields such as refrigeration, gas mixture separation, natural gas liquefaction, and cryogenics. The objective of this study is to design and fabricate the twin thermoacoustic heat engine (TAHE) producing the acoustic waves with high resonance frequencies which is used to drive a thermoacoustic refrigerator efficiently by the influence of geometrical parameters and working fluids. Twin TAHE has gained significant attention due to the production of high intensity acoustic waves than single TAHE. In order to drive an efficient thermoacoustic refrigerator, a twin thermoacoustic heat engine is built up and its performance are analysed by varying the resonator length and working fluid. The performance is measured in terms of onset temperature difference, resonance frequency and pressure amplitude of the oscillations generated from twin TAHE. The simulation is performed using free software DeltaEC, from LANL, USA. The simulated DeltaEC results are compared with experimental results and the deviations are found within +10%.

CLAP: A web-server for automatic classification of proteins with special reference to multi-domain proteins

Background: The function of a protein can be deciphered with higher accuracy from its structure than from its amino acid sequence. Due to the huge gap in the available protein sequence and structural space, tools that can generate functionally homogeneous clusters using only the sequence information, hold great importance. For this, traditional alignment-based tools work well in most cases and clustering is performed on the basis of sequence similarity. But, in the case of multi-domain proteins, the alignment quality might be poor due to varied lengths of the proteins, domain shuffling or circular permutations. Multi-domain proteins are ubiquitous in nature, hence alignment-free tools, which overcome the shortcomings of alignment-based protein comparison methods, are required. Further, existing tools classify proteins using only domain-level information and hence miss out on the information encoded in the tethered regions or accessory domains. Our method, on the other hand, takes into account the full-length sequence of a protein, consolidating the complete sequence information to understand a given protein better. Results: Our web-server, CLAP (Classification of Proteins), is one such alignment-free software for automatic classification of protein sequences. It utilizes a pattern-matching algorithm that assigns local matching scores (LMS) to residues that are a part of the matched patterns between two sequences being compared. CLAP works on full-length sequences and does not require prior domain definitions. Pilot studies undertaken previously on protein kinases and immunoglobulins have shown that CLAP yields clusters, which have high functional and domain architectural similarity. Moreover, parsing at a statistically determined cut-off resulted in clusters that corroborated with the sub-family level classification of that particular domain family. Conclusions: CLAP is a useful protein-clustering tool, independent of domain assignment, domain order, sequence length and domain diversity. Our method can be used for any set of protein sequences, yielding functionally relevant clusters with high domain architectural homogeneity. The CLAP web server is freely available for academic use at http://nslab.mbu.iisc.ernet.in/clap/.

Dataflow analysis for data-race free programs

Memory models for shared-memory concurrent programming languages typically guarantee sequential consistency (SC) semantics for datarace-free (DRF) programs, while providing very weak or no guarantees for non-DRF programs. In effect programmers are expected to write only DRF programs, which are then executed with SC semantics. With this in mind, we propose a novel scalable solution for dataflow analysis of concurrent programs, which is proved to be sound for DRF programs with SC semantics. We use the synchronization structure of the program to propagate dataflow information among threads without requiring to consider all interleavings explicitly. Given a dataflow analysis that is sound for sequential programs and meets certain criteria, our technique automatically converts it to an analysis for concurrent programs.

Model-free simulations for compressible mixing layer

Confined supersonic mixing layer is explored through model-free simulations. Both two- and three-dimensional spatio-temporal simulations were carried out employing higher order finite difference scheme as well as finite volume scheme based on open source software (OpenFOAM) to understand the effect of three-dimensionality on the development of mixing layer. It is observed that although the instantaneous structures exhibit three-dimensional features, the average pressure and velocities are predominantly two-dimensional. The computed wall pressures match well with experimental results fairly well, although three-dimensional simulation underpredicts the wall pressure in the downstream direction. The self-similarity of the velocity profiles is obtained within the duct length for all the simulations. Although the mixing layer thicknesses differ among different simulations, their growth rate is nearly the same. Significant differences are observed for species and temperature distribution between two- and three-dimensional calculations, and two-dimensional calculations do not match the experimental observation of smooth variations in species mass fraction profiles as reported in literature. Reynolds stress distribution for three-dimensional calculations show profiles with less peak values compared to two-dimensional calculations; while normal stress anisotropy is higher for three-dimensional case.

Microstructural characterization of ultrafine-grain interstitial-free steel by X-ray diffraction line profile analysis

This paper highlights the microstructural features of commercially available interstitial free (IF) steel specimens deformed by equal channel angular pressing (ECAP) up to four passes following the route A. The microstructure of the samples was studied by different techniques of X-ray diffraction peak profile analysis as a function of strain (epsilon). It was found that the crystallite size is reduced substantially already at epsilon=2.3 and it does not change significantly during further deformation. At the same time, the dislocation density increases gradually up to epsilon=4.6. The dislocation densities estimated from X-ray diffraction study are found to correlate very well with the experimentally obtained yield strength of the samples.

Singularity-free path planning for the Stewart platform manipulator

This paper addresses the problem of singularity-free path planning for the six-degree-of-freedom parallel manipulator known as the Stewart platform manipulator. Unlike serial manipulators, the Stewart platform possesses singular configurations within the workspace where the manipulator is uncontrollable. An algorithm has been developed to construct continuous paths within the workspace of the manipulator by avoiding singularities and ill-conditioning. Given two end-poses of the manipulator, the algorithm finds out safe (well-conditioned) via points and plans a continuous path from the initial pose to the final one. When the two end-poses belong to different branches and no singularity-free path is possible, the algorithm indicates the impossibility of a valid path. A numerical example has also been presented as illustration of the path planning strategy.

Unsteady free convection flow in the stagnation-point region of a rotating sphere

The unsteady free convection boundary-layer flow in the forward stagnation-point region of a sphere, which is rotating with time-dependent angular velocity in an ambient fluid, has been studied. Both constant wall temperature and constant hear flux conditions have been considered. The non-linear coupled parabolic partial differential equations governing the flow have been solved numerically using an implicit finite-difference scheme. The skin friction and the heat transfer are enhanced by the buoyancy force. The effect of the buoyancy force is found to be more pronounced for smaller Prandtl numbers than for larger Prandtl numbers. For a given buoyancy force, the heat transfer increases with an increase in Prandtl number, but the skin friction decreases.

Unsteady free convection flow in the stagnation-point region of a three-dimensional body

The unsteady free convection flow in the stagnation-point region of a heated three-dimensional body placed in an ambient fluid is studied under boundary layer approximations. We have considered the case where there is an initial steady state that is perturbed by a step-change in the wall temperature. The non-linear coupled partial differential equations governing the free convection flow are solved numerically using a finite difference scheme. The presented results show the temporal development of the momentum and thermal boundary layer characteristics.

Free Energy Gap Dependence of the Electron-Transfer Rate from the Inverted to the Normal Region

numerical study of the free energy gap (FEG) dependence of the electron-transfer rate in polar solvents is presented. This study is based on the generalized multidimensional hybrid model, which not only includes the solvent polarization and the molecular vibration modes, but also the biphasic polar response of the solvent. The free energy gap dependence is found to be sensitive to several factors, including the solvent relaxation rate, the electronic coupling between the surfaces, the frequency of the high-frequency quantum vibrational mode, and the magnitude of the solvent reorganization energy. It is shown that in some cases solvent relaxation can play an important role even in the Marcus normal regime. The minimal hybrid model involves a large number of parameters, giving rise to a diverse non-Marcus FEG behavior which is often determined collectively by these parameters. The model gives the linear free energy gap dependence of the logarithmic rate over a substantial range of FEG, spanning from the normal to the inverted regime. However, even for favorable values of the relevant parameters, a linear free energy gap dependence of the rate could be obtained only over a range of 5000-6000 cm(-1) (compared to the experimentally observed range of 10000 cm(-1) reported by Benniston et al.). The present work suggests several extensions/generalizations of the hybrid model which might be necessary to fully understand the observed free energy gap dependence.

Free energy landscape of a dense hard-sphere system

The topography of the free energy landscape in phase space of a dense hard-sphere system characterized by a discretized free energy functional of the Ramakishnan-Yussouff form is investigated numerically using a specially devised Monte Carlo procedure. We locate a considerable number of glassy local minima of the free energy and analyze the distributions of the free energy at a minimum and an appropriately defined phase-space "distance" between different minima. We find evidence for the existence of pairs of closely related glassy minima("two-level systems"). We also investigate the way the system makes transitions as it moves from the basin of attraction of a minimum to that of another one after a start under nonequilibrium conditions. This allows us to determine the effective height of free energy barriers that separate a glassy minimum from the others. The dependence of the height of free energy barriers on the density is investigated in detail. The general appearance of the free energy landscape resembles that of a putting green: relatively deep minima separated by a fairly flat structure. We discuss the connection of our results with the Vogel-Fulcher law and relate our observations to other work on the glass transition.

Free vibration of a kinked cantilever with attached masses

In this paper free vibration characteristics of a centrally kinked cantilever beam of unit mass carrying masses at the kink (m(k)) and at the tip (m(t)) are analyzed. Frequency factors are presented for the first two modes for different combinations of m(k),m(t) and the kink angle delta. A relationship of the form f(m(k),m(t), delta) = m(k) + m(t)(4 + 10/3 cos delta+ 2/3 cos(2) delta)=const appears to give the same fundamental frequency for a given delta and different combinations of [m(k), m(t)]. Mode shapes as well as bending moments at the support and at the kink are also discussed. The utility of a discrete beam model in understanding the free vibration characteristics is also highlighted.

Extended Kalman filters using explicit and derivative-free local linearizations

We propose three variants of the extended Kalman filter (EKF) especially suited for parameter estimations in mechanical oscillators under Gaussian white noises. These filters are based on three versions of explicit and derivative-free local linearizations (DLL) of the non-linear drift terms in the governing stochastic differential equations (SDE-s). Besides a basic linearization of the non-linear drift functions via one-term replacements, linearizations using replacements through explicit Euler and Newmark expansions are also attempted in order to ensure higher closeness of true solutions with the linearized ones. Thus, unlike the conventional EKF, the proposed filters do not need computing derivatives (tangent matrices) at any stage. The measurements are synthetically generated by corrupting with noise the numerical solutions of the SDE-s through implicit versions of these linearizations. In order to demonstrate the effectiveness and accuracy of the proposed methods vis-à-vis the conventional EKF, numerical illustrations are provided for a few single degree-of-freedom (DOF) oscillators and a three-DOF shear frame with constant parameters.