Search results for: molecular dynamics simulations

Authors: Sakshi Piplani, Ajit Kumar

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Valproic acid (VPA) is the first synthetic therapeutic agent used to treat epileptic disorders, which account for affecting nearly 1% world population. Teratogenicity caused by VPA has prompted the search for next generation drug with better efficacy and lower side effects. Recent studies have posed HDAC8 as direct target of VPA that causes the teratogenic effect in foetus. We have employed molecular dynamics (MD) and docking simulations to understand the binding mode of VPA and their analogues onto HDAC8. A total of twenty 3D-structures of human HDAC8 isoforms were selected using BLAST-P search against PDB. Multiple sequence alignment was carried out using ClustalW and PDB-3F07 having least missing and mutated regions was selected for study. The missing residues of loop region were constructed using MODELLER and energy was minimized. A set of 216 structural analogues (>90% identity) of VPA were obtained from Pubchem and ZINC database and their energy was optimized with Chemsketch software using 3-D CHARMM-type force field. Four major neurotransmitters (GABAt, SSADH, α-KGDH, GAD) involved in anticonvulsant activity were docked with VPA and its analogues. Out of 216 analogues, 75 were selected on the basis of lower binding energy and inhibition constant as compared to VPA, thus predicted to have anti-convulsant activity. Selected hHDAC8 structure was then subjected to MD Simulation using licenced version YASARA with AMBER99SB force field. The structure was solvated in rectangular box of TIP3P. The simulation was carried out with periodic boundary conditions and electrostatic interactions and treated with Particle mesh Ewald algorithm. pH of system was set to 7.4, temperature 323K and pressure 1atm respectively. Simulation snapshots were stored every 25ps. The MD simulation was carried out for 20ns and pdb file of HDAC8 structure was saved every 2ns. The structures were analysed using castP and UCSF Chimera and most stabilized structure (20ns) was used for docking study. Molecular docking of 75 selected VPA-analogues with PDB-3F07 was performed using AUTODOCK4.2.6. Lamarckian Genetic Algorithm was used to generate conformations of docked ligand and structure. The docking study revealed that VPA and its analogues have more affinity towards ‘hydrophobic active site channel’, due to its hydrophobic properties and allows VPA and their analogues to take part in van der Waal interactions with TYR24, HIS42, VAL41, TYR20, SER138, TRP137 while TRP137 and SER138 showed hydrogen bonding interaction with VPA-analogues. 14 analogues showed better binding affinity than VPA. ADMET SAR server was used to predict the ADMET properties of selected VPA analogues for predicting their druggability. On the basis of ADMET screening, 09 molecules were selected and are being used for in-vivo evaluation using Danio rerio model.

Keywords: HDAC8, docking, molecular dynamics simulation, valproic acid

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Authors: Worrapol Koranuntachai, Tonkid Chantrasmi, Udomkiat Nontakaew

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Medical latex gloves are made from the latex compound in production lines. Latex dipping is considered one of the most important processes that directly affect the final product quality. In a continuous production line, a chain conveyor carries the formers through the process and partially submerges them into an open channel flow in a latex dipping tank. In general, the conveyor speed is determined by the desired production capacity, and the latex-dipping tank can then be designed accordingly. It is important to understand the flow behavior in the dipping tank in order to achieve high quality in the process. In this work, Computational Fluid Dynamics (CFD) was used to simulate the flow past an array of formers in a simplified latex dipping process. The computational results showed both the flow structure and the vortex generation between two formers. The maximum shear stress over the surface of the formers was used as the quality metric of the latex-dipping process when adjusting operation parameters.

Keywords: medical latex gloves, latex dipping, dipping tank, computational fluid dynamics

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Authors: Naseem Uddin

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Impinging jets are used in variety of engineering and industrial applications. This paper is based on numerical simulations of heat transfer by turbulent impinging jet with velocity field excitations using different Reynolds Averaged Navier-Stokes Equations models. Also Detached Eddy Simulations are conducted to investigate the differences in the prediction capabilities of these two simulation approaches. In this paper the excited jet is simulated in non-commercial CFD code OpenFOAM with the goal to understand the influence of dynamics of impinging jet on heat transfer. The jet’s frequencies are altered keeping in view the preferred mode of the jet. The Reynolds number based on mean velocity and diameter is 23,000 and jet’s outlet-to-target wall distance is 2. It is found that heat transfer at the target wall can be influenced by judicious selection of amplitude and frequencies.

Keywords: excitation, impinging jet, natural frequency, turbulence models

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Authors: Jorge Lopez

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In this work, we introduce fractional calculus in order to study the dynamics of a damped multistory building with some symmetry. Initially we make a review of the dynamics of a free and damped multistory building. Then we introduce those concepts of fractional calculus that will be involved in our study. It has been noticed that fractional calculus provides models with less parameters than those based on classical calculus. In particular, a damped classical oscilator is more naturally described by using fractional derivatives. Accordingly, we model our multistory building as a set of coupled fractional oscillators and compare its dynamics with the results coming from traditional methods.

Keywords: coupled oscillators, fractional calculus, fractional oscillator, structural dynamics

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Authors: Jiahui Song

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In order to predict or explain a complicated biological process, it is important first to construct mathematical models that can be used to yield analytical solutions. Through numerical simulation, mathematical model results can be used to test scenarios that might not be easily attained in a laboratory experiment, or to predict parameters or phenomena. High-intensity, nanosecond pulse electroporation has been a recent development in bioelectrics. The dynamic pore model can be achieved by including a dynamic aspect and a dependence on the pore population density into pore formation energy equation to analyze and predict such electroporation effects. For greater accuracy, with inclusion of atomistic details, molecular dynamics (MD) simulations were also carried out during this study. Besides inducing pores in cells, external voltages could also be used in principle to modulate action potential generation in nerves. This could have an application in electrically controlled ‘pain management’. Also a simple model-based rate equation treatment of the various cellular bio-chemical processes has been used to predict the pulse number dependent cell survival trends.

Keywords: model, high-intensity, nanosecond, bioelectrics

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Authors: Carlos A. Acosta, Amar Bhalla, Ruyan Guo

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Scraped surface heat exchangers (SSHE) use a rotor shaft assembly with scraping blades to homogenize viscous fluids during the heat transfer process. Obtaining in-situ measurements is difficult because the rotor and scraping blades spin continuously inside the mixing chamber, obstructing the instrumentation pathway. Computational fluid dynamics simulations provide useful insight into the flow behavior around the scraper blades for a variety of fluids and blade geometries. However, numerical solutions often focus on the fluid dynamics and heat transfer phenomena of rotating flow, ignoring the glass-transition temperature and freezing point depression. This research studies the multi-phase fluid dynamics and freezing point depression inside the SSHE with non-isothermal conditions in a time dependent process using an aqueous solution that contains 13.5 wt.% high fructose corn syrup and CO₂. The computational results were validated with in-situ pressure, temperature, and optical spectroscopy measurements. Results from the numerical model show good quantitatively agreement with experimental values.

Keywords: computational fluid dynamics, freezing point depression, phase-transition temperature, multi-phase flow

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Authors: Lokesh Soni, Sushanta Kumar Sethi, Gaurav Manik

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This work attempts to use molecular simulations to create equilibrated structures of a range of commercially used polymers. Generated equilibrated structures for polyvinyl acetate (isotactic), polyvinyl alcohol (atactic), polystyrene, polyethylene, polyamide 66, poly dimethyl siloxane, poly carbonate, poly ethylene oxide, poly amide 12, natural rubber, poly urethane, and polycarbonate (bisphenol-A) and poly ethylene terephthalate are employed to estimate the correct chain length that will correctly predict the chain parameters and properties. Further, the equilibrated structures are used to predict some properties like density, solubility parameter, cohesive energy density, surface energy, and Flory-Huggins interaction parameter. The simulated densities for polyvinyl acetate, polyvinyl alcohol, polystyrene, polypropylene, and polycarbonate are 1.15 g/cm3, 1.125 g/cm3, 1.02 g/cm3, 0.84 g/cm3 and 1.223 g/cm3 respectively are found to be in good agreement with the available literature estimates. However, the critical repeating units or the degree of polymerization after which the solubility parameter showed saturation were 15, 20, 25, 10 and 20 respectively. This also indicates that such properties that dictate the miscibility of two or more polymers in their blends are strongly dependent on the chosen polymer or its characteristic properties. An attempt has been made to correlate such properties with polymer properties like Kuhn length, free volume and the energy term which plays a vital role in predicting the mentioned properties. These results help us to screen and propose a useful library which may be used by the research groups in estimating the polymer properties using the molecular simulations of chains with the predicted critical lengths. The library shall help to obviate the need for researchers to spend efforts in finding the critical chain length needed for simulating the mentioned polymer properties.

Keywords: Kuhn length, Flory Huggins interaction parameter, cohesive energy density, free volume

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Authors: Surbhi Rani, Sunita Gakkhar

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The four-dimensional food web system consisting of two prey species for a generalist middle predator and a top predator is proposed and investigated. The middle predator is predating both the prey species with a modified Holling type-II functional response. The food web model is found to be well-posed, bounded, and dissipative. The proposed model's essential dynamical features are studied in terms of local stability. The four species' survival is explored, and persistence conditions are established. The numerical simulations reveal the persistence in the form of a chaotic attractor or stable focus. The conclusion is that providing additional food to the middle predator may help to control the food chain's chaos.

Keywords: predator-prey model, existence of equilibrium points, local stability, chaos, numerical simulations

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Authors: Haijie Li, Xuping Zhang

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This paper presents a computationally efficient method for the modeling of robot manipulators with flexible links and joints. This approach combines the Discrete Time Transfer Matrix Method with the Finite Segment Method, in which the flexible links are discretized by a number of rigid segments connected by torsion springs; and the flexibility of joints are modeled by torsion springs. The proposed method avoids the global dynamics and has the advantage of modeling non-uniform manipulators. Experiments and simulations of a single-link flexible manipulator are conducted for verifying the proposed methodologies. The simulations of a three-link robot arm with links and joints flexibility are also performed.

Keywords: flexible manipulator, transfer matrix method, linearization, finite segment method

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Authors: Mohammad Salehi, Mohammad Erfan Doraki

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In this paper, airflow analysis inside a desktop computer case is performed by simulating computational fluid dynamics. The purpose is to investigate the cooling process of the central processing unit (CPU) with thermal capacities of 80 and 130 watts. The airflow inside the computer enclosure, selected from the microATX model, consists of the main components of heat production such as CPU, hard disk drive, CD drive, floppy drive, memory card and power supply unit; According to the amount of thermal power produced by the CPU with 80 and 130 watts of power, two different geometries have been used for a direct and radial heat sink. First, the independence of the computational mesh and the validation of the solution were performed, and after ensuring the correctness of the numerical solution, the results of the solution were analyzed. The simulation results showed that changes in CPU temperature and other components linearly increased with increasing CPU heat output. Also, the ambient air temperature has a significant effect on the maximum processor temperature.

Keywords: computational fluid dynamics, CPU cooling, computer case simulation, heat sink

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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: H. E. Ferrari, R. Farengo, C. F. Clauser

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Tungsten (W) will be used in ITER as one of the plasma facing components (PFCs). The W could migrate to the plasma center. This could have a potentially deleterious effect on plasma confinement. Electron cyclotron resonance heating (ECRH) can be used to prevent W accumulation. We simulated a series of H mode discharges in ASDEX U with PFC containing W, where central ECRH was used to prevent W accumulation in the plasma center. The experiments showed that the W density profiles were flat after a sawtooth crash, and become hollow in between sawtooth crashes when ECRH has been applied. It was also observed that a saturated kink mode was active in these conditions. We studied the effect of saturated kink like instabilities on the redistribution of W impurities. The kink was modeled as the sum of a simple analytical equilibrium (large aspect ratio, circular cross section) plus the perturbation produced by the kink. A numerical code that follows the exact trajectories of the impurity ions in the total fields and includes collisions was employed. The code is written in Cuda C and runs in Graphical Processing Units (GPUs), allowing simulations with a large number of particles with modest resources. Our simulations show that when the W ions have a thermal velocity distribution, the kink has no effect on the W density. When we consider the plasma rotation, the kink can affect the W density. When the average passing frequency of the W particles is similar to the frequency of the kink mode, the expulsion of W ions from the plasma core is maximum, and the W density shows a hollow structure. This could have implications for the mitigation of W accumulation.

Keywords: impurity transport, kink instability, tungsten accumulation, tungsten dynamics

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Authors: K. Ghosh, S. N. Tripathi, Manish Joshi, Y. S. Mayya, Arshad Khan, B. K. Sapra

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We have developed a CFD coupled aerosol microphysics model in the context of aerosol generation from a glowing wire. The governing equations can be solved implicitly for mass, momentum, energy transfer along with aerosol dynamics. The computationally efficient framework can simulate temporal behavior of total number concentration and number size distribution. This formulation uniquely couples standard K-Epsilon scheme with boundary layer model with detailed aerosol dynamics through residence time. This model uses measured temperatures (wire surface and axial/radial surroundings) and wire compositional data apart from other usual inputs for simulations. The model predictions show that bulk fluid motion and local heat distribution can significantly affect the aerosol behavior when the buoyancy effect in momentum transfer is considered. Buoyancy generated turbulence was found to be affecting parameters related to aerosol dynamics and transport as well. The model was validated by comparing simulated predictions with results obtained from six controlled experiments performed with a laboratory-made hot wire nanoparticle generator. Condensation particle counter (CPC) and scanning mobility particle sizer (SMPS) were used for measurement of total number concentration and number size distribution at the outlet of reactor cell during these experiments. Our model-predicted results were found to be in reasonable agreement with observed values. The developed model is fast (fully implicit) and numerically stable. It can be used specifically for applications in the context of the behavior of aerosol particles generated from glowing wire technique and in general for other similar large scale domains. Incorporation of CFD in aerosol microphysics framework provides a realistic platform to study natural convection driven systems/ applications. Aerosol dynamics sub-modules (nucleation, coagulation, wall deposition) have been coupled with Navier Stokes equations modified to include buoyancy coupled K-Epsilon turbulence model. Coupled flow-aerosol dynamics equation was solved numerically and in the implicit scheme. Wire composition and temperature (wire surface and cell domain) were obtained/measured, to be used as input for the model simulations. Model simulations showed a significant effect of fluid properties on the dynamics of aerosol particles. The role of buoyancy was highlighted by observation and interpretation of nucleation zones in the planes above the wire axis. The model was validated against measured temporal evolution, total number concentration and size distribution at the outlet of hot wire generator cell. Experimentally averaged and simulated total number concentrations were found to match closely, barring values at initial times. Steady-state number size distribution matched very well for sub 10 nm particle diameters while reasonable differences were noticed for higher size ranges. Although tuned specifically for the present context (i.e., aerosol generation from hotwire generator), the model can also be used for diverse applications, e.g., emission of particles from hot zones (chimneys, exhaust), fires and atmospheric cloud dynamics.

Keywords: nanoparticles, k-epsilon model, buoyancy, CFD, hot wire generator, aerosol dynamics

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Authors: Innocent O. Arukalam, Emeka E. Oguzie

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Interest in the development of eco-friendly anti-corrosion coatings using bio-based renewable materials is gaining momentum recently. To this effect, chitin biopolymer, which is non-toxic, biodegradable, and inherently possesses anti-microbial property, was successfully synthesized from snail shells and used as a filler in the preparation of epoxy coating. The chitin particles were characterized with contact angle goniometer, scanning electron microscope (SEM), Fourier transform infrared (FTIR) spectrophotometer, and X-ray diffractometer (XRD). The performance of the coatings was evaluated by immersion and electrochemical impedance spectroscopy (EIS) tests. Electronic structure properties of the coating ingredients and molecular level interaction of the corrodent and coated Q235 steel were appraised by quantum chemical computations (QCC) and molecular dynamics (MD) simulation techniques, respectively. The water contact angle (WCA) measurement of chitin particles was found to be 129.3o while that of chitin particles modified with amino trimethoxy silane (ATMS) was 149.6o, suggesting it is highly hydrophobic. Immersion and EIS analyses revealed that epoxy coating containing silane-modified chitin exhibited lowest water absorption and highest barrier as well as anti-corrosion performances. The QCC showed that quantum parameters for the coating containing silane-modified chitin are optimum and therefore corresponds to high corrosion protection. The high negative value of adsorption energies (Eads) for the coating containing silane-modified chitin indicates the coating molecules interacted and adsorbed strongly on the steel surface. The observed results have shown that silane-modified epoxy-chitin coating would perform satisfactorily for surface protection of metal structures in saline environment.

Keywords: chitin, EIS, epoxy coating, hydrophobic, molecular dynamics simulation, quantum chemical computation

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Authors: Virginie Hergault, Siham Chebbah, Bertrand Frere

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Following in-house objectives, Central laboratory of Paris police Prefecture conducted a general review on models and Computational Fluid Dynamics (CFD) codes used to simulate pollutant dispersion in the atmosphere. Starting from that review and considering main features of Large Eddy Simulation, Central Laboratory Of Paris Police Prefecture (LCPP) postulates that the Fire Dynamics Simulator (FDS) model, from National Institute of Standards and Technology (NIST), should be well suited for air pollutant dispersion modeling. This paper focuses on the implementation and the evaluation of FDS in the frame of the European COST ES1006 Action. This action aimed at quantifying the performance of modeling approaches. In this paper, the CUTE dataset carried out in the city of Hamburg, and its mock-up has been used. We have performed a comparison of FDS results with wind tunnel measurements from CUTE trials on the one hand, and, on the other, with the models results involved in the COST Action. The most time-consuming part of creating input data for simulations is the transfer of obstacle geometry information to the format required by SDS. Thus, we have developed Python codes to convert automatically building and topographic data to the FDS input file. In order to evaluate the predictions of FDS with observations, statistical performance measures have been used. These metrics include the fractional bias (FB), the normalized mean square error (NMSE) and the fraction of predictions within a factor of two of observations (FAC2). As well as the CFD models tested in the COST Action, FDS results demonstrate a good agreement with measured concentrations. Furthermore, the metrics assessment indicate that FB and NMSE meet the tolerance acceptable.

Keywords: numerical simulations, atmospheric dispersion, cost ES1006 action, CFD model, cute experiments, wind tunnel data, numerical results

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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: Ali Oveysi Sarabi

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In this paper, controller design for the attitude and altitude dynamics of an outdoor quadrotor, which is constructed with low cost actuators and drivers, is aimed. Before designing the controller, the quadrotor is modeled mathematically in Matlab-Simulink environment. To control attitude dynamics, linear quadratic regulator (LQR) based controllers are designed, simulated and applied to the system. Two different proportional-integral-derivative action (PID) controllers are designed to control yaw and altitude dynamics. During the implementation of the designed controllers, different test setups are used. Designed controllers are implemented and tuned on the real system using xPC Target. Tests show that these basic control structures are successful to control the attitude and altitude dynamics.

Keywords: helicopter balance, flight dynamics, autonomous landing, control robotics

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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: S. Perera, T. R. Walsh, M. Solvang

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The structure-property relationships of calcium aluminosilicate (CAS) glass surfaces are of scientific and technological interest regarding dissolution phenomena. Molecular dynamics (MD) simulations can provide atomic-scale insights into the structure and properties of the CAS interfaces in vacuo as the first step to conducting computational dissolution studies on CAS surfaces. However, one limitation to date is that although the bulk properties of CAS glasses have been well studied by MD simulation, corresponding efforts on CAS surface properties are relatively few in number (both theoretical and experimental). Here, a systematic computational protocol to create CAS surfaces in vacuo is developed by evaluating the sensitivity of the resultant surface structure with respect to different factors. Factors such as the relative thickness of the surface layer, the relative thickness of the bulk region, the cooling rate, and the annealing schedule (time and temperature) are explored. Structural features such as ring size distribution, defect concentrations (five-coordinated aluminium (AlV), non-bridging oxygen (NBO), and tri-cluster oxygen (TBO)), and linkage distribution are identified as significant features in dissolution studies.

Keywords: MD simulation, CAS glasses, surface structure, structure-property, CAS interface

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Authors: Divya Vats, Sanjay Mahajani

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The clarification of sugarcane juice plays a pivotal role in the production of non-centrifugal sugar (NCS), profoundly influencing the quality of the final NCS product. In this study, we have investigated the kinetics and mathematical modeling of the batch clarification process. The turbidity of the clarified cane juice (NTU) emerges as the determinant of the end product’s color. Moreover, this parameter underscores the significance of considering other variables as performance indicators for accessing the efficacy of the clarification process. Temperature-controlled experiments were meticulously conducted in a laboratory-scale batch mode. The primary objective was to discern the essential and optimized parameters crucial for augmenting the clarity of cane juice. Additionally, we explored the impact of pH and flocculant loading on the kinetics. Particle Image Velocimetry (PIV) is employed to comprehend the particle-particle and fluid-particle interaction. This technique facilitated a comprehensive understanding, paving the way for the subsequent multiphase computational fluid dynamics (CFD) simulations using the Eulerian-Lagrangian approach in the Ansys fluent. Impressively, these simulations accurately replicated comparable velocity profiles. The final mechanism of this study helps to make a mathematical model and presents a valuable framework for transitioning from the traditional batch process to a continuous process. The ultimate aim is to attain heightened productivity and unwavering consistency in product quality.

Keywords: non-centrifugal sugar, particle image velocimetry, computational fluid dynamics, mathematical modeling, turbidity

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Authors: Naveed Ahmad, Farooq Ahmad, Abdul Aal

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The effect of iron contents on the rheological behavior of sPP/iron composites in the melt phase was investigated using a series of syndiotactic polypropylene/iron (sPP/iron) composite samples. Using the Advanced Rheometric Expansion System, studies with small amplitude oscillatory shear were conducted (ARES). It was discovered that the plateau modulus rose along with the iron loading. Also it was found that both entanglement molecular weight and packing length decrease with increase in iron loading.. This finding demonstrates how iron content in polymer/iron composites affects chain parameters and dimensions, which in turn affects the entire chain dynamics.

Keywords: plateau modulus, packing lenght, polymer/iron composites, rheology, entanglement molecular weight

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Authors: Zhijie Li, Wenhui Peng, Zelong Yuan, Jianchun Wang

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Turbulence is a complex phenomenon that plays a crucial role in various fields, such as engineering, atmospheric science, and fluid dynamics. Predicting and understanding its behavior over long time scales have been challenging tasks. Traditional methods, such as large-eddy simulation (LES), have provided valuable insights but are computationally expensive. In the past few years, machine learning methods have experienced rapid development, leading to significant improvements in computational speed. However, ensuring stable and accurate long-term predictions remains a challenging task for these methods. In this study, we introduce the implicit U-net enhanced Fourier neural operator (IU-FNO) as a solution for stable and efficient long-term predictions of the nonlinear dynamics in three-dimensional (3D) turbulence. The IU-FNO model combines implicit re-current Fourier layers to deepen the network and incorporates the U-Net architecture to accurately capture small-scale flow structures. We evaluate the performance of the IU-FNO model through extensive large-eddy simulations of three types of 3D turbulence: forced homogeneous isotropic turbulence (HIT), temporally evolving turbulent mixing layer, and decaying homogeneous isotropic turbulence. The results demonstrate that the IU-FNO model outperforms other FNO-based models, including vanilla FNO, implicit FNO (IFNO), and U-net enhanced FNO (U-FNO), as well as the dynamic Smagorinsky model (DSM), in predicting various turbulence statistics. Specifically, the IU-FNO model exhibits improved accuracy in predicting the velocity spectrum, probability density functions (PDFs) of vorticity and velocity increments, and instantaneous spatial structures of the flow field. Furthermore, the IU-FNO model addresses the stability issues encountered in long-term predictions, which were limitations of previous FNO models. In addition to its superior performance, the IU-FNO model offers faster computational speed compared to traditional large-eddy simulations using the DSM model. It also demonstrates generalization capabilities to higher Taylor-Reynolds numbers and unseen flow regimes, such as decaying turbulence. Overall, the IU-FNO model presents a promising approach for long-term dynamics prediction in 3D turbulence, providing improved accuracy, stability, and computational efficiency compared to existing methods.

Keywords: data-driven, Fourier neural operator, large eddy simulation, fluid dynamics

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Authors: Ankur Chaudhuri, Sibani Sen Chakraborty

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In human, glutaminyl cyclase activity is highly abundant in neuronal and secretory tissues and is preferentially restricted to hypothalamus and pituitary. The N-terminal modification of β-amyloids (Aβs) peptides by the generation of a pyro-glutamyl (pGlu) modified Aβs (pE-Aβs) is an important process in the initiation of the formation of neurotoxic plaques in Alzheimer’s disease (AD). This process is catalyzed by glutaminyl cyclase (QC). The expression of QC is characteristically up-regulated in the early stage of AD, and the hallmark of the inhibition of QC is the prevention of the formation of pE-Aβs and plaques. A computer-aided drug design (CADD) process was employed to give an idea for the designing of potentially active compounds to understand the inhibitory potency against human glutaminyl cyclase (QC). This work elaborates the ligand-based and structure-based pharmacophore exploration of glutaminyl cyclase (QC) by using the known inhibitors. Three dimensional (3D) quantitative structure-activity relationship (QSAR) methods were applied to 154 compounds with known IC50 values. All the inhibitors were divided into two sets, training-set, and test-sets. Generally, training-set was used to build the quantitative pharmacophore model based on the principle of structural diversity, whereas the test-set was employed to evaluate the predictive ability of the pharmacophore hypotheses. A chemical feature-based pharmacophore model was generated from the known 92 training-set compounds by HypoGen module implemented in Discovery Studio 2017 R2 software package. The best hypothesis was selected (Hypo1) based upon the highest correlation coefficient (0.8906), lowest total cost (463.72), and the lowest root mean square deviation (2.24Å) values. The highest correlation coefficient value indicates greater predictive activity of the hypothesis, whereas the lower root mean square deviation signifies a small deviation of experimental activity from the predicted one. The best pharmacophore model (Hypo1) of the candidate inhibitors predicted comprised four features: two hydrogen bond acceptor, one hydrogen bond donor, and one hydrophobic feature. The Hypo1 was validated by several parameters such as test set activity prediction, cost analysis, Fischer's randomization test, leave-one-out method, and heat map of ligand profiler. The predicted features were then used for virtual screening of potential compounds from NCI, ASINEX, Maybridge and Chembridge databases. More than seven million compounds were used for this purpose. The hit compounds were filtered by drug-likeness and pharmacokinetics properties. The selective hits were docked to the high-resolution three-dimensional structure of the target protein glutaminyl cyclase (PDB ID: 2AFU/2AFW) to filter these hits further. To validate the molecular docking results, the most active compound from the dataset was selected as a reference molecule. From the density functional theory (DFT) study, ten molecules were selected based on their highest HOMO (highest occupied molecular orbitals) energy and the lowest bandgap values. Molecular dynamics simulations with explicit solvation systems of the final ten hit compounds revealed that a large number of non-covalent interactions were formed with the binding site of the human glutaminyl cyclase. It was suggested that the hit compounds reported in this study could help in future designing of potent inhibitors as leads against human glutaminyl cyclase.

Keywords: glutaminyl cyclase, hit lead, pharmacophore model, simulation

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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: Jonathan Galvan-Colin, Ariel Valladares, Renela Valladares, Alexander Valladares

Abstract:

Both porous materials and bulk metallic glasses have been studied due to their potential applications and their exceptional physical and chemical properties. However, each material presents certain drawbacks which have been thought to be overcome by generating bulk metallic glass foams (BMGF). Although some experimental reports have been performed on multicomponent BMGF, still no ab initio works have been published, as far as we know. We present an approach based on the expanding lattice (EL) method to generate binary amorphous nanoporous Cu64Zr36. Starting from two different configurations: a 108-atom crystalline cubic supercell (cCu64Zr36) and a 108-atom amorphous supercell (aCu64Zr36), both with an initial density of 8.06 g/cm3, we applied EL method to halve the density and to get 50% of porosity. After the lattice expansion the supercells were subject to ab initio molecular dynamics for 500 steps at constant room temperature. Then, the samples were geometry-optimized and characterized with the pair and radial distribution functions, bond-angle distributions and a coordination number analysis. We found that pores appeared along specific spatial directions different from one to another and that they differed in size and form as well, which we think is related to the initial structure. Due to the lack of experimental counterparts our results should be considered predictive and further studies are needed in order to handle a larger number of atoms and its implication on pore topology.

Keywords: ab initio molecular dynamics, bulk mettalic glass, porous alloy

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Authors: Sourav Ray, Christoph Stein, Marcus Weber

Abstract:

A new class of drug candidates, initially derived from mathematical modeling of ligand-receptor interactions, activate the μ-opioid receptor (MOR) preferentially at acidic extracellular pH-levels, as present in injured tissues. This is of commercial interest because it may preclude the adverse effects of conventional MOR agonists like fentanyl, which include but are not limited to addiction, constipation, sedation, and apnea. Animal studies indicate the importance of taking the pH value of the chemical environment of MOR into account when designing new drugs. Hydrogen bonds (HBs) play a crucial role in stabilizing protein secondary structure and molecular interaction, such as ligand-protein interaction. These bonds may depend on the pH value of the chemical environment. For the MOR, antagonist naloxone and agonist [D-Ala2,N-Me-Phe4,Gly5-ol]-enkephalin (DAMGO) form HBs with ionizable residue HIS 297 at physiological pH to modulate signaling. However, such interactions were markedly reduced at acidic pH. Although fentanyl-induced signaling is also diminished at acidic pH, HBs with HIS 297 residue are not observed at either acidic or physiological pH for this strong agonist of the MOR. Molecular dynamics (MD) simulations can provide greater insight into the interaction between the ligand of interest and the HIS 297 residue. Amino acid protonation states are adjusted to the model difference in system acidity. Unbiased and unrestrained MD simulations were performed, with the ligand in the proximity of the HIS 297 residue. Ligand-receptor complexes were embedded in 1-palmitoyl-2-oleoyl-sn glycero-3-phosphatidylcholine (POPC) bilayer to mimic the membrane environment. The occurrence of HBs between the different ligands and the HIS 297 residue of MOR at acidic and physiological pH values were tracked across the various simulation trajectories. No HB formation was observed between fentanyl and HIS 297 residue at either acidic or physiological pH. Naloxone formed some HBs with HIS 297 at pH 5, but no such HBs were noted at pH 7. Interestingly, DAMGO displayed an opposite yet more pronounced HB formation trend compared to naloxone. Whereas a marginal number of HBs could be observed at even pH 5, HBs with HIS 297 were more stable and widely present at pH 7. The HB formation plays no and marginal role in the interaction of fentanyl and naloxone, respectively, with the HIS 297 residue of MOR. However, HBs play a significant role in the DAMGO and HIS 297 interaction. Post DAMGO administration, these HBs might be crucial for the remediation of opioid tolerance and restoration of opioid sensitivity. Although experimental studies concur with our observations regarding the influence of HB formation on the fentanyl and DAMGO interaction with HIS 297, the same could not be conclusively stated for naloxone. Therefore, some other supplementary interactions might be responsible for the modulation of the MOR activity by naloxone binding at pH 7 but not at pH 5. Further elucidation of the mechanism of naloxone action on the MOR could assist in the formulation of cost-effective naloxone-based treatment of opioid overdose or opioid-induced side effects.

Keywords: effect of system acidity, hydrogen bond formation, opioid action, receptor activation

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

Abstract:

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: Salim Al Jadidi, Shian Gao, Shivananda Moolya

Abstract:

Computational Fluid Dynamic (CFD) technique coupled with Sub-Grid-Scale (SGS) model is used to study the flow behavior of heavy oil-water-air flow in a horizontal pipe by adapting ANSYS Fluent CFD software. The technique suitable for the transport of water-lubricated heavy viscous oil in a horizontal pipe is the Core Annular flow (CAF) technique. The present study focuses on the numerical study of CAF adapting Large Eddy Simulations (LES). The basic objective of the present study is to gain a basic knowledge of the flow behavior of heavy oil using turbulent CAF through a conventional horizontal pipe. This work also focuses on the success and applicability of LES. The simulation of heavy oil-water-air three-phase flow and two-phase flow of heavy oil–water in a conventional horizontal pipe is performed using ANSYS Fluent 16.2 software. The influence of three-phase heavy oil-water air flow in a selected pipe is affected by gravity. It is also observed from the result that the air phase and the variation in the temperature impact the behavior of the annular stream and pressure drop. Some results obtained during the study are validated with the results gained from part of the literature experiments and simulations, and the results show reasonably good agreement between the studies.

Keywords: computational fluid dynamics, gravity, heavy viscous oil, three-phase flow

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Authors: Sanja Podunavac-Kuzmanović, Strahinja Kovačević, Lidija Jevrić, Evgenija Djurendić, Jovana Ajduković

Abstract:

In the present study, the molecular modeling of a series of 24 17-picolyl and 17-picolinylidene androstane derivatives whit significant anticancer activity was carried out. Modelling of studied compounds was performed by CS ChemBioDraw Ultra v12.0 program for drawing 2D molecular structures and CS ChemBio3D Ultra v12.0 for 3D molecular modelling. The obtained 3D structures were subjected to energy minimization using molecular mechanics force field method (MM2). The cutoff for structure optimization was set at a gradient of 0.1 kcal/Åmol. Full geometry optimization was done by the Austin Model 1 (AM1) until the root mean square (RMS) gradient reached a value smaller than 0.0001 kcal/Åmol using Molecular Orbital Package (MOPAC) program. The obtained physicochemical, lipophilicity and topological descriptors were used for analysis of molecular similarities and dissimilarities applying suitable chemometric methods (principal component analysis and cluster analysis). These results are the part of the project No. 114-451-347/2015-02, financially supported by the Provincial Secretariat for Science and Technological Development of Vojvodina and CMST COST Action CM1306.

Keywords: androstane derivatives, anticancer activity, chemometrics, molecular descriptors

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Authors: Sergio Curilef, Boris Atenas

Abstract:

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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