Search results for: protein-protein interaction

Authors: Kyi Lin Lin Kyaw

Abstract:

Nowadays, we are facing with network threats that cause enormous damage to the Internet community day by day. In this situation, more and more people try to prevent their network security using some traditional mechanisms including firewall, Intrusion Detection System, etc. Among them honeypot is a versatile tool for a security practitioner, of course, they are tools that are meant to be attacked or interacted with to more information about attackers, their motives and tools. In this paper, we will describe usefulness of low-interaction honeypot and high-interaction honeypot and comparison between them. And then we propose hybrid honeypot architecture that combines low and high -interaction honeypot to mitigate the drawback. In this architecture, low-interaction honeypot is used as a traffic filter. Activities like port scanning can be effectively detected by low-interaction honeypot and stop there. Traffic that cannot be handled by low-interaction honeypot is handed over to high-interaction honeypot. In this case, low-interaction honeypot is used as proxy whereas high-interaction honeypot offers the optimal level realism. To prevent the high-interaction honeypot from infections, containment environment (VMware) is used.

Keywords: Low-interaction honeypot, High-interactionhoneypot, VMware, Proxy

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 2953

Authors: C. Thassana, W. Techitdheera

Abstract:

This calculation focus on the effect of exchange interaction J and Coulomb interaction U on spin magnetic moments (ms) of MnO by using the local spin density approximation plus the Coulomb interaction (LSDA+U) method within full potential linear muffin-tin orbital (FP-LMTO). Our calculated results indicated that the spin magnetic moments correlated to J and U. The relevant results exhibited the increasing spin magnetic moments with increasing exchange interaction and Coulomb interaction. Furthermore, equations of spin magnetic moment, which h good correspondence to the experimental data 4.58μB, are defined ms = 0.11J +4.52μB and ms = 0.03U+4.52μB. So, the relation of J and U parameter is obtained, it is obviously, J = -0.249U+1.346 eV.

Keywords: exchange interaction J, the Coulomb interaction U, spin magnetic moment, LSDA+U, MnO.

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 1740

Authors: Martin Henkel

Abstract:

Different forms of interaction are an integral part of modern courses. Traditional courses held on-campus might focus on teacher-student interaction, or student-student interaction, or both. However when these traditional on-campus courses are to be held as distance courses there is a risk that these well-designed interactions will be difficult or impossible to uphold. For example, studentstudent interaction in traditional project assignments might not work well if the students are scattered across the world. Thus, even a welldesigned traditional on-site course cannot without modification be turned into a distance course. Traditional on-site courses simply have to be redesigned to become true distance courses. This paper describes a structured approach which facilitates the redesign of a traditional course into a distance course. The approach is based on that the desired forms of course flexibility are identified, and thereafter that the course activities are redesigned to facilitate interaction in a distance course. The approach is making use of known patterns of pedagogic interaction and existing guidelines for distance education design. The approach is illustrated with an example course in the field of information systems design.

Keywords: Distance education, interaction in education, course design.

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 1422

Authors: Razvan Bocu, Sabin Tabirca

Abstract:

The study of proteomics reached unexpected levels of interest, as a direct consequence of its discovered influence over some complex biological phenomena, such as problematic diseases like cancer. This paper presents a new technique that allows for an accurate analysis of the human interactome network. It is basically a two-step analysis process that involves, at first, the detection of each protein-s absolute importance through the betweenness centrality computation. Then, the second step determines the functionallyrelated communities of proteins. For this purpose, we use a community detection technique that is based on the edge betweenness calculation. The new technique was thoroughly tested on real biological data and the results prove some interesting properties of those proteins that are involved in the carcinogenesis process. Apart from its experimental usefulness, the novel technique is also computationally effective in terms of execution times. Based on the analysis- results, some topological features of cancer mutated proteins are presented and a possible optimization solution for cancer drugs design is suggested.

Keywords: Betweenness centrality, interactome networks, proteinprotein interactions, protein communities, cancer.

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 1294

Authors: Alireza Bozorgian, Navid Majdi Nasab, Abdolreza Memari

Abstract:

A continuum model is presented to study vdW interaction on buckling analysis of multi-walled walled carbon nanotube. In previous studies, only the vdW interaction between adjacent two layers was considered and the vdW interaction between the other two layers was neglected. The results show that the vdW interaction cofficients are dependent on the change of interlayer spacing and the radii of tubes. With increase of radii the vdW coefficients approach a constant value. The numerical results show that the effect of vdW interaction on the critical strain for a doublewalled CNT is negligible when the radius is large enough for the both the cases of before and after buckling.

Keywords: Buckling, Carbon nanotube, van der Waals interaction, Multi-walled Carbon nanotube, Critical Strain, Prebuckling Pressure

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 1379

Authors: M. Dehestani, M. Ghasemi-Kooch

Abstract:

In this work, adsorption of chlorophylls a and b pigments in aqueous solution on the inner and outer surfaces of single-walled carbon nanotube (SWCNT) has been studied using molecular dynamics simulation. The linear interaction energy algorithm has been used to calculate the binding free energy. The results show that the adsorption of two pigments is fine on the both positions. Although there is the close similarity between these two pigments, their interaction with the nanotube is different. This result is useful to separate these pigments from one another. According to interaction energy between the pigments and carbon nanotube, interaction between these pigments-SWCNT on the inner surface is stronger than the outer surface. The interaction of SWCNT with chlorophylls phytol tail is stronger than the interaction of SWCNT with porphyrin ring of chlorophylls.

Keywords: Dynamic simulation, single walled carbon nanotube, chlorophyll, adsorption.

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 897

Authors: M. Rahimnejad, B. Vahidi, B. Ebrahimi Hoseinzadeh, F. Yazdian, P. Motamed Fath, R. Jamjah

Abstract:

In this study, we developed and simulated nano-drug delivery systems efficacy in compare to free drug prescription. Computational models can be utilized to accelerate experimental steps and control the experiments high cost. Molecular dynamics simulation (MDS), in particular NAMD was utilized to better understand the anti-cancer drug interaction with cell membrane model. Paclitaxel (PTX) and dipalmitoylphosphatidylcholine (DPPC) were selected for the drug molecule and as a natural phospholipid nanocarrier, respectively. This work focused on two important interaction parameters between molecules in terms of center of mass (COM) and van der Waals interaction energy. Furthermore, we compared the simulation results of the PTX interaction with the cell membrane and the interaction of DPPC as a nanocarrier loaded by the drug with the cell membrane. The molecular dynamic analysis resulted in low energy between the nanocarrier and the cell membrane as well as significant decrease of COM amount in the nanocarrier and the cell membrane system during the interaction. Thus, the drug vehicle showed notably better interaction with the cell membrane in compared to free drug interaction with the cell membrane.

Keywords: Anti-cancer drug, center of Mass, interaction energy, molecular dynamics simulation, nanocarrier.

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 1322

Authors: Omar GACI, Stefan BALEV, Antoine DUTOT

Abstract:

In this paper we introduce the notion of protein interaction network. This is a graph whose vertices are the protein-s amino acids and whose edges are the interactions between them. Using a graph theory approach, we observe that according to their structural roles, the nodes interact differently. By leading a community structure detection, we confirm this specific behavior and describe thecommunities composition to finally propose a new approach to fold a protein interaction network.

Keywords: interaction network, protein structure, community structure detection.

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 1519

Authors: Huynh Quyet Thang, Le Hai Quan

Abstract:

Interaction Model plays an important role in Modelbased Intelligent Interface Agent Architecture for developing Intelligent User Interface. In this paper we are presenting some improvements in the algorithms for development interaction model of interface agent including: the action segmentation algorithm, the action pair selection algorithm, the final action pair selection algorithm, the interaction graph construction algorithm and the probability calculation algorithm. The analysis of the algorithms also presented. At the end of this paper, we introduce an experimental program called “Personal Transfer System".

Keywords: interface agent, interaction model, user model.

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 2197

Authors: A. Maitarad, P. Maitarad

Abstract:

In order to find the particular interaction energy between cylcloguanil and the amino acids surrounding the pocket of wild type and quadruple mutant type PfDHFR enzymes, the MP2 method with basis set 6-31G(d,p) level of calculations was performed. The obtained interaction energies found that Asp54 has the strongest interaction energy to both wild type and mutant type of - 12.439 and -11.250 kcal/mol, respectively and three amino acids; Asp54, Ile164 and Ile14 formed the H-bonding with cycloguanil drug. Importantly, the mutation at Ser108Asn was the key important of cycloguanil resistant with showing repulsive interaction energy.

Keywords: Cycloguanil, DHFR, malaria disease, interactionenergy, quantum calculations

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 1412

Authors: R. K. Apalowo, D. Chronopoulos

Abstract:

A Finite Element (FE) based scheme is presented for quantifying guided wave interaction with Localised Nonlinear Structural Damage (LNSD) within structures of arbitrary layering and geometric complexity. The through-thickness mode-shape of the structure is obtained through a wave and finite element method. This is applied in a time domain FE simulation in order to generate time harmonic excitation for a specific wave mode. Interaction of the wave with LNSD within the system is computed through an element activation and deactivation iteration. The scheme is validated against experimental measurements and a WFE-FE methodology for calculating wave interaction with damage. Case studies for guided wave interaction with crack and delamination are presented to verify the robustness of the proposed method in classifying and identifying damage.

Keywords: Layered Structures, nonlinear ultrasound, wave interaction with nonlinear damage, wave finite element, finite element.

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 546

Authors: Swapnoneel Roy, Minhazur Rahman, Ashok Kumar Thakur

Abstract:

Bioinformatics and computational biology involve the use of techniques including applied mathematics, informatics, statistics, computer science, artificial intelligence, chemistry, and biochemistry to solve biological problems usually on the molecular level. Research in computational biology often overlaps with systems biology. Major research efforts in the field include sequence alignment, gene finding, genome assembly, protein structure alignment, protein structure prediction, prediction of gene expression and proteinprotein interactions, and the modeling of evolution. Various global rearrangements of permutations, such as reversals and transpositions,have recently become of interest because of their applications in computational molecular biology. A reversal is an operation that reverses the order of a substring of a permutation. A transposition is an operation that swaps two adjacent substrings of a permutation. The problem of determining the smallest number of reversals required to transform a given permutation into the identity permutation is called sorting by reversals. Similar problems can be defined for transpositions and other global rearrangements. In this work we perform a study about some genome rearrangement primitives. We show how a genome is modelled by a permutation, introduce some of the existing primitives and the lower and upper bounds on them. We then provide a comparison of the introduced primitives.

Keywords: Sorting Primitives, Genome Rearrangements, Transpositions, Block Interchanges, Strip Exchanges.

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 2161

Authors: Kuan-Liang Liu, Eric Lee, Jung-Jyh Lee, Jyh-Ping Hsu

Abstract:

The electrical interaction between two axisymmetric spheroidal particles in an electrolyte solution is examined numerically. A Galerkin finite element method combined with a Newton-Raphson iteration scheme is proposed to evaluate the spatial variation in the electrical potential, and the result obtained used to estimate the interaction energy between two particles. We show that if the surface charge density is fixed, the potential gradient is larger at a point, which has a larger curvature, and if surface potential is fixed, surface charge density is proportional to the curvature. Also, if the total interaction energy against closest surface-to-surface curve exhibits a primary maximum, the maximum follows the order (oblate-oblate) > (sphere-sphere)>(oblate-prolate)>(prolate-prolate), and if the curve has a secondary minimum, the absolute value of the minimum follows the same order.

Keywords: interaction energy, interaction force, Poisson-Boltzmann equation, spheroid.

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 1471

Authors: A. Jawahar

Abstract:

In this paper, the dependence of soliton pulses with respect to phase in a 10Gbps, single channel, dispersion uncompensated telecommunication system was studied. The characteristic feature of periodic soliton interaction was noted at the Interaction point (I=6202.5Km) in one collision length of L=12405.1 Km. The interaction point is located for 10Gbps system with an initial relative spacing (qo) of soliton as 5.28 using Perturbation theory. It is shown that, when two in-phase solitons are launched, they interact at the point I=6202.5 Km, but the interaction could be restricted with introduction of different phase initially. When the phase of the input solitons increases, the deviation of soliton pulses at the ‘I’ also increases. We have successfully demonstrated this effect in a telecommunication set-up in terms of Quality factor (Q), where the Q=0 for in-phase soliton. The Q was noted to be 125.9, 38.63, 47.53, 59.60, 161.37, and 78.04 for different phases such as 10o, 20o, 30o, 45o, 60o and 90o degrees respectively at Interaction point (I).

Keywords: Soliton interaction, Initial relative spacing, phase, Perturbation theory and telecommunication system.

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 1865

Authors: Waleed Maqableh, Ahmad Al-Hamad, Manjit Sidhu

Abstract:

Augmented reality (AR) technology has the capability to provide many benefits in the field of education as a modern technology which aided learning and improved the learning experience. This paper evaluates AR based application with multiple markers interaction technique (touch-to-print) which is designed for analyzing the kinematics of 4BL mechanism in mechanical engineering. The application is termed as AR-4BL-MAST and it allows the users to touch the symbols on a paper in natural way of interaction. The evaluation of this application was performed with mechanical engineering students and human–computer interaction (HCI) experts to test its effectiveness as a tangible user interface application where the statistical results show its ability as an interaction technique, and it gives the users more freedom in interaction with the virtual mechanical objects.

Keywords: Augmented reality, engineering, four-bar linkage, Multimedia, user interface, visualization.

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 1429

Authors: Vinicius Binotte, Guilherme Baldo, Christiane Goulart, Carlos Valadão, Eliete Caldeira, Teodiano Bastos

Abstract:

Socially assistive robotic has become increasingly active and it is present in therapies of people affected for several neurobehavioral conditions, such as Autism Spectrum Disorder (ASD). In fact, robots have played a significant role for positive interaction with children with ASD, by stimulating their social and cognitive skills. This work introduces a mobile socially-assistive robot, which was built for interaction with children with ASD, using non-linear control techniques for this interaction.

Keywords: Socially assistive robotics, mobile robot, autonomous control, autism.

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 1574

Authors: Paolo Pilloni, Fabrizio Mulas, Salvatore Carta

Abstract:

Nowadays, several research studies point up that an active lifestyle is essential for physical and mental health benefits. Mobile phones have greatly influenced people’s habits and attitudes also in the way they exercise. Our research work is mainly focused on investigating how to exploit mobile technologies to favour people’s exertion experience. To this end, we developed an exertion framework users can exploit through a real world mobile application, called EverywhereSport Run (EWRun), designed to act as a virtual personal trainer to support runners during their trainings. In this work, inspired by both previous findings in the field of interaction design for people with visual impairments, feedback gathered from real users of our framework, and positive results obtained from two experimentations, we present some new interaction facilities we designed to enhance the interaction experience during a training. The positive obtained results helped us to derive some interaction design recommendations we believe will be a valid support for designers of future mobile systems conceived to be used in circumstances where there are limited possibilities of interaction.

Keywords: Human Computer Interaction, Interaction Design Guidelines, Persuasive Mobile Technologies for Sport and Health.

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 1947

Authors: Mella Ismelina Farma Rahayu

Abstract:

Environmental problems could not be separated from unethical human perspectives and behaviors toward the environment. There is a fundamental error in the philosophy of people’s perspective about human and nature and their relationship with the environment, which in turn will create an inappropriate behavior in relation to the environment. The aim of this study is to investigate and to understand the ethics of the environment in the context of humans interacting with the environment by using the hermeneutic approach. The related theories and concepts collected from literature review are used as data, which were analyzed by using interpretation, critical evaluation, internal coherence, comparisons, and heuristic techniques. As a result of this study, there will be a picture related to the interaction of human and environment in the perspective of environmental ethics, as well as the problems of the value of ecological justice in the interaction of humans and environment. We suggest that the interaction between humans and environment need to be based on environmental ethics, in a spirit of mutual respect between humans and the natural world.

Keywords: The environment, environmental ethics, the interaction, value.

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 1599

Authors: Dowluru Ravi Kumar, Bhima Prabhakara Rao

Abstract:

Propagation of solitons in single-mode birefringent fibers is considered under the presence of third-order dispersion (TOD). The behavior of two neighboring solitons and their interaction is investigated under the presence of third-order dispersion with different group velocity dispersion (GVD) parameters. It is found that third-order dispersion makes the resultant soliton to deviate from its ideal position and increases the interaction between adjacent soliton pulses. It is also observed that this deviation due to third-order dispersion is considerably small when the optical pulse propagates at wavelengths relatively far from the zerodispersion. Modified coupled nonlinear Schrödinger-s equations (CNLSE) representing the propagation of optical pulse in single mode fiber with TOD are solved using split-step Fourier algorithm. The results presented in this paper reveal that the third-order dispersion can substantially increase the interaction between the solitons, but large group velocity dispersion reduces the interaction between neighboring solitons.

Keywords: Birefringence, Group velocity dispersion, Polarization mode dispersion, Soliton interaction, Third order dispersion.

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 1225

Authors: Yuan-Hsiang Chang, Pin-Chi Lin, Li-Der Jeng

Abstract:

Advance in techniques of image and video processing has enabled the development of intelligent video surveillance systems. This study was aimed to automatically detect moving human objects and to analyze events of dual human interaction in a surveillance scene. Our system was developed in four major steps: image preprocessing, human object detection, human object tracking, and motion trajectory analysis. The adaptive background subtraction and image processing techniques were used to detect and track moving human objects. To solve the occlusion problem during the interaction, the Kalman filter was used to retain a complete trajectory for each human object. Finally, the motion trajectory analysis was developed to distinguish between the interaction and non-interaction events based on derivatives of trajectories related to the speed of the moving objects. Using a database of 60 video sequences, our system could achieve the classification accuracy of 80% in interaction events and 95% in non-interaction events, respectively. In summary, we have explored the idea to investigate a system for the automatic classification of events for interaction and non-interaction events using surveillance cameras. Ultimately, this system could be incorporated in an intelligent surveillance system for the detection and/or classification of abnormal or criminal events (e.g., theft, snatch, fighting, etc.). 

Keywords: Motion detection, motion tracking, trajectory analysis, video surveillance.

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 1732

Authors: Hsuan-Chia Yang, Yan-Jhih Haung, Yu-Chuan Li

Abstract:

Researchers of drug-drug interaction alert systems have often suggested that there were high overridden rate for alerts and also too false alerts. However, research about decreasing false alerts is scant. Therefore, the aim of this article attempts to proactive identification of false alert for drug-drug interaction and provide solution to decrease false alerts. This research involved retrospective analysis prescribing database and calculated false alert rate by using MYSQL and JAVA. Results of this study showed 17% of false alerts and the false alert rate in the hospitals (37%) was more than in the clinics. To conclude, this study described the importance that drug-drug interaction alert system should not only detect drug name but also detect frequency or route, as well as in providing solution to decrease false alerts.

Keywords: drug-drug interaction, proactive identification, false alert

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 1765

Authors: Ricardo A. Martins, Matheus S. da Silva, Gabriel H. F. Iarossi, Helen C. M. Senefonte, Cinthyan R. S. C. de Barbosa

Abstract:

This paper is the development of a concept of the man/robot interaction. More accurately in developing of an autistic child that have more troubles with interaction, here offers an efficient solution, even though simple; however, less studied for this public. This concept is based on code applied thought out the Lego NXT kit, built for the interpretation of the robot, thereby can create this interaction in a constructive way for children suffering with Autism.

Keywords: Lego NXT, autism, ANN (Artificial Neural Network), Backpropagation.

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 883

Authors: Chewa Thassana, Wicharn Techitdheera

Abstract:

The spin (ms) and orbital (mo) magnetic moment of the antiferromagnetic NiO and MnO have been studied in the local spin density approximation (LSDA+U) within full potential linear muffin-tin orbital (FP-LMTO method with in the coulomb interaction U varying from 0 to 10eV, exchange interaction J, from 0 to 1.0eV, and volume compression VC in range of 0 to 80%. Our calculated results shown that the spin magnetic moments and the orbital magnetic moments increase linearly with increasing U and J. While the interesting behaviour appears when volume compression is greater than 70% for NiO and 50% for MnO at which ms collapses. Further increase of volume compression to be at 80% leads to the disappearance of both magnetic moments.

Keywords: spin-orbital magnetic moment, Coulomb interaction U and exchange interaction J, volume compression VC, LSDA+U.

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 2204

Authors: Omar Gaci, Stefan Balev

Abstract:

In this paper we introduce the notion of protein interaction network. This is a graph whose vertices are the protein-s amino acids and whose edges are the interactions between them. Using a graph theory approach, we identify a number of properties of these networks. We compare them to the general small-world network model and we analyze their hierarchical structure.

Keywords: interaction network, protein structure, small-world network.

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 1579

Authors: Nazar Zaki, Safaai Deris, Hany Alashwal

Abstract:

Detecting protein-protein interactions is a central problem in computational biology and aberrant such interactions may have implicated in a number of neurological disorders. As a result, the prediction of protein-protein interactions has recently received considerable attention from biologist around the globe. Computational tools that are capable of effectively identifying protein-protein interactions are much needed. In this paper, we propose a method to detect protein-protein interaction based on substring similarity measure. Two protein sequences may interact by the mean of the similarities of the substrings they contain. When applied on the currently available protein-protein interaction data for the yeast Saccharomyces cerevisiae, the proposed method delivered reasonable improvement over the existing ones.

Keywords: Protein-Protein Interaction, support vector machine, feature extraction, pairwise alignment, Smith-Waterman score.

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 1937

Authors: Mohammad Shoyaib, M. Abdullah-Al-Wadud, Oksam Chae

Abstract:

Proteomics is one of the largest areas of research for bioinformatics and medical science. An ambitious goal of proteomics is to elucidate the structure, interactions and functions of all proteins within cells and organisms. Predicting Protein-Protein Interaction (PPI) is one of the crucial and decisive problems in current research. Genomic data offer a great opportunity and at the same time a lot of challenges for the identification of these interactions. Many methods have already been proposed in this regard. In case of in-silico identification, most of the methods require both positive and negative examples of protein interaction and the perfection of these examples are very much crucial for the final prediction accuracy. Positive examples are relatively easy to obtain from well known databases. But the generation of negative examples is not a trivial task. Current PPI identification methods generate negative examples based on some assumptions, which are likely to affect their prediction accuracy. Hence, if more reliable negative examples are used, the PPI prediction methods may achieve even more accuracy. Focusing on this issue, a graph based negative example generation method is proposed, which is simple and more accurate than the existing approaches. An interaction graph of the protein sequences is created. The basic assumption is that the longer the shortest path between two protein-sequences in the interaction graph, the less is the possibility of their interaction. A well established PPI detection algorithm is employed with our negative examples and in most cases it increases the accuracy more than 10% in comparison with the negative pair selection method in that paper.

Keywords: Interaction graph, Negative training data, Protein-Protein interaction, Support vector machine.

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 1702

Authors: M. Z. Fathiah, R. G. Edyvean

Abstract:

Electrostatic interaction energy (ΔEEDL) is a part of the Extended Derjaguin-Landau-Verwey-Overbeek (XDLVO) theory, which, together with van der Waals (ΔEVDW) and acid base (ΔEAB) interaction energies, has been extensively used to investigate the initial adhesion of bacteria to surfaces. Electrostatic or electrical double layer interaction energy is considerably affected by surface potential; however it cannot be determined experimentally and is usually replaced by zeta (ζ) potential via electrophoretic mobility. This paper focusses on the effect of ionic concentration as a function of pH and the effect of mineral grain size on ζ potential. It was found that both ionic strength and mineral grain size play a major role in determining the value of ζ potential for the adhesion of P. putida to hematite and quartz surfaces. Higher ζ potential values lead to higher electrostatic interaction energies and eventually to higher total XDLVO interaction energy resulting in bacterial repulsion.

Keywords: XDLVO, Electrostatic interaction energy, zeta potential, P. putida, mineral.

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 2605

Authors: S. Arun Prakash, V. Malathi, M. S. Mani Rajan

Abstract:

The analytical bright two soliton solution of the 3- coupled nonlinear Schrödinger equations with variable coefficients in birefringent optical fiber is obtained by Darboux transformation method. To the design of ultra-speed optical devices, Soliton interaction and control in birefringence fiber is investigated. Lax pair is constructed for N coupled NLS system through AKNS method. Using two-soliton solution, we demonstrate different interaction behaviors of solitons in birefringent fiber depending on the choice of control parameters. Our results shows that interactions of optical solitons have some specific applications such as construction of logic gates, optical computing, soliton switching, and soliton amplification in wavelength division multiplexing (WDM) system.

Keywords: Optical soliton, soliton interaction, soliton switching, WDM.

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 2159

Authors: Eduardo Álvarez, Gerardo Quiroga, Jorge Orozco, Gabriel Chavira

Abstract:

AmI proposes a new way of thinking about computers, which follows the ideas of the Ubiquitous Computing vision of Mark Weiser. In these, there is what is known as a Disappearing Computer Initiative, with users immersed in intelligent environments. Hence, technologies need to be adapted so that they are capable of replacing the traditional inputs to the system by embedding these in every-day artifacts. In this work, we present an approach, which uses Radiofrequency Identification (RFID) and Near Field Communication (NFC) technologies. In the latter, a new form of interaction appears by contact. We compare both technologies by analyzing their requirements and advantages. In addition, we propose using a combination of RFID and NFC.

Keywords: Touching interaction, ambient intelligence, NFC, RFID.

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 1628

Authors: Seung Pil Pack

Abstract:

Deaminated lesions were produced via nitrosative oxidation of natural nucleobases; uracul (Ura, U) from cytosine (Cyt, C), hypoxanthine (Hyp, H) from adenine (Ade, A), and xanthine (Xan, X) and oxanine (Oxa, O) from guanine (Gua, G). Such damaged nucleobases may induce mutagenic problems, so that much attentions and efforts have been poured on the revealing of their mechanisms in vivo or in vitro. In this study, we employed these deaminated lesions as useful probes for analysis of DNA-binding/recognizing proteins or enzymes. Since the pyrimidine lesions such as Hyp, Oxa and Xan are employed as analogues of guanine, their comparative uses are informative for analyzing the role of Gua in DNA sequence in DNA-protein interaction. Several DNA oligomers containing such Hyp, Oxa or Xan substituted for Gua were designed to reveal the molecular interaction between DNA and protein. From this approach, we have got useful information to understand the molecular mechanisms of the DNA-recognizing enzymes, which have not ever been observed using conventional DNA oligomer composed of just natural nucleobases.

Keywords: Deaminated lesion, DNA-protein interaction, DNA-recognizing enzymes

Procedia APA BibTeX Chicago EndNote Harvard JSON MLA RIS XML ISO 690 PDF Downloads 1292