Search results for: molecular docking simulations

Authors: Sumit Sharma, Rakesh Chandra, Pramod Kumar, Navin Kumar

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Molecular dynamics (MD) simulation has been used to study the effect of carbon nanofiber (CNF) volume fraction (Vf) and aspect ratio (l/d) on mechanical properties of CNF reinforced polypropylene (PP) composites. Materials Studio 5.5 has been used as a tool for finding the modulus and damping in composites. CNF composition in PP was varied by volume from 0 to 16%. Aspect ratio of CNF was varied from l/d=5 to l/d=100. To the best of the knowledge of the authors, till date there is no study, either experimental or analytical, which predict damping for CNF-PP composites at the nanoscale. Hence, this will be a valuable addition in the area of nanocomposites. Results show that with only 2% addition by volume of CNF in PP, E11 increases 748%. Increase in E22 is very less in comparison to the increase in E11. With increase in CNF aspect ratio (l/d) till l/d=60, the longitudinal loss factor (η11) decreases rapidly. Results of this study have been compared with those available in literature.

Keywords: carbon nanofiber, elasticity, mechanical properties, molecular dynamics

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Authors: Petter Eklund, Jonathan Sjölund, Sandra Eriksson, Mats Leijon

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The spoke type rotor can be used to obtain magnetic flux concentration in permanent magnet machines. This allows the air gap magnetic flux density to exceed the remanent flux density of the permanent magnets but gives problems with leakage fluxes in the magnetic circuit. The end leakage flux of one spoke type permanent magnet rotor design is studied through measurements and finite element simulations. The measurements are performed in the end regions of a 12 kW prototype generator for a vertical axis wind turbine. The simulations are made using three dimensional finite elements to calculate the magnetic field distribution in the end regions of the machine. Also two dimensional finite element simulations are performed and the impact of the two dimensional approximation is studied. It is found that the magnetic leakage flux in the end regions of the machine is equal to about 20% of the flux in the permanent magnets. The overestimation of the performance by the two dimensional approximation is quantified and a curve-fitted expression for its behavior is suggested.

Keywords: end effects, end leakage flux, permanent magnet machine, spoke type rotor

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Authors: Nadim Zgheib, Sivaramakrishnan Balachandar

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We present results on the initial formation of ripples from an initially flattened erodible bed. We use direct numerical simulations (DNS) of turbulent open channel flow over a fixed sinusoidal bed coupled with hydrodynamic stability analysis. We use the direct forcing immersed boundary method to account for the presence of the sediment bed. The resolved flow provides the bed shear stress and consequently the sediment transport rate, which is needed in the stability analysis of the Exner equation. The approach is different from traditional linear stability analysis in the sense that the phase lag between the bed topology, and the sediment flux is obtained from the DNS. We ran 11 simulations at a fixed shear Reynolds number of 180, but for different sediment bed wavelengths. The analysis allows us to sweep a large range of physical and modelling parameters to predict their effects on linear growth. The Froude number appears to be the critical controlling parameter in the early linear development of ripples, in contrast with the dominant role of particle Reynolds number during the equilibrium stage.

Keywords: direct numerical simulation, immersed boundary method, sediment-bed interactions, turbulent multiphase flow, linear stability analysis

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Authors: Alya Harichane, Abderraouf Achour, Abdelbaki Benmounah

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The main difficulty encountered in the formulation of high-performance concrete (HPC) consists in choosing the most efficient cement-superplasticizer pair allowing to obtain maximum water reduction, good workability of the concrete in the fresh state, and very good mechanical resistance in the hardened state. The aim of this work is to test the efficiency of three polycarboxylate ether-based superplasticizers (PCE) marketed in Algeria with CEMI 52.5 R cement and to study the effect of chemical structure of PCE on zeta potential, rheological and mechanical properties of cement pastes. The property of the polymers in cement was tested by a Malvern Zetasizer 2000 apparatus and VT 550 viscometer. Results showed that the zeta potential and its rheological properties are related to the molecular weight and the density carboxylic of PCE. The PCE with a moderate molecular weight and the highest carboxylic groups had the best dispersion (high value of zeta potential) and lowest viscosity. The effect of the chemical structure of PCEs on mechanical properties is evaluated by the formulation of cement mortar with these PCEs. The result shows that there is a correlation between the zeta potential of polymer and the compressive strength of cement paste.

Keywords: molecular weight, polycarboxylate-ether superplasticizer, rheology, zeta potential

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Authors: Chaudhari S. G., Saxena, S.

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We systematically and quantitatively investigated the effect of glucose as a model of natural molecular crowding agent on the structure and thermodynamics of Watson-Crick base paired three duplexes (named as D1, D2 and D3) of different base compositions and lengths. Structural analyses demonstrated that duplexes (D1 and D2) folded into B-form with different cations in the absence and presence of glucose while duplex (D3) folded into mixed A and B-form. Moreover, we demonstrated that the duplex was more stable in the absence of glucose, and marginally destabilized in its presence because glucose act as a weak structure breaker on the tetrahedral network of water. In the absence of glucose, the values of ΔG°25 for duplex (D1) were -13.56, -13.76, -12.46, and -12.36 kcal/mol, for duplex (D2) were -13.64, -12.93, -12.86, and -12.30 kcal/mol, for duplex (D3) were -10.05, -11.76, -9.91, -9.70 kcal/mol in the presence of Na+, K+, Na+ + Mg++ and K+ + Mg++ respectively. At high concentration of glucose (1:10000), there was increase in ΔG°25 for duplex (D1) -12.47, -12.37, -11.96, -11.55 kcal/mol, for duplex (D2) -12.37, -11.47, -11.98, -11.01 kcal/mol and for duplex (D3) -8.47, -9.17, -9.16, -8.66 kcal/mol. Our results provide the information that structure and stability of DNA duplex depends on the structure of molecular crowding agent present in its close vicinity. In this study, I have taken the hydration of simple sugar as an essential model for understanding interactions between hydrophilic groups and interfacial water molecules and its effect on hydrogen bonded DNA duplexes. On the basis of these relatively simple building blocks I hope to gain some insights for understanding more generally the properties of sugar–water–salt systems with DNA duplexes.

Keywords: natural molecular crowding, DNA Duplex, structure of DNA, bioengineering and life sciences

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Authors: Mrinalini Amritkar, Disha Patil, Swapna Kulkarni, Sukratu Barve, Suresh Gosavi

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Micro-mixers play an important role in the lab-on-a-chip applications and micro total analysis systems to acquire the correct level of mixing for any given process. The mixing process can be classified as active or passive according to the use of external energy. Literature of microfluidics reports that most of the work is done on the models of steady laminar flow; however, the study of unsteady laminar flow is an active area of research at present. There are wide applications of this, out of which, we consider nanoparticle synthesis in micro-mixers. In this work, we have developed a model for unsteady flow to study the mixing performance of a passive micro mixer for reactants used for such synthesis. The model is developed in Finite Volume Method (FVM)-based software, OpenFOAM. The model is tested by carrying out the simulations at Re of 0.5. Mixing performance of the micro-mixer is investigated using simulated concentration values of mixed species across the width of the micro-mixer and calculating the variance across a line profile. Experimental validation is done by passing dyes through a Y shape micro-mixer fabricated using polydimethylsiloxane (PDMS) polymer and comparing variances with the simulated ones. Gold nanoparticles are later synthesized through the micro-mixer and collected at two different times leading to significantly different size distributions. These times match with the time scales over which reactant concentrations vary as obtained from simulations. Our simulations could thus be used to create design aids for passive micro-mixers used in nanoparticle synthesis.

Keywords: Lab-on-chip, LOC, micro-mixer, OpenFOAM, PDMS

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Authors: D. M. Eric, D. Milosevic, F. D. Eric

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Concurrent engineering technologies are a modern concept in manufacturing engineering. One of the key goals in designing modern technological processes is further reduction of production costs, both in the prototype and the preparatory part, as well as during the serial production. Thanks to many segments of concurrent engineering, these goals can be accomplished much more easily. In this paper, we give an overview of the advantages of using modern software simulations in relation to the classical aspects of designing technological processes of metal deformation. Significant savings are achieved thanks to the electronic simulation and software detection of all possible irregularities in the functional-working regime of the technological process. In order for the expected results to be optimal, it is necessary that the input parameters are very objective and that they reliably represent the values ​of these parameters in real conditions. Since it is a metal deformation treatment here, the particularly important parameters are the coefficient of internal friction between the working material and the tools, as well as the parameters related to the flow curve of the processing material. The paper will give a presentation for the experimental determination of some of these parameters.

Keywords: production technologies, metal processing, software simulations, effects of application

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Authors: Hyery Kang, Dong-Yeun Koh, Yun-Ho Ahn, Huen Lee

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Terahertz time-domain spectroscopy (THz-TDS) was used to observe the THF clathrate hydrate system with dosage of polyvinylpyrrolidone (PVP) with three different average molecular weights (10,000 g/mol, 40,000 g/mol, 360,000 g/mol). Distinct footprints of phase transition in the THz region (0.4 - 2.2 THz) were analyzed and absorption coefficients and complex refractive indices are obtained and compared in the temperature range of 253 K to 288 K. Along with the optical properties, ring breathing and stretching modes for different molecular weights of PVP in THF hydrate are analyzed by Raman spectroscopy.

Keywords: clathrate hydrate, terahertz, polyvinylpyrrolidone (PVP), THz-TDS, inhibitor

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Authors: Pierre Kancir, Jean-Philippe Diguet, Marc Sevaux

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One of the main difficulties in developing multi-robot systems (MRS) is related to the simulation and testing tools available. Indeed, if the differences between simulations and real robots are too significant, the transition from the simulation to the robot won’t be possible without another long development phase and won’t permit to validate the simulation. Moreover, the testing of different algorithmic solutions or modifications of robots requires a strong knowledge of current tools and a significant development time. Therefore, the availability of tools for MRS, mainly with flying drones, is crucial to enable the industrial emergence of these systems. This research aims to present the most commonly used tools for MRS simulations and their main shortcomings and presents complementary tools to improve the productivity of designers in the development of multi-vehicle solutions focused on a fast learning curve and rapid transition from simulations to real usage. The proposed contributions are based on existing open source tools as Gazebo simulator combined with ROS (Robot Operating System) and the open-source multi-platform autopilot ArduPilot to bring them to a broad audience.

Keywords: ROS, ArduPilot, MRS, simulation, drones, Gazebo

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Authors: T. Walczak, J. K. Grabski, P. Fritzkowski, M. Stopa

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Objectives of the study are i) to perform numerical simulations that permit an analysis of the dynamics of subretinal fluid when an implant has induced scleral intussusception and ii) assess the impact of the physical parameters of the model on the flow rate. Computer simulations were created using finite element method (FEM) based on a model that takes into account the interaction of a viscous fluid (subretinal fluid) with a hyperelastic body (retina). The purpose of the calculation was to investigate the dependence of the flow rate of subretinal fluid through a hole in the retina on different factors such as viscosity of subretinal fluid, material parameters of the retina, and the offset of the implant from the retina’s hole. These simulations were performed for different speeds of eye movement that reflect the behavior of the eye when reading, REM, and saccadic movements. Similar to other works in the field of subretinal fluid flow, it was assumed stationary, single sided, forced fluid flow in the considered area simulating the subretinal space. Additionally, a hyperelastic material model of the retina and parameterized geometry of the considered model was adopted. The calculations also examined the influence the direction of the force of gravity due to the position of the patient’s head on the trend of outflow of fluid. The simulations revealed that fluid outflow from the retina becomes significant with eyeball movement speed of 100°/sec. This speed is greater than in the case of reading but is four times less than saccadic movement. The increase of viscosity of the fluid increased beneficial effect. Further, the simulation results suggest that moderate eye movement speed is optimal and that the conventional prescription of the avoidance of routine eye movement following retinal detachment surgery should be relaxed. Additionally, to verify numerical results, some calculations were repeated with use of meshless method (method of fundamental solutions), which is relatively fast and easy to implement. The paper has been supported by 02/21/DSPB/3477 grant.

Keywords: CFD simulations, FEM analysis, meshless method, retinal detachment

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Authors: Mahdi Golriz

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The aim of this work is to estimate the change in molecular structure of linear low-density polyethylene (LLDPE) during peroxide modification can be detected by a simple rheological method. For this purpose a commercial grade LLDPE (Exxon MobileTM LL4004EL) was reacted with different doses of dicumyl peroxide (DCP). The samples were analyzed by size-exclusion chromatography coupled with a light scattering detector. The dynamic shear oscillatory measurements showed a deviation of the δ-׀G ׀٭curve from that of the linear LLDPE, which can be attributed to the presence of long-chain branching (LCB). By the use of a simple rheological method that utilizes melt rheology, transformations in molecular architecture induced on an originally linear low density polyethylene during the early stages of reactive modification were indicated. Reasonable and consistent estimates are obtained, concerning the degree of LCB, the volume fraction of the various molecular species produced in peroxide modification of LLDPE.

Keywords: linear low-density polyethylene, peroxide modification, long-chain branching, rheological method

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Authors: Ali Abbas Zaidi

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In free settling or sedimentation, particles form clusters at high Reynolds number and dilute suspensions. It is due to the entrapment of particles in the wakes of upstream particles. In this paper, the effect of bi-dispersity of settling particles on particle clustering is investigated using particle-resolved direct numerical simulation. Immersed boundary method is used for particle fluid interactions and discrete element method is used for particle-particle interactions. The solid volume fraction used in the simulation is 1% and the Reynolds number based on Sauter mean diameter is 350. Both solid volume fraction and Reynolds number lie in the clustering regime of sedimentation. In simulations, the particle diameter ratio (i.e. diameter of larger particle to smaller particle (d₁/d₂)) is varied from 2:1, 3:1 and 4:1. For each case of particle diameter ratio, solid volume fraction for each particle size (φ₁/φ₂) is varied from 1:1, 1:2 and 2:1. For comparison, simulations are also performed for monodisperse particles. For studying particles clustering, radial distribution function and instantaneous location of particles in the computational domain are studied. It is observed that the degree of particle clustering decreases with the increase in the bi-dispersity of settling particles. The smallest degree of particle clustering or dispersion of particles is observed for particles with d₁/d₂ equal to 4:1 and φ₁/φ₂ equal to 1:2. Simulations showed that the reduction in particle clustering by increasing bi-dispersity is due to the difference in settling velocity of particles. Particles with larger size settle faster and knockout the smaller particles from clustered regions of particles in the computational domain.

Keywords: dispersion in bi-disperse settling particles, particle microstructures in bi-disperse suspensions, particle resolved direct numerical simulations, settling of bi-disperse particles

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Authors: Soraya Abtouche, Zeyneb Ghoualem, Syrine Daoudi, Lina Ouldmohamed, Xavier Assfeld

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This work reports density functional theory calculations of the optimized geometries, molecular reactivity, energy gap,and thermodynamic properties of the free base (H2P) and their Zn (II) metallated (ZnP), bearing one, two, or three carboxylic acid groups using the hybrid functional B3LYP, Cam-B3lYP, wb97xd with 6-31G(d,p) basis sets. When donating groups are attached to the molecular dye, the bond lengths are slightly decreased, which is important for the easy transfer of an electron from donating to the accepting group. For all dyes, the highest occupied molecular orbital/lowest occupied molecular orbital analysis results in positive outcomes upon electron injection to the semiconductor and subsequent dye regeneration by the electrolyte. The ionization potential increases with increasing conjugation; therefore, the compound dye attached to one carboxylic acid group has the highest ionization potential. The results show higher efficiencies of those sensitized with ZnP. These results have been explained, taking into account the electronic character of the metal ion, which acts as a mediator in the injection step, and, on the other hand, considering the number of anchoring groups to which it binds to the surface of TiO2.

Keywords: DSSC, porphyrin, TD-DFT, electronic properties, donor-acceptor groups

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Authors: Mustafa Sahin, İlkay Yavrucuk

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This paper presents a wind turbine envelope protection control algorithm that protects Variable Speed Variable Pitch (VSVP) wind turbines from damage during operation throughout their below and above rated regions, i.e. from cut-in to cut-out wind speed. The proposed approach uses a neural network that can adapt to turbines and their operating points. An algorithm monitors instantaneous wind and turbine states, predicts a wind speed that would push the turbine to a pre-defined envelope limit and, when necessary, realizes an avoidance action. Simulations are realized using the MS Bladed Wind Turbine Simulation Model for the NREL 5 MW wind turbine equipped with baseline controllers. In all simulations, through the proposed algorithm, it is observed that the turbine operates safely within the allowable limit throughout the below and above rated regions. Two example cases, adaptations to turbine operating points for the below and above rated regions and protections are investigated in simulations to show the capability of the proposed envelope protection system (EPS) algorithm, which reduces excessive wind turbine loads and expectedly increases the turbine service life.

Keywords: adaptive envelope protection control, limit detection and avoidance, neural networks, ultimate load reduction, wind turbine power control

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Authors: Ahmet Kaya

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Quantum mechanism is one of the most important approaches to calculating non-ruin probability. We apply standard Dirac notation to model given Hamiltonians. By using the traditional method and eigenvector basis, non-ruin probability is found for several examples. Also, non-ruin probability is calculated for two different Hamiltonian by using the tensor product. Finally, the path integral method is applied to the examples and comparison is made for stochastic simulations and path integral calculation.

Keywords: quantum physics, Hamiltonian system, path integral, tensor product, ruin probability

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Authors: Amir Doustgani

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Melt electrospinning is a safe and simple technique for the production of micro and nanofibers which can be an alternative to conventional solvent electrospinning. The effects of various melt-electrospinning parameters, including molecular weight, electric field strength, flow rate and temperature on the morphology and fiber diameter of polylactic acid were studied. It was shown that molecular weight was the predominant factor in determining the obtainable fiber diameter of the collected fibers. An orthogonal design was used to examine process parameters. Results showed that molecular weight is the most effective parameter on the average fiber diameter of melt electrospun PLA nanofibers and the flow rate has the less important impact. Mean fiber diameter increased by increasing MW and flow rate, but decreased by increasing electric field strength and temperature. MFD of optimized fibers was below 100 nm and the result of software was in good agreement with the experimental condition.

Keywords: fiber formation, processing, spinning, melt blowing

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Authors: Natesan Balasubramanian, Palpandi Pounpandi, Venkatraman Thamil Priya, Vellasamy Shanmugaiah, Karubbiah Balakrishnan, Mandayam Anandam Thirunarayan

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Streptococcus agalactiae is commonly known as Group B Streptococcus (GBS) and it is the most common cause of life-threatening bacterial infection. GBS first considered as a veterinary pathogen causing mastitis in cattle later becomes a human pathogen for severe neonatal infections. In this present study, a total of 20 new clinical isolates of S. agalactiae were collected from male (6) and female patient (14) with different age group. The isolates were from Urinary tract infection (UTI), blood, pus and eye ulcer. All the 20 S. agalactiae isolates has clear hemolysis properties on blood agar medium and were identified by serogrouping and MALTI-TOF-MS analysis. Antibiotic susceptibility/resistance test was performed for 20 S. agalactiae isolates, further phenotypic resistance pattern was observed for tetracycline, vancomycin, ampicillin and penicillin. Genotypically we found two antibiotic resistance genes such as Betalactem antibiotic resistance gene (Tem) (70%) and tetracycline resistance gene Tet(O) 15% in our isolates. Six virulence factors encoding genes were performed by PCR in twenty GBS isolates, cfb gene (100%), followed by, cylE(90.47%), lmp(85.7%), bca(71.42%), rib (38%) and low frequency in bac gene (4.76%) were determined. Most of the S. agalactiae isolates produced strong biofilm in the polystyrene surface (hydrophobic), and low-level biofilm formation was found in glass tube (hydrophilic) surface. lytR is secreted protein and localized in bacterial cell wall, extra cellular membrane, and cytoplasm. In silico docking studies were performed for lytR protein with four antibiofilm compounds, including a peptide (PR39) with the docking study showed peptide has strong interaction followed by ellagic acid and interaction length is 2.95, 2.97 and 2.95 A°. In ligand EGCGO10 and O11 two atoms intract with lytR (Leu271), with binding bond affinity length is 3.24 and 3.14. The aminoacid Leu 271 is act as an impartant aminoacid, since ellagic acid and EGCG interact with same aminoacid.

Keywords: antibiotics, biofilms, clinical isolates, S. agalactiae, virulence

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Authors: Mohammad Hossein Modarressi, Mozhgan Mondeali, Khabat Barkhordari, Ali Etemadi

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The COVID-19 pandemic, caused by SARS-CoV-2, has led to significant concerns worldwide due to its catastrophic effects on public health. The SARS-CoV-2 infection is initiated with the binding of the receptor-binding domain (RBD) in its spike protein to the ACE2 receptor in the host cell membrane. Due to the error-prone entity of the viral RNA-dependent polymerase complex, the virus genome, including the coding region for the RBD, acquires new mutations, leading to the appearance of multiple variants. These variants can potentially impact transmission, virulence, antigenicity and evasive immune properties. S477N mutation located in the RBD has been observed in the SARS-CoV-2 omicron (B.1.1. 529) variant. In this study, we investigated the consequences of S477N mutation at the molecular level using computational approaches such as molecular dynamics simulation, protein-protein interaction analysis, immunoinformatics and free energy computation. We showed that displacement of Ser with Asn increases the stability of the spike protein and its affinity to ACE2 and thus increases the transmission potential of the virus. This mutation changes the folding and secondary structure of the spike protein. Also, it reduces antibody neutralization, raising concern about re-infection, vaccine breakthrough and therapeutic values.

Keywords: S477N, COVID-19, molecular dynamic, SARS-COV2 mutations

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Authors: Varun Dongre, Stefan Pirker, Stefan Heinrich

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Over the last decades, the numerical modelling of fluidized bed processes has become feasible even for industrial processes. Commonly, continuous two-fluid models are applied to describe large-scale fluidization. In order to allow for coarse grids novel two-fluid models account for unresolved sub-grid heterogeneities. However, computational efforts remain high – in the order of several hours of compute-time for a few seconds of real-time – thus preventing the representation of long-term phenomena such as heating or particle conversion processes. In order to overcome this limitation, data-based recurrence computational fluid dynamics (rCFD) has been put forward in recent years. rCFD can be regarded as a data-based method that relies on the numerical predictions of a conventional short-term simulation. This data is stored in a database and then used by rCFD to efficiently time-extrapolate the flow behavior in high spatial resolution. This study will compare the numerical predictions of rCFD simulations with those of corresponding full CFD reference simulations for lab-scale and pilot-scale fluidized beds. In assessing the predictive capabilities of rCFD simulations, we focus on solid mixing and secondary gas holdup. We observed that predictions made by rCFD simulations are highly sensitive to numerical parameters such as diffusivity associated with face swaps. We achieved a computational speed-up of four orders of magnitude (10,000 time faster than classical TFM simulation) eventually allowing for real-time simulations of fluidized beds. In the next step, we apply the checkerboarding technique by introducing gas tracers subjected to convection and diffusion. We then analyze the concentration profiles by observing mixing, transport of gas tracers, insights about the convective and diffusive pattern of the gas tracers, and further towards heat and mass transfer methods. Finally, we run rCFD simulations and calibrate them with numerical and physical parameters compared with convectional Two-fluid model (full CFD) simulation. As a result, this study gives a clear indication of the applicability, predictive capabilities, and existing limitations of rCFD in the realm of fluidization modelling.

Keywords: multiphase flow, recurrence CFD, two-fluid model, industrial processes

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Authors: Midiya Khademi, Ali Nikoo, Shabnam Rahimnezhad Baghche Jooghi

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Cardiovascular diseases (CVDs) are the main cause of death globally. Most CVDs can be prevented by avoiding habitual risk factors. Separate from the habitual risk factors, there are some inherent factors in each individual that can increase the risk potential of CVDs. Vessel shapes and geometry are influential factors, having great impact on the blood flow and the hemodynamic behavior of the vessels. In the present study, the influence of bifurcation angle on blood flow characteristics is studied. In order to approach this topic, by simplifying the details of the bifurcation, three models with angles 30°, 45°, and 60° were created, then by using CFD analysis, the response of these models for stable flow and pulsatile flow was studied. In the conducted simulation in order to eliminate the influence of other geometrical factors, only the angle of the bifurcation was changed and other parameters remained constant during the research. Simulations are conducted under dynamic and stable condition. In the stable flow simulation, a steady velocity of 0.17 m/s at the inlet plug was maintained and in dynamic simulations, a typical LAD flow waveform is implemented. The results show that the bifurcation angle has an influence on the maximum speed of the flow. In the stable flow condition, increasing the angle lead to decrease the maximum flow velocity. In the dynamic flow simulations, increasing the bifurcation angle lead to an increase in the maximum velocity. Since blood flow has pulsatile characteristics, using a uniform velocity during the simulations can lead to a discrepancy between the actual results and the calculated results.

Keywords: coronary artery, cardiovascular disease, bifurcation, atherosclerosis, CFD, artery wall shear stress

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Authors: Neha Kanodia, M. Kamil

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Properties of mono layers of Pluronic F127 at air/water interface have been investigated by using Langmuir trough method. Pluronic F127 is a triblock copolymer of poly (ethyleneoxide) (PEO groups)– poly (propylene oxide) (PO groups)–poly(ethylene oxide) (PEO groups). Surface pressure versus mean molecular area isotherms is studied. The isotherm of the mono layer showed the characteristics of a pancake-to-brush transition upon compression of the mono layer. The effect of adding surfactant (SDS) to polymer and the effect of increasing loading on polymer was also studied. The effect of repeated compression and expansion cycle (or hysteresis curve) is investigated to know about stability of the film formed. Static elasticity of mono layer gives information about molecular arrangement, phase structure and phase transition.

Keywords: surface-pressure, mean molecular area isotherms, hysteresis, static elasticity

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Authors: Mohamed Sahli, David Bassir, Thierry Barriere, Xavier Roizard

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Predicting the behaviour of the Ti-6Al-4V alloy during the turning operation was very important in the choice of suitable cutting tools and also in the machining strategies. In this study, a 3D model with thermo-mechanical coupling has been proposed to study the influence of cutting parameters and also lubrication on the performance of cutting tools. The constants of the constitutive Johnson-Cook model of Ti-6Al-4V alloy were identified using inverse analysis based on the parameters of the orthogonal cutting process. Then, numerical simulations of the finishing machining operation were developed and experimentally validated for the cylindrical stock removal stage with the finishing cutting tool.

Keywords: titanium turning, cutting tools, FE simulation, chip

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Authors: An-Shik Yang, Chin-Ting Kuo, Yung-Chun Yang, Wen-Hsin Hsieh, Chiang-Ho Cheng

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Optical biosensors have become a powerful detection and analysis tool for wide-ranging applications in biomedical research, pharmaceuticals and environmental monitoring. This study carried out the computational fluid dynamics (CFD)-based simulations to explore the dispersion phenomenon in the microchannel of a optical biosensor. The predicted time sequences of concentration contours were utilized to better understand the dispersion development occurred in different geometric shapes of microchannels. The simulation results showed the surface concentrations at the sensing probe (with the best performance of a grating coupler) in respect of time to appraise the dispersion effect and therefore identify the design configurations resulting in minimum dispersion.

Keywords: CFD simulations, dispersion, microfluidic, optical waveguide sensors

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Authors: Mohamed Rajab Peer Mohamed, Thiruvenkatasamy Kannabiran

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In the present investigation, the scour around a circular pier subjected to a steady current were studied numerically using two-dimensional MIKE21 Flow Model (FM) and Sand Transport (ST)Modulewhich is developed by Danish Hydraulic Institute (DHI), Denmark. The unstructured flexible mesh generated with rectangular flume dimension of 10 m wide, 1 m deep, and 30 m long. The grain size of the sand was d50 = 0.16 mm, sediment size, sediment gradation=1.16, pier diameter D= 30 mm and depth-averaged current velocity, U = 0.449 m/s are considered in the model. The estimated scour depth obtained from this model is validated and it is observed that the results of the model have good agreement with flume experimental results.In order to estimate the scour depth, several simulations were made for three cases viz., Case I:change in sediment transport model description in the numerical model viz, i) Engelund-Hansen model, ii) Engelund-Fredsøe model, and iii) Van Rijn model, Case II: change in current velocity for keeping constant pile diameter D=0.03 m and Case III:change in pier diameter for constant depth averaged current speed U=0.449 m/s.In case I simulations, the results indicate that the scour depth S/D is the order of 1.73 for Engelund-Hansen model, 0.64 for Engelund-Fredsøe model and 0.46 for VanRijn model. The scour depth estimates using Engelund-Hansen method compares well the experimental results.In case II, simulations show that the scour depth increases with increasing current component of the flow.In case III simulations, the results indicate that the scour depth increases with increase in pier diameter and it stabilize attains steady value when the Froude number> 2.71.All the results of the numerical simulations are clearly matches with reported values of the experimental results. Hence, this MIKE21 FM –Sand Transport model can be used as a suitable tool to estimate the scour depth for field applications. Moreover, to provide suitable scour protection methods, the maximum scour depth is to be predicted, Engelund-Hansen method can be adopted to estimate the scour depth in the steady current region.

Keywords: circular pier, MIKE21, numerical model, scour, sediment transport

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

Abstract:

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: Rachit Ahuja, Ayush Chugh

Abstract:

Aerodynamic forces and moments, as well as tire-road forces largely affects the maneuverability of the vehicle. Car manufacturers are largely fascinated and influenced by various aerodynamic improvements made in formula cars. There is constant effort of applying these aerodynamic improvements in road vehicles. In motor racing, the key differentiating factor in a high performance car is its ability to maintain highest possible acceleration in appropriate direction. One of the main areas of concern in motor racing is balance of aerodynamic forces and stream line the flow of air across the body of the vehicle. At present, formula racing cars are regulated by stringent FIA norms, there are constrains for dimensions of the vehicle, engine capacity etc. So one of the fields in which there is a large scope of improvement is aerodynamics of the vehicle. In this project work, an attempt has been made to design a formula- student (FS) car, improve its aerodynamic characteristics through steady state CFD simulations and simultaneously calculate its lap time. Initially, a CAD model of a formula student car is made using SOLIDWORKS as per the given dimensions and a steady-state external air-flow simulation is performed on the baseline model of the formula student car without any add on device to evaluate and analyze the air-flow pattern around the car and aerodynamic forces using FLUENT Solver. A detailed survey on different add-on devices used in racing application like: - front wing, diffuser, shark pin, T- wing etc. is made and geometric model of these add-on devices are created. These add-on devices are assembled with the baseline model. Steady state CFD simulations are done on the modified car to evaluate the aerodynamic effects of these add-on devices on the car. Later comparison of lap time simulation of the formula student car with and without the add-on devices is done with the help of MATLAB. Aerodynamic performances like: - lift, drag and their coefficients are evaluated for different configuration and design of the add-on devices at different speed of the vehicle. From parametric CFD simulations on formula student car attached with add-on devices, there is a considerable amount of drag and lift force reduction besides streamlining the airflow across the car. The best possible configuration of these add-on devices is obtained from these CFD simulations and also use of these add-on devices have shown an improvement in performance of the car which can be compared by various lap time simulations of the car.

Keywords: aerodynamic performance, front wing, laptime simulation, t-wing

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Authors: Serena Gomez, Raeesa Tanseen, Netra Shaligram, Nithin Francis, Sandesh B. J.

Abstract:

The human gut consists of a community of microbes which has a lot of effects on human health disease. Metabolic modeling can help to predict relative populations of stable microbes and their effect on health disease. In order to study and visualize microbes in the human gut, we developed a tool that offers the following modules: Build a tool that can be used to perform Flux Balance Analysis for microbes in the human gut using the Artificial Bee Colony optimization algorithm. Run simulations for an individual microbe in different conditions, such as aerobic and anaerobic and visualize the results of these simulations.

Keywords: microbes, metabolic modeling, flux balance analysis, artificial bee colony

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Authors: Shokofeh Ebrtahimi

Abstract:

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

Procedia PDF Downloads 278