Search results for: first-principle molecular dynamics simulation of multiscale shock technique

Authors: Qiuhao Chang, Liangliang Huang, Xingru Wu

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In the United States, over 90% of the roads are paved with asphalt. The aging of asphalt is the most serious problem that causes the deterioration of asphalt pavement. Waste cooking oils (WCOs) have been found they can restore the properties of aged asphalt and promote the reuse of aged asphalt pavement. In our previous study, it was found the optimal WCO concentration to restore the aged asphalt sample should be in the range of 10~15 wt% of the aged asphalt sample. After the WCO concentration exceeds 15 wt%, as the WCO concentration increases, some important properties of the asphalt sample can be weakened by the addition of WCO, such as cohesion energy density, surface free energy density, bulk modulus, shear modulus, etc. However, maximizing the utilization of WCO can create environmental and economic benefits. Therefore, in this study, a new idea about using the waste polymer is another additive to restore the WCO modified asphalt that contains a high concentration of WCO (15-25 wt%) is proposed, which has never been reported before. In this way, both waste polymer and WCO can be utilized. The molecular dynamics simulation is used to study the effect of waste polymer on properties of WCO modified asphalt and understand the corresponding mechanism at the molecular level. The radial distribution function, self-diffusion, cohesion energy density, surface free energy density, bulk modulus, shear modulus, adhesion energy between asphalt and aggregate are analyzed to validate the feasibility of combining the waste polymer and WCO to restore the aged asphalt. Finally, the optimal concentration of waste polymer and WCO are determined.

Keywords: reclaim aged asphalt pavement, waste cooking oil, waste polymer, molecular dynamics simulation

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Authors: A. A. Abid

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The magnetospheric multiscale (MMS) satellite observations in the inner magnetosphere were used to detect the proton band of the electromagnetic ion cyclotron (EMIC) waves on December 14, 2015, which have been significantly contributing to the dynamics of the magnetosphere. It has been examined that the intensity of EMIC waves gradually increases by decreasing the L shell. The waves are triggered by hot proton thermal anisotropy. The low-energy cold protons (ions) can be activated by the EMIC waves when the EMIC wave intensity is high. As a result, these previously invisible protons are now visible. As a result, the EMC waves also excite the helium ions. The EMIC waves, whose frequency in the magnetosphere of the Earth ranges from 0.001 Hz to 5 Hz, have drawn a lot of attention for their ability to carry energy. Since these waves act as a mechanism for the loss of energetic electrons from the Van Allen radiation belt to the atmosphere, therefore, it is necessary to understand how and where they can be produced, as well as the direction of waves along the magnetic field lines. This work examines how the excitation of EMIC waves is affected by the energy of hot proton temperature anisotropy, and It has a minimum resonance energy of 6.9 keV and a range of 7 to 26 keV. On the hot protons, however, the reverse effect can be seen for energies below the minimum resonance energy. It is demonstrated that throughout the energy range of 1 eV to 100 eV, the number density and temperature anisotropy of the protons likewise rise as the intensity of the EMIC waves increases. Key Points: 1. The analysis of EMIC waves produced by hot proton temperature anisotropy using MMS data. 2. The number density and temperature anisotropy of the cold protons increases owing to high-intensity EMIC waves. 3. The cold protons with an energy range of 1-100eV are energized by EMIC waves using the Magnetospheric Multiscale (MMS) satellite not been discussed before

Keywords: EMIC waves, temperature anisotropy of hot protons, energization of the cold proton, magnetospheric multiscale (MMS) satellite observations

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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: Son Nguyen, Thanh Van, Ly Le

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Ca2+ - dependent calmodulin kinase IIa (CaMKIIa) has recently been found to associate with protein tau missorting and polymerization in Alzheimer’s Disease (AD). However, there has yet inhibitors targeting CaMKIIa to investigate the correlation between CaMKIIa activity and protein tau polymer formation. Combining virtual screening and our statistics in binding contribution scoring function (BCSF), we rationally identified potential compounds that bind to specific CaMKIIa active site and specificity-affinity distribution of the ligand within the active site. Using molecular dynamics simulation, we identified structural stability of CaMKIIa and potent inhibitors, and site-directed bonding, separating non-specific and specific molecular interaction features. Despite of variation in confirmation of simulation time, interactions of the potent inhibitors were found to be strongly associated with the unique chemical features extracted from molecular binding poses. In addition, competitive inhibitors within CaMKIIa showed an important molecular recognition pattern toward specific ligand features. Our approach combining virtual screening with BCSF may provide an universally applicable method for precise identification in the discovery of compounds.

Keywords: Alzheimer’s disease, Ca 2+ -dependent calmodulin kinase IIa, protein tau, molecular docking

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Authors: Tobias Schramm, Günther Prokop

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Degraded vehicle shock absorbers represent a risk for road safety. The exact effect of degraded vehicle dampers on road safety is still the subject of research. This work is intended to contribute to estimating the effect of degraded twin-tube dampers of passenger cars on road safety. An axle model was built using a damper model to simulate different degradation levels. To parameterize the model, a realistic parameter space was estimated based on test rig measurements and database analyses, which is intended to represent the vehicle field in Germany. Within the parameter space, simulations of the axle model were carried out, which calculated the transmittable lateral forces of the various axle configurations as a function of vehicle speed, road surface, damper conditions and axle parameters. A degraded damper has the greatest effect on the transmittable lateral forces at high speeds and in poor road conditions. If a vehicle is traveling at a speed of 100 kph on a Class D road, a degraded damper reduces the transmissible lateral forces of an axle by 20 % on average. For individual parameter configurations, this value can rise to 50 %. The axle parameters that most influence the effect of a degraded damper are the vertical stiffness of the tire, the unsprung mass and the stabilizer stiffness of the axle.

Keywords: vehicle dynamics, vehicle simulation, vehicle component degradation, shock absorber model, shock absorber degradation

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

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The inhibition of SH2 domain regulated protein-protein interactions is an attractive target for developing an effective chemotherapeutic approach in the treatment of disease. Molecular simulation is a useful tool for developing new drugs and for studying molecular recognition. In this study, we searched potential drug compounds for the inhibition of SH2 domain by performing structural similarity search in PubChem Compound Database. A total of 37 compounds were screened from the database, and then we used the LibDock docking program to evaluate the inhibition effect. The best three compounds (AP22408, CID 71463546 and CID 9917321) were chosen for MD simulations after the LibDock docking. Our results show that the compound CID 9917321 can produce a more stable protein-ligand complex compared to other two currently known inhibitors of Src SH2 domain. The compound CID 9917321 may be useful for the inhibition of SH2 domain based on these computational results. Subsequently experiments are needed to verify the effect of compound CID 9917321 on the SH2 domain in the future studies.

Keywords: nonpeptide inhibitor, Src SH2 domain, LibDock, molecular dynamics simulation

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Authors: Stewart A. Keir, Faik A. Hamad

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This study aims to use both analytical and experimental methods of analysis to examine the accuracy of Computational Fluid Dynamics (CFD) models that can then be used for more complex analyses, accurately representing more elaborate flow phenomena such as internal shockwaves and boundary layers. The geometry used in the analytical study and CFD model is taken from the experimental rig. The analytical study is undertaken using isentropic and adiabatic relationships and the output of the analytical study, the 'shockwave location tool', is created. The results from the analytical study are then used to optimize the redesign an experimental rig for more favorable placement of pressure taps and gain a much better representation of the shockwaves occurring in the divergent section of the nozzle. The CFD model is then optimized through the selection of different parameters, e.g. turbulence models (Spalart-Almaras, Realizable k-epsilon & Standard k-omega) in order to develop an accurate, robust model. The results from the CFD model can then be directly compared to experimental and analytical results in order to gauge the accuracy of each method of analysis. The CFD model will be used to visualize the variation of various parameters such as velocity/Mach number, pressure and turbulence across the shock. The CFD results will be used to investigate the interaction between the shock wave and the boundary layer. The validated model can then be used to modify the nozzle designs which may offer better performance and ease of manufacture and may present feasible improvements to existing high-speed flow applications.

Keywords: CFD, nozzle, fluent, gas dynamics, shock-wave

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Authors: Elisa Y. M. Ang, Teng Yong Ng, Jingjie Yeo, Rongming Lin, Zishun Liu, K. R. Geethalakshmi

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By stacking carbon nanotubes (CNT) one on top of another, single layer CNT arrays can perform water-salt separation with ultra-high permeability and selectivity. Such outer-wall CNT slit membrane is named as the transverse flow CNT membrane. By adjusting the slit size between neighboring CNTs, the membrane can be configured to sieve out different solutes, right down to the separation of monovalent salt ions from water. Molecular dynamics (MD) simulation results show that the permeability of transverse flow CNT membrane is more than two times that of conventional axial-flow CNT membranes, and orders of magnitude higher than current reverse osmosis membrane. In addition, by carrying out MD simulations with different CNT size, it was observed that the variance in desalination performance with CNT size is small. This insensitivity of the transverse flow CNT membrane’s performance to CNT size is a distinct advantage over axial flow CNT membrane designs. Not only does the membrane operate well under constant pressure desalination operation, but MD simulations further indicate that oscillatory operation can further enhance the membrane’s desalination performance, making it suitable for operation such as electrodialysis reversal. While there are still challenges that need to be overcome, particularly on the physical fabrication of such membrane, it is hope that this versatile membrane design can bring the idea of using low dimensional structures for desalination closer to reality.

Keywords: carbon nanotubes, membrane desalination, transverse flow carbon nanotube membrane, molecular dynamics

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Authors: Sakina Fatima, Joseph-Patrick W. E. Clarke, Patricia A. Thibault, Subha Kalyaanamoorthy, Michael Levin, Aravindhan Ganesan

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Heteronuclear ribonucleoprotein (hnRNPA1 or A1) is associated with the pathology of different diseases, including neurological disorders and cancers. In particular, the aggregation and dysfunction of A1 have been identified as a critical driver for neurodegeneration (NDG) in Multiple Sclerosis (MS). Structurally, A1 includes a low-complexity domain (LCD) and two RNA-recognition motifs (RRMs), and their interdomain coordination may play a crucial role in A1 aggregation. Previous studies propose that RNA-inhibitors or nucleoside analogs that bind to RRMs can potentially prevent A1 self-association. Therefore, molecular-level understanding of the structures, dynamics, and nucleotide interactions with A1 RRMs can be useful for developing therapeutics for NDG in MS. In this work, a combination of computational modelling and biochemical experiments were employed to analyze a set of RNA-A1 RRM complexes. Initially, the atomistic models of RNA-RRM complexes were constructed by modifying known crystal structures (e.g., PDBs: 4YOE and 5MPG), and through molecular docking calculations. The complexes were optimized using molecular dynamics simulations (200-400 ns), and their binding free energies were computed. The binding affinities of the selected complexes were validated using a thermal shift assay. Further, the most important molecular interactions that contributed to the overall stability of the RNA-A1 RRM complexes were deduced. The results highlight that adenine and guanine are the most suitable nucleotides for high-affinity binding with A1. These insights will be useful in the rational design of nucleotide-analogs for targeting A1 RRMs.

Keywords: hnRNPA1, molecular docking, molecular dynamics, RNA-binding proteins

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Authors: Christian Angerer, Markus Lienkamp

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Electric vehicles offer a high variety of possible drivetrain topologies with up to 4 motors. Multi-motor-designs can have several advantages regarding traction, vehicle dynamics, safety and even efficiency. With a rising number of motors, the whole drivetrain becomes more complex. All permutations of gearings, drivetrain-layouts, motor-types and –sizes lead up in a very large solution space. Single elements of this solution space can be analyzed by simulation methods. In addition to longitudinal vehicle behavior, which most optimization-approaches are restricted to, also lateral dynamics are important for vehicle dynamics, stability and efficiency. In order to compete large solution spaces and to find an optimal result, genetic algorithm based optimization is state-of-the-art. As lateral dynamics simulation is way more CPU-intensive, optimization takes much more time than in case of longitudinal-only simulation. Therefore, this paper shows an approach how to create meta-models from a 14-degree of freedom vehicle model in order to enable a numerically efficient drivetrain-layout optimization process under consideration of lateral dynamics. Different meta-modelling approaches such as neural networks or DoE are implemented and comparatively discussed.

Keywords: driving dynamics, drivetrain layout, genetic optimization, meta-modeling, lateral dynamicx

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Authors: A. K. Visnuprasad, P. J. Jojo, Reshma Bhaskaran

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Computational fluid dynamics (CFD) is used to simulate the distribution of indoor radon concentration in a living room with elevated levels of radon concentration which varies from 22 Bqm-3 to 1533 Bqm-3 in 24 hours. Finite volume method (FVM) was used for the simulation. The simulation results were experimentally validated at 16 points in two horizontal planes (y=1.4m & y=2.0m) using pin-hole dosimeters and at 3 points using scintillation radon monitor (SRM). Passive measurement using pin-hole dosimeters were performed in all seasons. Another simulation was done to find a suitable position for a passive ventilation system for the effective mitigation of radon.

Keywords: indoor radon, computational fluid dynamics, radon flux, ventilation rate, pin-hole dosimeter

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Authors: Aldin Justin Sundararaj, Austin Lord Tennyson, Divya Jose, A. N. Subash

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Blast waves are generated due to the explosions of high energy materials. An explosion yielding a blast wave has the potential to cause severe damage to buildings and its personnel. In order to understand the physics of effects of blast pressure on buildings, studies in the shock tube on generic configurations are carried out at various pressures on discrete models. The strength of shock wave is systematically varied by using different driver gases and diaphragm thickness. The basic material of the diaphragm is Aluminum. To simulate the effect of shock waves on discrete models a shock tube was used. Generic models selected for this study are suitably scaled cylinder, cone and cubical blocks. The experiments were carried out with 2mm diaphragm with burst pressure ranging from 28 to 31 bar. Numerical analysis was carried out over these discrete models. A 3D model of shock-tube with different discrete models inside the tube was used for CFD computation. It was found that cone has dissipated most of the shock pressure compared to cylinder and cubical block. The robustness and the accuracy of the numerical model were validation with the analytical and experimental data.

Keywords: shock wave, blast wave, discrete models, shock tube

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Authors: Muhammad Asif ShakoorI, Maogang He, Aamir Shahzad

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Dusty (complex) plasmas contained micro-sized charged dust particles in addition to ions, electrons, and neutrals. It is typically low-temperature plasma and exists in a wide variety of physical systems. In this work, the effects of an external electric field on the diffusion coefficient and share viscosity are investigated through equilibrium molecular dynamics (EMD) simulations in three-dimensional (3D) strongly coupled (SC) dusty plasmas (DPs). The effects of constant and varying normalized electric field strength (E*) have been computed along with different combinations of plasma states on the diffusion of dust particles using EMD simulations. Diffusion coefficient (D) and share viscosity (η) along with varied system sizes, in the limit of varying E* values, is accounted for an appropriate range of plasma coupling (Γ) and screening strength (κ) parameters. At varying E* values, it is revealed that the 3D diffusion coefficient increases with increasing E* and κ; however, it decreases with an increase of Γ but within statistical limits. The share viscosity increases with increasing E*and Γ and decreases with increasing κ. New simulation results are outstanding that the combined effects of electric field and screening strengths give well-matched values of Dandη at low-intermediate to large Γ with varying small-intermediate to large N. The current EMD simulation outcomes under varying electric field strengths are in satisfactory well-matched with previous known simulation data of EMD simulations of the SC-DPs. It has been shown that the present EMD simulation data enlarged the range of E* strength up to 0.1 ≤ E*≤ 1.0 in order to find the linear range of the DPs system and to demonstrate the fundamental nature of electric field linearity of 3D SC-DPs.

Keywords: strongly coupled dusty plasma, diffusion coefficient, share viscosity, molecular dynamics simulation, electric field strength

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Authors: M. R. Ghasemi, R. Ghiasi, H. Varaee

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Surrogate model has received increasing attention for use in detecting damage of structures based on vibration modal parameters. However, uncertainties existing in the measured vibration data may lead to false or unreliable output result from such model. In this study, an efficient approach based on Monte Carlo simulation is proposed to take into account the effect of uncertainties in developing a surrogate model. The probability of damage existence (PDE) is calculated based on the probability density function of the existence of undamaged and damaged states. The kriging technique allows one to genuinely quantify the surrogate error, therefore it is chosen as metamodeling technique. Enhanced version of ideal gas molecular movement (EIGMM) algorithm is used as main algorithm for model updating. The developed approach is applied to detect simulated damage in numerical models of 72-bar space truss and 120-bar dome truss. The simulation results show the proposed method can perform well in probability-based damage detection of structures with less computational effort compared to direct finite element model.

Keywords: probability-based damage detection (PBDD), Kriging, surrogate modeling, uncertainty quantification, artificial intelligence, enhanced ideal gas molecular movement (EIGMM)

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Authors: Christy Rosaline, Rathankar Roa, Waheeta Hopper

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Persistence of tuberculosis, emergence of multidrug-resistance and extensively drug-resistant forms of the disease, has increased the interest in developing new antitubercular drugs. Developing inhibitors for 3-deoxy-D-arabino-heptulosonate 7-phosphate synthase from Mycobacterium tuberculosis (MtbDAH7Ps), an enzyme involved in shikimate pathway, gives a selective target for antitubercular agents. MtbDAH7Ps was screened against ZINC database, and shortlisted compounds were subjected to induce fit docking. Prime/Molecular Mechanics Generalized Born Surface Area calculation was used to validate the binding energy of ligand-protein complex. Molecular Dynamics analysis for of the lead compounds–MtbDAH7Ps complexes showed that the backbone of MtbDAH7Ps in their complexes were stable. These results suggest that the shortlisted lead compounds ZINC04097114, ZINC15163225, ZINC16857013, ZINC06275603, and ZINC05331260 could be developed into novel drug leads to inhibit DAH7Ps in Mycobacterium tuberculosis.

Keywords: MtbDAH7Ps, Mycobacterium tuberculosis, HTVS, molecular dynamics

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Authors: A. E. Kobryn

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We present both descriptive and predictive modeling of structural properties of blends of PCBM or organic-inorganic hybrid perovskites of the type CH3NH3PbX3 (X=Cl, Br, I) with P3HT, P3BT or squaraine SQ2 dye sensitizer, including adsorption on TiO2 clusters having rutile (110) surface. In our study, we use a methodology that allows computing the microscopic structure of blends on the nanometer scale and getting insight on miscibility of its components at various thermodynamic conditions. The methodology is based on the integral equation theory of molecular liquids in the reference interaction site representation/model (RISM) and uses the universal force field. Input parameters for RISM, such as optimized molecular geometries and charge distribution of interaction sites, are derived with the use of the density functional theory methods. To compare the diffusivity of the PCBM in binary blends with P3HT and P3BT, respectively, the study is complemented with MD simulation. A very good agreement with experiment and the reports of alternative modeling or simulation is observed for PCBM in P3HT system. The performance of P3BT with perovskites, however, seems as expected. The calculated nanoscale morphologies of blends of P3HT, P3BT or SQ2 with perovskites, including adsorption on TiO2, are all new and serve as an instrument in rational design of organic/hybrid photovoltaics. They are used in collaboration with experts who actually make prototypes or devices for practical applications.

Keywords: multiscale theory and modeling, nanoscale morphology, organic-inorganic halide perovskites, three dimensional distribution

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Authors: Abdul Wajid Ali

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Supersonic flight promises speed, but the design of the air inlet faces an obstacle: shock waves. They prevent air flow in the mixed compression ports, which reduces engine performance. Our research investigates this using supersonic wind tunnels and schlieren imaging to reveal the complex dance between shock waves and airflow. The findings show clear patterns of shock wave formation influenced by internal/external pressure surfaces. We looked at the boundary layer, the slow-moving air near the inlet walls, and its interaction with shock waves. In addition, the study emphasizes the dependence of the shock wave behaviour on the Mach number, which highlights the need for adaptive models. This knowledge is key to optimizing the combined compression inputs, paving the way for more powerful and efficient supersonic vehicles. Future engineers can use this knowledge to improve existing designs and explore innovative configurations for next-generation ultrasonic applications.

Keywords: oblique shock formation, boundary layer interaction, schlieren images, double wedge surface

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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: Mouna Baassi, Mohamed Moussaoui, Sanchaita Rajkhowa, Hatim Soufi, Said Belaaouad

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The objective of this paper is to address the challenging task of targeting Human Immunodeficiency Virus type 1 Reverse Transcriptase (HIV-1 RT) in the treatment of AIDS. Reverse Transcriptase inhibitors (RTIs) have limitations due to the development of Reverse Transcriptase mutations that lead to treatment resistance. In this study, a combination of statistical analysis and bioinformatics tools was adopted to develop a mathematical model that relates the structure of compounds to their inhibitory activities against HIV-1 Reverse Transcriptase. Our approach was based on a series of compounds recognized for their HIV-1 RT enzymatic inhibitory activities. These compounds were designed via software, with their descriptors computed using multiple tools. The most statistically promising model was chosen, and its domain of application was ascertained. Furthermore, compounds exhibiting comparable biological activity to existing drugs were identified as potential inhibitors of HIV-1 RT. The compounds underwent evaluation based on their chemical absorption, distribution, metabolism, excretion, toxicity properties, and adherence to Lipinski's rule. Molecular docking techniques were employed to examine the interaction between the Reverse Transcriptase (Wild Type and Mutant Type) and the ligands, including a known drug available in the market. Molecular dynamics simulations were also conducted to assess the stability of the RT-ligand complexes. Our results reveal some of the new compounds as promising candidates for effectively inhibiting HIV-1 Reverse Transcriptase, matching the potency of the established drug. This necessitates further experimental validation. This study, beyond its immediate results, provides a methodological foundation for future endeavors aiming to discover and design new inhibitors targeting HIV-1 Reverse Transcriptase.

Keywords: QSAR, ADMET properties, molecular docking, molecular dynamics simulation, reverse transcriptase inhibitors, HIV type 1

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Authors: Sergio Curilef, Boris Atenas

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Systems with long-range interactions are very common in nature. They are observed from the atomic scale to the astronomical scale and exhibit anomalies, such as inequivalence of ensembles, negative heat capacity, ergodicity breaking, nonequilibrium phase transitions, quasistationary states, and anomalous diffusion. These anomalies are exacerbated when special initial conditions are imposed; in particular, we use the so-called water bag initial conditions that stand for a uniform distribution. Several theoretical and practical implications are discussed here. A potential energy inspired by dipole-dipole interactions is proposed to build the dipole-type Hamiltonian mean-field model. As expected, the dynamics is novel and general to the behavior of systems with long-range interactions, which is obtained through molecular dynamics technique. Two plateaus sequentially emerge before arriving at equilibrium, which are corresponding to two different quasistationary states. The first plateau is a type of quasistationary state the lifetime of which depends on a power law of N and the second plateau seems to be a true quasistationary state as reported in the literature. The general behavior of the model according to its dynamics and thermodynamics is described. Using numerical simulation we characterize the mean kinetic energy, caloric curve, and the diffusion law through the mean square of displacement. The present challenge is to characterize the distributions in phase space. Certainly, the equilibrium state is well characterized by the Gaussian distribution, but quasistationary states in general depart from any Gaussian function.

Keywords: dipole-type interactions, dynamics and thermodynamics, mean field model, quasistationary states

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Authors: Aamir Shahzad, Mao-Gang He

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Currently, dusty plasmas motivated the researchers' widespread interest. Since the last two decades, substantial efforts have been made by the scientific and technological community to investigate the transport properties and their nonlinear behavior of three-dimensional and two-dimensional nonideal complex (dusty plasma) liquids (NICDPLs). Different calculations have been made to sustain and utilize strongly coupled NICDPLs because of their remarkable scientific and industrial applications. Understanding of the thermophysical properties of complex liquids under various conditions is of practical interest in the field of science and technology. The determination of thermal conductivity is also a demanding question for thermophysical researchers, due to some reasons; very few results are offered for this significant property. Lack of information of the thermal conductivity of dense and complex liquids at different parameters related to the industrial developments is a major barrier to quantitative knowledge of the heat flux flow from one medium to another medium or surface. The exact numerical investigation of transport properties of complex liquids is a fundamental research task in the field of thermophysics, as various transport data are closely related with the setup and confirmation of equations of state. A reliable knowledge of transport data is also important for an optimized design of processes and apparatus in various engineering and science fields (thermoelectric devices), and, in particular, the provision of precise data for the parameters of heat, mass, and momentum transport is required. One of the promising computational techniques, the homogenous nonequilibrium molecular dynamics (HNEMD) simulation, is over viewed with a special importance on the application to transport problems of complex liquids. This proposed work is particularly motivated by the FIRST TIME to modify the problem of heat conduction equations leads to polynomial velocity and temperature profiles algorithm for the investigation of transport properties with their nonlinear behaviors in the NICDPLs. The aim of proposed work is to implement a NEMDS algorithm (Poiseuille flow) and to delve the understanding of thermal conductivity behaviors in Yukawa liquids. The Yukawa system is equilibrated through the Gaussian thermostat in order to maintain the constant system temperature (canonical ensemble ≡ NVT)). The output steps will be developed between 3.0×105/ωp and 1.5×105/ωp simulation time steps for the computation of λ data. The HNEMD algorithm shows that the thermal conductivity is dependent on plasma parameters and the minimum value of lmin shifts toward higher G with an increase in k, as expected. New investigations give more reliable simulated data for the plasma conductivity than earlier known simulation data and generally the plasma λ0 by 2%-20%, depending on Γ and κ. It has been shown that the obtained results at normalized force field are in satisfactory agreement with various earlier simulation results. This algorithm shows that the new technique provides more accurate results with fast convergence and small size effects over a wide range of plasma states.

Keywords: molecular dynamics simulation, thermal conductivity, nonideal complex plasma, Poiseuille flow

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Authors: Jatinder Kumar, Ajay Bansal

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Simulation of a photocatalytic reactor helps in understanding the complex behavior of the photocatalytic degradation. Simulation also aids the designing and optimization of the photocatalytic reactor. Lack of simulation strategies is a huge hindrance in the commercialization of the photocatalytic technology. With the increased performance of computational resources, and development of simulation software, computational fluid dynamics (CFD) is becoming an affordable engineering tool to simulate and optimize reactor designs. In the present paper, a CFD (Computational fluid dynamics) model for simulating the performance of an immobilized-titanium dioxide based annular photocatalytic reactor was developed. The computational model integrates hydrodynamics, species mass transport, and chemical reaction kinetics using a commercial CFD code Fluent 6.3.26. The CFD model was based on the intrinsic kinetic parameters determined experimentally in a perfectly mixed batch reactor. Rhodamine B, a complex organic compound, was selected as a test pollutant for photocatalytic degradation. It was observed that CFD could become a valuable tool to understand and improve the photocatalytic systems.

Keywords: simulation, computational fluid dynamics (CFD), annular photocatalytic reactor, titanium dioxide

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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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Authors: Qiang Bu

Abstract:

This paper compares the explanatory power of sentiment level and sentiment shock. The preliminary test results show that sentiment shock plays a more significant role in explaining stocks returns, including the raw return and abnormal return. We also find that sentiment shock beta has a higher statistical significance than sentiment beta. These finding sheds new light on the relationship between investor sentiment and stock returns.

Keywords: sentiment level, sentiment shock, explanatory power, abnormal stock return, beta

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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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Authors: Apisaraporn Baicharoen, Prapasiri Pongprayoon

Abstract:

Betaine aldehyde dehydrogenase 2 (BADH2) is an enzyme that inhibits the accumulation of 2-acetyl-1-pyrroline (2AP), a potent flavor compound in rice fragrance. BADH2 contains three domains (NAD-binding, substrate-binding, and oligomerization domains). It catalyzes the oxidation of amino aldehydes. The lack of BADH2 results in the formation of 2AP and consequently an increase in rice fragrance. To date, inadequate data on BADH2 structure and function are available. An insight into the nature of BADH2 can serve as one of key starting points for the production of high quality fragrant rice. In this study, we therefore constructed the homology model of BADH2 and employed 500-ns Molecular Dynamics simulations (MD) to primarily understand the structural and dynamic properties of BADH2. Initially, Ramachandran plot confirms the good quality of modeled protein structure. Principle Component Analysis (PCA) was also calculated to capture the protein dynamics. Among 3 domains, the results show that NAD binding site is found to be more flexible. Moreover, interactions from key amino acids (N162, E260, C294, and Y419) that are crucial for function are investigated.

Keywords: betaine aldehyde dehydrogenase 2, fragrant rice, homology modeling, molecular dynamics simulations

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Authors: Raj K. Gupta, X. Gary Tan, Andrzej Przekwas

Abstract:

Bomb blasts from Improvised Explosive Devices (IEDs) account for vast majority of terrorist attacks worldwide. Injuries caused by IEDs result from a combination of the primary blast wave, penetrating fragments, and human body accelerations and impacts. This paper presents a multiscale computational model of coupled blast physics, whole human body biodynamics and injury biomechanics of sensitive organs. The disparity of the involved space- and time-scales is used to conduct sequential modeling of an IED explosion event, CFD simulation of blast loads on the human body and FEM modeling of body biodynamics and injury biomechanics. The paper presents simulation results for blast-induced brain injury coupling macro-scale brain biomechanics and micro-scale response of sensitive neuro-axonal structures. Validation results on animal models and physical surrogates are discussed. Results of our model can be used to 'replicate' filed blast loadings in laboratory controlled experiments using animal models and in vitro neuro-cultures.

Keywords: blast waves, improvised explosive devices, injury biomechanics, mathematical models, traumatic brain injury

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Authors: Muleya Nqobile, Winston Garira

Abstract:

We presented a compartmental deterministic multi-scale model which encompass internal plant defensive mechanism and pathogen interaction, then we consider nesting the model into the epidemiological model. The objective was to improve our understanding of the transmission dynamics of within host and between host of Guignardia citricapa Kiely. The inflow of infected class was scaled down to individual level while the outflow was scaled up to average population level. Conceptual model and mathematical model were constructed to display a theoretical framework which can be used for predicting or identify disease pattern.

Keywords: epidemiological model, mathematical modelling, multi-scale modelling, immunological model

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Authors: Thiago Victor Cordeiro Marcos, Joao Felipe de Araujo Martos, Ronaldo de Lima Cardoso, David Romanelli Pinto, Paulo Gilberto de Paula Toro, Israel da Silveira Rego, Antonio Carlos de Oliveira

Abstract:

Currently, the use of 3D rapid prototyping, also known as 3D printing, has been investigated by some universities around the world as an innovative technique, fast, flexible and cheap for a direct plastic models manufacturing that are lighter and with complex geometries to be tested for hypersonic shock tunnel. Initially, the purpose is integrated prototyped parts with metal models that actually are manufactured through of the conventional machining and hereafter replace them with completely prototyped models. The mechanical design models to be tested in hypersonic shock tunnel are based on conventional manufacturing processes, therefore are limited forms and standard geometries. The use of 3D rapid prototyping offers a range of options that enables geometries innovation and ways to be used for the design new models. The conception and project of a prototyped model for hypersonic shock tunnel should be rethought and adapted when comparing the conventional manufacturing processes, in order to fully exploit the creativity and flexibility that are allowed by the 3D prototyping process. The objective of this paper is to compare the conception and project of a 3D rapid prototyping model and a conventional machining model, while showing the advantages and disadvantages of each process and the benefits that 3D prototyping can bring to the manufacture of models to be tested in hypersonic shock tunnel.

Keywords: 3D printing, 3D prototyping, experimental research, hypersonic shock tunnel

Procedia PDF Downloads 435