Search results for: molecular dynamic

Authors: Inci Kesilmis, Manolya Akin, Mehmet Melih Kesilmis

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The aim of this research was to compare dynamic balance ability (bipedal, right, left foot) and plantar-dorsi flexion range of motion in fencers and swimmers. 43 fencers participated as volunteer with mean age 15.74±1.90year and mean training year 4.97±2.37year. 25 swimmers participated as volunteer with mean age 15.36±1.65 yr. and mean training year 5.98±2.35 yr. Dynamic balance measured while participants were standing in the anatomical position with prokin tecno body for bipedal, right, left foot. Plantar and dorsal flexion range of motion measured while participants in seated position on the examination table and goniometer placed on the lateral malleolus. For statistical analyses; independent samples t test was used. There were significant differences between bipedal (p < 0.05), right foot (p < 0.05), left foot (p < 0.05) dynamic balance ability in favor of fencers. Also there was significant difference between right and left foot dorsal flexion range of motion (p < 0.001) in favor of fencers. There was no significant difference in plantar flexion range of motion between fencers and swimmers. The difference observed in fencers may be due to the use of more dorsal flexion in action moves and that swimming does not impact loading sport and it is performed in pool.

Keywords: fencing, swimming, dynamic balance, flexibility

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Authors: Farzad Yavari, Fereydoun Ohadi

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Today, with the development and growth of technology and extreme environmental changes, organizations need to identify opportunities and create creativity and innovation in order to be able to maintain or improve their position in competition with others. In this regard, it is necessary that the resources and assets of the organization are coordinated and reviewed in accordance with the orientation of the strategy. One of the competitive advantages of the present age is knowledge management, which is to equip the organization with the knowledge of the day and disseminate among employees and use it in the development of products and services. Therefore, in the forthcoming research, the impact of dynamic capabilities components (sense, seize, and reconfiguration) has been investigated on knowledge management processes (acquisition, integration and knowledge utilization) in the MAPNA Engineering and Construction Company using a field survey and applied research method. For this purpose, a questionnaire was filled out in the form of 15 questions for dynamic components and 15 questions for measuring knowledge management components and distributed among 46 employees of the knowledge management organization. Validity of the questionnaire was evaluated through content validity and its reliability with Cronbach's coefficient. Pearson correlation test and structural equation technique were used to analyze the data. The results of the research indicate a positive significant correlation between the components of dynamic capabilities and knowledge management.

Keywords: dynamic capabilities, knowledge management, sense capability, seize capability, reconfigurable capability, knowledge acquisition, knowledge integrity, knowledge utilization

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Authors: Mansouri Nabila, Ben Jemaa Yousra, Motamed Cina, Watelain Eric

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Research and development efforts in intelligent Advanced Driver Assistance Systems (ADAS) seek to save lives and reduce the number of on-road fatalities. For traffic and emergency monitoring, the essential but challenging task is vehicle detection and tracking in reasonably short time. This purpose needs first of all a powerful dynamic car detector model. In fact, this paper presents an optimized HOG process based on shape and motion parameters fusion. Our proposed approach mains to compute HOG by bloc feature from foreground blobs using configurable research window and pathway in order to overcome the shortcoming in term of computing time of HOG descriptor and improve their dynamic application performance. Indeed we prove in this paper that HOG by bloc descriptor combined with motion parameters is a very suitable car detector which reaches in record time a satisfactory recognition rate in dynamic outside area and bypasses several popular works without using sophisticated and expensive architectures such as GPU and FPGA.

Keywords: car-detector, HOG, motion, computing time

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Authors: Behzad Mohammadzadeh, Huyk Chun Noh

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The plate is one of the popular structural elements used in a wide range of industries and structures. They may be subjected to blast loads during explosion events, missile attacks or aircraft attacks. This study is to investigate dynamic responses of the rectangular plate subjected to explosive loads. The effects of material properties and plate thickness on responses of the plate are to be investigated. The compressive pressure is applied to the surface of the plate. Different amounts of thickness in the range from 10mm to 30mm are considered for the plate to evaluate the changes in responses of the plate with respect to the plate thickness. Two different properties are considered for the steel. First, the analysis is performed by considering only the elastic-plastic properties for the steel plate. Later on damping is considered to investigate its effects on the responses of the plate. To do analysis, the numerical method using a finite element based package ABAQUS is applied. Finally, dynamic responses and graphs showing the relation between maximum displacement of the plate and aim parameters are provided.

Keywords: impulsive loaded plates, dynamic analysis, ABAQUS, material nonlinearity

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

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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: Radhwan Yousif Sedik Al-Jawadi

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Optimization is necessary for finding appropriate solutions to a range of real-life problems. In particular, genetic (or more generally, evolutionary) algorithms have proved very useful in solving many problems for which analytical solutions are not available. In this paper, we present an optimization algorithm called Dynamic Schema with Dissimilarity and Similarity of Chromosomes (DSDSC) which is a variant of the classical genetic algorithm. This approach constructs new chromosomes from a schema and pairs of existing ones by exploring their dissimilarities and similarities. To show the effectiveness of the algorithm, it is tested and compared with the classical GA, on 15 two-dimensional optimization problems taken from literature. We have found that, in most cases, our method is better than the classical genetic algorithm.

Keywords: chromosome injection, dynamic schema, genetic algorithm, similarity and dissimilarity

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

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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: Elias K. Maragos, Petros E. Maravelakis

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In Dynamic Data Envelopment Analysis (DDEA), which is a subfield of Data Envelopment Analysis (DEA), the productivity of Decision Making Units (DMUs) is considered in relation to time. In this case, as it is accepted by the most of the researchers, there are outputs, which are produced by a DMU to be used as inputs in a future time. Those outputs are known as intermediates. The common models, in DDEA, do not take into account the shape of the distribution of those inputs, outputs or intermediates data, assuming that the distribution of the virtual value of them does not deviate from linearity. This weakness causes the limitation of the accuracy of the analytical power of the traditional DDEA models. In this paper, the authors, using the concept of piecewise linear inputs and outputs, propose an extended DDEA model. The proposed model increases the flexibility of the traditional DDEA models and improves the measurement of the dynamic performance of DMUs.

Keywords: Dynamic Data Envelopment Analysis, DDEA, piecewise linear inputs, piecewise linear outputs

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Authors: Alok Shiomurti Tripathi, Ajay Kumar Timiri, Papiya Mitra Mazumder, Anil Chandewar

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The present study evaluates the possible drug interaction between glimepiride (GLIM) and sildenafil citrate (SIL) in streptozotocin (STZ) induced in diabetic nephropathic (DN) animals and also postulates the possible mechanism of interaction by molecular modeling studies. Diabetic nephropathy was induced by single dose of STZ (60 mg/kg, ip) and confirms it by assessing the blood and urine biochemical parameters on 28th day of its induction. Selected DN animals were used for the drug interaction between GLIM (0.5mg/kg, p.o.) and SIL (2.5 mg/kg, p.o.) after 29th and 70th day of protocol. Drug interaction were assessed by evaluating the plasma drug concentration using HPLC-UV and also determine the change in the biochemical parameter in blood and urine. Mechanism of the interaction was postulated by molecular modeling study using Maestro module of Schrodinger software. DN was confirmed as there was significant alteration in the blood and urine biochemical parameter in STZ treated groups. The concentration of SIL increased significantly (p<0.001) in rat plasma when co administered with GLIM after 70th day of protocol. Molecular modelling study revealed few important interactions with rat serum albumin and CYP2C9.GLIM has strong hydrophobic interaction with binding site residues of rat serum albumin compared to SIL. Whereas, for CYP2C9, GLIM has strong hydrogen bond with polar contacts and hydrophobic interactions than SIL. Present study concludes that bioavailability of SIL increases when co-administered chronically with GLIM in the management of DN animals and mechanism has been supported by molecular modeling studies.

Keywords: diabetic nephropathy, glimepiride, sildenafil citrate, pharmacokinetics, homology modeling, schrodinger

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Authors: S. B. Kerur, B. S. Murgayya

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The development of micro and nano particle is challenging task and the study of the behavior of material at the micro level is gaining importance as their behavior at micro/nano level is different. These micro particle are being used as a sensing element to measure and detects the hazardous chemical, gases, explosives and biological agents. In the present study, finite element method is used for static and dynamic analysis of simple and composite cantilever beams of different shapes. The present FE model is validated with available analytical results and various parameters like shape, materials properties, damped and undamped conditions are considered for the numerical study. The results show the effects of shape change on the natural frequency and as these are used with fluid for chemical applications, the effect of damping due to viscous nature of fluid are simulated by considering different damping coefficient effect on the dynamic behavior of cantilever beams. The obtained results show the effect of these parameters can be effectively utilized based on system requirements.

Keywords: micro, FEM, dynamic, cantilever beam

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Authors: Nahush Modak, Meena Pangarkar, Anand Pathak, Ankita Tamhane

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Background: Breast cancer is the prominent cause of cancer and mortality among women. This study was done to show the statistical analysis of a cohort of over 250 patients detected with breast cancer diagnosed by oncologists using Immunohistochemistry (IHC). IHC was performed by using ER; PR; HER2; Ki-67 antibodies. Materials and methods: Formalin fixed Paraffin embedded tissue samples were obtained by surgical manner and standard protocol was followed for fixation, grossing, tissue processing, embedding, cutting and IHC. The Ventana Benchmark XT machine was used for automated IHC of the samples. Antibodies used were supplied by F. Hoffmann-La Roche Ltd. Statistical analysis was performed by using SPSS for windows. Statistical tests performed were chi-squared test and Correlation tests with p<.01. The raw data was collected and provided by National Cancer Insitute, Jamtha, India. Result: Luminal B was the most prevailing molecular subtype of Breast cancer at our institute. Chi squared test of homogeneity was performed to find equality in distribution and Luminal B was the most prevalent molecular subtype. The worse prognostic indicator for breast cancer depends upon expression of Ki-67 and her2 protein in cancerous cells. Our study was done at p <.01 and significant dependence was observed. There exists no dependence of age on molecular subtype of breast cancer. Similarly, age is an independent variable while considering Ki-67 expression. Chi square test performed on Human epidermal growth factor receptor 2 (HER2) statuses of patients and strong dependence was observed in percentage of Ki-67 expression and Her2 (+/-) character which shows that, value of Ki depends upon Her2 expression in cancerous cells (p<.01). Surprisingly, dependence was observed in case of Ki-67 and Pr, at p <.01. This shows that Progesterone receptor proteins (PR) are over-expressed when there is an elevation in expression of Ki-67 protein. Conclusion: We conclude from that Luminal B is the most prevalent molecular subtype at National Cancer Institute, Jamtha, India. There was found no significant correlation between age and Ki-67 expression in any molecular subtype. And no dependence or correlation exists between patients’ age and molecular subtype. We also found that, when the diagnosis is Luminal A, out of the cohort of 257 patients, no patient shows >14% Ki-67 value. Statistically, extremely significant values were observed for dependence of PR+Her2- and PR-Her2+ scores on Ki-67 expression. (p<.01). Her2 is an important prognostic factor in breast cancer. Chi squared test for Her2 and Ki-67 shows that the expression of Ki depends upon Her2 statuses. Moreover, Ki-67 cannot be used as a standalone prognostic factor for determining breast cancer.

Keywords: breast cancer molecular subtypes , correlation, immunohistochemistry, Ki-67 and HR, statistical analysis

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Authors: Mohamed Amine Ben Abdallah, Imed Khemili, Nizar Aifaoui

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This work denotes an insight into dynamic synthesis of multibody systems. A set of mechanism parameters design variable are synthetized based on a desired mechanism response, such as, velocity, acceleration and bodies deformations. Moreover, knowing the work space, for a robot, and mechanism response allow defining optimal parameters mechanism handling with the desired target response. To this end, evolutionary genetic algorithm has been deployed. A demonstrative example for imperfect mechanism has been treated, mainly, a slider crank mechanism with a flexible connecting rod. The transversal deflection of the connecting rod has been chosen as response to identify the mechanism design parameters.

Keywords: dynamic response, evolutionary genetic algorithm, flexible bodies, optimization

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Authors: M. Benlebna, B. Serier, B. Bachir Bouiadjra, S. Khalkhal

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This study focuses on the mechanical behavior of a dental prosthesis subjected to dynamic loads chewing. It covers a three-dimensional analysis by the finite element method, the level of distribution of equivalent stresses induced in the bone between the implants (depending on the number of implants). The studied structure, consisting of a braced, implant and mandibular bone is subjected to dynamic loading of variable amplitude in three directions corrono-apical, mesial-distal and bucco-lingual. These efforts simulate those of mastication. We show that compared to the implantation of a single implant, implantology using two implants promotes the weakening of the bones. This weakness is all the more likely that the implants are located in close proximity to one another.

Keywords: stress, bone, dental implant, distribution, stress levels, dynamic, effort, interaction, prosthesis

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Authors: Rizwan H. Khan, Saima Nusrat

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Despite the fact that amyloid associated neurodegenerative diseases and non-neuropathic systemic amyloidosis have allured the research endeavors, as no curative drugs have been proclaimed up till now except for symptomatic cure. Therapeutic compounds which can diminish or disaggregate such toxic oligomers and fibrillar species have been examined and more are on its way. In the present study, we had reported an extensive biophysical, microscopic and computational study, revealing that L-3, 4-dihydroxyphenylalanine (L-Dopa) possess undeniable potency to inhibit heat induced human lysozyme (HL) amyloid fibrillation and also retain the fibril disaggregating potential. L-Dopa interferes in the amyloid fibrillogenesis process by interacting hydrophobically and also by forming hydrogen bonds with the amino acid residues found in amyloid fibril forming prone region of HL as elucidated by molecular docking results. L-Dopa also disaggregates the mature amyloid fibrils into some unorganised species. Thus, L-Dopa and related compounds can work as a promising inhibitor for the therapeutic advancement prospective against systemic amyloidosis.

Keywords: amyloids, disaggregation, human lysozyme, molecular docking

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Authors: Shehret Tilvaldyev, Jorge Flores-Garay, Alfredo Villanueva, Erwin Martinez, Lazaro Rico

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The efficiency of modern transportation is severely compromised by the prevalence of turbulent drag. The high level of turbulent skin-friction occurring, e.g., on the surface of an aircraft, automobiles or the carriage of a high-speed train, is responsible for excess fuel consumption and increased carbon emissions. The environmental, political, and economic pressure to improve fuel efficiency and reduce carbon emissions associated with transportation means that reducing turbulent skin-friction drag is a pressing engineering problem. The dynamic pressure of subsonic airflow around solid objects creates lift, but also induces drag force. This paper is presenting the results of laboratory experiments, investigating appearance and magnitude of dynamic pressure in micro scale of subsonic air flow around right cylinder and symmetrical airfoil.

Keywords: airflow, dynamic pressure, micro scale, symmetric object

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Authors: Jia-Jang Wu

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The objective of this research is to develop a general technique so that one may predict the dynamic behaviour of a three-dimensional scale crane model subjected to time-dependent moving point forces by means of conventional finite element computer packages. To this end, the whole scale crane model is divided into two parts: the stationary framework and the moving substructure. In such a case, the dynamic responses of a scale crane model can be predicted from the forced vibration responses of the stationary framework due to actions of the four time-dependent moving point forces induced by the moving substructure. Since the magnitudes and positions of the moving point forces are dependent on the relative positions between the trolley, moving substructure and the stationary framework, it can be found from the numerical results that the time histories for the moving speeds of the moving substructure and the trolley are the key factors affecting the dynamic responses of the scale crane model.

Keywords: moving load, moving substructure, dynamic responses, forced vibration responses

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Authors: Osama Brinji, Wing Kong Chiu, Graham Tew

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Understanding the stability of rail ballast is one of the most important aspects in the railways. An unstable track may cause some issues such as unnecessary vibration and ultimately loss of track quality. The track foundation plays an important role in the stabilization of the railway. The dynamic response of rail ballast in the vicinity of the rail sleeper can affect the stability of the rail track and this has not been studied in detail. A review of literature showed that most of the works focused on the area under the concrete sleeper. Although there are some theories about the shear (longitudinal) effect of the rail ballast, these have not properly been studied and hence are not well understood. The stability of a rail track will depend on the compactness of the ballast in its vicinity. This paper will try to determine the dynamic response of the ballast to identify its resonant behaviour. This preliminary research is one of several studies that examine the vibration response of the granular materials. The main aim is to use this information for future design of sleepers to ensure that any dynamic response of the sleeper will not compromise the state of compactness of the ballast. This paper will report on the dependence of damping and the natural frequency of the ballast as a function of depth and distance from the point of excitation introduced through a concrete block. The concrete block is used to simulate a sleeper and the ballast is simulated with gravel. In spite of these approximations, the results presented in the paper will show an agreement with theories and the assumptions that are used in study the mechanical behaviour of the rail ballast.

Keywords: ballast, dynamic response, sleeper, stability

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Authors: Ebrahim Hassan Kapeel, Ahmed Mohsen Kamel, Hossan Hendy, Yehia Z. Elhalwagy

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Interest in autopilot design has been raised intensely as a result of recent advancements in Unmanned Aerial vehicles (UAVs). Due to the enormous number of applications that UAVs can achieve, the number of applied control theories used for them has increased in recent years. These small fixed-wing UAVs are suffering high non-linearity, sensitivity to disturbances, and coupling effects between their channels. In this work, the nonlinear dynamic inversion (NDI) control lawisdesigned for a nonlinear small fixed-wing UAV model. The NDI is preferable for varied operating conditions, there is no need for a scheduling controller. Moreover, it’s applicable for high angles of attack. For the designed flight controller validation, a nonlinear Modified PI-D controller is performed with our model. A comparative study between both controllers is achieved to evaluate the NDI performance. Simulation results and analysis are proposed to illustrate the effectiveness of the designed controller based on NDI.

Keywords: UAV dynamic model, attitude control, nonlinear PID, dynamic inversion

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Authors: Kuan-Chou Chen

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This paper will demonstrate a simulation model of an information security system by using the systems dynamic approach. The relationships in the system model are designed to be simple and functional and do not necessarily represent any particular information security environments. The purpose of the paper aims to develop a generic system dynamic information security system model with implications on information security research. The interrelated and interdependent relationships of five primary sectors in the system dynamic model will be presented in this paper. The integrated information security systems model will include (1) information security characteristics, (2) users, (3) technology, (4) business functions, and (5) policy and management. Environments, attacks, government and social culture will be defined as the external sector. The interactions within each of these sectors will be depicted by system loop map as well. The proposed system dynamic model will not only provide a conceptual framework for information security analysts and designers but also allow information security managers to remove the incongruity between the management of risk incidents and the management of knowledge and further support information security managers and decision makers the foundation for managerial actions and policy decisions.

Keywords: system thinking, information security systems, security management, simulation

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Authors: Shokofeh Ebrtahimi

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Let G be the chemical graph of a molecule. The matrix D = [dij ] is called the detour matrix of G, if dij is the length of longest path between atoms i and j. The sum of all entries above the main diagonal of D is called the detour index of G.Chemical graph theory is the topology branch of mathematical chemistry which applies graph theory to mathematical modelling of chemical phenomena.[1] The pioneers of the chemical graph theory are Alexandru Balaban, Ante Graovac, Ivan Gutman, Haruo Hosoya, Milan Randić and Nenad TrinajstićLet G be the chemical graph of a molecule. The matrix D = [dij ] is called the detour matrix of G, if dij is the length of longest path between atoms i and j. The sum of all entries above the main diagonal of D is called the detour index of G. In this paper, a new program for computing the detour index of molecular graphs of nanotubes by heptagons is determineded. Some Conjectures about detour index of Molecular graphs of nanotubes is included.

Keywords: chemical graph, detour matrix, Detour index, carbon nanotube

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Authors: Mohsin Ali Shaikh, Song Weiguo, Muhammad Kashan Surahio, Usman Shahid, Rehmat Karim

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This study investigated a catastrophic arson fire incident that occurred at a textile garment building in Karachi, Pakistan. Unfortunately, a catastrophic event led to the loss of 262 lives and caused 55 severe injuries. The primary objective is to analyze the aspects of the fire incident and understand the causes of arson fire disasters. The study utilized Fire Dynamic Simulation (F.D.S) was employed to simulate fire propagation, visibility, harmful gas concentration, fire temperature, and numerical results. The analysis report has determined the specific circumstances that created the unpleasant incident in the present study. The significance of the current findings lies in their potential to prevent arson fires, improve fire safety measures, and the development of safety plans in building design. The fire dynamic simulation findings can serve as a theoretical basis for the investigation of arson fires and evacuation planning in textile garment buildings.

Keywords: investigation, fire arson incident, textile garment, fire dynamic simulation (FDS)

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Authors: Abdelsalam Omar

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This paper presents simulation-based case study that indicate the need for accurate dynamic modeling of distance protection relay. In many cases, a static analysis based on current and voltage phasors may be sufficient to assess the performance of distance protection. There are several circumstances under which such a simplified study does not provide the depth of analysis necessary to obtain accurate results, however. This letter present study of the influences of magnetizing inrush and power swing on the performance of distance protection relay. One type of numerical distance protection relay has been investigated: 7SA511. The study has been performed in order to demonstrate the relay response when dynamic model of distance relay is utilized.

Keywords: distance protection, magnitizing inrush, power swing, dynamic model of protection relays, simulatio

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Authors: A. Didaoui, N. Benhalima, M. Elkeurti, A. Chouaih, F. Hamzaoui

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The monomer and dimer structures of the title molecule have been obtained from density functional theory (DFT) B3LYP method with 6-31G (d,p) as basis set calculations. The optimized geometrical parameters obtained by B3LYP/6-31G (d,p) method show good agreement with xperimental X-ray data. The polarizability and first order hyperpolarizabilty of the title molecule were calculated and interpreted. the intermolecular N–H•••O hydrogen bonds are discussed in dimer structure of the molecule. The vibrational wave numbers and their assignments were examined theoretically using the Gaussian 03 set of quantum chemistry codes. The predicted frontier molecular orbital energies at B3LYP/6-31G(d,p) method set show that charge transfer occurs within the molecule. The frontier molecular orbital calculations clearly show the inverse relationship of HOMO–LUMO gap with the total static hyperpolarizability. The results also show that N-(2-Methylphenyl)-2-nitrobenzenesulfonamide molecule may have nonlinear optical (NLO) comportment with non-zero values.

Keywords: DFT, Gaussian 03, NLO, N-(2-Methylphenyl)-2-nitrobenzenesulfonamide

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Authors: N. Khelloul, N. Benhalima, A. Chouaih, F. Hamzaoui

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The monomer and dimer structures of the title molecule have been obtained from density functional theory (DFT) B3LYP method with 6-31G (d,p) as basis set calculations. The optimized geometrical parameters obtained by B3LYP/6-31G (d,p) method shows good agreement with experimental X-ray data. The polarizability and first order hyperpolarizabilty of the title molecule were calculated and interpreted. The intermolecular N–H•••O hydrogen bonds are discussed in dimer structure of the molecule. The vibrational wave numbers and their assignments were examined theoretically using the Gaussian 09 set of quantum chemistry codes. The predicted frontier molecular orbital energies at B3LYP/6-31G(d,p) method set show that charge transfer occurs within the molecule. The frontier molecular orbital calculations clearly show the inverse relationship of HOMO–LUMO gap with the total static hyperpolarizability. The results also show that 2-Chloro-N-(2-methylphenyl) benzamide 2 molecule may have nonlinear optical (NLO) comportment with non-zero values.

Keywords: DFT, HOMO, LUMO, NLO

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Authors: Martynova Alina, Lyubov Buzoleva

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Streptococcus pneumoniae is the causative agent of pneumonias and meningitids throught all the world. Having high genetic diversity, this microorganism can cause different clinical forms of pneumococcal infections and microbiologically it is really difficult diagnosed by routine methods. Also, epidemiological surveillance requires more developed methods of molecular typing because the recent method of serotyping doesn't allow to distinguish invasive and non-invasive isolates properly. Non-coding genome of bacteria seems to be the interesting source for seeking of highly distinguishable markers to discriminate the subspecies of such a variable bacteria as Streptococcus pneumoniae. Technically, we proposed scheme of discrimination of S.pneumoniae strains with amplification of non-coding region (SP_1932) with the following restriction with 2 types of enzymes of Alu1 and Mn1. Aim: This research aimed to compare different methods of typing and their application for molecular epidemiology purposes. Methods: we analyzed population of 100 strains of S.pneumoniae isolated from different patients by different molecular epidemiology methods such as pulse-field gel electophoresis (PFGE), restriction polymorphism analysis (RFLP) and multilolocus sequence typing (MLST), and all of them were compared with classic typing method as serotyping. The discriminative power was estimated with Simpson Index (SI). Results: We revealed that the most discriminative typing method is RFLP (SI=0,97, there were distinguished 42 genotypes).PFGE was slightly less discriminative (SI=0,95, we identified 35 genotypes). MLST is still the best reference method (SI=1.0). Classic method of serotyping showed quite weak discriminative power (SI=0,93, 24 genotypes). In addition, sensivity of RFLP was 100%, specificity was 97,09%. Conclusion: the most appropriate method for routine epidemiology surveillance is RFLP with non-coding region of Streptococcsu pneumoniae, then PFGE, though in some cases these results should be obligatory confirmed by MLST.

Keywords: molecular epidemiology typing, non-coding genome, Streptococcus pneumoniae, MLST

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Authors: Ewelina Nowak, Anna Wisla-Swider, Gohar Khachatryan, Krzysztof Danel

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Complexes of ionic liquids with different heterocyclic-rings were synthesized by ion exchange reactions with pure salmon DNA. Ionic liquids (ILs) like 1-hexyl-3-methylimidazolium chloride, 1-butyl-4-methylpyridinium chloride and 1-ethyl-1-methylpyrrolidinium bromide were used. The ILs were built into helical state and confirmed by IR spectrometric techniques. Patterns of UV-Vis, photoluminescence, IR, and CD spectra indicated inclusion of small molecules into DNA structure. Molecular weight and radii of gyrations values of ILs-DNA complexes chains were established by HPSEC–MALLS–RI method. Modification DNA with 1-ethyl-1-methylpyrrolidinium bromide gives more uniform material and leads to elimination of high molecular weight chains. Thus, the incorporation DNA double helical structure with both 1-hexyl-3-methylimidazolium chloride and 1-butyl-4-methylpyridinium chloride exhibited higher molecular weight values. Scanning electron microscopy images indicate formation of nanofibre structures in all DNA complexes. Fluorescence depends strongly on the environment in which the chromophores are inserted and simultaneously on the molecular interactions with the biopolymer matrix. The most intensive emission was observed for DNA-imidazole ring complex. Decrease in intensity UV-Vis peak absorption is a consequence of a reduction in the spatial order of polynucleotide strands and provides different π–π stacking structure. Changes in optical properties confirmed by spectroscopy methods make DNA-ILs complexes potential biosensor applications.

Keywords: biopolymers, biosensors, cationic surfactant, DNA, DNA-gels

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Authors: Amir Zeb, Shailima Rampogu, Minky Son, Ayoung Baek, Sang H. Yoon, Keun W. Lee

Abstract:

Neurotoxic insults activate calpain, which in turn produces truncated p25 from p35. p25 forms hyperactivated Cdk5/p25 complex, and thereby induces severe neuropathological aberrations including hyperphosphorylated tau, neuroinflammation, apoptosis, and neuronal death. Inhibition of Cdk5/p25 complex alleviates aberrant phosphorylation of tau to mitigate AD pathology. PHA-793887 and Roscovitine have been investigated as selective inhibitors of Cdk5/p25 with IC50 values 5nM and 160nM, respectively, but their mechanistic studies remain unknown. Herein, computational simulations have explored the binding mode and interaction mechanism of PHA-793887 and Roscovitine with Cdk5/p25. Docking results suggested that PHA-793887 and Rsocovitine have occupied the ATP-binding site of Cdk5 and obtained highest docking (GOLD) score of 66.54 and 84.03, respectively. Furthermore, molecular dynamics (MD) simulation demonstrated that PHA-793887 and Roscovitine established stable RMSD of 1.09 Å and 1.48 Å with Cdk5/p25, respectively. Profiling of polar interactions suggested that each inhibitor formed hydrogen bonds (H-bond) with catalytic residues of Cdk5 and could remain stable throughout the molecular dynamics simulation. Additionally, binding free energy calculation by molecular mechanics/Poisson–Boltzmann surface area (MM/PBSA) suggested that PHA-793887 and Roscovitine had lowest binding free energies of -150.05 kJ/mol and -113.14 kJ/mol, respectively with Cdk5/p25. Free energy decomposition demonstrated that polar energy by H-bond between the Glu81 of Cdk5 and PHA-793887 is the essential factor to make PHA-793887 highly selective towards Cdk5/p25. Overall, this study provided substantial evidences to explore mechanistic interactions of the selective inhibitors of Cdk5/p25 and could be used as fundamental considerations in the development of structure-based selective inhibitors of Cdk5/p25.

Keywords: Cdk5/p25 inhibition, molecular modeling of Cdk5/p25, PHA-793887 and roscovitine, selective inhibition of Cdk5/p25

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Authors: Che Hsiu Chen, Kuo Wei Tseng, Zih Jian Huang, Hon Wen Cheng

Abstract:

A typical warm-up contains both stretching exercises and jogging. The static stretching prior to training or competition may cause detrimental effects to athletic performance. However, it is unclear whether different types of dynamic stretching exercises had different acute effects on knee flexors stiffness, flexibility, and strength. The purpose of this study was to analyze the knee flexors stiffness, flexibility, and strength gains after dynamic straight leg raise (DSLR) and dynamic modified toe-touch (MTT) stretching. Sixteen healthy university active men (height 176.27 ± 4.03 cm; weight 72.27 ± 8.90 kg; age 22.09 ± 2.31 years). After 5 minutes (8km/h) of running subjects performed 2 randomly ordered stretching protocols: DSLR and MTT stretching protocols. There were a total of six, 30 seconds bouts of dynamic stretching (15 repetitions) with 30seconds rest between bouts. The outcome measures were maximal voluntary isokinetic concentric hamstring strength (60°/s), muscle flexibility test by passive straight leg raise (PSLR), active straight leg raise (ASLR), and muscle stiffness using ultrasound Acoustic Radiation Forced Impulse (ARFI) elastography before and immediately after stretching. The muscle stiffness and concentric strength decreased significantly (p < .05), the flexibility no significant change after DSLR protocol (p > .05). The concentric strength decreased significantly (p < .05), the flexibility and muscle stiffness no significant change after MTT protocol (p > .05), whereas no significant differences were found for the DSLR and MTT. Our findings suggest that dynamic stretching (30s x 6 bouts) resulted in change in muscle stiffness or may be induced slack in the musculotendinous unit thereby, reducing force production. Therefore, 30s x 6 bouts of dynamic stretching adversely affects efforts of hamstring muscle maximal concentric strength.

Keywords: sport injury, ultrasound, eccentric exercise, performance

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Authors: Fouzia Perveen, Rumana Qureshi

Abstract:

The presently studied twelve anticancer drugs are the cytotoxic agents which inhibit the replication of DNA and activity of enzymes involved in DNA replication namely topoisomerase-II, polymerase and helicase and have shown remarkable anticancer activity in clinical trials. In this study, we performed molecular docking studies of twelve antitumor drugs against DNA and DNA enzymes in the presence and absence of ascorbic acid (AA) and developed the quantitative structure-activity relationship (QSAR) model for anticancer activity screening. A number of electronic and steric descriptors were calculated using MOE software package. QSAR was established showing a correlation of binding strength with various physicochemical descriptors. Out of these twelve, eight cytotoxic drugs were tested on Non-Small Cell Lung Cancer cell lines (H-157 and H-1299) in the absence and presence of ascorbic acid and experimental IC50 values were calculated. From the docking studies, binding constants were calculated indicating the strength of drug-DNA and drug-enzyme complex formation and it was correlated to the IC50 values (both experimental and theoretical). These results can offer useful references for directing the molecular design of DNA enzyme inhibitor with improved anticancer activity.

Keywords: ascorbic acid, binding constant, cytotoxic agents, cell culture, DNA, DNA enzymes, molecular docking

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Authors: Igor B. Sivaev

Abstract:

Design of molecular machines is an extraordinary growing and very important area of research that it was recognized by awarding Sauvage, Stoddart and Feringa the Nobel Prize in Chemistry in 2016 'for the design and synthesis of molecular machines'. Based on the type of motion being performed, molecular machines can be divided into two main types: molecular motors and molecular switches. Molecular switches are molecules or supramolecular complexes having bistability, i.e., the ability to exist in two or more stable forms, among which may be reversible transitions under external influence (heating, lighting, changing the medium acidity, the action of chemicals, exposure to magnetic or electric field). Molecular switches are the main structural element of any molecular electronics devices. Therefore, the design and the study of molecules and supramolecular systems capable of performing mechanical movement is an important and urgent problem of modern chemistry. There is growing interest in molecular switches and other devices of molecular electronics based on transition metal complexes; therefore choice of suitable stable organometallic unit is of great importance. An example of such unit is bis(dicarbollide) complexes of transition metals [3,3’-M(1,2-C₂B₉H₁₁)₂]ⁿ⁻. The control on the ligand rotation in such complexes can be reached by introducing substituents which could provide stabilization of certain rotamers due to specific interactions between the ligands, on the one hand, and which can participate as Lewis bases in complex formation with external metals resulting in a change in the rotation angle of the ligands, on the other hand. A series of isomeric methyl sulfide derivatives of cobalt bis(dicarbollide) complexes containing methyl sulfide substituents at boron atoms in different positions of the pentagonal face of the dicarbollide ligands [8,8’-(MeS)₂-3,3’-Co(1,2-C₂B₉H₁₀)₂]⁻, rac-[4,4’-(MeS)₂-3,3’-Co(1,2-C₂B₉H₁₀)₂]⁻ and meso-[4,7’-(MeS)₂-3,3’-Co(1,2-C₂B₉H₁₀)₂]⁻ were synthesized by the reaction of CoCl₂ with the corresponding methyl sulfide carborane derivatives [10-MeS-7,8-C₂B₉H₁₁)₂]⁻ and [10-MeS-7,8-C₂B₉H₁₁)₂]⁻. In the case of asymmetrically substituted cobalt bis(dicarbollide) complexes the corresponding rac- and meso-isomers were successfully separated by column chromatography as the tetrabutylammonium salts. The compounds obtained were studied by the methods of ¹H, ¹³C, and ¹¹B NMR spectroscopy, single crystal X-ray diffraction, cyclic voltammetry, controlled potential coulometry and quantum chemical calculations. It was found that in the solid state, the transoid- and gauche-conformations of the 8,8’- and 4,4’-isomers are stabilized by four intramolecular CH···S(Me)B hydrogen bonds each one (2.683-2.712 Å and 2.709-2.752 Å, respectively), whereas gauche-conformation of the 4,7’-isomer is stabilized by two intramolecular CH···S hydrogen bonds (2.699-2.711 Å). The existence of the intramolecular CH·S(Me)B hydrogen bonding in solutions was supported by the 1H NMR spectroscopy. These data are in a good agreement with results of the quantum chemical calculations. The corresponding iron and nickel complexes were synthesized as well. The reaction of the methyl sulfide derivatives of cobalt bis(dicarbollide) with various labile transition metal complexes results in rupture of intramolecular hydrogen bonds and complexation of the methyl sulfide groups with external metal. This results in stabilization of other rotational conformation of cobalt bis(dicarbollide) and can be used in design of molecular switches. This work was supported by the Russian Science Foundation (16-13-10331).

Keywords: molecular switches, NMR spectroscopy, single crystal X-ray diffraction, transition metal bis(dicarbollide) complexes, quantum chemical calculations

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