Search results for: molecular mechanics.

Authors: M. Jahanandish, Gh. Sadeghian, M. H. Daneshvar, M. H. Jahanandish

Abstract:

The amount of resistance of a particular medium like soil to the moving objects is the interest of many areas in science. These include soil mechanics, geotechnical engineering, powder mechanics etc. Knowledge of drag force is also used for estimating the amount of momentum of fired objects like bullets. This paper focuses on measurement of drag force of sand on a cone when it moves at a low constant speed. A 30-degree apex angle cone has been used for this purpose. The study consisted of both loose and dense conditions of the soil. The applied speed has been in the range of 0.1 to 10 mm/min. The results indicate that the required force is basically independent of the cone speed; but, it is very dependent on the material densification and confining stress.

Keywords: Drag force, sand, moving speed, friction angle, densification, confining stress.

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Authors: Samira Laidaoui, Mohammed Djermane, Nazihe Terfaya

Abstract:

The fluid-structure coupling is a natural phenomenon which reflects the effects of two continuums: fluid and structure of different types in the reciprocal action on each other, involving knowledge of elasticity and fluid mechanics. The solution for such problems is based on the relations of continuum mechanics and is mostly solved with numerical methods. It is a computational challenge to solve such problems because of the complex geometries, intricate physics of fluids, and complicated fluid-structure interactions. The way in which the interaction between fluid and solid is described gives the largest opportunity for reducing the computational effort. In this paper, a problem of fluid structure interaction is investigated with two-way coupling method. The formulation Arbitrary Lagrangian-Eulerian (ALE) was used, by considering a dynamic grid, where the solid is described by a Lagrangian formulation and the fluid by a Eulerian formulation. The simulation was made on the ANSYS software.

Keywords: ALE, coupling, FEM, fluid-structure interaction, one-way method, two-way method.

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Authors: R. Pilafkan, M. Kaffash Irzarahimi, S. F. Asbaghian Namin

Abstract:

The biaxial buckling behavior of single-layered graphene sheets (SLGSs) is studied in the present work. To consider the size-effects in the analysis, Eringen’s nonlocal elasticity equations are incorporated into classical plate theory (CLPT). A Generalized Differential Quadrature Method (GDQM) approach is utilized and numerical solutions for the critical buckling loads are obtained. Then, molecular dynamics (MD) simulations are performed for a series of zigzag SLGSs with different side-lengths and with various boundary conditions, the results of which are matched with those obtained by the nonlocal plate model to numerical the appropriate values of nonlocal parameter relevant to each type of boundary conditions.

Keywords: Biaxial buckling, single-layered graphene sheets, nonlocal elasticity, molecular dynamics simulation, classical plate theory.

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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: Aomar Anane, Omar Chakrone, Loubna Moutaouekkil

Abstract:

As p-Laplacian equations have been widely applied in field of the fluid mechanics and nonlinear elastic mechanics, it is necessary to investigate the periodic solutions of functional differential equations involving the scalar p-Laplacian. By using Mawhin’s continuation theorem, we study the existence of periodic solutions for p-Laplacian neutral Rayleigh equation (ϕp(x(t)−c(t)x(t − r))) + f(x(t)) + g1(x(t − τ1(t, |x|∞))) + β(t)g2(x(t − τ2(t, |x|∞))) = e(t), It is meaningful that the functions c(t) and β(t) are allowed to change signs in this paper, which are different from the corresponding ones of known literature.

Keywords: periodic solution, neutral Rayleigh equation, variable sign, Deviating argument, p-Laplacian, Mawhin’s continuation.

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Authors: Rado Flajs

Abstract:

In the present paper the extreme shear stresses with the corresponding planes are established using the freely available computer tools like the Gnuplot, Sage, R, Python and Octave. In order to support these freely available computer tools, their strong symbolical and graphical abilities are illustrated. The nature of the stationary points obtained by the Method of Lagrangian Multipliers can be determined using freely available computer symbolical tools like Sage. The characters of the stationary points can be explained in the easiest way using freely available computer graphical tools like Gnuplot, Sage, R, Python and Octave. The presented figures improve the understanding of the problem and the obtained solutions for the majority of students of civil or mechanical engineering.

Keywords: engineering, continuum mechanics, extreme shear stresses, Gnuplot, Sage, R, Python, Octave

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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: 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: 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: Ružarovský, Roman, Danišová, Nina, Velíšek, Karol

Abstract:

In this contribution is presented a complex design of individual objects identification in the workplace of intelligent assembly cell. Intelligent assembly cell is situated at Institute of Manufacturing Systems and Applied Mechanics and is used for pneumatic actuator assembly. Pneumatic actuator components are pneumatic roller, cover, piston and spring. Two identification objects alternatives for assembly are designed in the workplace of industrial robot. In the contribution is evaluated and selected suitable alternative for identification – 2D codes reader. The complex design of individual object identification is going out of intelligent manufacturing systems knowledge. Intelligent assembly and manufacturing systems as systems of new generation are gradually loaded in to the mechanical production, when they are removeing human operation out of production process and they also short production times.

Keywords: system, cell, intelligent, mechanics, device

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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: 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: Mahmoud Zarrini, R. N. Pralhad

Abstract:

We estimate snow velocity and snow drift density on hilly terrain under the assumption that the drifting snow mass can be represented using a micro-continuum approach (i.e. using a nonclassical mechanics approach assuming a class of fluids for which basic equations of mass, momentum and energy have been derived). In our model, the theory of coupled stress fluids proposed by Stokes [1] has been employed for the computation of flow parameters. Analyses of bulk drift velocity, drift density, drift transport and mass transport of snow particles have been carried out and computations made, considering various parametric effects. Results are compared with those of classical mechanics (logarithmic wind profile). The results indicate that particle size affects the flow characteristics significantly.

Keywords: Snow velocity, snow drift density, mass transport of snow particles, snow avalanche.

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Authors: Shagufta Tabassum

Abstract:

The study of dielectric properties in a binary mixture of liquids is very useful to understand the liquid structure, molecular interaction, dynamics, and kinematics of the mixture. Time-domain reflectometry (TDR) is a powerful tool for studying the cooperation and molecular dynamics of the H-bonded system. Here we discuss the basic calibration and normalization procedure for TDR measurements. Our aim is to explain different types of error occur during TDR measurements and how to minimize it.

Keywords: time domain reflectometry measurement technique, cable and connector loss, oscilloscope loss, normalization technique

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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: Raouf Mbarki, Fadi Al Khatib, Malek Adouni

Abstract:

Knee collateral ligaments play a significant role in restraining excessive frontal motion (varus/valgus rotations). In this investigation, a multiscale frame was developed based on structural hierarchies of the collateral ligaments starting from the bottom (tropocollagen molecule) to up where the fibred reinforced structure established. Experimental data of failure tensile test were considered as the principal driver of the developed model. This model was calibrated statistically using Bayesian calibration due to the high number of unknown parameters. Then the model is scaled up to fit the real structure of the collateral ligaments and simulated under realistic boundary conditions. Predications have been successful in describing the observed transient response of the collateral ligaments during tensile test under pre- and post-damage loading conditions. Collateral ligaments maximum stresses and strengths were observed near to the femoral insertions, a results that is in good agreement with experimental investigations. Also for the first time, damage initiation and propagation were documented with this model as a function of the cross-link density between tropocollagen molecules.

Keywords: Multiscale model, tropocollagen, fibrils, ligaments.

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Authors: Mahmoud Zarrini

Abstract:

Avalanche release of snow has been modeled in the present studies. Snow is assumed to be represented by semi-solid and the governing equations have been studied from the concept of continuum approach. The dynamical equations have been solved for two different zones [starting zone and track zone] by using appropriate initial and boundary conditions. Effect of density (ρ), Eddy viscosity (η), Slope angle (θ), Slab depth (R) on the flow parameters have been observed in the present studies. Numerical methods have been employed for computing the non linear differential equations. One of the most interesting and fundamental innovation in the present studies is getting initial condition for the computation of velocity by numerical approach. This information of the velocity has obtained through the concept of fracture mechanics applicable to snow. The results on the flow parameters have found to be in qualitative agreement with the published results.

Keywords: Snow avalanche, fracture mechanics, avalanche velocity, avalanche zones.

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Authors: R. Haddad, K. Morris, V. Buchanan-Wollaston

Abstract:

Biochemical and molecular analysis of some antioxidant enzyme genes revealed different level of gene expression on oilseed (Brassica napus). For molecular and biochemical analysis, leaf tissues were harvested from plants at eight different developmental stages, from young to senescence. The levels of total protein and chlorophyll were increased during maturity stages of plant, while these were decreased during the last stages of plant growth. Structural analysis (nucleotide and deduced amino acid sequence, and phylogenic tree) of a complementary DNA revealed a high level of similarity for a family of Catalase genes. The expression of the gene encoded by different Catalase isoforms was assessed during different plant growth phase. No significant difference between samples was observed, when Catalase activity was statistically analyzed at different developmental stages. EST analysis exhibited different transcripts levels for a number of other relevant antioxidant genes (different isoforms of SOD and glutathione). The high level of transcription of these genes at senescence stages was indicated that these genes are senescenceinduced genes.

Keywords: Biochemical analysis, Oilseed, Expression pattern, Growth phases

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Authors: Tomio Iwasaki, Yosuke Kawahito

Abstract:

The adhesion strength and wettability at the interfaces between a polyetheretherketone (PEEK) resin and titanium dioxide (TiO2) have become more important because direct joining of PEEK resin and titanium (Ti), whose surface has usually the oxide (TiO2), is needed not only in vehicles such as airplanes, automobiles, and space vehicles, but also in medical devices such as implants. To realize strong joint between the PEEK resin and TiO2, the dependence of the adhesion strength and wettability on crystal orientations of rutile TiO2 were investigated by using molecular simulations. Molecular dynamics simulations were conducted by combining quantum-mechanics equation of electrons with Newton’s equation of motion of nuclear coordinates (atomic coordinates). By putting a PEEK-resin sphere on a rutile TiO2 surface and by heating the system to 650 K, the contact angles at the interfaces were calculated to evaluate the wettability. After the system is cooled to 300 K from 650 K, to evaluate the adhesin strength, the adhesive fracture energy is calculated as the difference between the energy of the PEEK-TiO2 attached state and that of the PEEK-TiO2 detached state. The results of the contact angles showed that PEEK resin on the TiO2(100) and that on the TiO2(001) surface has low wettability with large contact angles. On the other hand, PEEK resin on the TiO2(110) surface has high wettability with a small contact angle. The results of the adhesive fracture energies showed that the adhesion at the PEEK-resin/TiO2(100) and PEEK-resin/TiO2(001) interfaces are weak. On the other hand, the adhesion at the PEEK-resin/TiO2(110) interface is strong. To clarify the reason that the higher wettability and stronger adhesion are obtained at the PEEK/TiO2(110) interface than at the at the PEEK/TiO2(100) and PEEK/TiO2(001) interfaces, atomic configurations at the interfaces were visualized. The atomic configuration at the PEEK/TiO2(110) interface showed that the lattice-matched coherent interface is realized, and the atomic density is high. On the other hand, the atomic configuration at the PEEK/TiO2(001) interface showed the lattice-unmatched incoherent interface. The atomic configuration at the PEEK/TiO2(100) interface showed that the atomic density is very low although the lattice-matched interface is realized. Therefore, the lattice matching and the high atomic density at the PEEK/TiO2(001) interface are considered to be dominant factors in the high wettability and strong adhesion.

Keywords: Adhesion, direct joining, PEEK, TiO2, wettability.

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Authors: Chanin Park, Sundarapandian Thangapandian, Yuno Lee, Minky Son, Shalini John, Young-sik Sohn, Keun Woo Lee

Abstract:

Hypertension is characterized with stress on the heart and blood vessels thus increasing the risk of heart attack and renal diseases. The Renin angiotensin system (RAS) plays a major role in blood pressure control. Renin is the enzyme that controls the RAS at the rate-limiting step. Our aim is to develop new drug-like leads which can inhibit renin and thereby emerge as therapeutics for hypertension. To achieve this, molecular dynamics (MD) simulation and receptor-based pharmacophore modeling were implemented, and three rennin-inhibitor complex structures were selected based on IC50 value and scaffolds of inhibitors. Three pharmacophore models were generated considering conformations induced by inhibitor. The compounds mapped to these models were selected and subjected to drug-like screening. The identified hits were docked into the active site of renin. Finally, hit1 satisfying the binding mode and interaction energy was selected as possible lead candidate to be used in novel renin inhibitors.

Keywords: Renin inhibitor, Molecular dynamics simulation, Structure-based pharmacophore modeling

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Authors: Yu-Kai Ting, Jia-Ying Tu, Chung-Chun Hsiao

Abstract:

New physical insights into the nonlinear Lorenz equations related to flow resistance is discussed in this work. The chaotic dynamics related to Lorenz equations has been studied in many papers, which is due to the sensitivity of Lorenz equations to initial conditions and parameter uncertainties. However, the physical implication arising from Lorenz equations about convectional motion attracts little attention in the relevant literature. Therefore, as a first step to understand the related fluid mechanics of convectional motion, this paper derives the Lorenz equations again with different forced conditions in the model. Simulation work of the modified Lorenz equations without the viscosity or buoyancy force is discussed. The time-domain simulation results may imply that the states of the Lorenz equations are related to certain flow speed and flow resistance. The flow speed of the underlying fluid system increases as the flow resistance reduces. This observation would be helpful to analyze the coupling effects of different fluid parameters in a convectional model in future work.

Keywords: Galerkin method, Lorenz equations, Navier-Stokes equations.

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Authors: Syhalath Xaphakdy, Toshio Nagata, Saykham Phommathat, Pavy Souwannavong, Vilayvanh Srithilat, Phoxay Sengdala, Bounaom Phetarnousone, Boualay Siharath, Xaya Chemcheng

Abstract:

The National University of Laos (NUOL) invited a group of volunteers from the Japan International Cooperation Agency (JICA) to revise the physics experiments to utilize the materials that were already available to students. The intension was to review and revise the materials regularly utilized in physics class. The project had access to limited materials and a small budget for the class in the unit; however, by developing experimental textbooks related to mechanics, electricity, and wave and vibration, the group found a way to apply them in the classroom and enhance the students teaching activities. The aim was to introduce a way to incorporate the materials and practices in the classroom to enhance the students learning and teaching skills, particularly when they graduate and begin working as high school teachers.

Keywords: NUOL, JICA, physics experiment materials, small budget, mechanics, electricity.

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Authors: Jeong-Won Kang

Abstract:

Graphene, a single-atom sheet, has been considered as the most promising material for making future nanoelectromechanical systems as well as purely electrical switching with graphene transistors. Graphene-based devices have advantages in scaled-up device fabrication due to the recent progress in large area graphene growth and lithographic patterning of graphene nanostructures. Here we investigated its mechanical responses of circular graphene nanoflake under the nanoindentation using classical molecular dynamics simulations. A correlation between the load and the indentation depth was constructed. The nanoindented force in this work was applied to the center point of the circular graphene nanoflake and then, the resonance frequency could be tuned by a nanoindented depth. We found the hardening or the softening of the graphene nanoflake during its nanoindented-deflections, and such properties were recognized by the shift of the resonance frequency. The calculated mechanical parameters in the force-vs-deflection plot were in good agreement with previous experimental and theoretical works. This proposed schematics can detect the pressure via the deflection change or/and the resonance frequency shift, and also have great potential for versatile applications in nanoelectromechanical systems.

Keywords: Graphene, pressure sensor, circular graphene nanoflake, molecular dynamics.

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Authors: Raju Bhukya, DVLN Somayajulu

Abstract:

Pattern matching is one of the fundamental applications in molecular biology. Searching DNA related data is a common activity for molecular biologists. In this paper we explore the applicability of a new pattern matching technique called Index based Forward Backward Multiple Pattern Matching algorithm(IFBMPM), for DNA Sequences. Our approach avoids unnecessary comparisons in the DNA Sequence due to this; the number of comparisons of the proposed algorithm is very less compared to other existing popular methods. The number of comparisons rapidly decreases and execution time decreases accordingly and shows better performance.

Keywords: Comparisons, DNA Sequence, Index.

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Authors: Jianwei Zhang, Dazhi Jiang, Huaxin Peng, Chunqi Wang

Abstract:

Stress-strain curve of inter-tube connected carbon nanotube (CNT) reinforced polymer composite under axial loading generated from molecular dynamics simulation is presented. Comparison of the response to axial mechanical loading between this composite system with composite systems reinforced by long, continuous CNTs (replicated via periodic boundary conditions) and short, discontinuous CNTs has been made. Simulation results showed that the inter-tube connection improved the mechanical properties of short discontinuous CNTs dramatically. Though still weaker than long CNT/polymer composite, more remarkable increase in the stiffness relative to the polymer was observed in the inter-tube connected CNT/polymer composite than in the discontinuous CNT/polymer composite. The manually introduced bridge break process resulted in a stress-strain curve of ductile fracture mode, which is consistent with the experimental result.

Keywords: Carbon nanotube, inter-tube connection, molecular dynamics, stress-strain curve

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Authors: Ravinu Garg, Naresh V. Datla

Abstract:

We study the fracture mechanics of peeling of thin films perfectly bonded to a rigid substrate of any random surface topology using an analytical formulation. A generalized theoretical model has been developed to determine the peel strength of thin elastic films. It is demonstrated that an improvement in the peel strength can be achieved by modifying the surface characteristics of the rigid substrate. Characterization study has been performed to analyze the effect of different parameters on effective peel force from the rigid surface. Different surface profiles such as circular and sinusoidal has been considered to demonstrate the bonding characteristics of film-substrate interface. Condition for the instability in the debonding of the film is analyzed, where the localized self-debonding arises depending upon the film and surface characteristics. This study is towards improved adhesion strength of thin films to rigid substrate using different textured surfaces.

Keywords: Debonding, fracture mechanics, surface topology, thin film adhesion.

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Authors: Nurul Bahiyah Ahmad Khairudin, Habibah A Wahab

Abstract:

A new approach to predict the 3D structures of proteins by combining the knowledge-based method and Molecular Dynamics Simulation is presented on the chicken villin headpiece subdomain (HP-36). Comparative modeling is employed as the knowledge-based method to predict the core region (Ala9-Asn28) of the protein while the remaining residues are built as extended regions (Met1-Lys8; Leu29-Phe36) which then further refined using Molecular Dynamics Simulation for 120 ns. Since the core region is built based on a high sequence identity to the template (65%) resulting in RMSD of 1.39 Å from the native, it is believed that this well-developed core region can act as a 'nucleation center' for subsequent rapid downhill folding. Results also demonstrate that the formation of the non-native contact which tends to hamper folding rate can be avoided. The best 3D model that exhibits most of the native characteristics is identified using clustering method which then further ranked based on the conformational free energies. It is found that the backbone RMSD of the best model compared to the NMR-MDavg is 1.01 Å and 3.53 Å, for the core region and the complete protein, respectively. In addition to this, the conformational free energy of the best model is lower by 5.85 kcal/mol as compared to the NMR-MDavg. This structure prediction protocol is shown to be effective in predicting the 3D structure of small globular protein with a considerable accuracy in much shorter time compared to the conventional Molecular Dynamics simulation alone.

Keywords: 3D model, Chicken villin headpiece subdomain, Molecular dynamic simulation NMR-MDavg, RMSD.

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Authors: Eda Gök

Abstract:

Peridynamics is a new modeling concept of non-local interactions for solid structures. The formulations of Peridynamic (PD) theory are based on integral equations rather than differential equations. Through, undefined equations of associated problems are avoided. PD theory might be defined as continuum version of molecular dynamics. The medium is usually modeled with mass particles bonded together. Particles interact with each other directly across finite distances through central forces named as bonds. The main assumption of this theory is that the body is composed of material points which interact with other material points within a finite distance. Although, PD theory developed for discontinuities, it gives good results for structures which have no discontinuities. In this paper, displacement control of the isotropic plate under the effect of tensile and bending loading has been investigated by means of PD theory. A MATLAB code is generated to create PD bonds and corresponding surface correction factors. Using generated MATLAB code the geometry of the specimen is generated, and the code is implemented in Finite Element Software. The results obtained from non-local continuum theory are compared with the Finite Element Analysis results and analytical solution. The results show good agreement.

Keywords: Flexural loading, non-local continuum mechanics, Peridynamic theory, solid structures, tensile loading.

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Authors: A. Hung, K. Mithraratne, M. Sagar, P. Hunter

Abstract:

A biophysically based multilayer continuum model of the facial soft tissue composite has been developed for simulating wrinkle formation. The deformed state of the soft tissue block was determined by solving large deformation mechanics equations using the Galerkin finite element method. The proposed soft tissue model is composed of four layers with distinct mechanical properties. These include stratum corneum, epidermal-dermal layer (living epidermis and dermis), subcutaneous tissue and the underlying muscle. All the layers were treated as non-linear, isotropic Mooney Rivlin materials. Contraction of muscle fibres was approximated using a steady-state relationship between the fibre extension ratio, intracellular calcium concentration and active stress in the fibre direction. Several variations of the model parameters (stiffness and thickness of epidermal-dermal layer, thickness of subcutaneous tissue layer) have been considered.

Keywords: Bio-physically based, soft tissue mechanics, facialtissue composite, wrinkling.

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Authors: S. Desouky, A. Al sabagh , M. Betiha, A. Badawi, A. Ghanem, S. Khalil

Abstract:

Two Amphiphilic catalysts, iron (III) dodecylbenzene sulfonate and nickel (II) dodecylbenzene sulfonate, were synthesized and used in the catalytic aquathermolysis of heavy crude oil to reduce its viscosity. The prepared catalysts exhibited good performance in the aquathermolysis and the viscosity is reduced by ~ 78.9 % for Egyptian heavy crude oil. The chemical and physical properties of heavy oil both before and after reaction were investigated by FT-IR, dynamic viscosity, molecular weight and SARA analysis. The results indicated that the content of resin, asphaltene, average molecular weight and sulfur content of heavy oil is reduced after the catalytic aquathermolysis.

Keywords: Amphiphilic catalyst, Aquathermolysis, Heavy oil, Viscosity reduction.

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