Computational Study Research Articles

The role of claudins in renal transepithelial transport and kidney disease.

25 years after the discovery of claudins as the central constituents of tight junctions, the "hunter-gatherer phase" of claudin research is coming to an end. Deficiency in individual claudins as a cause of rare hereditary diseases is well documented. However, knowledge about the involvement of renal claudins in common kidney diseases and strategies to utilize claudins or their regulators for intervention are still scarce. The present review summarizes novel approaches to address these questions. Publicly accessible omics data provide new insights not only into general claudin expression patterns along the nephron, but also into sex-specific differences in claudin expression and into claudin dysregulation in renal injury. Computational association studies identify claudin variants as risk factors for kidney disease such as nephrolithiasis or loss of filtration capacity. The establishment of innovative cell culture and organoid models contributes to a better understanding of junctional and extra-junctional functions of individual claudins. The current studies lay the foundation for the identification of upstream regulators of renal claudin expression and thus for the development of new concepts for the treatment of kidney disease.

Mechanism of Z-Selective Allylic Functionalization via Thianthrenium Salts.

A detailed mechanistic study of the Z-selective allylic functionalization via thianthrenium salts is presented. Kinetic analyses, deuterium labeling experiments, and computational methods are used to rationalize the observed reactivity and selectivity. We find that the reaction proceeds via a rate-determining and stereodetermining allylic deprotonation of an alkenylthianthrenium species. The Z-configuration of the resultant allylic ylide is translated into the Z-allylic amine product through a sequence of subsequent fast and irreversible steps: protonation to form a Z-allylic thianthrenium electrophile and then regioselective substitution by the nucleophile. In the stereodetermining deprotonation step, computational studies identified a series of stabilizing nonbonding interactions in the Z-alkene-forming transition state that contribute to the stereoselectivity.

The Race of Artificial Intelligence and Challenges

In today’s era Artificial Intelligence (AI) has become an increasingly prominent field of research and development over the past few decades. In recent years, the development of AI has been accelerating, with more and more resources being devoted to the creation of increasingly sophisticated and capable AI systems. With more and more countries being in an AI arm race, companies competing and racing to be the one with the next most disruptive and transformative AI system. Artificial Intelligence (AI) is the science and engineering of making intelligent machines, especially intelligent computer programs. It is related to the similar task of using computers to understand human intelligence, but AI does not have to limited itself to procedures that are biologically observable. While no exact definition of Artificial Intelligence (AI) exists, AI is broadly characterized as the study of computations that allow for reason, perception and action. Today, the amount of data that is generated, by both humans and machines, far outpaces humans’ ability to absorb, interpret, and make complex decisions based on that data. Artificial intelligence forms the basis for all computer learning and is the future of all complex decision making. This paper focuses features of artificial Intelligence, introduction, history, applications, growth and achievements. This paper also analyzes the current state of artificial intelligence progresses, and how the current AI race with recent trends.

Pd-catalyzed asymmetric Larock reaction for the atroposelective synthesis of N─N chiral indoles.

Atropisomeric indoles defined by a N─N axis are an important class of heterocycles in synthetic and medicinal chemistry and material sciences. However, they remain heavily underexplored due to limited synthetic methods and challenging stereocontrol over the short N─N bonds. Here, we report highly atroposelective access to N─N axially chiral indoles via the asymmetric Larock reaction. This protocol leveraged the powerful role of chiral phosphoramidite ligand to attenuate the common ligand dissociation in the original Larock reaction, forming N─N chiral indoles with excellent functional group tolerance and high enantioselectivity via palladium-catalyzed intermolecular annulation between readily available o-iodoaniline and alkynes. The multifunctionality in the prepared chiral indoles allowed diverse post-coupling synthetic transformations, affording a broad array of functionalized chiral indoles. Experimental and computational studies have been conducted to explore the reaction mechanism, elucidating the enantio-determining and rate-limiting steps.

Electrochemically Benzyl Cation‐Triggered Alkylacetoxylation of Terminal Alkynes and Carboxylic Acids

A catalyst‐free electrochemical alkylacetoxylation reaction of terminal alkynes with (thio)xanthenes and carboxylic acids is developed. Treating the addition products with K2CO3 as a base in methanol affords the ketones in moderate to good yields. Preliminary experimental and computational studies indicate that the benzylic cation generated from the (thio)xanthenes triggers the electrophilic addition to alkynes.

Characterization of curing status of commercial tire compounds with vein graphite powder and its particle sizes—Experimental and computational study

AbstractThe use of solid tires in demanding industrial applications, subjected to substantial mechanical loads, poses significant challenges due to heat generation from hysteresis and tread friction. Managing this heat is crucial to mitigate the risk of tire blowouts and layer separation. This research investigates the impact of introducing vein graphite powder, varying in particle size, into a commercially used solid tire compound, both experimentally and computationally. The research findings presented in this paper reveal substantial changes in thermal conductivity, specific heat capacity, rate constant, induction time, and the order of reaction in solid tires. Contemporary industry trends involve predictive methods for monitoring the curing process in tire manufacturing. A tire curing simulation model based on finite (FE) element analysis is developed. FE modeling is favored due to its accuracy and adaptability, especially when dealing with the intricate geometry and multi‐layered, multi‐compound structure of tires. The complex interplay between heat transfer and curing processes is effectively addressed using user subroutines (UMATHT) in commercial FE software like ABAQUS. In this analysis, thermal conductivity, heat capacity, order of reaction, rate constant, and induction time of the commercial tire compound are considered as temperature‐dependent variables. The computational model not only demonstrates its potential to significantly enhance the efficiency and quality of tire manufacturing processes but also contributes to a deeper understanding of the curing behavior of graphite powder‐based solid tire compounds. Consequently, it provides a valuable tool for optimizing tire manufacturing procedures and ensuring the safe and reliable performance of solid tires under demanding operational conditions. This research bridges the gap between the traditional commercial tire compound and the use of vein graphite powder in tire manufacturing and advanced computational methods, facilitating improvements in tire quality and safety.

Manipulating Spin‐Lattice Coupling in Layered Magnetic Topological Insulator Heterostructure via Interface Engineering

AbstractInduced magnetic order in a topological insulator (TI) can be realized either by depositing magnetic adatoms on the surface of a TI or engineering the interface with epitaxial thin film or stacked assembly of 2D van der Waals (vdW) materials. Herein, the observation of spin‐phonon coupling in the otherwise non‐magnetic TI Bi2Te3 is reported, due to the proximity of FePS3 (an antiferromagnet (AFM), TN ≈ 120 K), in a vdW heterostructure framework. Temperature‐dependent Raman spectroscopic studies reveal deviation from the usual phonon anharmonicity originated from spin‐lattice coupling at the Bi2Te3/FePS3 interface at/below 60 K in the peak position (self‐energy) and linewidth (lifetime) of the characteristic phonon modes of Bi2Te3 (106 and 138 cm−1) in the stacked heterostructure. The Ginzburg‐Landau (GL) formalism, where the respective phonon frequencies of Bi2Te3 couple to phonons of similar frequencies of FePS3 in the AFM phase, is adopted to understand the origin of the hybrid magneto‐elastic modes. At the same time, the reduction of characteristic TN of FePS3 from 120 K in isolated flakes to 65 K in the heterostructure, possibly due to the interfacial strain, which leads to smaller Fe‐S‐Fe bond angles as corroborated by computational studies using density functional theory (DFT). Besides, inserting hexagonal boron nitride within Bi2Te3/FePS3 stacking regains the anharmonicity in Bi2Te3. Controlling interfacial spin‐phonon coupling in stacked heterostructure can have potential application in surface code spin logic devices.

Alkyl chain length affecting the structure and interactions of choline-based amino acid ionic liquids: Insights from a computational study

The influences of the alkyl chain length of amino acid anions on the structure and interactions of choline-based amino acid ([Cho][AA]) ionic liquids were investigated based on density functional theory (DFT) and molecular dynamics (MD) simulations. The most stable configuration of the individual [Cho][AA] ion pair was determined, revealing negligible variations in the binding energy between choline cation ([Cho]+) and different amino acid anions ([AA]−). To further characterize the intermolecular interactions between charged entities, the atoms in molecules theory (AIM) and independent gradient model based on Hirshfeld partition (IGMH) were employed, which highlight the presence of robust hydrogen bonds between [Cho]+ and [AA] −, underscoring their significance in shaping the structure of [Cho][AA] ion pairs. The MD studies exhibited the aggregation of anions in [Cho][AA] ILs, which was attributed to side chain interactions of anions. This aggregation effect becomes more pronounced with the elongation of anionic alkyl chain. Simultaneously, radial distribution functions (RDF) analysis revealed a higher probability of hydrogen bonds occurring between [Cho]+ and [AA]− as the alkyl chain in [AA]− lengthened. Additionally, the hydrogen bond lifetimes roughly display an increasing trend as the alkyl chain of the [AA]− increases, which may be due to the reduced diffusion coefficients of ions. Hopefully, our results would contribute fundamental knowledge regarding the impact of alkyl chain length of anions on the structure and interactions in the choline-based amino acid ionic liquids.

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.

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.