Computer Simulation Study Research Articles

Modeling of carbon and tungsten transient dust influx in tokamak edge plasma

The paper presents computer simulation studies of burst injection of carbon and tungsten dust particles in DIII-D-like edge plasmas. The injection causes a large transient influx of the low- and high-Z impurities associated with the dust ablation in the plasmas. The dust transport and the effects of the ablated impurities on the edge plasma dynamics in a modern mid-size tokamak geometry are investigated for low- and high-power plasma discharge conditions. The core plasma contamination with dust-ablated impurities and the factors affecting it are evaluated.

Thermal kinetics and molecular modeling studies of ZnII-poly (vinyl alcohol-nicotinic acid) complexes

Complexes of poly (vinyl alcohol-nicotinic acid) with ZnII (ZnII/PVA-NA) were synthesized by incipient wetness impregnation. The successful synthesis of PVA-NA and ZnII/PVA-NA was examined using FT-IR, TGA, XRD, HR-SEM, and 1H NMR spectroscopy. The 1H NMR resonance of HOCO-nicotinic moiety close to 11 ppm disappeared from the spectrum of PVA-NA, revealing conversion to ester is complete. The 1711 and 1326 cm-1 bands, assigned to νCO and νCN, respectively, shifted downward as the ring nitrogen atom of NA and carboxyl group of PVA chelate to the ZnII center in ZnII/PVA-NA. The changes related to activation enthalpy (∆H*), entropy (∆S*), and Gibbs free energy (∆G*) during the thermal degradation process of PVA-NA and ZnII/ PVA-NA copolymers were assessed. The ∆H* values given at the 4th step and a heating rate of 30 K min-1 for the ZnII/PVA-NA degradation were: Coats-Redfern: 3503.695, Horowitz-Metzger: 1545.92 and Kissinger: 6.455 kJ mol-1. TGA profile of ZnII/ PVA-NA run at 30 K min−1 indicated an increased activation energy (E*), as the degraded ligand species strongly bound to ZnII. The computational simulation study was carried out using the Builder module of the wave function, and the molecular structure for each compound was fully optimized. The HOMO and LUMO simulation, band-gap, and electrostatic potential (MEP) maps were also examined. Besides, the stability of docked ligand was assessed through a molecular dynamics simulation study, showing the high stability of the tested structures in the active sites. The antimicrobial activity for the tested ZnII/PVA-NA complexes against six pathogens indicated promising antibacterial and antifungal activities.

Structure and dynamics of a glucose-based cryoprotectant mixture: a computer simulation study

Structure and dynamics of a glucose-based cryoprotectant mixture: a computer simulation study

Nonstationary but quasisteady states in self-organized criticality.

The notion of self-organized criticality (SOC) was conceived to interpret the spontaneous emergence of long-range correlations in nature. Since then many different models have been introduced to study SOC. All of them have a few common features: externally driven dynamical systems self-organize themselves to nonequilibrium stationary states exhibiting fluctuations of all length scales as the signatures of criticality. In contrast, we have studied here in the framework of the sandpile model a system that has mass inflow but no outflow. There is no boundary, and particles cannot escape from the system by any means. Therefore, there is no current balance, and consequently it is not expected that the system would arrive at a stationary state. In spite of that, it is observed that the bulk of the system self-organizes to a quasisteady state where the grain density is maintained at a nearly constant value. Power law distributed fluctuations of all lengths and time scales have been observed, which are the signatures of criticality. Our detailed computer simulation study gives the set of critical exponents whose values are very close to their counterparts in the original sandpile model. This study indicates that (i) a physical boundary and (ii) the stationary state, though sufficient, may not be the necessary criteria for achieving SOC.

Concept development, design and validation of a novel continuous casting equipment

PurposeThe purpose of this paper is to develop a concept and design to cast Al alloys/metal matrix composites (MMCs) by continuous casting process. The various steps involved in the evolution of the design have been reported and discussed in this study.Design/methodology/approachOn the basis of developed design concept, initial prototype design has been prepared in this study. The casting process's melt flow pattern was studied via computer simulation, and the resulting changes were implemented in the original design. The single-phase fluid flow pattern through bottom feeding technique is studied. The equipment was fabricated based on computer simulation and water modelling studies. Finally, validation was performed for the preparation of Al alloys/ MMCs after parameter optimisation. The results were observed in the optical metallography to confirm the alloying and Al MMC preparation.FindingsThe developed continuous casting process with bottom feeding technique for the addition of constituent particles shows more efficiency in comparison to the existing batch processes. The final manufactured setup demonstrates effective Al alloy/MMC production as the basis for final fabrication has been accomplished by both computer simulation and water model test. In addition, the microstructure exhibits homogeneous distribution, validating the reliability of the setup.Originality/valueIntegrating continuous casting with continuous reinforcement or master alloy addition is novel in this area. The constraints that batch production had that have been rectified will also lower the contemporary cost of production.

SELF-OSCILLATING PARAMETRIC HUMIDITY SENSOR WITH FREQUENCY OUTPUT SIGNAL

A self-oscillating parametric humidity sensor has been developed that implements the principle of "humidity-frequency" conversion into hybrid integrated circuit based on a microelectronic transistor structure with a negative differential resistance, in which the humidity-sensitive element is a resistor of the HR202 type. For the purposes of determining parameters self-oscillating parametric humidity sensor with frequency output a mathematical model has been developed that takes into account the effect of humidity on a sensitive resistive element, which is an integral element of the device. Based on the mathematical model, analytical expressions for the transformation function and the sensitivity equation are obtained. It is shown that the main contribution to the conversion function is made by relative humidity. The computer simulation and experimental studies of a self-oscillating parametric humidity sensor with a frequency output signal contributed to obtaining the main parameters and characteristics, such as the dependence of the generation frequency on changes in relative humidity in the range from 30% to 99%, the change in sensitivity on relative humidity, the dependence of the active and reactive components of the impedance in the frequency range from 50 kHz to 2 GHz; standing wave ratio, change in logarithmic magnitude and spectra of the output signal of a parametric humidity sensor with a frequency output signal in the LTE-800 Downlink frequency range. The obtained electrical characteristics confirm the operability of the developed device. The sensitivity of the developed self-oscillating parametric humidity sensor in the range of relative humidity change from 30% to 99% has a value from 332.8 kHz/% to 130.2 kHz/%.

Crosslinking and Gelation of Polymer Brushes and Free Polymer Chains in a Confined Space during Controlled Radical Polymerization─A Computer Simulation Study

The confinement effect on crosslinking and gelation during controlled/living copolymerization of a monovinyl and a divinyl monomer was studied by Monte Carlo computer simulation using the dynamic lattice liquid method. The simulated reactions took place in plane-parallel slits of various widths for various grafting densities (GDs) and various initial initiator/crosslinker ratios ([X]0/[Ini]0). Monomers and crosslinkers were initially randomly distributed in the slit, but initiators were either anchored to one solid plane (polymer brushes) or randomly distributed (free chains). For brushes, the gel point (GP) depended on GD and [X]0/[Ini]0. The higher these parameters, the lower was the gel point. The gel point was also affected by the slit width. For free, nongrafted chains, the dependence of GP on slit width was negligible. For brushes, a nonuniform density of crosslinks was found, the highest density was close to the wall. This asymmetry was high at the gel point and decreased at higher conversions.

Structure of adsorbed linear and cyclic block copolymers: A computer simulation study

A study of the adsorption of linear and cyclic mutiblock copolymers on a planar surface was performed using extensive computer simulations. A coarse-grained off-lattice model was designed and polymer chains were modeled as sequences of beads forming solvophilic and solvophobic blocks. A Monte Carlo simulation algorithm employing the Replica Exchange technique was used to determine properties of the model chains. The structure of collapsed and adsorbed chains was determined. The increase of the surface attraction and the number of blocks shifted the transition towards lower temperatures. It was also shown that the influence of the macromolecular architecture and the number of blocks in chains on polymer size is weak.

Bearings can dislocate with smaller femoral components and thicker bearings in Oxford™ medial unicompartmental knee arthroplasty

BackgroundA mobile bearing can dislocate when joint laxity is larger than jumping height, the height difference between the bottom and the peak of the bearing (the highest point of the upper bearing surface on each side). Significant laxity due to improper gap balancing should therefore be avoided. However, once the bearing rotates vertically on the tibial component, the bearing can dislocate with smaller laxity than the jumping height. We mathematically calculated the required laxity for dislocation (RLD) and the required rotation of the bearing for dislocation (RRD). The current study addressed the question: 1) could the femoral component size and the bearing thickness affect the RLD and RRD? HypothesisThe femoral component size and the bearing thickness could affect the MLD and MRD. MethodsThe RLD and RRD were calculated using the bearing dimensions provided by the manufacturer with femoral component size, bearing thickness, and directions (anterior, posterior, and medial/lateral) as the variables on a two-dimensional basis. ResultsThe RLD was 3.4 to 5.5mm in the anterior, 2.3 to 3.8mm in the posterior, and 1.4 to 2.4mm in the medial or lateral directions. The RLD decreased with a smaller femoral size or a thicker bearing. Similarly, the RRD decreased with a smaller femoral size or a thicker bearing thickness in all directions. ConclusionsIncreased bearing thickness and decreased femoral component size deceased the RLD and RRD, which would relate to an increased risk of dislocation. Selecting the femoral component as large as possible and the bearing as thin as possible would therefore be helpful in the prevention of dislocation. Level of evidenceIII; comparative computer simulation study.

Crosslinking Rapidly Cured Epoxy Resin Thermosets: Experimental and Computational Modeling and Simulation Study.

The power of computational modeling and simulation for establishing clear links between materials' intrinsic properties and their atomic structure has more and more increased the demand for reliable and reproducible protocols. Despite this increased demand, no one approach can provide reliable and reproducible outcomes to predict the properties of novel materials, particularly rapidly cured epoxy-resins with additives. This study introduces the first computational modeling and simulation protocol for crosslinking rapidly cured epoxy resin thermosets based on solvate ionic liquid (SIL). The protocol combines several modeling approaches, including quantum mechanics (QMs) and molecular dynamics (MDs). Furthermore, it insightfully provides a wide range of thermo-mechanical, chemical, and mechano-chemical properties, which agree with experimental data.

Aggregation and crystallization of small alkanes.

We present a computer simulation study of the aggregation and ordering of short alkane chains using a united atom model description. Our simulation approach allows us to determine the density of states of our systems and, from those, their thermodynamics for all temperatures. All systems show a first order aggregation transition followed by a low-temperature ordering transition. For a few chain aggregates of intermediate lengths (up to N = 40), we show that these ordering transitions resemble the quaternary structure formation in peptides. In an earlier publication, we have already shown that single alkane chains fold into low-temperature structures, best described as secondary and tertiary structure formation, thus completing this analogy here. The aggregation transition in the thermodynamic limit can be extrapolated in pressure to the ambient pressure for which it agrees well with experimentally known boiling points of short alkanes. Similarly, the chain length dependence of the crystallization transition agrees with known experimental results for alkanes. For small aggregates, for which volume and surface effects are not yet well separated, our method allows us to identify the crystallization in the core of the aggregate and at its surface, individually.

High performance aptasensing platform development through in silico aptamer engineering for aflatoxin B1 monitoring

Due to the technical challenges of small binding aptamer development, reliable computational simulation studies can be considered as effective tools to design novel and high functional mycotoxin aptameric probes. Here, two novel aflatoxin B1(AFB1) binding aptamers were successfully exploited as recognition elements in the lateral flow aptasensors and the reflective phantom interface (RPI) platform. Using the parent aptamer previously designed through genetic algorithm based in silico maturation (ISM) strategy, F20, a new variant, F20-T, was obtained here via coupling truncating strategy and computational simulation approaches. Two aptamer-gold nanoparticle strip biosensors were developed based on the designed probes for the simple and rapid detection of AFB1 in competitive format. The F20-based strip was more sensitive than that exploiting the truncated aptamer, with limits of detection (LOD) of 0.1 and 0.5 ng/mL, respectively. Based on the in silico and experimental selectivity evaluations of both test strips towards other mycotoxins, including aflatoxin B 2 , M 1 , G 1 , G 2 , Ochratoxin A and Zearalenone, F20-T based test strip revealed higher selectivity for AFB1. Both developed aptasensors successfully detected AFB1 in maize flour within 30 min using a simple strip reader. Exploiting of F20 and F20-T aptamers in an exclusive technology called RPI platform led to successful AFB1 detection, as well. Both designed aptameric probes can be regarded as potential recognition elements to develop screening tools for rapid, low cost and on-site AFB1 detection. Our findings highlighted the reliable and robust application of computational simulation studies for novel small binding aptamer development and consequently open up a much-needed avenue to design various aptasensing platforms in green and cost effective ways. • A new truncated Aflatoxin B1 binding aptamer was designed via in silico studies. • The truncated and the parent aptamer were successfully applied to build aptasensors. • The redesigned aptasensing platforms provided high sensitive AFB1 detection. • In silico engineered aptamers can be costly exploited for new aptasensor development.

Mapping allosteric pathway in NIa‐Pro using computational approach

BackgroundComputer simulation studies complement in vitro experiments and provide avenue to understand allosteric regulation in the absence of other molecular viewing techniques. Molecular dynamics captures internal motion within the protein and enables tracing the communication path between a catalytic site and a distal allosteric site. In this article, we have identified the communication pathway between the viral protein genome linked (VPg) binding region and catalytic active site in nuclear inclusion protein‐a protease (NIa‐Pro).MethodsMolecular dynamics followed by in silico analyses have been used to map the allosteric pathway.ResultsThis study delineates the residue interaction network involved in allosteric regulation of NIa‐Pro activity by VPg. Simulation studies indicate that point mutations in the VPg interaction interface of NIa‐Pro lead to disruption in these networks and change the orientation of catalytic residues. His142Ala and His167Ala mutations do not show a substantial change in the overall protease structure, but rather in the residue interaction network and catalytic site geometry.ConclusionOur mutagenic study delineates the allosteric pathway and facilitates the understanding of the modulation of NIa‐Pro activity on a molecular level in the absence of the structure of its complex with the known regulator VPg. Additionally, our in silico analysis explains the molecular concepts and highlights the dynamics behind the previously reported wet lab study findings.

GB1 Dimerization in Crowders: A Multiple Resolution Approach.

In-cell protein-protein association, which is crucial in enzyme catalysis and polymerization, occurs in an environment that is highly heterogeneous and crowded. The crowder molecules exclude the reactant molecules from occupying certain regions of the cell, resulting in changes in the reaction thermodynamics and kinetics. Recent studies, both experiment and simulations, revealed that the nature of the interaction between crowder and protein species, in particular the soft interactions, plays an important role in crowder induced effects on protein association. To this end, from a simulation perspective, it is important to decipher the level of structural resolution in a protein-crowder model that can faithfully capture the influence of crowding on protein association. Here, we investigate the dimerization of model system GB1 in the presence of lysozyme crowders at two structural resolutions. The lower resolution model assumes both protein and crowder species as spherical beads, similar to the analytical scaled particle theory model, whereas the higher resolution model retains residue specific structural details for protein and crowder species. From the higher resolution model, it is found that GB1 dimer formation is destabilized in the presence of lysozyme crowders, and the destabilization is more for the side-by-side dimer compared to the domain-swapped dimer, in qualitative agreement with experimental findings. However, the low resolution CG model predicts stabilization of the dimers in the presence of the lysozyme crowder, similar to the SPT model. Our results indicate a nontrivial role of the choice of model resolution in computer simulation studies investigating crowder induced effects.

Investigating the biophysical interaction of serum albumins-gold nanorods using hybrid spectroscopic and computational approaches with the intent of enhancing cytotoxicity efficiency of targeted drug delivery

In this contribution, biophysical aspects of binding interaction, conformational changes, and molecular simulation studies of human and bovine serum albumins (HSA and BSA) exposed to gold nanorods (AuNRs) are thoroughly investigated and their bio-nanoconjugates were then used in in-vitro cytotoxic studies. The structural variations of AuNRs in the presence of serum proteins were confirmed by absorbance and high-resolution transmission electron microscopic (HR-TEM) pictures. According to the results of the steady-state emission quenching, AuNRs affect the intrinsic emission of HSA and BSA by a static mechanism. Synchronous emission spectrum results showed that the microenvironment near the tryptophan and tyrosine amino acid residues of serum proteins is altered, and the impact is stronger toward tryptophan than tyrosine. Furthermore, it was demonstrated by infrared, absorbance, and three-dimensional (3D) luminescence spectroscopic methods that the binding of AuNRs can arouse concerns and cause changes in the structural and/or microenvironmental characteristics of HSA and BSA. An outcome of the computational molecular simulation study supports the stability of the bio-nanoconjugate, and molecular docking interaction investigations suggest that the two-dimensional AuNRs surface associated with the cysteine residue of HSA and BSA contains sulphur atoms. Furthermore, using an in vitro model using the A-549 and MCF-7 cell lines, we calculated the toxicity and the effectiveness of cellular absorption of the AuNRs and their bio-nanoconjugates as a function of supplied dosage. These cytotoxicity findings demonstrate that protein adsorption affects AuNRs' physicochemical characteristics as well as enhances their subsequent biological function.

The effect of patient positioning on measurements of bone mineral density of the proximal femur: a simulation study using computed tomographic images.

Several studies have analyzed the effect of hip rotation on the measurement of bone mineral density (BMD) of the proximal femur by dual-energy x-ray absorptiometry (DXA). However, as the effects of hip flexion and abduction on BMD measurements remain uncertain, a computational simulation study using CT images was performed in this study. Hip CT images of 120 patients (33 men and 87 women; mean age, 82.1 ± 9.4 years) were used for analysis. Digitally reconstructed radiographs of the proximal femur region were generated from CT images to calculate the BMD of the proximal femur region. BMD at the neutral position was quantified, and the percent changes in BMD when hip internal rotation was altered from -30° to 15°, when hip flexion was altered from 0° to 30°, and when hip abduction was altered from -15° to 30° were quantified. Analyses were automatically performed with a 1° increment in each direction using computer programming. The alteration of hip angles in each direction affected BMD measurements, with the largest changes found for hip flexion (maximum change of 17.7% at 30° flexion) and the smallest changes found for hip rotation (maximum change of 2.2% at 15° internal rotation). The BMD measurements increased by 0.34% for each 1° of hip abduction, and the maximum change was 12.3% at 30° abduction. This simulation study quantified the amount of BMD change induced by altering the hip position. Based on these results, we recommend that patients be positioned carefully when acquiring DXA images.

Electronic, intermolecular, quantum computational investigations, molecular docking and simulation studies of the potent antiviral drug EIDD-2801

In this work, an analysis has been done to describe the molecular structure, spectroscopic, reduced density gradient, topological properties, atomic charges, Lipinski rule, Natural bond orbital analysis, docking and molecular dynamics simulation of the potent antiviral drug EIDD-2801 in the effective treatment against COVID-19. Intramolecular charge distribution is well understood by three schemes such as AIM, Mulliken and NBO analysis and non-covalent interactions have been understood through reduced density gradient. Topological properties, such as charge density and Laplacian of charge density along with the electron localization function, make it easy to obtain comprehensive information about bond strengths and critical points. The details obtained from the calculation of global reactivity descriptors and Lipinski rule are useful for understanding the nature of molecular reactivity and site selectivity. Electrostatic potentials help to identify potential electrophilic and nucleophilic sites for interaction between EIDD-2801 and target proteins. The molecular docking combined with molecular dynamic simulation studies enables us to get better picture about the ligand-protein interaction.

Computer simulation study of ion-water and water-water hydrogen bonds in methanesulfonic acid solutions at room temperature

Classical molecular dynamics simulations of aqueous methanesulfonic acid solutions have been conducted at room temperature in the entire composition range. The dissociation of the acid has been considered according to the available experimental data. Then, the systems are constituted by the following molecular species: water and methanesulfonic acid molecules, hydronium cations, and mesylate anions. The simulations have been carried out employing a reliable force field, which provides density values that show an excellent agreement with the available experimental data. The shear viscosity, the diffusion coefficients of the molecular species, and the radial distribution functions, which involve water molecules, have also been computed. We have observed that water molecules diffuse faster than the other species at all concentrations. Moreover, the shear viscosity and the diffusion coefficients exhibit a noticeable unimodal concentration dependence with extrema located at 90 wt% (0.628 mol fraction). A detailed hydrogen bond analysis, concerning water molecules, has also been made. At low dilutions, water exhibits its well-known hydrogen bond tetrahedral structure, which vanishes as the acid concentration increases. The most labile water molecules are those bonded to the anions. At large concentrations, the lability of the water molecules, bonded to other water molecules, increases, and that of the water molecules, bonded to the cations, decreases. The interrupted lifetimes also show a unimodal dependence with maxima located at 90 wt%. This behavior could be related to the appearance of the methanesulfonic acid hydrogen bond network, which emerges at large weight percentage values because the acid almost completely dissociates up to concentrations of 70 wt% (0.304 mole fraction).

A computer simulation study of extended DLVO interactions between calcite nanoparticles and real rough surfaces

The interaction energy between calcite nanoparticles and real rough surfaces in calcium carbonate supersaturated solutions was numerically calculated according to the extended Derjaguin-Landau-Verwey-Overbeek (XDLVO) theory and the surface element integration method. Three different surfaces, namely polished stainless steel, plasma-treated stainless steel, and fluorine-doped diamond-like carbon film, were prepared by mechanical polishing, plasma sputtering and film deposition, and characterized by atomic force microscopy. These images were then used as inputs in numerical simulations, where particle radius, solution concentration, surface electric potential, and surface tension components were varied. A total of 4052 simulations were performed. It was obtained that smaller particles interact more strongly with the surface and therefore are more attracted or repelled by the surface than larger ones. The effect of surface roughness on the particle interaction, however, depends on the physicochemical properties of the system and, therefore, a given surface may change its fouling behavior when the set of experimental conditions is changed. The effect of particle size on particle-surface interaction was found to be dependent on the relative sizes of the particle and the typical roughness features of the surface. A new local roughness metric – the minimum distance between the south pole of the particle and the rough substrate – can be used to predict the contact energy. These results may be important to engineer better antifouling surfaces for a wide range of applications, such as oil and gas exploitation and water treatment and desalination.

Physiochemical insight into the solution behavior of cationic gemini surfactant in water and ethanol–water systems

AbstractSurfactants in water and both alcohol‐water mixed solutions are used extensively in a host of industrial applications. This work presents the solution behavior and micellar transition of a cationic gemini surfactant (GS): N,N′‐dihexadecyl‐N,N,N′,N′‐tetramethyl‐N,N′‐ethanediyl‐diammonium dibromide (16‐2‐16) in water and mixed water‐ethanol media. Phase behavior for 16‐2‐16 in the ethanol–water system was investigated at ambient temperature. The rheological data obtained for these systems at varying alcohol concentrations showed that the system viscosity (η) decreased with as the ethanol concentration increased. Small‐angle neutron scattering (SANS) was used to probe the structural details of the cationic micelles as a function of ethanol concentration and temperature. The scattering data inferred a structural transition from unilamellar vesicles (ULV) through rod‐like micelles to ellipsoidal micelles occurs that is dependent on the solvent composition and temperature indicating the behavior of ethanol molecules as a cosolvent in the process of micelle breaking. The plausible physicochemical interactions in the 16‐2‐16‐ethanol mixed system were further investigated using a computational simulation study employing density functional theory (DFT)/B3LYP (Gauss View 5.0.9) utilizing a 3‐21G basis set.