Computational Study Research Articles

Radical scavenging mechanism of aryl carbamate: a computational case study using 3-morpholinopropyl phenyl carbamate

Radical scavenging mechanism of aryl carbamate: a computational case study using 3-morpholinopropyl phenyl carbamate

Unravelling the La dopant induced physicochemical changes and the electrical behaviour on BaFeO3 under oxidising and reducing atmospheres

Electroceramic oxides like La-doped BaFeO3 garner greater interest owing to their tunability of mixed ionic conduction. However, reports on the effect of La on the microstructural changes, the type of conduction mechanism under different atmospheres and the negative charge transfer influenced by the Fe-O hybridization in Ba1−xLaxFeO3−δ are hardly available. Doping La induces cation vacancies and Fe reduction, creating nanorod decorated surface after the high-temperature treatment. Conductivity studies expose the rate-limiting steps for hydrogen oxidation reaction (HOR) and oxygen reduction reaction (ORR) as the ohmic resistances and Ba segregation effects. Among the samples studied, Ba0.9La0.1FeO3−δ performs better at 800 °C with an activation energy of ∼0.35 eV under both oxidizing and reducing atmospheres. Surface analysis after EIS reveals Fe and O with different oxidation states that enhance the total conductivity. The amount of hydroxyl species retained (23.66% for Ba0.9La0.1FeO3−δ ) and the ratio of the adsorbed to the lattice oxygen (15.33% for Ba0.9La0.1FeO3−δ ) gives insight on HOR and ORR activities. Also, computational studies validated the negative charge transfer mechanism of the samples under thermally assisted oxidation. The results indicate Ba0.9La0.1FeO3−δ as a tuneable electrode for solid oxide cells.

Asymmetric Synthesis of SCF3-Substituted Alkylboronates by Copper-Catalyzed Hydroboration of 1-Trifluoromethylthioalkenes.

A synthetic method for preparation of optically active trifluoromethylthio (SCF3) compounds by a copper-catalyzed regio- and enantioselective hydroboration of 1-trifluoromethylthioalkenes with H-Bpin has been developed. The enantioselective hydrocupration of an in situ generated CuH species and subsequent boration reaction generate a chiral SCF3-containing alkylboronate, of which Bpin moiety can be further transformed to deliver various optically active SCF3 molecules. Computational studies suggest that the SCF3 group successfully controls the regioselectivity in the reaction.

A Monometallic Bis(cyaphido) Complex.

The first example of a bis(cyaphido) complex, trans-[Ru(dppe)2(CºP)2], is described, unequivocally demonstrating the synthetic accessibility and stability of complexes that feature more than one cyaphido ligand. Synthesis is achieved from the precedent cation [Ru(dppe)2(CΞP)]+ via sequential coordination and desilylation of the phosphaalkyne Me3SiCΞP. The heteroleptic analogue trans-[Ru(dppe)2(CΞN)(CΞP)] is also prepared from the same cation and NaCN; both cyaphido complexes are structurally characterized, enabling the first direct comparison of cyaphide with cyanide, its isoelectronic and isolobal counterpart. This demonstrates an enhanced p-acidity for -CΞP over -CΞN, while computational studies reveal also a degree of p-donor character for the cyaphido ligand.

Asymmetric Synthesis of SCF3‐Substituted Alkylboronates by Copper‐Catalyzed Hydroboration of 1‐Trifluoromethylthioalkenes

AbstractA synthetic method for preparation of optically active trifluoromethylthio (SCF3) compounds by a copper‐catalyzed regio‐ and enantioselective hydroboration of 1‐trifluoromethylthioalkenes with H‐Bpin has been developed. The enantioselective hydrocupration of an in situ generated CuH species and subsequent boration reaction generate a chiral SCF3‐containing alkylboronate, of which Bpin moiety can be further transformed to deliver various optically active SCF3 molecules. Computational studies suggest that the SCF3 group successfully controls the regioselectivity in the reaction.

The binding energy distribution of H2S: why it is not the major sulphur reservoir of the interstellar ices

Abstract Despite hydrogen sulfide (H2S) has been predicted to be the major reservoir of S-bearing species on the icy mantles of interstellar grains, no solid H2S has been detected so far. A crucial parameter that governs whether or not a species remains frozen onto the grain mantles is its binding energy (BE). We present a new computational study of the H2S BE on a large amorphous water ice surface, constituted by 200 water molecules. The resulting H2S BE distribution ranges from 57 K (0.5 kJ/mol) to 2406 K (20.0 kJ/mol), with the average μ = 984 K (8.2 kJ/mol). We discuss the reasons why the low bound of the newly computed BE distribution, which testifies to the very weak interaction of H2S with the ice surface, has never been found by previous theoretical or experimental works before. In addition, the low H2S BEs may also explain why frozen H2S is not detected in interstellar ices. Following previous molecular dynamics studies that show that the energy of reactions occurring on ice surfaces is quickly absorbed by the water molecules of the ice and conservatively assuming that 10% of the HS + H → H2S formation energy (-369.5 kJ/mol) is left to the newly formed H2S, its energy is more than twice the largest BE and 5 times the average BE and, hence, H2S will most likely leave the water surface.

Combined DFT and ionic model computational study of the effect of alkali metal cations on the structure, bonding and properties of molten cryolites, M3AlF6 (M = li, Na, K, Rb, and Cs)

ABSTRACT Ionic melts, in the form of ionic liquids and molten salts, are important in many technological aspects such as metal production and energy applications. Cryolite melts constitute an important family especially for the industrial production of Al. The present computational study aims to analyse the effect of different cations on the structure and properties of Al (III) fluorocomplexes in cryolite melts. Cation effects are discussed as the ion pair interactions due to alkali metal cations of cryolite compounds M3AlF6 with M= Li, Na, K, Rb, or Cs for various microclusters using ionic interaction model (IM) and DFT calculations. DFT results for different ion complexes are compared with the energy calculations using a pseudoclassical model for isolated clusters. QTAIM and ELF analyses were performed to understand the nature of interactions in detail. A link between open-shell interactions and decreased ionic conductivity is proposed within the series of K, Rb, and Cs. Environmental effects, such as temperature and presence of other ions, are investigated in detail by DFT analysis.

Exploring the impact of tailored π-linkers on perovskite solar cell efficiency: a computational study in triphenylamine-based hole transport material design

Exploring the impact of tailored π-linkers on perovskite solar cell efficiency: a computational study in triphenylamine-based hole transport material design

Computational study of diffraction image formation from XFEL irradiated single ribosome molecule

Single particle imaging at atomic resolution is perhaps one of the most desired goals for ultrafast X-ray science with X-ray free-electron lasers. Such a capability would create great opportunity within the biological sciences, as high-resolution structural information of biosamples that may not crystallize is essential for many research areas therein. In this paper, we report on a comprehensive computational study of diffraction image formation during single particle imaging of a macromolecule, containing over one hundred thousand non-hydrogen atoms. For this study, we use a dedicated simulation framework, SIMEX, available at the European XFEL facility. Our results demonstrate the full feasibility of computational single-particle imaging studies for biological samples of realistic size. This finding is important as it shows that the SIMEX platform can be used for simulations to inform relevant single-particle-imaging experiments and help to establish optimal parameters for these experiments. This will enable more focused and more efficient single-particle-imaging experiments at XFEL facilities, making the best use of the resource-intensive XFEL operation.

Experiment and Computational Study on Pd‐Catalyzed MIA‐Directed Ortho‐C‐H Alkynlation of Phenylalanine

The direct ortho‐alkynylation of substituted phenylalanine has been successfully achieved through methoxyiminoacyl (MIA)‐mediated Pd‐catalyzed C‐H functionalization. This innovative protocol showcases the ability to apply a diverse range of phenylalanine substrates, resulting in the efficient synthesis of alkynylation benzylamine derivatives with notable effectiveness. Computational investigations further revealed that the fluoride ion enhances the electropositivity of Pd(IV) and the interaction between C1 and C2 within the transition state of the reductive elimination, which significantly expedites the reductive elimination step in the alkynylation process.

Selective intrafascicular stimulation of myelinated and unmyelinated nerve fibers through a longitudinal electrode: A computational study

Carbon nanotube (CNT) fiber electrodes have demonstrated exceptional spatial selectivity and sustained reliability in the context of intrafascicular electrical stimulation, as evidenced through rigorous animal experimentation. A significant presence of unmyelinated C fibers, known to induce uncomfortable somatosensory experiences, exists within peripheral nerves. This presence poses a considerable challenge to the excitation of myelinated Aβ fibers, which are crucial for tactile sensation. To achieve nuanced tactile sensory feedback utilizing CNT fiber electrodes, the selective stimulation of Aβ sensory afferents emerges as a critical factor.In confronting this challenge, the present investigation sought to refine and apply a rat sciatic-nerve model leveraging the capabilities of the COMSOL-NEURON framework. This approach enables a systematic evaluation of the influence exerted by stimulation parameters and electrode geometry on the activation dynamics of both myelinated Aβ and unmyelinated C fibers. The findings advocate for the utilization of current pulses featuring a pulse width of 600 μs, alongside the deployment of CNT fibers characterized by a diminutive diameter of 10 μm, with an exclusively exposed cross-sectional area, to facilitate reduced activation current thresholds. Comparative analysis under monopolar and bipolar electrical stimulation conditions revealed proximate activation thresholds, albeit with bipolar stimulation exhibiting superior fiber selectivity relative to its monopolar counterpart. Concerning pulse waveform characteristics, the adoption of an anodic-first biphasic stimulation modality is favored, taking into account the dual criteria of activation threshold and fiber selectivity optimization. Consequently, this investigation furnishes an efficacious stimulation paradigm for the selective activation of touch-related nerve fibers, alongside provisioning a comprehensive theoretical foundation for the realization of natural tactile feedback within the domain of prosthetic hand applications.

A Novel Numerical Model Considering Unsaturated Soil Properties and Computational Study on Heat and Moisture Transfer Characteristics of Helix Ground Heat Exchanger

Abstract A novel three-dimensional numerical simulation model for the helix ground heat exchanger was proposed in this paper, which takes into account unsaturated soil properties. This model is more suitable for real working conditions. To validate its accuracy, a miniature model heat transfer experimental platform was constructed. Additionally, the study conducted simulation research using three types of soil with significantly different thermal and moisture characteristics. Moreover, the comprehensive thermal conductivity and water diffusion coefficient of these three soil types were determined by relevant literature and experimental tests. The aim was to comprehensively explore the impact of different soil types on the heat and mass transfer of the helix ground heat exchanger. The results indicate that the numerical model developed in this paper accurately captures the heat and mass transfer characteristics of the helix ground heat exchanger to a certain extent. Increasing the comprehensive thermal conductivity and water diffusion coefficient of the soil can significantly enhance the heat exchange capacity of the exchanger. For instance, under sandy loam conditions, the heat exchange capacity is approximately 20.73% higher compared to clay loam conditions. The study also identifies two distinct areas around the helix ground heat exchanger: the severe change region and the soft change region. In the severe change region, there is a notable decrease in soil water content near the exchanger, which inevitably weakens the thermal conductivity of the soil. It is advised to minimize this effect through measures like active water spraying.

Unsteady MHD flow analysis of hybrid nanofluid over a shrinking surface with porous media and heat generation: Computational study on entropy generation and Bejan number

The use of hybrid nanofluids in real-world situations is essential for enhancing the efficiency of heat transmission, especially in cooling semiconductor technology and industrial processes. The entropy generation on unsteady Al2O3-Cu/H2O hybrid nanofluid flow over a three-dimensional shrinking sheet is addressed numerically in this study, taking into account the effects of magnetohydrodynamic (MHD), nonlinear thermal radiation, porous media, heat generation, viscous dissipation, joule heating, and convective conditions. Using well-known non-similarity transformations, the model is carefully converted from partial differential equations (PDEs) to ordinary differential equations (ODEs). Afterwards, the behaviors of critical physical characteristics are uncovered across different parameter configurations by a numerical solution using the finite difference technique in bvp4c MATLAB. The velocity profiles of hybrid nanofluid grow proportionately with increases in the values of ϕ2,M,A,K and λ parameters. As Rd,θw,Ec,Bi,H and ϕ2 increase, the temperature of the hybrid nanofluid rises, but as M and A increase, the temperature falls. The local skin friction in both the x and y- directions is increased by enhancing the unsteadiness A, nanoparticle volume fraction ϕ2, magnetic M, porous media K, and the ratio of strain rate λ parameter on the shrinking surface. The local Nusselt number is improved by cumulative the unsteadiness A, nanoparticle volume fraction ϕ2, magnetic M, and Biot number Bi parameter in the direction of a shrinking surface, while the Nusselt number decreases when Eckert number Ec, thermal radiation Rd, heat production H, and temperature ratio θw are improved. An upsurge in the magnetic parameter leads to the development of entropy generation. Increasing levels of the magnetic parameters led to a reduction in the Bejan number. At a nanoparticle volume fraction of 1 % and a nonlinearity radiation scenario, where the unsteadiness values are 0.5, the Nusselt number for hybrid nanofluid shows an estimated improvement of 10.55 % compared to regular nanofluid.

A bioinformatic analysis of T-cell epitope diversity in SARS-CoV-2 variants: association with COVID-19 clinical severity in the United States population

Long-term immunity against severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) requires the identification of T-cell epitopes affecting host immunogenicity. In this computational study, we explored the CD8+ epitope diversity estimated in 27 of the most common HLA-A and HLA-B alleles, representing most of the United States population. Analysis of 16 SARS-CoV-2 variants [B.1, Alpha (B.1.1.7), five Delta (AY.100, AY.25, AY.3, AY.3.1, AY.44), and nine Omicron (BA.1, BA.1.1, BA.2, BA.4, BA.5, BQ.1, BQ.1.1, XBB.1, XBB.1.5)] in analyzed MHC class I alleles revealed that SARS-CoV-2 CD8+ epitope conservation was estimated at 87.6%–96.5% in spike (S), 92.5%–99.6% in membrane (M), and 94.6%–99% in nucleocapsid (N). As the virus mutated, an increasing proportion of S epitopes experienced reduced predicted binding affinity: 70% of Omicron BQ.1-XBB.1.5 S epitopes experienced decreased predicted binding, as compared with ~3% and ~15% in the earlier strains Delta AY.100–AY.44 and Omicron BA.1–BA.5, respectively. Additionally, we identified several novel candidate HLA alleles that may be more susceptible to severe disease, notably HLA-A*32:01, HLA-A*26:01, and HLA-B*53:01, and relatively protected from disease, such as HLA-A*31:01, HLA-B*40:01, HLA-B*44:03, and HLA-B*57:01. Our findings support the hypothesis that viral genetic variation affecting CD8 T-cell epitope immunogenicity contributes to determining the clinical severity of acute COVID-19. Achieving long-term COVID-19 immunity will require an understanding of the relationship between T cells, SARS-CoV-2 variants, and host MHC class I genetics. This project is one of the first to explore the SARS-CoV-2 CD8+ epitope diversity that putatively impacts much of the United States population.

Computational Insights into the Interplay of Mechanical Forces in Angiogenesis

This study employs a meshless computational model to investigate the impacts of compression and traction on angiogenesis, exploring their effects on vascular endothelial growth factor (VEGF) diffusion and subsequent capillary network formation. Three distinct initial domain geometries were defined to simulate variations in endothelial cell sprouting and VEGF release. Compression and traction were applied, and the ensuing effects on VEGF diffusion coefficients were analysed. Compression promoted angiogenesis, increasing capillary network density. The reduction in the VEGF diffusion coefficient under compression altered VEGF concentration, impacting endothelial cell migration patterns. The findings were consistent across diverse simulation scenarios, demonstrating the robust influence of compression on angiogenesis. This computational study enhances our understanding of the intricate interplay between mechanical forces and angiogenesis. Compression emerges as an effective mediator of angiogenesis, influencing VEGF diffusion and vascular pattern. These insights may contribute to innovative therapeutic strategies for angiogenesis-related disorders, fostering tissue regeneration and addressing diseases where angiogenesis is crucial.

Reinforcement Learning for Closed-loop Regulation of Cardiovascular System with Vagus Nerve Stimulation: A Computational Study.

(Objective). Vagus nerve stimulation (VNS) is being investigated as a potential therapy for cardiovascular diseases including heart failure, cardiac arrhythmia, and hypertension. The lack of a systematic approach for controlling and tuning the VNS parameters poses a significant challenge. Closed-loop VNS strategies combined with artificial intelligence (AI) approaches offer a framework for systematically learning and adapting the optimal stimulation parameters. In this study, we presented an interactive AI framework using reinforcement learning (RL) for automated data-driven design of closed-loop VNS control systems in a computational study. (Approach). Multiple simulation environments with a standard application programming interface were developed to facilitate the design and evaluation of the automated data-driven closed-loop VNS control systems. These environments simulate the hemodynamic response to multi-location VNS using biophysics-based computational models of healthy and hypertensive rat cardiovascular systems in resting and exercise states. We designed and implemented the RL-based closed-loop VNS control frameworks in the context of controlling the heart rate (HR) and the mean arterial pressure (MAP) for a set point tracking task. Our experimental design included two approaches; a general policy using deep RL algorithms and a sample-efficient adaptive policy using probabilistic inference for learning and control (PILCO). (Main results). Our simulation results demonstrated the capabilities of the closed-loop RL-based approaches to learn optimal VNS control policies and to adapt to variations in the target set points and the underlying dynamics of the cardiovascular system. Our findings highlighted the trade-off between sample-efficiency and generalizability, providing insights for proper algorithm selection. Finally, we demonstrated that transfer learning improves the sample efficiency of Deep RL algorithms allowing the development of more efficient and personalized closed-loop VNS systems. (Significance). We demonstrated the capability of RL-based closed-loop VNS systems. Our approach provided a systematic adaptable framework for learning control strategies without requiring prior knowledge about the underlying dynamics.

Computational Study on Influence Factors and Vortical Structures in Static Drift Tests

This paper conducted a computational study on the KCS benchmark model at static drift conditions. At the first instance, the roles played by the grid size, turbulence model, and time step are qualitatively and quantitatively analyzed with the orthogonal experimental method (OEM). After the verification of simulated results compared with experimental data in a Static Oblique Towing Test (OTT), hydrodynamic performance is obtained with the employment of the SST κ-ω turbulence model. The grid size is set as 0.07 m while the time step as 0.01 s. The characteristics of the wake field are illustrated in different forms, such as contours of the free surface, distribution of pressure and hydrodynamic forces, variation of turbulent kinetic energy (TKE), and so on. For a deep insight into the physical mechanisms of the asymmetrical flow field, the Detached Eddy Simulation (DES) method is also utilized to capture vortical structures occurring around the hull, in comparison with results obtained through the Reynolds Averaged Navier Stokes (RANS) model. With the aim of a hydrodynamic derivative estimation or detailed flow characteristics analysis, corresponding selections of the computational method are disparate.

Experimental and computational study on antioxidant activity and molecular properties of novel ferrocenyl Schiff bases

In this study, antioxidant and molecular properties of some important novel ferrocenyl Schiff bases were studied. The 4-Ferrocenyl aniline synthetic pathway was chosen as the general procedure for the synthesis of Schiff bases. Two experimental techniques, UV–Visible spectroscopy and cyclic voltammetry, and one theoretical DFT method was employed to find out their antioxidant activity and molecular properties of some novel ferrocenyl Schiff bases and compared it with standard antioxidant (Ascorbic acid). Maximum wavelength, extinction coefficient, IC30 and IC50 were estimated by using UV–Visible spectroscopy. For theoretical investigations, computational Amsterdam density function software was employed to study the molecular properties and reaction parameters based on density functional theory calculations. The cyclic voltammetry (CV) measurements in electrochemical experiments were done at room temperature while diffusion coefficient was estimated by using CV graphs. UV–Vis spectra of these compounds exhibited similar peaks with greater intensity ranges from 312 nm to 314 nm and smaller intensity ranges 471 nm to 473 nm which occurred because of the only substituent R (naphthoxy, phenoxy and phenoxy) in these compounds. Registered Amsterdam density function was utilized to determine the optimized structure, FTIR spectra, UV–Visible spectra, HOMO, LUMO, dipole moment, ionization potential, electron affinity, band gap, hardness, chemical potential and electrophility index. The overall electrode processes were found to be diffusion controlled and the novel compounds showed appreciable antioxidant activities.

Attenuation of Inlet Distortion Effects on Fans Using Asymmetric Inlet Guide Vanes

Abstract This research proposes and preliminarily analyzes a novel concept to passively reduce the negative impact of deep inlet distortion on the fan of an aero-engine. It consists of placing a row of non-axisymmetric inlet guide vanes (IGVs) just upstream of the fan rotor to induce a spatially varying swirl distribution. The swirl distribution is tailored so as to reduce flow incidence in the distorted flow region and increase it in the undistorted flow region to decrease the fluctuation in aerodynamic force on the fan blades under large inlet distortion that can lead to blade failure, as well as attenuate the negative effect of flow non-uniformity on fan/engine aerodynamic performance. A computational study is carried out on a high-speed (transonic) fan rotor (NASA Rotor 67) from a published distortion study using full-annulus unsteady 3D computational fluid dynamics (CFD) simulations. The asymmetric IGV is designed through a process of manual iterations and CFD simulations to take into account the change in flow redistribution with IGV geometry. The asymmetric IGV design, though not optimized, reduces the aerodynamic force variation amplitude by around two-thirds. Moreover, it allows the fan to recover over half of the loss in total pressure rise due to inlet distortion. The asymmetric IGV is also able to reduce the total pressure distortion at the fan rotor exit. Spanwise analysis indicates that the effectiveness of the asymmetric IGV can be improved on all three metrics if better 3D IGV shaping is performed.

Self‐Assembled Cyclotriguaiacyclene‐Integrated Supramolecular Systems for Liquid Crystal and Self‐Assembly Behavior

AbstractAn advanced tri‐substituted supramolecular material was synthesized via conversion of cyclotriveratrylene to cyclotriguaiacyclene with further esterification reaction with fluorescein unit embedded with side‐arms. All four luminescent materials exhibited columnar hexagonal type mesophase on both heating and cooling conditions. The materials with hexadecyloxy and octadecyloxy tail group exhibit liquid crystalline behavior at room temperature indicating the presence of a mesophase even under ambient conditions. By combining polarizing optical microscopy, differential scanning calorimetry, and high‐temperature X‐Ray diffraction techniques to understanding the optical, thermal, and molecular packing behavior of the compounds in the liquid crystalline state. The cyclotriguaiacyclene core with high fluorescent nature displayed columnar hexagonal type self‐assembly at room temperature. All four supramolecular mesogens showed higher thermal stability of mesophase. The computational study provides the importance of the electronic nature of the compounds.