Search results for: molecular dynamic simulation
Commenced in January 2007
Frequency: Monthly
Edition: International
Paper Count: 9755

Search results for: molecular dynamic simulation

9755 Investigation of Acidizing Corrosion Inhibitors for Mild Steel in Hydrochloric Acid: Theoretical and Experimental Approaches

Authors: Ambrish Singh

Abstract:

The corrosion inhibition performance of pyran derivatives (AP) on mild steel in 15% HCl was investigated by electrochemical impedance spectroscopy (EIS), potentiodynamic polarization, weight loss, contact angle, and scanning electron microscopy (SEM) measurements, DFT and molecular dynamic simulation. The adsorption of APs on the surface of mild steel obeyed Langmuir isotherm. The potentiodynamic polarization study confirmed that inhibitors are mixed type with cathodic predominance. Molecular dynamic simulation was applied to search for the most stable configuration and adsorption energies for the interaction of the inhibitors with Fe (110) surface. The theoretical data obtained are, in most cases, in agreement with experimental results.

Keywords: acidizing inhibitor, pyran derivatives, DFT, molecular simulation, mild steel, EIS

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9754 Molecular Clustering and Velocity Increase in Converging-Diverging Nozzle in Molecular Dynamics Simulation

Authors: Jeoungsu Na, Jaehawn Lee, Changil Hong, Suhee Kim

Abstract:

A molecular dynamics simulation in a converging-diverging nozzle was performed to study molecular collisions and their influence to average flow velocity according to a variety of vacuum levels. The static pressures and the dynamic pressure exerted by the molecule collision on the selected walls were compared to figure out the intensity variances of the directional flows. With pressure differences constant between the entrance and the exit of the nozzle, the numerical experiment was performed for molecular velocities and directional flows. The result shows that the velocities increased at the nozzle exit as the vacuum level gets higher in that area because less molecular collisions.

Keywords: cavitation, molecular collision, nozzle, vacuum, velocity increase

Procedia PDF Downloads 398
9753 Molecular Dynamics Analysis onI mpact Behaviour of Carbon Nanotubes and Graphene Sheets

Authors: Sajjad Seifoori

Abstract:

Impact behavior of striker on graphene sheet and carbon nanotube is investigated based on molecular dynamics (MD) simulations. A MD simulation is conducted to obtain the maximum dynamic deflections of a square and rectangular single-layered graphene sheets (SLGSs) with various values of side-length and striker parameter. Effect of (i) chirality, (ii) graphene side-length and nanotube length, (iii) striker mass on the maximum dynamic deflections of graphene and nanotube are investigated. The effect of different types of boundary condition on the maximum dynamic deflections is studied for zigzag and armchair SWCNTs with various aspect ratios (Length/Diameter).

Keywords: impact, molecular dynamic, graphene, spring mass

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9752 Assessment of Drug Delivery Systems from Molecular Dynamic Perspective

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

Abstract:

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

Keywords: anti-cancer drug, center of mass, interaction energy, molecular dynamics simulation, nanocarrier

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9751 Damping Function and Dynamic Simulation of GUPFC Using IC-HS Algorithm

Authors: Galu Papy Yuma

Abstract:

This paper presents a new dynamic simulation of a power system consisting of four machines equipped with the Generalized Unified Power Flow Controller (GUPFC) to improve power system stability. The dynamic simulation of the GUPFC consists of one shunt converter and two series converters based on voltage source converter, and DC link capacitor installed in the power system. MATLAB/Simulink is used to arrange the dynamic simulation of the GUPFC, where the power system is simulated in order to investigate the impact of the controller on power system oscillation damping and to show the simulation program reliability. The Improved Chaotic- Harmony Search (IC-HS) Algorithm is used to provide the parameter controller in order to lead-lag compensation design. The results obtained by simulation show that the power system with four machines is suitable for stability analysis. The use of GUPFC and IC-HS Algorithm provides the excellent capability in fast damping of power system oscillations and improve greatly the dynamic stability of the power system.

Keywords: GUPFC, IC-HS algorithm, Matlab/Simulink, damping oscillation

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9750 Molecular Dynamics Simulation of Beta-Glucosidase of Streptomyces

Authors: Adam Abate, Elham Rasti, Philip Romero

Abstract:

Beta-glucosidase is the key enzyme component present in cellulase and completes the final step during cellulose hydrolysis by converting the cellobiose to glucose. The regulatory properties of beta-glucosidases are most commonly found for the retaining and inverting enzymes. Hydrolysis of a glycoside typically occurs with general acid and general base assistance from two amino acid side chains, normally glutamic or aspartic acids. In order to obtain more detailed information on the dynamic events origination from the interaction with enzyme active site, we carried out molecular dynamics simulations of beta-glycosidase in protonated state (Glu-H178) and deprotonated state (Glu178). The theoretical models generated from our molecular dynamics simulations complement and advance the structural information currently available, leading to a more detailed understanding of Beta-glycosidase structure and function. This article presents the important role of Asn307 in enzyme activity of beta-glucosidase

Keywords: Beta-glucosidase, GROMACS, molecular dynamics simulation, structural parameters

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9749 Predicting the Solubility of Aromatic Waste Petroleum Paraffin Wax in Organic Solvents to Separate Ultra-Pure Phase Change Materials (PCMs) by Molecular Dynamics Simulation

Authors: Fathi Soliman

Abstract:

With the ultimate goal of developing the separation of n-paraffin as phase change material (PCM) by means of molecular dynamic simulations, we attempt to predict the solubility of aromatic n-paraffin in two organic solvents: Butyl Acetate (BA) and Methyl Iso Butyl Ketone (MIBK). A simple model of aromatic paraffin: 2-hexadecylantharacene with amorphous molecular structure and periodic boundary conditions was constructed. The results showed that MIBK is the best solvent to separate ultra-pure phase change materials and this data was compatible with experimental data done to separate ultra-pure n-paraffin from waste petroleum aromatic paraffin wax, the separated n-paraffin was characterized by XRD, TGA, GC and DSC, moreover; data revealed that the n-paraffin separated by using MIBK is better as PCM than that separated using BA.

Keywords: molecular dynamics simulation, n-paraffin, organic solvents, phase change materials, solvent extraction

Procedia PDF Downloads 152
9748 An Insight into the Conformational Dynamics of Glycan through Molecular Dynamics Simulation

Authors: K. Veluraja

Abstract:

Glycan of glycolipids and glycoproteins is playing a significant role in living systems particularly in molecular recognition processes. Molecular recognition processes are attributed to their occurrence on the surface of the cell, sequential arrangement and type of sugar molecules present in the oligosaccharide structure and glyosidic linkage diversity (glycoinformatics) and conformational diversity (glycoconformatics). Molecular Dynamics Simulation study is a theoretical-cum-computational tool successfully utilized to establish glycoconformatics of glycan. The study on various oligosaccharides of glycan clearly indicates that oligosaccharides do exist in multiple conformational states and these conformational states arise due to the flexibility associated with a glycosidic torsional angle (φ,ψ) . As an example: a single disaccharide structure NeuNacα(2-3) Gal exists in three different conformational states due to the differences in the preferential value of glycosidic torsional angles (φ,ψ). Hence establishing three dimensional structural and conformational models for glycan (cartesian coordinates of every individual atoms of an oligosaccharide structure in a preferred conformation) is quite crucial to understand various molecular recognition processes such as glycan-toxin interaction and glycan-virus interaction. The gycoconformatics models obtained for various glycan through Molecular Dynamics Simulation stored in our 3DSDSCAR (3DSDSCAR.ORG) a public domain database and its utility value in understanding the molecular recognition processes and in drug design venture will be discussed.

Keywords: glycan, glycoconformatics, molecular dynamics simulation, oligosaccharide

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9747 Development of Immuno-Modulators: Application of Molecular Dynamics Simulation

Authors: Ruqaiya Khalil, Saman Usmani, Zaheer Ul-Haq

Abstract:

The accurate characterization of ligand binding affinity is indispensable for designing molecules with optimized binding affinity. Computational tools help in many directions to predict quantitative correlations between protein-ligand structure and their binding affinities. Molecular dynamics (MD) simulation is a modern state-of-the-art technique to evaluate the underlying basis of ligand-protein interactions by characterizing dynamic and energetic properties during the event. Autoimmune diseases arise from an abnormal immune response of the body against own tissues. The current regimen for the described condition is limited to immune-modulators having compromised pharmacodynamics and pharmacokinetics profiles. One of the key player mediating immunity and tolerance, thus invoking autoimmunity is Interleukin-2; a cytokine influencing the growth of T cells. Molecular dynamics simulation techniques are applied to seek insight into the inhibitory mechanisms of newly synthesized compounds that manifested immunosuppressant potentials during in silico pipeline. In addition to estimation of free energies associated with ligand binding, MD simulation yielded us a great deal of information about ligand-macromolecule interactions to evaluate the pattern of interactions and the molecular basis of inhibition. The present study is a continuum of our efforts to identify interleukin-2 inhibitors of both natural and synthetic origin. Herein, we report molecular dynamics simulation studies of Interluekin-2 complexed with different antagonists previously reported by our group. The study of protein-ligand dynamics enabled us to gain a better understanding of the contribution of different active site residues in ligand binding. The results of the study will be used as the guide to rationalize the fragment based synthesis of drug-like interleukin-2 inhibitors as immune-modulators.

Keywords: immuno-modulators, MD simulation, protein-ligand interaction, structure-based drug design

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9746 Dynamic Fault Tree Analysis of Dynamic Positioning System through Monte Carlo Approach

Authors: A. S. Cheliyan, S. K. Bhattacharyya

Abstract:

Dynamic Positioning System (DPS) is employed in marine vessels of the offshore oil and gas industry. It is a computer controlled system to automatically maintain a ship’s position and heading by using its own thrusters. Reliability assessment of the same can be analyzed through conventional fault tree. However, the complex behaviour like sequence failure, redundancy management and priority of failing of events cannot be analyzed by the conventional fault trees. The Dynamic Fault Tree (DFT) addresses these shortcomings of conventional Fault Tree by defining additional gates called dynamic gates. Monte Carlo based simulation approach has been adopted for the dynamic gates. This method of realistic modeling of DPS gives meaningful insight into the system reliability and the ability to improve the same.

Keywords: dynamic positioning system, dynamic fault tree, Monte Carlo simulation, reliability assessment

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9745 Preventing Neurodegenerative Diseases by Stabilization of Superoxide Dismutase by Natural Polyphenolic Compounds

Authors: Danish Idrees, Vijay Kumar, Samudrala Gourinath

Abstract:

Amyotrophic lateral sclerosis (ALS) is a neurodegenerative disease caused by misfolding and aggregation of Cu, Zn superoxide dismutase (SOD1). The use of small molecules has been shown to stabilize the SOD1 dimer and preventing its dissociation and aggregation. In this study, we employed molecular docking, molecular dynamics simulation and surface plasmon resonance (SPR) to study the interactions between SOD1 and natural polyphenolic compounds. In order to explore the noncovalent interaction between SOD1 and natural polyphenolic compounds, molecular docking and molecular dynamic (MD) simulations were employed to gain insights into the binding modes and free energies of SOD1-polyphenolic compounds. MM/PBSA methods were used to calculate free energies from obtained MD trajectories. The compounds, Hesperidin, Ergosterol, and Rutin showed the excellent binding affinity in micromolar range with SOD1. Ergosterol and Hesperidin have the strongest binding affinity to SOD1 and was subjected to further characterization. Biophysical experiments using Circular Dichroism and Thioflavin T fluorescence spectroscopy results show that the binding of these two compounds can stabilize SOD1 dimer and inhibit the aggregation of SOD1. Molecular simulation results also suggest that these compounds reduce the dissociation of SOD1 dimers through direct interaction with the dimer interface. This study will be helpful to develop other drug-like molecules which may have the effect to reduce the aggregation of SOD1.

Keywords: amyotrophic lateral sclerosis, molecular dynamics simulation, surface plasmon resonance, superoxide dismutase

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9744 Analyzing and Predicting the CL-20 Detonation Reaction Mechanism Based on Artificial Intelligence Algorithm

Authors: Kaining Zhang, Lang Chen, Danyang Liu, Jianying Lu, Kun Yang, Junying Wu

Abstract:

In order to solve the problem of a large amount of simulation and limited simulation scale in the first-principle molecular dynamics simulation of energetic material detonation reaction, we established an artificial intelligence model for analyzing and predicting the detonation reaction mechanism of CL-20 based on the first-principle molecular dynamics simulation of the multiscale shock technique (MSST). We employed principal component analysis to identify the dominant charge features governing molecular reactions. We adopted the K-means clustering algorithm to cluster the reaction paths and screen out the key reactions. We introduced the neural network algorithm to construct the mapping relationship between the charge characteristics of the molecular structure and the key reaction characteristics so as to establish a calculation method for predicting detonation reactions based on the charge characteristics of CL-20 and realize the rapid analysis of the reaction mechanism of energetic materials.

Keywords: energetic material detonation reaction, first-principle molecular dynamics simulation of multiscale shock technique, neural network, CL-20

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9743 Molecular Dynamic Simulation of CO2 Absorption into Mixed Aqueous Solutions MDEA/PZ

Authors: N. Harun, E. E. Masiren, W. H. W. Ibrahim, F. Adam

Abstract:

Amine absorption process is an approach for mitigation of CO2 from flue gas that produces from power plant. This process is the most common system used in chemical and oil industries for gas purification to remove acid gases. On the challenges of this process is high energy requirement for solvent regeneration to release CO2. In the past few years, mixed alkanolamines have received increasing attention. In most cases, the mixtures contain N-methyldiethanolamine (MDEA) as the base amine with the addition of one or two more reactive amines such as PZ. The reason for the application of such blend amine is to take advantage of high reaction rate of CO2 with the activator combined with the advantages of the low heat of regeneration of MDEA. Several experimental and simulation studies have been undertaken to understand this process using blend MDEA/PZ solvent. Despite those studies, the mechanism of CO2 absorption into the aqueous MDEA is not well understood and available knowledge within the open literature is limited. The aim of this study is to investigate the intermolecular interaction of the blend MDEA/PZ using Molecular Dynamics (MD) simulation. MD simulation was run under condition 313K and 1 atm using NVE ensemble at 200ps and NVT ensemble at 1ns. The results were interpreted in term of Radial Distribution Function (RDF) analysis through two system of interest i.e binary and tertiary. The binary system will explain the interaction between amine and water molecule while tertiary system used to determine the interaction between the amine and CO2 molecule. For the binary system, it was observed that the –OH group of MDEA is more attracted to water molecule compared to –NH group of MDEA. The –OH group of MDEA can form the hydrogen bond with water that will assist the solubility of MDEA in water. The intermolecular interaction probability of –OH and –NH group of MDEA with CO2 in blended MDEA/PZ is higher than using single MDEA. This findings show that PZ molecule act as an activator to promote the intermolecular interaction between MDEA and CO2.Thus, blend of MDEA with PZ is expecting to increase the absorption rate of CO2 and reduce the heat regeneration requirement.

Keywords: amine absorption process, blend MDEA/PZ, CO2 capture, molecular dynamic simulation, radial distribution function

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9742 Molecular Dynamics Simulation on Nanoelectromechanical Graphene Nanoflake Shuttle Device

Authors: Eunae Lee, Oh-Kuen Kwon, Ki-Sub Kim, Jeong Won Kang

Abstract:

We investigated the dynamic properties of graphene-nanoribbon (GNR) memory encapsulating graphene-nanoflake (GNF) shuttle in the potential to be applicable as a non-volatile random access memory via molecular dynamics simulations. This work explicitly demonstrates that the GNR encapsulating the GNF shuttle can be applied to nonvolatile memory. The potential well was originated by the increase of the attractive vdW energy between the GNRs when the GNF approached the edges of the GNRs. So the bistable positions were located near the edges of the GNRs. Such a nanoelectromechanical non-volatile memory based on graphene is also applicable to the development of switches, sensors, and quantum computing.

Keywords: graphene nanoribbon, graphene nanoflake, shuttle memory, molecular dynamics

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9741 Molecular Dynamics Simulation for Buckling Analysis at Nanocomposite Beams

Authors: Babak Safaei, A. M. Fattahi

Abstract:

In the present study we have investigated axial buckling characteristics of nanocomposite beams reinforced by single-walled carbon nanotubes (SWCNTs). Various types of beam theories including Euler-Bernoulli beam theory, Timoshenko beam theory and Reddy beam theory were used to analyze the buckling behavior of carbon nanotube-reinforced composite beams. Generalized differential quadrature (GDQ) method was utilized to discretize the governing differential equations along with four commonly used boundary conditions. The material properties of the nanocomposite beams were obtained using molecular dynamic (MD) simulation corresponding to both short-(10,10) SWCNT and long-(10,10) SWCNT composites which were embedded by amorphous polyethylene matrix. Then the results obtained directly from MD simulations were matched with those calculated by the mixture rule to extract appropriate values of carbon nanotube efficiency parameters accounting for the scale-dependent material properties. The selected numerical results were presented to indicate the influences of nanotube volume fractions and end supports on the critical axial buckling loads of nanocomposite beams relevant to long- and short-nanotube composites.

Keywords: nanocomposites, molecular dynamics simulation, axial buckling, generalized differential quadrature (GDQ)

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9740 Molecular Dynamic Simulation of Cold Spray Process

Authors: Aneesh Joshi, Sagil James

Abstract:

Cold Spray (CS) process is deposition of solid particles over a substrate above a certain critical impact velocity. Unlike thermal spray processes, CS process does not melt the particles thus retaining their original physical and chemical properties. These characteristics make CS process ideal for various engineering applications involving metals, polymers, ceramics and composites. The bonding mechanism involved in CS process is extremely complex considering the dynamic nature of the process. Though CS process offers great promise for several engineering applications, the realization of its full potential is limited by the lack of understanding of the complex mechanisms involved in this process and the effect of critical process parameters on the deposition efficiency. The goal of this research is to understand the complex nanoscale mechanisms involved in CS process. The study uses Molecular Dynamics (MD) simulation technique to understand the material deposition phenomenon during the CS process. Impact of a single crystalline copper nanoparticle on copper substrate is modelled under varying process conditions. The quantitative results of the impacts at different velocities, impact angle and size of the particles are evaluated using flattening ratio, von Mises stress distribution and local shear strain. The study finds that the flattening ratio and hence the quality of deposition was highest for an impact velocity of 700 m/s, particle size of 20 Å and an impact angle of 90°. The stress and strain analysis revealed regions of shear instabilities in the periphery of impact and also revealed plastic deformation of the particles after the impact. The results of this study can be used to augment our existing knowledge in the field of CS processes.

Keywords: cold spray process, molecular dynamics simulation, nanoparticles, particle impact

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9739 Coarse-Grained Molecular Simulations to Estimate Thermophysical Properties of Phase Equilibria

Authors: Hai Hoang, Thanh Xuan Nguyen Thi, Guillaume Galliero

Abstract:

Coarse-Grained (CG) molecular simulations have shown to be an efficient way to estimate thermophysical (static and dynamic) properties of fluids. Several strategies have been developed and reported in the literature for defining CG molecular models. Among them, those based on a top-down strategy (i.e. CG molecular models related to macroscopic observables), despite being heuristic, have increasingly gained attention. This is probably due to its simplicity in implementation and its ability to provide reasonable results for not only simple but also complex systems. Regarding simple Force-Fields associated with these CG molecular models, it has been found that the four parameters Mie chain model is one of the best compromises to describe thermophysical static properties (e.g. phase diagram, saturation pressure). However, parameterization procedures of these Mie-chain GC molecular models given in literature are generally insufficient to simultaneously provide static and dynamic (e.g. viscosity) properties. To deal with such situations, we have extended the corresponding states by using a quantity associated with the liquid viscosity. Results obtained from molecular simulations have shown that our approach is able to yield good estimates for both static and dynamic thermophysical properties for various real non-associating fluids. In addition, we will show that on simple (e.g. phase diagram, saturation pressure) and complex (e.g. thermodynamic response functions, thermodynamic energy potentials) static properties, results of our scheme generally provides improved results compared to existing approaches.

Keywords: coarse-grained model, mie potential, molecular simulations, thermophysical properties, phase equilibria

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9738 Accelerated Molecular Simulation: A Convolution Approach

Authors: Jannes Quer, Amir Niknejad, Marcus Weber

Abstract:

Computational Drug Design is often based on Molecular Dynamics simulations of molecular systems. Molecular Dynamics can be used to simulate, e.g., the binding and unbinding event of a small drug-like molecule with regard to the active site of an enzyme or a receptor. However, the time-scale of the overall binding event is many orders of magnitude longer than the time-scale of simulation. Thus, there is a need to speed-up molecular simulations. In order to speed up simulations, the molecular dynamics trajectories have to be ”steared” out of local minimizers of the potential energy surface – the so-called metastabilities – of the molecular system. Increasing the kinetic energy (temperature) is one possibility to accelerate simulated processes. However, with temperature the entropy of the molecular system increases, too. But this kind ”stearing” is not directed enough to stear the molecule out of the minimum toward the saddle point. In this article, we give a new mathematical idea, how a potential energy surface can be changed in such a way, that entropy is kept under control while the trajectories are still steared out of the metastabilities. In order to compute the unsteared transition behaviour based on a steared simulation, we propose to use extrapolation methods. In the end we mathematically show, that our method accelerates the simulations along the direction, in which the curvature of the potential energy surface changes the most, i.e., from local minimizers towards saddle points.

Keywords: extrapolation, Eyring-Kramers, metastability, multilevel sampling

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9737 Molecular Dynamics Study of Ferrocene in Low and Room Temperatures

Authors: Feng Wang, Vladislav Vasilyev

Abstract:

Ferrocene (Fe(C5H5)2, i.e., di-cyclopentadienyle iron (FeCp2) or Fc) is a unique example of ‘wrong but seminal’ in chemistry history. It has significant applications in a number of areas such as homogeneous catalysis, polymer chemistry, molecular sensing, and nonlinear optical materials. However, the ‘molecular carousel’ has been a ‘notoriously difficult example’ and subject to long debate for its conformation and properties. Ferrocene is a dynamic molecule. As a result, understanding of the dynamical properties of ferrocene is very important to understand the conformational properties of Fc. In the present study, molecular dynamic (MD) simulations are performed. In the simulation, we use 5 geometrical parameters to define the overall conformation of Fc and all the rest is a thermal noise. The five parameters are defined as: three parameters d---the distance between two Cp planes, α and δ to define the relative positions of the Cp planes, in which α is the angle of the Cp tilt and δ the angle the two Cp plane rotation like a carousel. Two parameters to position the Fe atom between two Cps, i.e., d1 for Fe-Cp1 and d2 for Fe-Cp2 distances. Our preliminary MD simulation discovered the five parameters behave differently. Distances of Fe to the Cp planes show that they are independent, practically identical without correlation. The relative position of two Cp rings, α, indicates that the two Cp planes are most likely not in a parallel position, rather, they tilt in a small angle α≠ 0°. The mean plane dihedral angle δ ≠ 0°. Moreover, δ is neither 0° nor 36°, indicating under those conditions, Fc is neither in a perfect eclipsed structure nor a perfect staggered structure. The simulations show that when the temperature is above 80K, the conformers are virtually in free rotations, A very interesting result from the MD simulation is the five C-Fe bond distances from the same Cp ring. They are surprisingly not identical but in three groups of 2, 2 and 1. We describe the pentagon formed by five carbon atoms as ‘turtle swimming’ for the motion of the Cp rings of Fc as shown in their dynamical animation video. The Fe- C(1) and Fe-C(2) which are identical as ‘the turtle back legs’, Fe-C(3) and Fe-C(4) which are also identical as turtle front paws’, and Fe-C(5) ---’the turtle head’. Such as ‘turtle swimming’ analog may be able to explain the single substituted derivatives of Fc. Again, the mean Fe-C distance obtained from MD simulation is larger than the quantum mechanically calculated Fe-C distances for eclipsed and staggered Fc, with larger deviation with respect to the eclipsed Fc than the staggered Fc. The same trend is obtained for the five Fe-C-H angles from same Cp ring of Fc. The simulated mean IR spectrum at 7K shows split spectral peaks at approximately 470 cm-1 and 488 cm-1, in excellent agreement with quantum mechanically calculated gas phase IR spectrum for eclipsed Fc. As the temperature increases over 80K, the clearly splitting IR spectrum become a very board single peak. Preliminary MD results will be presented.

Keywords: ferrocene conformation, molecular dynamics simulation, conformer orientation, eclipsed and staggered ferrocene

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9736 Heat Capacity of a Soluble in Water Protein: Equilibrium Molecular Dynamics Simulation

Authors: A. Rajabpour, A. Hadizadeh Kheirkhah

Abstract:

Heat transfer is of great importance to biological systems in order to function properly. In the present study, specific heat capacity as one of the most important heat transfer properties is calculated for a soluble in water Lysozyme protein. Using equilibrium molecular dynamics (MD) simulation, specific heat capacities of pure water, dry lysozyme, and lysozyme-water solution are calculated at 300K for different weight fractions. It is found that MD results are in good agreement with ideal binary mixing rule at small weight fractions. Results of all simulations have been validated with experimental data.

Keywords: specific heat capacity, molecular dynamics simulation, lysozyme protein, equilibrium

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9735 Numerical Study of the Dynamic Behavior of an Air Conditioning with a Muti Confined Swirling Jet

Authors: Mohamed Roudane

Abstract:

The objective of this study is to know the dynamic behavior of a multi swirling jet used for air conditioning inside a room. To conduct this study, we designed a facility to ensure proper conditions of confinement in which we placed five air blowing devices with adjustable vanes, providing multiple swirling turbulent jets. The jets were issued in the same direction and the same spacing defined between them. This study concerned the numerical simulation of the dynamic mixing of confined swirling multi-jets, and examined the influence of important parameters of a swirl diffuser system on the dynamic performance characteristics. The CFD investigations are carried out by a hybrid mesh to discretize the computational domain. In this work, the simulations have been performed using the finite volume method and FLUENT solver, in which the standard k-ε RNG turbulence model was used for turbulence computations.

Keywords: simulation, dynamic behavior, swirl, turbulent jet

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9734 Investigation of Arson Fire Incident in Textile Garment Building Using Fire Dynamic Simulation

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

Abstract:

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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9733 Thick Disc Molecular Gas Fraction in NGC 6946

Authors: Narendra Nath Patra

Abstract:

Several recent studies reinforce the existence of a thick molecular disc in galaxies along with the dynamically cold thin disc. Assuming a two-component molecular disc, we model the disc of NGC 6946 as a four-component system consists of stars, HI, thin disc molecular gas, and thick disc molecular gas in vertical hydrostatic equilibrium. Following, we set up the joint Poisson-Boltzmann equation of hydrostatic equilibrium and solve it numerically to obtain a three-dimensional density distribution of different baryonic components. Using the density solutions and the observed rotation curve, we further build a three-dimensional dynamical model of the molecular disc and consecutively produce simulated CO spectral cube and spectral width profile. We find that the simulated spectral width profiles distinguishably differs for different assumed thick disc molecular gas fraction. Several CO spectral width profiles are then produced for different assumed thick disc molecular gas fractions and compared with the observed one to obtain the best fit thick disc molecular gas fraction profile. We find that the thick disc molecular gas fraction in NGC 6946 largely remains constant across its molecular disc with a mean value of 0.70 +/- 0.09. We also estimate the amount of extra-planar molecular gas in NGC 6946. We find 60% of the total molecular gas is extra-planar at the central region, whereas this fraction reduces to ~ 35% at the edge of the molecular disc. With our method, for the first time, we estimate the thick disc molecular gas fraction as a function of radius in an external galaxy with sub-kpc resolution.

Keywords: galaxies: kinematics and dynamic, galaxies: spiral, galaxies: structure , ISM: molecules, molecular data

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9732 Laboratory Simulation of Subway Dynamic Stray Current Interference with Cathodically Protected Structures

Authors: Mohammad Derakhshani, Saeed Reza Allahkaram, Michael Isakani-Zakaria, Masoud Samadian, Hojat Sharifi Rasaey

Abstract:

Dynamic stray currents tend to change their magnitude and polarity with time at their source which will create anodic and cathodic spots on a nearby interfered structure. To date, one of the biggest known dynamic stray current sources are DC traction systems. Laboratory simulation is a suitable method to apply theoretical principles in order to identify effective parameters in dynamic stray current influenced corrosion. Simulation techniques can be utilized for various mitigation methods applied in a small scales for selection of the most efficient method with regards to field applications. In this research, laboratory simulation of potential fluctuations caused by dynamic stray current on a cathodically protected structure was investigated. A lab model capable of generating DC static and dynamic stray currents and simulating its effects on cathodically protected samples were developed based on stray current induced (contact-less) polarization technique. Stray current pick-up and discharge spots on an influenced structure were simulated by inducing fluctuations in the sample’s stationary potential. Two mitigation methods for dynamic stray current interference on buried structures namely application of sacrificial anodes as preferred discharge point for the stray current and potentially controlled cathodic protection was investigated. Results showed that the application of sacrificial anodes can be effective in reducing interference only in discharge spot. But cathodic protection through potential controlling is more suitable for mitigating dynamic stray current effects.

Keywords: simulation, dynamic stray current, fluctuating potentials, sacrificial anode

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9731 Gas Aggregation and Nanobubbles Stability on Substrates Influenced by Surface Wettability: A Molecular Dynamics Study

Authors: Tsu-Hsu Yen

Abstract:

The interfacial gas adsorption presents a frequent challenge and opportunity for micro-/nano-fluidic operation. In this study, we investigate the wettability, gas accumulation, and nanobubble formation on various homogeneous surface conditions by using MD simulation, including a series of 3D and quasi-2D argon-water-solid systems simulation. To precisely determine the wettability on various substrates, several indicators were calculated. Among these wettability indicators, the water PMF (potential of mean force) has the most correlation tendency with interfacial water molecular orientation than depletion layer width and droplet contact angle. The results reveal that the aggregation of argon molecules on substrates not only depending on the level of hydrophobicity but also determined by the competition between gas-solid and water-solid interaction as well as water molecular structure near the surface. In addition, the surface nanobubble is always observed coexisted with the gas enrichment layer. The water structure adjacent to water-gas and water-solid interfaces also plays an important factor in gas out-flux and gas aggregation, respectively. The quasi-2D simulation shows that only a slight difference in the curved argon-water interface from the plane interface which suggests no noticeable obstructing effect on gas outflux from the gas-water interfacial water networks.

Keywords: gas aggregation, interfacial nanobubble, molecular dynamics simulation, wettability

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9730 Axle Load Estimation of Moving Vehicles Using BWIM Technique

Authors: Changgil Lee, Seunghee Park

Abstract:

Although vehicle driving test for the development of BWIM system is necessary, but it needs much cost and time in addition application of various driving condition. Thus, we need the numerical-simulation method resolving the cost and time problems of vehicle driving test and the way of measuring response of bridge according to the various driving condition. Using the precision analysis model reflecting the dynamic characteristic is contributed to increase accuracy in numerical simulation. In this paper, we conduct a numerical simulation to apply precision analysis model, which reflects the dynamic characteristic of bridge using Bridge Weigh-in-Motion technique and suggest overload vehicle enforcement technology using precision analysis model.

Keywords: bridge weigh-in-motion(BWIM) system, precision analysis model, dynamic characteristic of bridge, numerical simulation

Procedia PDF Downloads 249
9729 Molecular Dynamics Simulations of the Structural, Elastic and Thermodynamic Properties of Cubic GaBi

Authors: M. Zemouli, K. Amara, M. Elkeurti, Y. Benallou

Abstract:

We present the molecular dynamic simulations results of the structural and dynamical properties of the zinc-blende GaBi over a wide range of temperature (300-1000) K. Our simulation where performed in the framework of the three-body Tersoff potential, which accurately reproduces the lattice constants and elastic constants of the GaBi. A good agreement was found between our calculated results and the available theoretical data of the lattice constant, the bulk modulus and the cohesive energy. Our study allows us to predict the thermodynamic properties such as the specific heat and the lattice thermal expansion. In addition, this method allows us to check its ability to predict the phase transition of this compound. In particular, the transition pressure to the rock-salt phase is calculated and the results are compared with other available works.

Keywords: Gallium compounds, molecular dynamics simulations, interatomic potential thermodynamic properties, structural phase transition

Procedia PDF Downloads 400
9728 Computer-Aided Drug Repurposing for Mycobacterium Tuberculosis by Targeting Tryptophanyl-tRNA Synthetase

Authors: Neslihan Demirci, Serdar Durdağı

Abstract:

Mycobacterium tuberculosis is still a worldwide disease-causing agent that, according to WHO, led to the death of 1.5 million people from tuberculosis (TB) in 2020. The bacteria reside in macrophages located specifically in the lung. There is a known quadruple drug therapy regimen for TB consisting of isoniazid (INH), rifampin (RIF), pyrazinamide (PZA), and ethambutol (EMB). Over the past 60 years, there have been great contributions to treatment options, such as recently approved delamanid (OPC67683) and bedaquiline (TMC207/R207910), targeting mycolic acid and ATP synthesis, respectively. Also, there are natural compounds that can block the tryptophanyl-tRNA synthetase (TrpRS) enzyme, chuangxinmycin, and indolmycin. Yet, already the drug resistance is reported for those agents. In this study, the newly released TrpRS enzyme structure is investigated for potential inhibitor drugs from already synthesized molecules to help the treatment of resistant cases and to propose an alternative drug for the quadruple drug therapy of tuberculosis. Maestro, Schrodinger is used for docking and molecular dynamic simulations. In-house library containing ~8000 compounds among FDA-approved indole-containing compounds, a total of 57 obtained from the ChemBL were used for both ATP and tryptophan binding pocket docking. Best of indole-containing 57 compounds were subjected to hit expansion and compared later with virtual screening workflow (VSW) results. After docking, VSW was done. Glide-XP docking algorithm was chosen. When compared, VSW alone performed better than the hit expansion module. Best scored compounds were kept for ten ns molecular dynamic simulations by Desmond. Further, 100 ns molecular dynamic simulation was performed for elected molecules according to Z-score. The top three MMGBSA-scored compounds were subjected to steered molecular dynamic (SMD) simulations by Gromacs. While SMD simulations are still being conducted, ponesimod (for multiple sclerosis), vilanterol (β₂ adrenoreceptor agonist), and silodosin (for benign prostatic hyperplasia) were found to have a significant affinity for tuberculosis TrpRS, which is the propulsive force for the urge to expand the research with in vitro studies. Interestingly, top-scored ponesimod has been reported to have a side effect that makes the patient prone to upper respiratory tract infections.

Keywords: drug repurposing, molecular dynamics, tryptophanyl-tRNA synthetase, tuberculosis

Procedia PDF Downloads 77
9727 Dynamic Reroute Modeling for Emergency Evacuation: Case Study of Brunswick City, Germany

Authors: Yun-Pang Flötteröd, Jakob Erdmann

Abstract:

The human behaviors during evacuations are quite complex. One of the critical behaviors which affect the efficiency of evacuation is route choice. Therefore, the respective simulation modeling work needs to function properly. In this paper, Simulation of Urban Mobility’s (SUMO) current dynamic route modeling during evacuation, i.e. the rerouting functions, is examined with a real case study. The result consistency of the simulation and the reality is checked as well. Four influence factors (1) time to get information, (2) probability to cancel a trip, (3) probability to use navigation equipment, and (4) rerouting and information updating period are considered to analyze possible traffic impacts during the evacuation and to examine the rerouting functions in SUMO. Furthermore, some behavioral characters of the case study are analyzed with use of the corresponding detector data and applied in the simulation. The experiment results show that the dynamic route modeling in SUMO can deal with the proposed scenarios properly. Some issues and function needs related to route choice are discussed and further improvements are suggested.

Keywords: evacuation, microscopic traffic simulation, rerouting, SUMO

Procedia PDF Downloads 147
9726 Molecular Dynamics Simulation for Vibration Analysis at Nanocomposite Plates

Authors: Babak Safaei, A. M. Fattahi

Abstract:

Polymer/carbon nanotube nanocomposites have a wide range of promising applications Due to their enhanced properties. In this work, free vibration analysis of single-walled carbon nanotube-reinforced composite plates is conducted in which carbon nanotubes are embedded in an amorphous polyethylene. The rule of mixture based on various types of plate model namely classical plate theory (CLPT), first-order shear deformation theory (FSDT), and higher-order shear deformation theory (HSDT) was employed to obtain fundamental frequencies of the nanocomposite plates. Generalized differential quadrature (GDQ) method was used to discretize the governing differential equations along with the simply supported and clamped boundary conditions. The material properties of the nanocomposite plates were evaluated using molecular dynamic (MD) simulation corresponding to both short-(10,10) SWCNT and long-(10,10) SWCNT composites. Then the results obtained directly from MD simulations were fitted with those calculated by the rule of mixture to extract appropriate values of carbon nanotube efficiency parameters accounting for the scale-dependent material properties. The selected numerical results are presented to address the influences of nanotube volume fraction and edge supports on the value of fundamental frequency of carbon nanotube-reinforced composite plates corresponding to both long- and short-nanotube composites.

Keywords: nanocomposites, molecular dynamics simulation, free vibration, generalized, differential quadrature (GDQ) method

Procedia PDF Downloads 291