Search results for: molecular dynamic simulations

Authors: Duncan Oteki, Andebut Yeneneh, Daba Gedafa, Nabil Suleiman

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Most agencies lack the equipment required to measure the dynamic modulus (|E*|) of asphalt mixtures, necessitating the need to use predictive models. This study compared measured |E*| values for nine North Dakota asphalt mixes using the original Witczak, modified Witczak, and Hirsch models. The influence of temperature on the |E*| models was investigated, and Pavement ME simulations were conducted using measured |E*| and predictions from the most accurate |E*| model. The results revealed that the original Witczak model yielded the lowest Se/Sy and highest R² values, indicating the lowest bias and highest accuracy, while the poorest overall performance was exhibited by the Hirsch model. Using predicted |E*| as inputs in the Pavement ME generated conservative distress predictions compared to using measured |E*|. The original Witczak model was recommended for predicting |E*| for low-reliability pavements in North Dakota.

Keywords: asphalt mixture, binder, dynamic modulus, MEPDG, pavement ME, performance, prediction

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Authors: R. Mohan, V. Jadhav, A. Ahmed, J. Rivas, A. Kelkar

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Cementitious materials are an excellent example of a composite material with complex hierarchical features and random features that range from nanometer (nm) to millimeter (mm) scale. Multi-scale modeling of complex material systems requires starting from fundamental building blocks to capture the scale relevant features through associated computational models. In this paper, molecular dynamics (MD) modeling is employed to predict the effect of plasticizer additive on the mechanical properties of key hydrated cement constituent calcium-silicate-hydrate (CSH) at the molecular, nanometer scale level. Due to complexity, still unknown molecular configuration of CSH, a representative configuration widely accepted in the field of mineral Jennite is employed. The effectiveness of the Molecular Dynamics modeling to understand the predictive influence of material chemistry changes based on molecular/nanoscale models is demonstrated.

Keywords: cement composite, mechanical properties, molecular dynamics, plasticizer additives

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Authors: Chro Kawyan

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Endothelin-1 (ET-1), the principal individual from the newfound mammalian endothelin group of organically dynamic peptides, was initially distinguished as a 21 buildup powerful vasoconstrictor peptide in vascular endothelial cells. However, it has since been demonstrated to have a wide range of pharmacological activities in tissues both inside and outside the cardiovascular system. Additionally, peptides that have a striking resemblance to ET-1 have been identified as the primary toxic component of snake venom. In addition, late examinations have proposed that warm blooded creatures, including people, produce three unmistakable individuals from this peptide family, ET-1, ET-2 and ET-J, which might have various profiles of organic action and may follow up on particular subtypes of endothelin receptor. Masashi Yanagisawa and Tomoh Masaki survey the ongoing status of the organic chemistry and sub-atomic science of endothelin.

Keywords: thelin, microbiology, molecular biology, cell

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Authors: Divya Singh, Avinash Parashar

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Due to superior mechanical, creep and nuclear cross section, zirconium and niobium (Zr-Nb) based alloys are commonly used as nuclear materials for the manufacturing of fuel cladding and pressure tubes in nuclear power plants. In this work, symmetrical tilt grain boundary (STGB) structures in α-Zr are studied for their structure and energies along two tilt axes- [0001] and [0-110] using MD based simulations. Tilt grain boundaries are obtained along [0001] tilt axis, and special twin structures are obtained along [0-110] tilt axis in α-Zr. For Nb, STGBs are constructed along [100] and [110] axis using atomistic simulations. The correlation between GB structures and their energies is subsequently examined. A close relationship is found to exist between individual GB structure and its energy in both α-Zr and Nb. It is also concluded that the energies of the more coherent twin grain boundaries are lower than the symmetrical tilt grain boundaries.

Keywords: grain boundaries, molecular dynamics, grain boundary energy, hcp crystal

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Authors: Alireza Motamadnia, Roohollah Zohdi Oliayi, Hümeyra Bolakar, Ahmet Tortum

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Dynamic compression as a method of soil improvement in recent decades has been considered by engineers and experts. Three methods mainly, deep dynamic compaction, soil density, dynamic and rapid change have been proposed and implemented to improve subgrade conditions of highway road. Northern highway route in Tabriz (Pasdaran), Iran that was placed on the manual soil was the main concern. Engineering properties of soil have been investigated experimentally and theoretically. Among the three methods rapid dynamic compaction for highway has been suggested to improve the soil subgrade conditions.

Keywords: manual soil, subsidence, improvement, dynamic compression

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Authors: Ece A. Irmak, Amdulla O. Mekhrabov, M. Vedat Akdeniz

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There is a growing interest in the modeling and simulation of magnetic nanoalloys by various computational methods. Magnetic crystalline/amorphous nanoparticles (NP) are interesting materials from both the applied and fundamental points of view, as their properties differ from those of bulk materials and are essential for advanced applications such as high-performance permanent magnets, high-density magnetic recording media, drug carriers, sensors in biomedical technology, etc. As an important magnetic material, Fe-Ni based nanoalloys have promising applications in the chemical industry (catalysis, battery), aerospace and stealth industry (radar absorbing material, jet engine alloys), magnetic biomedical applications (drug delivery, magnetic resonance imaging, biosensor) and computer hardware industry (data storage). The physical and chemical properties of the nanoalloys depend not only on the particle or crystallite size but also on composition and atomic ordering. Therefore, computer modeling is an essential tool to predict structural, electronic, magnetic and optical behavior at atomistic levels and consequently reduce the time for designing and development of new materials with novel/enhanced properties. Although first-principles quantum mechanical methods provide the most accurate results, they require huge computational effort to solve the Schrodinger equation for only a few tens of atoms. On the other hand, molecular dynamics method with appropriate empirical or semi-empirical inter-atomic potentials can give accurate results for the static and dynamic properties of larger systems in a short span of time. In this study, structural evolutions, magnetic and electronic properties of Fe-Ni based nanoalloys have been studied by using molecular dynamics (MD) method in Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) and Density Functional Theory (DFT) in the Vienna Ab initio Simulation Package (VASP). The effects of particle size (in 2-10 nm particle size range) and temperature (300-1500 K) on stability and structural evolutions of amorphous and crystalline Fe-Ni bulk/nanoalloys have been investigated by combining molecular dynamic (MD) simulation method with Embedded Atom Model (EAM). EAM is applicable for the Fe-Ni based bimetallic systems because it considers both the pairwise interatomic interaction potentials and electron densities. Structural evolution of Fe-Ni bulk and nanoparticles (NPs) have been studied by calculation of radial distribution functions (RDF), interatomic distances, coordination number, core-to-surface concentration profiles as well as Voronoi analysis and surface energy dependences on temperature and particle size. Moreover, spin-polarized DFT calculations were performed by using a plane-wave basis set with generalized gradient approximation (GGA) exchange and correlation effects in the VASP-MedeA package to predict magnetic and electronic properties of the Fe-Ni based alloys in bulk and nanostructured phases. The result of theoretical modeling and simulations for the structural evolutions, magnetic and electronic properties of Fe-Ni based nanostructured alloys were compared with experimental and other theoretical results published in the literature.

Keywords: density functional theory, embedded atom model, Fe-Ni systems, molecular dynamics, nanoalloys

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Authors: R. Pravin Kumar, L. Roopa

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Enzymes are molecular machines used in various industries such as pharmaceuticals, cosmetics, food and animal feed, paper and leather processing, biofuel, and etc. Nevertheless, this has been possible only by the breath-taking efforts of the chemists and biologists to evolve/engineer these mysterious biomolecules to work the needful. Main agenda of this enzyme engineering project is to derive screening and selection tools to obtain focused libraries of enzyme variants with desired qualities. The methodologies for this research include the well-established directed evolution, rational redesign and relatively less established yet much faster and accurate insilico methods. This concept was initiated as a Receptor Rependent-4Dimensional Quantitative Structure Activity Relationship (RD-4D-QSAR) to predict kinetic properties of enzymes and extended here to study transaminase by a 7D QSAR approach. Induced-fit scenarios were explored using Quantum Mechanics/Molecular Mechanics (QM/MM) simulations which were then placed in a grid that stores interactions energies derived from QM parameters (QMgrid). In this study, the mutated enzymes were immersed completely inside the QMgrid and this was combined with solvation models to predict descriptors. After statistical screening of descriptors, QSAR models showed > 90% specificity and > 85% sensitivity towards the experimental activity. Mapping descriptors on the enzyme structure revealed hotspots important to enhance the enantioselectivity of the enzyme.

Keywords: QMgrid, QM/MM simulations, RD-4D-QSAR, transaminase

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Authors: Ahmed Tamer AlMotasem, Jens Bergström, Anders Gåård, Pavel Krakhmalev, Thijs Jan Holleboom

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In sheet metal forming processes, accumulation and transfer of sheet material to tool surfaces, often referred to as galling, is the major cause of tool failure. Initiation of galling is assumed to occur due to local adhesive wear between two surfaces. Therefore, reducing adhesion between the tool and the work sheet has a great potential to improve the tool materials galling resistance. Experimental observations and theoretical studies show that the presence of primary micro-sized carbides and/or nitrides in alloyed steels may significantly improve galling resistance. Generally, decreased adhesion between the ceramic precipitates and the sheet material counter-surface are attributed as main reason to the latter observations. On the other hand, adhesion processes occur at an atomic scale and, hence, fundamental understanding of galling can be obtained via atomic scale simulations. In the present study, molecular dynamics simulations are used, with utilizing second nearest neighbor embedded atom method potential to investigate the influence of nano-sized cementite precipitates embedded in tool atoms. The main aim of the simulations is to gain new fundamental knowledge on galling initiation mechanisms. Two tool/work piece configurations, iron/iron and iron-cementite/iron, are studied under dry sliding conditions. We find that the average frictional force decreases whereas the normal force increases for the iron-cementite/iron system, in comparison to the iron/iron configuration. Moreover, the average friction coefficient between the tool/work-piece decreases by about 10 % for the iron-cementite/iron case. The increase of the normal force in the case of iron-cementite/iron system may be attributed to the high stiffness of cementite compared to bcc iron. In order to qualitatively explain the effect of cementite on adhesion, the adhesion force between self-mated iron/iron and cementite/iron surfaces has been determined and we found that iron/cementite surface exhibits lower adhesive force than that of iron-iron surface. The variation of adhesion force with temperature was investigated up to 600 K and we found that the adhesive force, generally, decreases with increasing temperature. Structural analyses show that plastic deformation is the main deformation mechanism of the work-piece, accompanied with dislocations generation.

Keywords: adhesion, cementite, galling, molecular dynamics

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

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

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

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Authors: Aneesh Joshi, Sagil James

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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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Authors: A. Graa, I. Ziane, F. Benhamida, S. Souag

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This paper presents a comparative analysis study of an efficient and reliable quadratic programming (QP) to solve economic load dispatch (ELD) problem with considering transmission losses in a power system. The proposed QP method takes care of different unit and system constraints to find optimal solution. To validate the effectiveness of the proposed QP solution, simulations have been performed using Algerian test system. Results obtained with the QP method have been compared with other existing relevant approaches available in literatures. Experimental results show a proficiency of the QP method over other existing techniques in terms of robustness and its optimal search.

Keywords: economic dispatch, quadratic programming, Algerian network, dynamic load

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Authors: Carlos F. Sanz-Navarro, Sonia Fereres

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Binary and ternary mixtures of molten salts are excellent thermal energy storage systems and have been widely used in commercial tanks both in nuclear and solar thermal applications. However, the energy density of the commercially used mixtures is still insufficient, and therefore, new systems based on latent heat storage (or phase change materials, PCM) are currently being investigated. In order to shed some light on the macroscopic physical properties of the molten salt phases, knowledge of the microscopic structure and dynamics is required. Several molecular dynamics (MD) simulations have been performed to model the thermal behavior of (Li,K)2CO3 mixtures. Up to this date, this particular molten salt mixture has not been extensively studied but it is of fundamental interest for understanding the behavior of other commercial salts. Molten salt diffusivities, the internal electrical ion mobility, and the physical properties of the solid-liquid phase transition have been calculated and compared to available data from literature. The effect of anion polarization and the application of a strong external electric field have also been investigated. The influence of electrical ion mobility on local composition is explained through the Chemla effect, well known in electrochemistry. These results open a new way to design optimal high temperature energy storage materials.

Keywords: atomistic simulations, thermal storage, latent heat, molten salt, ion mobility

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Authors: Monisha Isaac

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Use of molecular markers for selecting plants with desired traits has been started long back. Due to their heritable characteristics, they are useful for identification and characterization of specific genotypes. The study involves various types of molecular markers used to select multiple desired characters in plants, their properties, and advantages to improve crop productivity in adverse climatological conditions for the purpose of providing food security to fast-growing global population. The study shows that genetic similarities obtained from molecular markers provide more accurate information and the genetic diversity can be better estimated from the genetic relationship obtained from the dendrogram. The information obtained from markers assisted characterization is more suitable for the crops of economic importance like sugarcane.

Keywords: molecular markers, crop productivity, genetic diversity, genotype

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Authors: Mergim Gasia, Bojan Milovanovica, Sanjin Gumbarevic

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Better energy performance of the building envelope is one of the most important aspects of energy savings if the goals set by the European Union are to be achieved in the future. Dynamic heat transfer simulations are being used for the calculation of building energy consumption because they give more realistic energy demands compared to the stationary calculations that do not take the building’s thermal mass into account. Software used for these dynamic simulation use methods that are based on the analytical models since numerical models are insufficient for longer periods. The analytical models used in this research fall in the category of the conduction transfer functions (CTFs). Two methods for calculating the CTFs covered by this research are the Laplace method and the State-Space method. The literature review showed that the main disadvantage of these methods is that they are inadequate for heavyweight façade elements and shorter time periods used for the calculation. The algorithms for both the Laplace and State-Space methods are implemented in Mathematica, and the results are compared to the results from EnergyPlus and TRNSYS since these software use similar algorithms for the calculation of the building’s energy demand. This research aims to check the efficiency of the Laplace and the State-Space method for calculating the building’s energy demand for heavyweight building elements and shorter sampling time, and it also gives the means for the improvement of the algorithms used by these methods. As the reference point for the boundary heat flux density, the finite difference method (FDM) is used. Even though the dynamic heat transfer simulations are superior to the calculation based on the stationary boundary conditions, they have their limitations and will give unsatisfactory results if not properly used.

Keywords: Laplace method, state-space method, conduction transfer functions, finite difference method

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Authors: Giulia Magi Meconi, Nicholas Ballard, José M. Asua, Ronen Zangi

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Experimental and computational studies are combined to elucidate the adsorption proprieties of ionic and nonionic surfactants on hydrophobic polymer surface such us poly(styrene). To present these two types of surfactants, sodium dodecyl sulfate and poly(ethylene glycol)-block-poly(ethylene), commonly utilized in emulsion polymerization, are chosen. By applying quartz crystal microbalance with dissipation monitoring it is found that, at low surfactant concentrations, it is easier to desorb (as measured by rate) ionic surfactants than nonionic surfactants. From molecular dynamics simulations, the effective, attractive force of these nonionic surfactants to the surface increases with the decrease of their concentration, whereas, the ionic surfactant exhibits mildly the opposite trend. The contrasting behavior of ionic and nonionic surfactants critically relies on two observations obtained from the simulations. The first is that there is a large degree of interweavement between head and tails groups in the adsorbed layer formed by the nonionic surfactant (PEO/PE systems). The second is that water molecules penetrate this layer. In the disordered layer, these nonionic surfactants generate at the surface, only oxygens of the head groups present at the interface with the water phase or oxygens next to the penetrating waters can form hydrogen bonds. Oxygens inside this layer lose this favorable energy, with a magnitude that increases with the surfactants density at the interface. This reduced stability of the surfactants diminishes their driving force for adsorption. All that is shown to be in accordance with experimental results on the dynamics of surfactants desorption. Ionic surfactants assemble into an ordered structure and the attraction to the surface was even slightly augmented at higher surfactant concentration, in agreement with the experimentally determined adsorption isotherm. The reason these two types of surfactants behave differently is because the ionic surfactant has a small head group that is strongly hydrophilic, whereas the head groups of the nonionic surfactants are large and only weakly attracted to water.

Keywords: emulsion polymerization process, molecular dynamics simulations, polymer surface, surfactants adsorption

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Authors: Pawel Flaszynski, Piotr Doerffer, Jan Holnicki-Szulc, Grzegorz Mikulowski

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Results of numerical simulations for transonic flow in a piezoelectric valve are presented. The valve is the main part of an adaptive pneumatic shock absorber. Flow structure in the valve domain and the influence of the flow non-uniformity in the valve on a mass flow rate is investigated. Numerical simulation results are compared with experimental data.

Keywords: pneumatic valve, transonic flow, numerical simulations, piezoelectric valve

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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: Hassan Nour, Nouh Mounadi, Oussama Abchir, Belaidi Salah, Samir Chtita

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Cholinesterase enzymes are biological catalysts essential for the transformation of acetylcholine, which is a neurotransmitter implicated in memory and learning, into acetic acid and choline, altering the neurotransmission process in Alzheimer’s disease patients. Therefore, inhibition of cholinesterase enzymes is a relevant strategy for the symptomatic treatment of Alzheimer’s disease. The current investigation aims to explore potential cholinesterase (ChE) inhibitors through a comprehensive computational approach. Forty-nine phytoconstituents extracted from Cannabis sativa L. were in-silico screened using molecular docking and pharmacokinetic and toxicological analysis to evaluate their possible inhibitory effect on the cholinesterase enzymes. Two phytoconstituents belonging to cannabinoid derivatives were revealed to be promising candidates for Alzheimer's therapy by acting as cholinesterase inhibitors. They have exhibited high binding affinities towards the cholinesterase enzymes and showed their ability to interact with key residues involved in cholinesterase enzymatic activity. In addition, they presented good ADMET profiles allowing them to be promising oral drug candidates. Furthermore, molecular dynamics (MD) simulations were executed to explore their interaction stability under mimetic biological conditions and thus support our findings. To corroborate the docking results, the binding free energy corresponding to the more stable ligand-ChE complexes was re-estimated by applying the MM-PBSA method. MD and MM-PBSA studies affirmed that the ligand-ChE recognition is a spontaneous reaction leading to stable complexes. The conducted investigations have led to great findings that would strongly guide the pharmaceutical industries toward the rational development of potent anti-Alzheimer agents.

Keywords: Alzheimer’s disease, molecular docking, Cannabis sativa L., cholinesterase inhibitors, molecular dynamics, ADMET, MM-PBSA

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Authors: Mohammad Reza Ghaani, Niall English

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Hydrogen is looked upon as the next-generation clean-energy carrier; the search for an efficient material and method for storing hydrogen has been, and is, pursued relentlessly. Clathrate hydrates are inclusion compounds wherein guest gas molecules like hydrogen are trapped in a host water-lattice framework. These types of materials can be categorised as potentially attractive hosting environments for physical hydrogen storage (i.e., no chemical reaction upon storage). Non-equilibrium molecular dynamics (NEMD) simulations have been performed to investigate thermal-driven break-up of propane-hydrate interfaces with liquid water at 270-300 K, with the propane hydrate containing either one or no hydrogen molecule in each of its small cavities. In addition, two types of hydrate-surface water-lattice molecular termination were adopted, at the hydrate edge with water: a 001-direct surface cleavage and one with completed cages. The geometric hydrate-ice-liquid distinction criteria of Báez and Clancy were employed to distinguish between the hydrate, ice lattices, and liquid-phase. Consequently, the melting temperatures of interface were estimated, and dissociation rates were observed to be strongly dependent on temperature, with higher dissociation rates at larger over-temperatures vis-à-vis melting. The different hydrate-edge terminations for the hydrate-water interface led to statistically-significant differences in the observed melting point and dissociation profile: it was found that the clathrate with the planar interface melts at around 280 K, whilst the melting temperature of the cage-completed interface was determined to be circa 270 K.

Keywords: hydrogen storage, clathrate hydrate, molecular dynamics, thermal dissociation

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Authors: Jeongim Kang, Moon Hee Kim, Seong Baeg Kim

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This paper proposes a novel e-learning model that is based on a dynamic formative evaluation. On evaluating the existing format of e-learning, conditions regarding repetitive learning to achieve mastery, causes issues for learners to lose tension and become neglectful of learning. The dynamic formative evaluation proposed is able to supplement limitation of the existing approaches. Since a repetitive learning method does not provide a perfect feedback, this paper puts an emphasis on the dynamic formative evaluation that is able to maximize learning achievement. Through the dynamic formative evaluation, the instructor is able to refer to the evaluation result when making estimation about the learner. To show the flow chart of learning, based on the dynamic formative evaluation, the model proves its effectiveness and validity.

Keywords: online learning, dynamic formative evaluation, mastery learning, repetitive learning method, learning achievement

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Authors: Ali Al-Zughaibi

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The purpose of this paper is to present a modeling and control of the quarter car active suspension system with unknown mass, unknown time-delay and road disturbance. The objective of designing the controller by deriving a control law to achieve stability of the system and convergence that can considerably improve the ride comfort and road disturbance handling. Thus is accomplished by using Routh-Herwitz criterion and based on some assumptions. A mathematical proof is given to show the ability of the designed controller to ensure stability and convergence of the active suspension system and dispersion oscillation of system with unknown mass, time-delay and road disturbances. Simulations were also performed for controlling quarter car suspension, where the results obtained from these simulations verify the validity of the proposed design.

Keywords: active suspension system, time-delay, disturbance rejection, dynamic uncertainty

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Authors: Ferid Hammami

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The molecular geometries of the possible conformations of pyruvic acid-water complexes (PA-(H₂O)ₙ = 1- 4) have been fully optimized at DFT/B3LYP/6-311G ++ (d, p) levels of calculation. Among several optimized molecular clusters, the most stable molecular arrangements obtained when one, two, three, and four water molecules are hydrogen-bonded to a central pyruvic acid molecule are presented in this paper. Apposite topological and geometrical parameters are considered as primary indicators of H-bond strength. Atoms in molecules (AIM) analysis shows that pyruvic acid can form a ring structure with water, and the molecular structures are stabilized by both strong O-H...O and C-H...O hydrogen bonds. In large clusters, classical O-H...O hydrogen bonds still exist between water molecules, and a cage-like structure is built around some parts of the central molecule of pyruvic acid. The electrostatic potential energy map (MEP) and the HOMO-LUMO molecular orbital (highest occupied molecular orbital-lowest unoccupied molecular orbital) analysis has been performed for all considered complexes.

Keywords: pyruvic acid, PA-water complex, hydrogen bonding, DFT, AIM, MEP, HOMO-LUMO

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Authors: Cristiana Ortigão, Antonio Couto, Thiago Gabriel

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In the wake of Samarco Fundão’s failure in 2015 followed by Vale’s Brumadinho disaster in 2019, the Brazilian National Mining Agency started a comprehensive dam safety programmed to rank dam safety risks and establish monitoring and analysis procedures. This paper focuses on the use of accelerometers for static and dynamic applications. Static applications may employ tiltmeters, as an example shown later in this paper. Dynamic monitoring of a structure with accelerometers yields its dynamic signature and this technique has also been successfully used in Brazil and this paper gives an example of tailings dam.

Keywords: instrumentation, dynamic, monitoring, tailings, dams, tiltmeters, automation

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Authors: Dodi Ikhsanshaleh

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When subjected to dynamic load, foundation oscillates in the way that depends on the soil behaviour, the geometry and inertia of the foundation and the dynamic exctation. The practical guideline to analysis block-type foundation excitated by dynamic load from vibrating machine is presented. The analysis use Lumped Mass Parameter Method to express dynamic properties such as stiffness and damping of soil. The numerical examples are performed on design block-type foundation supporting gas turbine compressor which is important equipment package in gas processing plant

Keywords: block foundation, dynamic load, lumped mass parameter

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Authors: Roberta Gentry

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The presentation will begin with a brief literature review of the use of computer simulation in teacher education programs. This information will be summarized. Additionally, based on the literature review, advantages and disadvantages of using computer simulation in higher education will be shared. Finally, a study in which computer simulations software was used with 50 initial licensure teacher candidates in both an introductory course and a behavior management course will be shared. Candidates reflected on their experiences with using computer simulation. The instructor of the course will also share lessons learned.

Keywords: simulations, teacher education, teacher preparation, educational research

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Authors: Leila Momenzadeh, Alexander V. Evteev, Elena V. Levchenko, Tanvir Ahmed, Irina Belova, Graeme Murch

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In this work, the phonon thermal conductivity of f.c.c. Al is investigated in detail in the temperature range 100 – 900 K within the framework of equilibrium molecular dynamics simulations making use of the Green-Kubo formalism and one of the most reliable embedded-atom method potentials. It is found that the heat current auto-correlation function of the f.c.c. Al model demonstrates a two-stage temporal decay similar to the previously observed for f.c.c Cu model. After the first stage of decay, the heat current auto-correlation function of the f.c.c. Al model demonstrates a peak in the temperature range 100-800 K. The intensity of the peak decreases as the temperature increases. At 900 K, it transforms to a shoulder. To describe the observed two-stage decay of the heat current auto-correlation function of the f.c.c. Al model, we employ decomposition model recently developed for phonon-mediated thermal transport in a monoatomic lattice. We found that the electronic contribution to the total thermal conductivity of f.c.c. Al dominates over the whole studied temperature range. However, the phonon contribution to the total thermal conductivity of f.c.c. Al increases as temperature decreases. It is about 1.05% at 900 K and about 12.5% at 100 K.

Keywords: aluminum, gGreen-Kubo formalism, molecular dynamics, phonon thermal conductivity

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Authors: Yew Mun Yip, Dawei Zhang

Abstract:

Proteins are the biological machinery that executes specific vital functions in every cell of the human body by folding into their 3D structures. When a protein misfolds from its native structure, the machinery will malfunction and lead to misfolding diseases. Although in vitro experiments are able to conclude that the mutations of the amino acid sequence lead to incorrectly folded protein structures, these experiments are unable to decipher the folding process. Therefore, molecular dynamic (MD) simulations are employed to simulate the folding process so that our improved understanding of the folding process will enable us to contemplate better treatments for misfolding diseases. MD simulations make use of force fields to simulate the folding process of peptides. Secondary structures are formed via the hydrogen bonds formed between the backbone atoms (C, O, N, H). It is important that the hydrogen bond energy computed during the MD simulation is accurate in order to direct the folding process to the native structure. Since the atoms involved in a hydrogen bond possess very dissimilar electronegativities, the more electronegative atom will attract greater electron density from the less electronegative atom towards itself. This is known as the polarization effect. Since the polarization effect changes the electron density of the two atoms in close proximity, the atomic charges of the two atoms should also vary based on the strength of the polarization effect. However, the fixed atomic charge scheme in force fields does not account for the polarization effect. In this study, we introduce the polarized structure-specific backbone charge (PSBC) model. The PSBC model accounts for the polarization effect in MD simulation by updating the atomic charges of the backbone hydrogen bond atoms according to equations derived between the amount of charge transferred to the atom and the length of the hydrogen bond, which are calculated from quantum-mechanical calculations. Compared to other polarizable models, the PSBC model does not require quantum-mechanical calculations of the peptide simulated at every time-step of the simulation and maintains the dynamic update of atomic charges, thereby reducing the computational cost and time while accounting for the polarization effect dynamically at the same time. The PSBC model is applied to two different β-peptides, namely the Beta3s/GS peptide, a de novo designed three-stranded β-sheet whose structure is folded in vitro and studied by NMR, and the trpzip peptides, a double-stranded β-sheet where a correlation is found between the type of amino acids that constitute the β-turn and the β-propensity.

Keywords: hydrogen bond, polarization effect, protein folding, PSBC

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Authors: Mei Hong, Wei Liu, Xuemin Dai, Yanxiong Pan, Xiangling Ji

Abstract:

Polyamic acid (PAA) is the precursor of polyimide (PI) prepared by a two-step method, its molecular weight and molecular weight distribution not only play an important role during the preparation and processing, but also influence the final performance of PI. However, precise characterization on molecular weight of PAA is still a challenge because of the existence of very complicated interactions in the solution system, including the electrostatic interaction, hydrogen bond interaction, dipole-dipole interaction, etc. Thus, it is necessary to establisha suitable strategy which can completely suppress these complex effects and get reasonable data on molecular weight. Herein, the gel permeation chromatography (GPC) coupled with differential refractive index (RI) and multi-angle laser light scattering (MALLS) detectors were applied to measure the molecular weight of (6FDA-DMB) PAA using different mobile phases, LiBr/DMF, LiBr/H3PO4/THF/DMF, LiBr/HAc/THF/DMF, and LiBr/HAc/DMF, respectively. It was found that combination of LiBr with HAc can shield the above-mentioned complex interactions and is more conducive to the separation of PAA than only addition of LiBr in DMF. LiBr/HAc/DMF was employed for the first time as a mild mobile phase to effectively separate PAA and determine its molecular weight. After a series of conditional experiments, 0.02M LiBr/0.2M HAc/DMF was fixed as an optimized mobile phase to measure the relative and absolute molecular weights of (6FDA-DMB) PAA prepared, and the obtained Mw from GPC-MALLS and GPC-RI were 35,300 g/mol and 125,000 g/mol, respectively. Particularly, such a mobile phase is also applicable to other PAA samples with different structures, and the final results on molecular weight are also reproducible.

Keywords: Polyamic acids, Polyelectrolyte effects, Gel permeation chromatography, Mobile phase, Molecular weight

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Authors: B. Umaru Mohammed, Faris A. Al-Maziad, Mohammad Y. Numan

Abstract:

One of the most important factors affecting the energy performance within a building is a carefully and efficiently designed facade. The primary aim of this research was to identify and present the potentiality of utilising Double-Skin Facade (DSF) construction and critically examine its effect on the energy consumption of an office building located within a maritime desert climate as to the conventional single-skin curtain wall system. A comparative analysis of the effect on the overall energy consumption within an office building was investigated in which a combination of various Double-Skin Facade configurations, systems, and cavity depths, glazing types and orientations were utilised. A computer dynamic modelling was utilised in order to ensure accurate calculations and efficient simulations of the various DSF systems due to the complex nature of the various functions within the Facade cavity. Through the use of the dynamic thermal modelling simulations, the best cavity size glazed type and orientation were determined to lead to a detailed analysis of the efficiency of each respective combination of Double-Skin Facade construction. As such the optimal facade combination for use within an office building located in a maritime desert climate was identified. Results demonstrated that a multi-story Facade, depending on its configuration, save up to 5% on annual cooling loads respect to a Corridor Facade and while vented can save unto 12% when compared to the single skin façade, on annual cooling load in the maritime desert climate. The selected configuration of the DSF from SSF saves an overall annual cooling load of 32%.A comparative analysis of the effect on the overall energy consumption within an office building was investigated in which a combination of various Double-Skin Facade configurations, systems, and cavity depths, glazing types and orientations were utilized. A computer dynamic modelling was utilized in order to ensure accurate calculations and efficient simulations of the various DSF systems due to the complex nature of the various functions within the Facade cavity. Through the use of the dynamic thermal modelling simulations, the best cavity size glazed type and orientation were determined to lead to a detailed analysis of the efficiency of each respective combination of Double-Skin Facade construction. As such the optimal facade combination for use within an office building located in a maritime desert climate was identified. Results demonstrated that a multi-story Facade, depending on its configuration, save up to 5% on annual cooling loads respect to a Corridor Facade and while vented can save unto 12% when compared to the single skin facade, on annual cooling load in the maritime desert climate. The selected configuration of the DSF from SSF saves an overall annual cooling load of 32%.

Keywords: computer dynamics modelling, comparative analysis, energy computation, double skin facade, single skin curtain wall, maritime desert climate

Procedia PDF Downloads 314

Authors: Seyedmajid Mehrnia, Maximilan Kuhr, Peter F. Pelz

Abstract:

Molecular Dynamics (MD) simulation is a proven method to inspect behaviours of lubricant oils in nano-scale gaps. However, most MD simulations on tribology have been performed with atomically smooth walls to determine wall slip and friction properties. This study will investigate the effect of porosity, specifically nano-porous walls, on wall slip properties of hydrocarbon oils confined between two walls in a Couette flow. Different pore geometries will be modelled to investigate the effect on wall slip and bulk shear. In this paper, the Polyalphaolefin (PAO) molecules are confined to a stationary and a moving wall. A hybrid force field consisting of different potential energy functions was employed in this MD simulation. Newton’s law defines how those forces will influence the atoms' movements. The interactions among surface atoms were simulated with an Embedded Atom Method (EAM) potential function which can represent the characteristics of metallic arrangements very strongly. We implemented NERD forcefield for intramolecular potential energy function. Also, Lennard-Jones potential was employed for nonbonded intermolecular interaction.

Keywords: slip length, molecular dynamics, critical shear rate, Couette flow

Procedia PDF Downloads 97