Search results for: Molecular Interaction

Authors: Thevaneyan K. David, John P. Forth

Abstract:

Integral Abutment Bridges (IAB) are defined as simple or multiple span bridges in which the bridge deck is cast monolithically with the abutment walls. This kind of bridges are becoming very popular due to different aspects such as good response under seismic loading, low initial costs, elimination of bearings, and less maintenance. However the main issue related to the analysis of this type of structures is dealing with soil-structure interaction of the abutment walls and the supporting piles. Various soil constitutive models have been used in studies of soil-structure interaction in this kind of structures by researchers. This paper is an effort to review the implementation of various finite elements model which explicitly incorporates the nonlinear soil and linear structural response considering various soil constitutive models and finite element mesh.

Keywords: Constitutive Models, FEM, Integral AbutmentBridges, Soil-structure Interactions

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Authors: D.Toghraie, A.R.Azimian

Abstract:

Molecular dynamics simulation of annular flow boiling in a nanochannel with 70000 particles is numerically investigated. In this research, an annular flow model is developed to predict the superheated flow boiling heat transfer characteristics in a nanochannel. To characterize the forced annular boiling flow in a nanochannel, an external driving force F ext ranging from 1to12PN (PN= Pico Newton) is applied along the flow direction to inlet fluid particles during the simulation. Based on an annular flow model analysis, it is found that saturation condition and superheat degree have great influences on the liquid-vapor interface. Also, the results show that due to the relatively strong influence of surface tension in small channel, the interface between the liquid film and vapor core is fairly smooth, and the mean velocity along the stream-wise direction does not change anymore.

Keywords: Lennard-Jones Potential, Molecular DynamicsSimulation, Periodic Boundary Conditions (PBC), Non-EquilibriumMolecular Dynamics (NEMD), Annular Flow Boiling

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Authors: Salima Hacini, Zahia Guessoum, Zizette Boufaïda

Abstract:

Human activities are increasingly based on the use of remote resources and services, and on the interaction between remotely located parties that may know little about each other. Mobile agents must be prepared to execute on different hosts with various environmental security conditions. The aim of this paper is to propose a trust based mechanism to improve the security of mobile agents and allow their execution in various environments. Thus, an adaptive trust mechanism is proposed. It is based on the dynamic interaction between the agent and the environment. Information collected during the interaction enables generation of an environment key. This key informs on the host-s trust degree and permits the mobile agent to adapt its execution. Trust estimation is based on concrete parameters values. Thus, in case of distrust, the source of problem can be located and a mobile agent appropriate behavior can be selected.

Keywords: Internet security, malicious host, mobile agent security, trust management

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Authors: Bhatti A., Nahavandi S., Hossny M.

Abstract:

Current advancements in nanotechnology are dependent on the capabilities that can enable nano-scientists to extend their eyes and hands into the nano-world. For this purpose, a haptics (devices capable of recreating tactile or force sensations) based system for AFM (Atomic Force Microscope) is proposed. The system enables the nano-scientists to touch and feel the sample surfaces, viewed through AFM, in order to provide them with better understanding of the physical properties of the surface, such as roughness, stiffness and shape of molecular architecture. At this stage, the proposed work uses of ine images produced using AFM and perform image analysis to create virtual surfaces suitable for haptics force analysis. The research work is in the process of extension from of ine to online process where interaction will be done directly on the material surface for realistic analysis.

Keywords: Haptics, AFM, force feedback, image analysis.

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Authors: Nilubon Kurubanjerdjit, Nattakarn Iam-On, Ka-Lok Ng

Abstract:

MicroRNAs are small non-coding RNA found in many different species. They play crucial roles in cancer such as biological processes of apoptosis and proliferation. The identification of microRNA-target genes can be an essential first step towards to reveal the role of microRNA in various cancer types. In this paper, we predict miRNA-target genes for lung cancer by integrating prediction scores from miRanda and PITA algorithms used as a feature vector of miRNA-target interaction. Then, machine-learning algorithms were implemented for making a final prediction. The approach developed in this study should be of value for future studies into understanding the role of miRNAs in molecular mechanisms enabling lung cancer formation.

Keywords: MicroRNA, miRNAs, lung cancer, machine learning, Naïve Bayes, SVM.

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Authors: Vladimir I. Ponomarenko, Mikhail D. Prokhorov, Anatoly S. Karavaev

Abstract:

The interaction between respiration and low-frequency rhythms of the cardiovascular system is studied. The obtained results count in favor of the hypothesis that low-frequency rhythms in blood pressure and R-R intervals are generated in different central neural structures involved in the autonomic control of the cardiovascular systems.

Keywords: Cardiovascular system, R-R intervals, blood pressure, synchronization.

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Authors: Bhatti A., Nahavandi S., Hossny M.

Abstract:

Current advancements in nanotechnology are dependent on the capabilities that can enable nano-scientists to extend their eyes and hands into the nano-world. For this purpose, a haptics (devices capable of recreating tactile or force sensations) based system for AFM (Atomic Force Microscope) is proposed. The system enables the nano-scientists to touch and feel the sample surfaces, viewed through AFM, in order to provide them with better understanding of the physical properties of the surface, such as roughness, stiffness and shape of molecular architecture. At this stage, the proposed work uses of ine images produced using AFM and perform image analysis to create virtual surfaces suitable for haptics force analysis. The research work is in the process of extension from of ine to online process where interaction will be done directly on the material surface for realistic analysis.

Keywords: Haptics, AFM, force feedback, image analysis.

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Authors: I. Mahmood

Abstract:

This survey was conducted to explore the hypothesis that excessive screen exposure combined with a subsequent decrease in parent-child interaction during infancy might be associated with autism. The main questions being asked are: Were children with autism exposed to long hours of screen time during the first 2 years of life? And what was the reason(s) for exposure at such an early age? Other variables were also addressed in this survey. An Arabic questionnaire was administered online (June 2019) via a Facebook page, relatively well-known in Arab countries. 1725 parents of children diagnosed with autism participated in this survey. Results show that 80.9% of children surveyed who were diagnosed with autism had been exposed to screens for long periods of time during the first 2 years of life. It can be inferred from the results of this survey that over-exposure to screens disrupt the parent-child interaction which is shown to be associated with ASD. The results of this survey highlight the harmful effects of screen exposure during infancy and the importance of parent-child interaction during the critical period of brain development. This paper attempts to further explore the connection between parent-child interaction and ASD, as well as serve as a call for further research and investigation of the relation between screens and parent-child interactions during infancy and Autism.

Keywords: Attachment disorder, autism, screen exposure, virtual autism.

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Authors: Abdulhamit Donder, Erhan Ilhan Konukseven

Abstract:

Grinding operation is performed in order to obtain desired surfaces precisely in machining process. The needed relative motion between the cutting tool and the workpiece is generally created either by the movement of the cutting tool or by the movement of the workpiece or by the movement of both of them as in our case. For all these cases, the coherence level between the movements and the interaction forces is a key influential parameter for efficient grinding. Therefore, in this work, spectral coherence analysis has been performed to investigate the coherence level between grinding interaction forces and the movement of the workpiece on our robotic-grinding experimental setup in METU Mechatronics Laboratory.

Keywords: Coherence analysis, correlation, FFT, grinding, Hanning window, machining, Piezo actuator, reverse arrangements test, spectral analysis.

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Authors: J. Tengrang, T. Rungrotmongkol, S. Hannongbua

Abstract:

Every 2-3 years the influenza B virus serves epidemics. Neuraminidase (NA) is an important target for influenza drug design. Although, oseltamivir, an oral neuraminidase drug, has been shown good inhibitory efficiency against wild-type of influenza B virus, the lower susceptibility to the R152K mutation has been reported. Better understanding of oseltamivir efficiency and resistance toward the influenza B NA wild-type and R152K mutant, respectively, could be useful for rational drug design. Here, two complex systems of wild-type and R152K NAs with oseltamivir bound were studied using molecular dynamics (MD) simulations. Based on 5-ns MD simulation, the loss of notable hydrogen bond and decrease in per-residue decomposition energy from the mutated residue K152 contributed to drug compared to those of R152 in wildtype were found to be a primary source of high-level of oseltamivir resistance due to the R152K mutation.

Keywords: Influenza B neuraminidase, Molecular dynamics simulation, Oseltamivir resistance, R152K mutant

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Authors: Byoung-Tak Zhang, Chan-Hoon Park

Abstract:

Hypernetworks are a generalized graph structure representing higher-order interactions between variables. We present a method for self-organizing hypernetworks to learn an associative memory of sentences and to recall the sentences from this memory. This learning method is inspired by the “mental chemistry" model of cognition and the “molecular self-assembly" technology in biochemistry. Simulation experiments are performed on a corpus of natural-language dialogues of approximately 300K sentences collected from TV drama captions. We report on the sentence completion performance as a function of the order of word-interaction and the size of the learning corpus, and discuss the plausibility of this architecture as a cognitive model of language learning and memory.

Keywords: Linguistic recall memory, sentence completion task, self-organizing hypernetworks, cognitive learning and memory.

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Authors: D. Toghraie, A. R. Azimian

Abstract:

In this paper, the Lennard -Jones potential is applied to molecules of liquid argon as well as its vapor and platinum as solid surface in order to perform a non-equilibrium molecular dynamics simulation to study the microscopic aspects of liquid-vapor-solid interactions. The channel is periodic in x and y directions and along z direction it is bounded by atomic walls. It was found that density of the liquids near the solid walls fluctuated greatly and that the structure was more like a solid than a liquid. This indicates that the interactions of solid and liquid molecules are very strong. The resultant surface tension, liquid density and vapor density are found to be well predicted when compared with the experimental data for argon. Liquid and vapor densities were found to depend on the cutoff radius which induces the use of P3M (particle-particle particle-mesh) method which was implemented for evaluation of force and surface tension.

Keywords: Lennard-Jones Potential, Molecular DynamicsSimulation, Periodic Boundary Conditions (PBC), Non-EquilibriumMolecular Dynamics (NEMD).

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Authors: Arturo Ayala-Hernandez, Humberto H´ıjar

Abstract:

We propose a new alternative method for imposing fluid-solid boundary conditions in simulations of Multiparticle Collision Dynamics. Our method is based on the introduction of an explicit potential force acting between the fluid particles and a surface representing a solid boundary. We show that our method can be used in simulations of plane Poiseuille flows. Important quantities characterizing the flow and the fluid-solid interaction like the slip coefficient at the solid boundary and the effective viscosity of the fluid, are measured in terms of the set of independent parameters defining the numerical implementation. We find that our method can be used to simulate the correct hydrodynamic flow within a wide range of values of these parameters.

Keywords: Multiparticle Collision Dynamics, Fluid-Solid Boundary Conditions, Molecular Dynamics.

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Authors: K. Khanafer

Abstract:

The aim of this investigation was to validate the fluid-structure interaction (FSI) model of type B aortic dissection with our experimental results from a bench-top-model. Another objective was to study the relationship between the size of a septectomy that increases the outflow of the false lumen and its effect on the values of the differential of pressure between true lumen and false lumen. FSI analysis based on Galerkin’s formulation was used in this investigation to study flow pattern and hemodynamics within a flexible type B aortic dissection model using boundary conditions from our experimental data. The numerical results of our model were verified against the experimental data for various tear size and location. Thus, CFD tools have a potential role in evaluating different scenarios and aortic dissection configurations.

Keywords: Aortic dissection, fluid-structure interaction, in vitro model, numerical.

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Authors: Giovanni Aloisio, Lucio T. De Paolis, Luciana Provenzano, Lucio Colizzi, Gianluca Pantile

Abstract:

One of the essential requirements in order to have a realistic surgical simulator is real-time interaction by means of a haptic interface is. In fact, reproducing haptic sensations increases the realism of the simulation. However, the interaction need to be performed in real-time, since a delay between the user action and the system reaction reduces the user immersion. In this paper, we present a prototype of the coronary stent implant simulator developed in the HERMES Project; this system allows real-time interactions with a artery by means of a specific haptic device; thus the user can interactively navigate in a reconstructed artery and force feedback is produced when contact occurs between the artery walls and the medical instruments

Keywords: Collision Detection, Haptic Interface, Real-Time Interaction, Surgical Simulator.

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Authors: Taewon Seo

Abstract:

The characteristics of physiological blood flow in human carotid arterial bifurcation model have been numerically studied using a fully coupled fluid-structure interaction (FSI) analysis. This computational model with the fluid-structure interaction is constructed to investigate the flow characteristics and wall shear stress in the carotid artery. As the flow begins to decelerate after the peak flow, a large recirculation zone develops at the non-divider wall of both internal carotid artery (ICA) and external carotid artery (ECA) in FSI model due to the elastic energy stored in the expanding compliant wall. The calculated difference in wall shear stress (WSS) in both Non-FSI and FSI models is a range of between 5 and 11% at the mean WSS. The low WSS corresponds to regions of carotid artery that are more susceptible to atherosclerosis.

Keywords: Carotid artery, Fluid-structure interaction, Hemodynamics, Wall shear stress.

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Authors: S. A. Kondratyev, O. I. Ibragimova

Abstract:

The authors discuss the collecting abilities of desorbable species (DS) of saturated fatty acids. The DS species of the reagent are understood as species capable of moving from the surface of the mineral particle to the bubble at the moment of the rupture of the interlayer of liquid separating these objects of interaction. DS species of carboxylic acids (molecules and ionic-molecular complexes) have the ability to spread over the surface of the bubble. The rate of their spreading at pH 7 and 10 over the water surface is determined. The collectibility criterion of saturated fatty acids is proposed. The values of forces exerted by the spreading DS species of reagents on liquid in the interlayer and the liquid flow rate from the interlayer are determined.

Keywords: Criterion of action of physically adsorbed reagent, flotation, saturated fatty acids, surface pressure.

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Authors: Vinay Gautam, Vivek Gautam

Abstract:

With increase in the unauthorized users access, it is required to increase the security in the Near Field Communication (NFC). In the paper we propose a user behavior based enhanced protocol entitled ‘User Behavior based Enhanced Protocol (UBEP)’ to increase the security in NFC enabled devices. The UBEP works on the history of interaction of a user with system.The propose protocol considers four different factors (touch, time and distance & angle) of user behavior to know the authenticity or authorization of the users. These factors can be same for a user during interaction with the system. The UBEP uses two phase user verification system to authenticate a user. Firstly the acquisition phase is used to acquire and store the user interaction with NFC device and the same information is used in future to detect the authenticity of the user. The second phase (recognition) uses analysis of current and previous scenario of user interaction and digital signature verification system to finally authenticate user. The analysis of user based input makes a NFC transaction more advance and secure. This security is very tactical because it is completely depends on usage of the device.

Keywords: Security, Network Field communication, NFC Protocol.

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Authors: W. P. Hu, J. V. Kumar, Jeffrey J. P. Tsai

Abstract:

The inhibition of SH2 domain regulated protein-protein interactions is an attractive target for developing an effective chemotherapeutic approach in the treatment of disease. Molecular simulation is a useful tool for developing new drugs and for studying molecular recognition. In this study, we searched potential drug compounds for the inhibition of SH2 domain by performing structural similarity search in PubChem Compound Database. A total of 37 compounds were screened from the database, and then we used the LibDock docking program to evaluate the inhibition effect. The best three compounds (AP22408, CID 71463546 and CID 9917321) were chosen for MD simulations after the LibDock docking. Our results show that the compound CID 9917321 can produce a more stable protein-ligand complex compared to other two currently known inhibitors of Src SH2 domain. The compound CID 9917321 may be useful for the inhibition of SH2 domain based on these computational results. Subsequently experiments are needed to verify the effect of compound CID 9917321 on the SH2 domain in the future studies.

Keywords: Nonpeptide inhibitor, Src SH2 domain, LibDock, molecular dynamics simulation.

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Authors: Shreya Thusoo, Karan Modi, Ankit Kumar Jha, Rajesh Kumar

Abstract:

Since the evolution of computational tools and simulation software, there has been considerable increase in research on Soil Structure Interaction (SSI) to decrease the computational time and increase accuracy in the results. To aid the designer with a proper understanding of the response of structure in different soil types, the presented paper compares the deformation, shear stress, acceleration and other parameters of multi-storey building for a specific input ground motion using Response-spectrum Analysis (RSA) method. The response of all the models of different heights have been compared in different soil types. Finite Element Simulation software, ANSYS, has been used for all the computational purposes. Overall, higher response is observed with SSI, while it increases with decreasing stiffness of soil.

Keywords: Soil-structure interaction, response-spectrum analysis, finite element method, multi-storey buildings.

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Authors: Rozhgar A. Khailany, Mehri Igci, Emine Bayraktar, Sakip Erturhan, Metin Karakok, Ahmet Arslan

Abstract:

Kidney cancer is the most lethal urological cancer accounting for 3% of adult malignancies. VHL, a tumor-suppressor gene, is best known to be associated with renal cell carcinoma (RCC). The VHL functions as negative regulator of hypoxia inducible factors. Recent sequencing efforts have identified several novel frequent mutations of histone modifying and chromatin remodeling genes in ccRCC (clear cell RCC) including PBRM1 and SETD2. The PBRM1 gene encodes the BAF180 protein, which involved in transcriptional activation and repression of selected genes. SETD2 encodes a histone methyltransferase, which may play a role in suppressing tumor development. In this study, RNAs of 30 paired tumor and normal samples that were grouped according to the types of kidney cancer and clinical characteristics of patients, including gender and average age were examined by RT-PCR, SSCP and sequencing techniques. VHL, PBRM1 and SETD2 expressions were relatively down-regulated. However, statistically no significance was found (Wilcoxon signed rank test, p>0.05). Interestingly, no mutation was observed on the contrary of previous studies. Understanding the molecular mechanisms involved in the pathogenesis of RCC has aided the development of molecular-targeted drugs for kidney cancer. Further analysis is required to identify the responsible genes rather than VHL, PBRM1 and SETD2 in kidney cancer.

Keywords: Kidney cancer, molecular biomarker, expression analysis, mutation screening.

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Authors: Hasan Furkan Kurt, Tugba Nur Atabey, Onat Cavit Dereli, Ahmad Salmanogli, H. Selcuk Gecim

Abstract:

In the article, the main goal is to study the effect of the plasmonic properties on the photocurrent generated by a photodetector. Fundamentally, a typical photodetector is designed and simulated using the finite element methods. To utilize the plasmonic effect, gold nanoparticles with different shape, size and morphology are buried into the intrinsic region. Plasmonic effect is arisen through the interaction of the incoming light with nanoparticles by which electrical properties of the photodetector are manipulated. In fact, using plasmonic nanoparticles not only increases the absorption bandwidth of the incoming light, but also generates a high intensity near-field close to the plasmonic nanoparticles. Those properties strongly affect the generated photocurrent. The simulation results show that using plasmonic nanoparticles significantly enhances the electrical properties of the photodetectors. More importantly, one can easily manipulate the plasmonic properties of the gold nanoparticles through engineering the nanoparticles' size, shape and morphology. Another important phenomenon is plasmon-plasmon interaction inside the photodetector. It is shown that plasmon-plasmon interaction improves the electron-hole generation rate by which the rate of the current generation is severely enhanced. This is the key factor that we want to focus on, to improve the photodetector electrical properties.

Keywords: Nanoparticles, plasmonic, plasmon-plasmon interaction, plasmonic photodetector.

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Authors: R. Manaffar, R. Maleki, S. Zare, N. Agh, S. Soltanian, B. Sehatnia, P. Sorgeloos, P. Bossier, G. Van Stappen

Abstract:

Artemia is one of the most conspicuous invertebrates associated with aquaculture. It can be considered as a model organism, offering numerous advantages for comprehensive and multidisciplinary studies using morphologic or molecular methods. Since DNA extraction is an important step of any molecular experiment, a new and a rapid method of DNA extraction from adult Artemia was described in this study. Besides, the efficiency of this technique was compared with two widely used alternative techniques, namely Chelex® 100 resin and SDS-chloroform methods. Data analysis revealed that the new method is the easiest and the most cost effective method among the other methods which allows a quick and efficient extraction of DNA from the adult animal.

Keywords: APD, Artemia, DNA extraction, Molecularexperiments

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Authors: A. Aljohani, M. Orif

Abstract:

The concentration of polycyclic aromatic hydrocarbons (PAH) in clams (A. glabrata) was examined in samples collected from Alseef Beach, 30 km south of Jeddah city. Gas chromatography-mass spectrometry (GC-MS) was used to analyze the 14 PAHs. The concentration of total PAHs was found to range from 11.521 to 40.149 ng/gdw with a mean concentration of 21.857 ng/gdw, which is lower compared to similar studies. The lower molecular weight PAHs with three rings comprised 18.14% of the total PAH concentrations in the clams, while the high molecular weight PAHs with four rings, five rings, and six rings account for 81.86%. Diagnostic ratios for PAH source distinction suggested pyrogenic or anthropogenic sources.

Keywords: Bivalves, biomonitoring, hydrocarbons, PAHs.

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Authors: Sérgio F. Sousa, Nuno M. F. S. A. Cerqueira, Marta A. S. Perez, Irina S. Moreira, António J. M.Ribeiro, Ana R. A. P. Neves, Maria J. Ramos, Pedro A. Fernandes

Abstract:

In this work we report the recent progresses that have been achieved by our group in the last half decade on the field of computational proteomics. Specifically, we discuss the application of Molecular Dynamics Simulations and Electronic Structure Calculations in drug design, in the clarification of the structural and dynamic properties of proteins and enzymes and in the understanding of the catalytic and inhibition mechanism of cancer-related enzymes. A set of examples illustrate the concepts and help to introduce the reader into this important and fast moving field.

Keywords: Enzyme, Molecular Dynamics, Protein, Quantum Mechanics.

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Authors: Yong H. Chung, Eun J. Han, Seil Lee, Sun Y. Park, Eun H. Yoon, Eun J. Cho, Jang H. Lee, Young J. Chu, Jang H. Ha, Jongseo Chai, Yu S. Kim, Min Y. Lee, Hyeyoung Lee

Abstract:

Cross sections of As radionuclides in the interaction of natGe with 14-30 MeV protons have been deduced by off-line y-ray spectroscopy to find optimal reaction channels leading to radiotracers for positron emission tomography. The experimental results were compared with the previous results and those estimated by the compound nucleus reaction model.

Keywords: Compound nucleus reaction model, off-line g-ray spectroscopy, radionuclide.

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Authors: Pavlo Selyshchev

Abstract:

We consider fluctuations of defects density taking into account their interaction. Stochastic field of displacement generation rate gives random defect distribution. We determinate statistical characteristics (mean and dispersion) of random field of point defect distribution as function of defect generation parameters, temperature and properties of irradiated crystal.

 

Keywords: Irradiation, Primary Defects, Interaction, Fluctuations.

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Authors: Assel S. Issabekova, Olga A. Berillo, Vladimir A. Khailenko, Shara A. Atambayeva, Mireille Regnier, Anatoly T. Ivachshenko

Abstract:

Regulatory relationships of 686 intronic miRNA and 784 intergenic miRNAs with mRNAs of 51 intronic miRNA coding genes were established. Interaction features of studied miRNAs with 5'UTR, CDS and 3'UTR of mRNA of each gene were revealed. Functional regions of mRNA were shown to be significantly heterogenous according to the number of binding sites of miRNA and to the location density of these sites.

Keywords: 5'UTR, 3'UTR, CDS, miRNA, target mRNA

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Authors: Xiaoli Shen, Yuehui Chen

Abstract:

Interactions among proteins are the basis of various life events. So, it is important to recognize and research protein interaction sites. A control set that contains 149 protein molecules were used here. Then 10 features were extracted and 4 sample sets that contained 9 sliding windows were made according to features. These 4 sample sets were calculated by Radial Basis Functional neutral networks which were optimized by Particle Swarm Optimization respectively. Then 4 groups of results were obtained. Finally, these 4 groups of results were integrated by decision fusion (DF) and Genetic Algorithm based Selected Ensemble (GASEN). A better accuracy was got by DF and GASEN. So, the integrated methods were proved to be effective.

Keywords: protein interaction sites, features, sliding windows, radial basis functional neutral networks, genetic algorithm basedselected ensemble.

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Authors: Fernando Miguel Campos, Carlos Ferreira, João Pestana, Pedro Campos, Nils Ehrenberg, Wojciech Hydzik

Abstract:

The current trend of organizations offering their workers open-office spaces and co-working offices has been primed for stimulating teamwork and collaboration. However, this is not always valid as these kinds of spaces bring other types of challenges that compromise workers productivity and creativity. We present an approach for improving creativity and productivity at the workspace by redesigning an office chair that incorporates subtle technological elements that help users focus, relax and being more productive and creative. This sheds light on how we can better design interactive furniture for such popular contexts, as we develop this new chair through a multidisciplinary approach using ergonomics, interior design, interaction design, hardware and software engineering and psychology.

Keywords: Creativity, co-working, ergonomics, human-computer interaction, interaction, interactive furniture, productivity.

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