Search results for: computational physics

Authors: Razib M. Othman, Safaai Deris, Rosli M. Illias

Abstract:

Annotation of a protein sequence is pivotal for the understanding of its function. Accuracy of manual annotation provided by curators is still questionable by having lesser evidence strength and yet a hard task and time consuming. A number of computational methods including tools have been developed to tackle this challenging task. However, they require high-cost hardware, are difficult to be setup by the bioscientists, or depend on time intensive and blind sequence similarity search like Basic Local Alignment Search Tool. This paper introduces a new method of assigning highly correlated Gene Ontology terms of annotated protein sequences to partially annotated or newly discovered protein sequences. This method is fully based on Gene Ontology data and annotations. Two problems had been identified to achieve this method. The first problem relates to splitting the single monolithic Gene Ontology RDF/XML file into a set of smaller files that can be easy to assess and process. Thus, these files can be enriched with protein sequences and Inferred from Electronic Annotation evidence associations. The second problem involves searching for a set of semantically similar Gene Ontology terms to a given query. The details of macro and micro problems involved and their solutions including objective of this study are described. This paper also describes the protein sequence annotation and the Gene Ontology. The methodology of this study and Gene Ontology based protein sequence annotation tool namely extended UTMGO is presented. Furthermore, its basic version which is a Gene Ontology browser that is based on semantic similarity search is also introduced.

Keywords: automatic clustering, bioinformatics tool, gene ontology, protein sequence annotation, semantic similarity search

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Authors: Philippe Jorrand

Abstract:

Research in quantum computation is looking for the consequences of having information encoding, processing and communication exploit the laws of quantum physics, i.e. the laws which govern the ultimate knowledge that we have, today, of the foreign world of elementary particles, as described by quantum mechanics. This paper starts with a short survey of the principles which underlie quantum computing, and of some of the major breakthroughs brought by the first ten to fifteen years of research in this domain; quantum algorithms and quantum teleportation are very biefly presented. The next sections are devoted to one among the many directions of current research in the quantum computation paradigm, namely quantum programming languages and their semantics. A few other hot topics and open problems in quantum information processing and communication are mentionned in few words in the concluding remarks, the most difficult of them being the physical implementation of a quantum computer. The interested reader will find a list of useful references at the end of the paper.

Keywords: Quantum information processing, quantum algorithms, quantum programming languages.

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Authors: Yuri Bizzoni, Marianne Reboul

Abstract:

Our program compares French and Italian translations of Homer’s Odyssey, from the XVIth to the XXth century. We focus on the third point, showing how distributional semantics systems can be used both to improve alignment between different French translations as well as between the Greek text and a French translation. Although we focus on French examples, the techniques we display are completely language independent.

Keywords: Translation studies, machine translation, computational linguistics, distributional semantics.

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Authors: B. Montero, M. Rico, A. Ares, R. Bouza

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The development of competences and practical capacities of students is getting an important incidence into the guidelines of the European Higher Education Area (EHEA). The methodology applied in this work is based on the education through directed resolution of practical cases. All cases are related to professional tasks that the students will have to develop in their future career. The method is intended to form the necessary competences of students of the Marine Engineering and Maritime Transport Degree in the matter of “Physics". The experience was applied in the course of 2011/2012. Students were grouped, and a practical task was assigned to them, that should be developed and solved within the team. The aim was to realize students learning by three ways: their own knowledge, the contribution of their teammates and the teacher's direction. The results of the evaluation were compared with those obtained previously by the traditional teaching method.

Keywords: Cooperation, Marine Engineering, Self-learning skills.

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Authors: I. Oral, E. Bozkurt, H. Guzel

Abstract:

The purpose of this study was to investigate the effect of combining Real Experimentation (RE) With Virtual Experimentation (VE) on students- conceptual understanding of photo electric effect. To achieve this, a pre–post comparison study design was used that involved 46 undergraduate students. Two groups were set up for this study. Participants in the control group used RE to learn photo electric effect, whereas, participants in the experimental group used RE in the first part of the curriculum and VE in another part. Achievement test was given to the groups before and after the application as pre-test and post test. The independent samples t- test, one way Anova and Tukey HSD test were used for testing the data obtained from the study. According to the results of analyzes, the experimental group was found more successful than the control group.

Keywords: Computer Based Teaching, Java, Physics Education, Virtual Laboratory.

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Authors: V.K.Ananthashayana, Geetha.K.S

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In this paper, a recursive algorithm for the computation of 2-D DCT using Ramanujan Numbers is proposed. With this algorithm, the floating-point multiplication is completely eliminated and hence the multiplierless algorithm can be implemented using shifts and additions only. The orthogonality of the recursive kernel is well maintained through matrix factorization to reduce the computational complexity. The inherent parallel structure yields simpler programming and hardware implementation and provides log 1 2 3 2 N N-N+ additions and N N 2 log 2 shifts which is very much less complex when compared to other recent multiplierless algorithms.

Keywords: DCT, Multilplerless, Ramanujan Number, Recursive.

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Authors: Thomas Jin-Chee Liu

Abstract:

In this paper, the thermo-electro-structural coupledfield in a cracked metal plate is studied using the finite element analysis. From the computational results, the compressive stresses reveal near the crack tip. This conclusion agrees with the past reference. Furthermore, the compressive condition can retard and stop the crack growth during the Joule heating process.

Keywords: Compressive stress, crack tip, Joule heating, finite element.

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Authors: Alexei M. Mikhailov

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The paper discusses the mathematics of pattern indexing and its applications to recognition of visual patterns that are found in video clips. It is shown that (a) pattern indexes can be represented by collections of inverted patterns, (b) solutions to pattern classification problems can be found as intersections and histograms of inverted patterns and, thus, matching of original patterns avoided.

Keywords: Artificial neural cortex, computational biology, data mining, pattern recognition.

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Authors: Faris Tarlochan, Siva Mahesh Tangutooru

Abstract:

Lateral Geniculate Nucleus (LGN) is the relay center in the visual pathway as it receives most of the input information from retinal ganglion cells (RGC) and sends to visual cortex. Low threshold calcium currents (IT) at the membrane are the unique indicator to characterize this firing functionality of the LGN neurons gained by the RGC input. According to the LGN functional requirements such as functional mapping of RGC to LGN, the morphologies of the LGN neurons were developed. During the neurological disorders like glaucoma, the mapping between RGC and LGN is disconnected and hence stimulating LGN electrically using deep brain electrodes can restore the functionalities of LGN. A computational model was developed for simulating the LGN neurons with three predominant morphologies each representing different functional mapping of RGC to LGN. The firings of action potentials at LGN neuron due to IT were characterized by varying the stimulation parameters, morphological parameters and orientation. A wide range of stimulation parameters (stimulus amplitude, duration and frequency) represents the various strengths of the electrical stimulation with different morphological parameters (soma size, dendrites size and structure). The orientation (0-1800) of LGN neuron with respect to the stimulating electrode represents the angle at which the extracellular deep brain stimulation towards LGN neuron is performed. A reduced dendrite structure was used in the model using Bush–Sejnowski algorithm to decrease the computational time while conserving its input resistance and total surface area. The major finding is that an input potential of 0.4 V is required to produce the action potential in the LGN neuron which is placed at 100 μm distance from the electrode. From this study, it can be concluded that the neuroprostheses under design would need to consider the capability of inducing at least 0.4V to produce action potentials in LGN.

Keywords: Lateral geniculate nucleus, visual cortex, finite element, glaucoma, neuroprostheses.

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Authors: Angela Ralli, Eleni Galiotou

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In this paper we describe the recognition process of Greek compound words using the PC-KIMMO software. We try to show certain limitations of the system with respect to the principles of compound formation in Greek. Moreover, we discuss the computational processing of phenomena such as stress and syllabification which are indispensable for the analysis of such constructions and we try to propose linguistically-acceptable solutions within the particular system.

Keywords: Morpho-phonological parsing, compound words, two-level morphology, natural language processing.

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Authors: Arpiruk Hokpunna, Michael Manhart

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We present a Large-Eddy simulation of a vortex cell with circular shaped. The results show that the flow field can be sub divided into four important zones, the shear layer above the cavity, the stagnation zone, the vortex core in the cavity and the boundary layer along the wall of the cavity. It is shown that the vortex core consits of solid body rotation without much turbulence activity. The vortex is mainly driven by high energy packets that are driven into the cavity from the stagnation point region and by entrainment of fluid from the cavity into the shear layer. The physics in the boundary layer along the cavity-s wall seems to be far from that of a canonical boundary layer which might be a crucial point for modelling this flow.

Keywords: Turbulent flow, Large eddy simulations, boundary layer and cavity flow, vortex cell flow.

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Authors: Ciprian Dobre

Abstract:

The scale, complexity and worldwide geographical spread of the LHC computing and data analysis problems are unprecedented in scientific research. The complexity of processing and accessing this data is increased substantially by the size and global span of the major experiments, combined with the limited wide area network bandwidth available. We present the latest generation of the MONARC (MOdels of Networked Analysis at Regional Centers) simulation framework, as a design and modeling tool for large scale distributed systems applied to HEP experiments. We present simulation experiments designed to evaluate the capabilities of the current real-world distributed infrastructure to support existing physics analysis processes and the means by which the experiments bands together to meet the technical challenges posed by the storage, access and computing requirements of LHC data analysis within the CMS experiment.

Keywords: Modeling and simulation, evaluation, large scale distributed systems, LHC experiments, CMS.

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Authors: Himanshu Shekhar Maharana, S. K .Dash

Abstract:

Economic Load Dispatch (ELD) proves to be a vital optimization process in electric power system for allocating generation amongst various units to compute the cost of generation, the cost of emission involving global warming gases like sulphur dioxide, nitrous oxide and carbon monoxide etc. In this dissertation, we emphasize ramp rate constriction factor based particle swarm optimization (RRCPSO) for analyzing various performance objectives, namely cost of generation, cost of emission, and a dual objective function involving both these objectives through the experimental simulated results. A 6-unit 30 bus IEEE test case system has been utilized for simulating the results involving improved weight factor advanced ramp rate limit constraints for optimizing total cost of generation and emission. This method increases the tendency of particles to venture into the solution space to ameliorate their convergence rates. Earlier works through dispersed PSO (DPSO) and constriction factor based PSO (CPSO) give rise to comparatively higher computational time and less good optimal solution at par with current dissertation. This paper deals with ramp rate and constriction factor based well defined ramp rate PSO to compute various objectives namely cost, emission and total objective etc. and compares the result with DPSO and weight improved PSO (WIPSO) techniques illustrating lesser computational time and better optimal solution. 

Keywords: Economic load dispatch, constriction factor based particle swarm optimization, dispersed particle swarm optimization, weight improved particle swarm optimization, ramp rate and constriction factor based particle swarm optimization.

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Authors: Sreeyuth Lal, Yohei Sato, Bojan Niceno

Abstract:

With the long-term objective of Critical Heat Flux (CHF) prediction, a Direct Numerical Simulation (DNS) framework for simulation of subcooled and saturated nucleate pool boiling is developed. One case of saturated, and three cases of subcooled boiling at different subcooling levels are simulated. Grid refinement study is also reported. Both boiling and condensation phenomena can be computed simultaneously in the proposed numerical framework. Computed bubble detachment diameters of the saturated nucleate pool boiling cases agree well with the experiment. The flow structures around the growing bubble are presented and the accompanying physics is described. The relation between heat flux evolution from the heated wall and the bubble growth is studied, along with investigations of temperature distribution and flow field evolutions.

Keywords: CFD, interface tracking method, phase change model, subcooled nucleate pool boiling.

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Authors: Jefri Marzal, Hong Xie, Chun Che Fung

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Visibility problems are central to many computational geometry applications. One of the typical visibility problems is computing the view from a given point. In this paper, a linear time procedure is proposed to compute the visibility subsets from a corner of a rectangular prism in an orthogonal polyhedron. The proposed algorithm could be useful to solve classic 3D problems.

Keywords: Visibility, rectangular prism, orthogonal polyhedron.

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Authors: A. Vairis, M. Petousis, B. Kandyla, C. Chrisoulakis

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The human knee joint has a three dimensional geometry with multiple body articulations that produce complex mechanical responses under loads that occur in everyday life and sports activities. To produce the necessary joint compliance and stability for optimal daily function various menisci and ligaments are present while muscle forces are used to this effect. Therefore, knowledge of the complex mechanical interactions of these load bearing structures is necessary when treatment of relevant diseases is evaluated and assisting devices are designed. Numerical tools such as finite element analysis are suitable for modeling such joints in order to understand their physics. They have been used in the current study to develop an accurate human knee joint and model its mechanical behavior. To evaluate the efficacy of this articulated model, static load cases were used for comparison purposes with previous experimentally verified modeling works drawn from literature.

Keywords: biomechanics, finite element modeling, knee joint

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Authors: Wang Wen-long, Li Hua, Pan Sha

Abstract:

Eight difference schemes and five limiters are applied to numerical computation of Riemann problem. The resolution of discontinuities of each scheme produced is compared. Numerical dissipation and its estimation are discussed. The result shows that the numerical dissipation of each scheme is vital to improve scheme-s accuracy and stability. MUSCL methodology is an effective approach to increase computational efficiency and resolution. Limiter should be selected appropriately by balancing compressive and diffusive performance.

Keywords: Scheme; Limiter, Numerical simulation, Riemannproblem.

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Authors: Ricardo Merlo

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In this paper, we analyzed the different didactic proposals for teaching about the free fall motion of bodies available online. An important aspect was the interpretation of the direction and sense of the acceleration of gravity and of the falling velocity of a body, which is why we found different applications of the Cartesian reference system used and also different graphical presentations of the velocity as a function of time and of the distance traveled vertically by the body in the period of time that it was dropped from a height h0. In this framework, a survey of previous concepts was applied to a voluntary group of first-year university students of an Engineering degree before and after the development of the class of the subject in question. Then, Hake's index (0.52) was determined, which resulted in an average learning gain from the meaningful use of the reference system and the respective graphs of velocity versus time and height versus time.

Keywords: Didactic gain, free–fall, physics teaching, previous knowledge.

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Authors: Le Chi Cuong

Abstract:

X-ray diffraction is an effective mean for analyzing material properties. This paper developed a new computational software for determining the properties of crystalline materials such as elastic constants, residual stresses, surface hardness, phase components, and etc. The results computed from the X-ray diffraction method were compared to those from the traditional methods and they are in the 95% confidential limits, showing that the newly developed software has high reproducibility, opening a possibility of its commercialization.

Keywords: X-ray diffraction, Nondestructive evaluation, Hardness, Residual stress, Phase determination.

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Authors: Luciana Montera

Abstract:

DNA shuffling is a powerful method used for in vitro evolute molecules with specific functions and has application in areas such as, for example, pharmaceutical, medical and agricultural research. The success of such experiments is dependent on a variety of parameters and conditions that, sometimes, can not be properly pre-established. Here, two computational models predicting DNA shuffling results is presented and their use and results are evaluated against an empirical experiment. The in silico and in vitro results show agreement indicating the importance of these two models and motivating the study and development of new models.

Keywords: Computer simulation, DNA shuffling, in silico andin vitro comparison.

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Authors: J. Urbánek Jiří, Krahulec Josef, Johanidesová Jitka, F. Urbánek Jiří

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This paper deals with using of prevailing operation system MS Office (SmartArt...) for mathematical models, using DYVELOP (Dynamic Vector Logistics of Processes) method. It serves for crisis situations investigation and modelling within the organizations of critical infrastructure. In first part of paper, it will be introduced entities, operators, and actors of DYVELOP method. It uses just three operators of Boolean algebra and four types of the entities: the Environments, the Process Systems, the Cases, and the Controlling. The Process Systems (PrS) have five “brothers”: Management PrS, Transformation PrS, Logistic PrS, Event PrS and Operation PrS. The Cases have three “sisters”: Process Cell Case, Use Case, and Activity Case. They all need for the controlling of their functions special Ctrl actors, except ENV – it can do without Ctrl. Model´s maps are named the Blazons and they are able mathematically - graphically express the relationships among entities, actors and processes. In second part of this paper, the rich blazons of DYVELOP method will be used for the discovering and modelling of the cycling cases and their phases. The blazons need live PowerPoint presentation for better comprehension of this paper mission. The crisis management of energetic crisis infrastructure organization is obliged to use the cycles for successful coping of crisis situations. Several times cycling of these cases is necessary condition for the encompassment for both emergency events and the mitigation of organization´s damages. Uninterrupted and continuous cycling process brings for crisis management fruitfulness and it is good indicator and controlling actor of organizational continuity and its sustainable development advanced possibilities. The research reliable rules are derived for the safety and reliable continuity of energetic critical infrastructure organization in the crisis situation.

Keywords: Blazons, computational assistance, DYVELOP method, critical infrastructure.

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Authors: Tainchi Lu, Chochih Lin

Abstract:

With a rapid growth in 3D graphics technology over the last few years, people are desired to see more flexible reacting motions of a biped in animations. In particular, it is impossible to anticipate all reacting motions of a biped while facing a perturbation. In this paper, we propose a three-level tracking method for animating a 3D humanoid character. First, we take the laws of physics into account to attach physical attributes, such as mass, gravity, friction, collision, contact, and torque, to bones and joints of a character. The next step is to employ PD controller to follow a reference motion as closely as possible. Once the character cannot tolerate a strong perturbation to prevent itself from falling down, we are capable of tracking a desirable falling-down action to avoid any falling condition inaccuracy. From the experimental results, we demonstrate the effectiveness and flexibility of the proposed method in comparison with conventional data-driven approaches.

Keywords: Character Animation, Forward Dynamics, Motion Tracking, PD Control.

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Authors: Erna T. Herdiani, Maman A. Djauhari

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In recent years, the use of vector variance as a measure of multivariate variability has received much attention in wide range of statistics. This paper deals with a more economic measure of multivariate variability, defined as vector variance minus all duplication elements. For high dimensional data, this will increase the computational efficiency almost 50 % compared to the original vector variance. Its sampling distribution will be investigated to make its applications possible.

Keywords: Asymptotic distribution, covariance matrix, likelihood ratio test, vector variance.

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Authors: Narasimham Challa, Jayaram Pradhan

Abstract:

Cryptographic algorithms play a crucial role in the information society by providing protection from unauthorized access to sensitive data. It is clear that information technology will become increasingly pervasive, Hence we can expect the emergence of ubiquitous or pervasive computing, ambient intelligence. These new environments and applications will present new security challenges, and there is no doubt that cryptographic algorithms and protocols will form a part of the solution. The efficiency of a public key cryptosystem is mainly measured in computational overheads, key size and bandwidth. In particular the RSA algorithm is used in many applications for providing the security. Although the security of RSA is beyond doubt, the evolution in computing power has caused a growth in the necessary key length. The fact that most chips on smart cards can-t process key extending 1024 bit shows that there is need for alternative. NTRU is such an alternative and it is a collection of mathematical algorithm based on manipulating lists of very small integers and polynomials. This allows NTRU to high speeds with the use of minimal computing power. NTRU (Nth degree Truncated Polynomial Ring Unit) is the first secure public key cryptosystem not based on factorization or discrete logarithm problem. This means that given sufficient computational resources and time, an adversary, should not be able to break the key. The multi-party communication and requirement of optimal resource utilization necessitated the need for the present day demand of applications that need security enforcement technique .and can be enhanced with high-end computing. This has promoted us to develop high-performance NTRU schemes using approaches such as the use of high-end computing hardware. Peer-to-peer (P2P) or enterprise grids are proven as one of the approaches for developing high-end computing systems. By utilizing them one can improve the performance of NTRU through parallel execution. In this paper we propose and develop an application for NTRU using enterprise grid middleware called Alchemi. An analysis and comparison of its performance for various text files is presented.

Keywords: Alchemi, GridNtru, Ntru, PKCS.

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Authors: M. Ebrahimi Shohani, S. M. Taheri, S. M. Golgoun

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Environmental radiation dosimeter is a kind of detector that measures the dose of the radiation area. Dosimeter registers the radiation and converts it to the dose according to the calibration parameters. The limit of a dose is different at each radiation area and this limit should be notified and reported to the user and health physics department. The stochastic nature of radiation is the reason for the fluctuation of any gamma detector dosimetry. In this research we investigated Geiger-Muller type of dosimeter and tried to improve the dose measurement. Geiger-Muller dosimeter is a counter that converts registered radiation to the dose. Therefore, for better data analysis, it is necessary to apply an algorithm to smooth statistical variations of registered radiation. We proposed a method to smooth these fluctuations much more and also proposed a dynamic way to trace rapid changes of radiations. Results show that our method is fast and reliable method in comparison the traditional method.

Keywords: Geiger-Muller, radiation detection, smoothing algorithms, dosimeter, dose calculation.

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Authors: Alexander L. Dmitriev, Sophia A. Bulgakova

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Temperature dependence of force of gravitation is one of the fundamental problems of physics. This problem has got special value in connection with that the general theory of relativity, supposing the weakest positive influence of a body temperature on its weight, actually rejects an opportunity of measurement of negative influence of temperature on gravity in laboratory conditions. Really, the recognition of negative temperature dependence of gravitation, for example, means basic impossibility of achievement of a singularity («a black hole») at a gravitational collapse. Laboratory experiments with exact weighing the heated up metal samples, indicating negative influence temperatures of bodies on their physical weight are described. Influence of mistakes of measurements is analyzed. Calculations of distribution of temperature in volume of the bar, agreed with experimental data of time dependence of weight of samples are executed. The physical substantiation of negative temperature dependence of weight of the bodies, based on correlation of acceleration at thermal movement of micro-particles of a body and its absolute temperature, are given.

Keywords: Gravitation, temperature, weight.

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Authors: Sharfi Dirar, Shihab Elhaj, Ahmed El Fatih

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Computational fluid dynamics were used to simulate and study the heated water boiler tube for both normal and rifled tube with a refinement of the mesh to check the convergence. The operation condition was taken from GARRI power station and used in a boundary condition accordingly. The result indicates the rifled tube has higher heat transfer efficiency than the normal tube.

Keywords: Boiler tube, Convergence Check, Normal Tube, Rifled Tube.

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Authors: Eric Y. Zhang, L. Acu

Abstract:

This paper is to point out the limitations of modern medical research and why the Traditional Chinese Medicine (TCM) can help address the limitations. Many of the modern medical research results are based on the findings in fundamental research disciplines, such as physics, and chemistry. However, this foundation is not as solid as it seems. The theory proposed in this paper, the Law of Chasm, or the Chasm Theory, states that there are two categories of objects to be studied. One is non-life objects, or lifeless objects; the other is living beings, or the objects that are alive. The laws and findings obtained by studying non-life objects may not all be extended to living beings, and vice versa. TCM is the study of medicine based on living beings. Therefore, TCM findings may not exist in the body of the knowledge obtained from studying non-life objects.

Keywords: TCM, Traditional Chinese Medicine, Law of Chasm, Chasm Theory, living-beings, non-life.

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Authors: A. Ruimi, S. Goyal, B. M. Nour

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Interactive web-based computer simulations are needed by the medical community to replicate the experience of surgical procedures as closely and realistically as possible without the need to practice on corpses, animals and/or plastic models. In this paper, we offer a review on current state of the research on simulations of surgical threads, identify future needs and present our proposed plans to meet them. Our goal is to create a physics-based simulator, which will predict the behavior of surgical thread when subjected to conditions commonly encountered during surgery. To that end, we will i) develop three dimensional finite element models based on the Cosserat theory of elasticity ii) test and feedback results with the medical community and iii) develop a web-based user interface to run/command our simulator and visualize the results. The impacts of our research are that i) it will contribute to the development of a new generation of training for medical school students and ii) the simulator will be useful to expert surgeons in developing new, better and less risky procedures.

Keywords: Cosserat rod-theory, FEM simulations, Modeling, Surgical thread.

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Authors: Francois T. Pronk, Steven J. Hulshoff

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A study of various turbulent inflow generation methods was performed to compare their relative effectiveness for LES computations of turbulent boundary layers. This study confirmed the quality of the turbulent information produced by the family of recycling and rescaling methods which take information from within the computational domain. Furthermore, more general inflow methods also proved applicable to such simulations, with a precursor-like inflow and a random inflow augmented with forcing planes showing promising results.

Keywords: Boundary layer, Flat plate, Inflow modeling, LES

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