Study Of Dynamics Research Articles

Enhanced heat transfer and thermal storage performance of molten K2CO3 by ZnO nanoparticles: A molecular dynamics study

Molten salt serves as a popular medium for thermal storage and transfer in concentrated solar power (CSP) systems. The existing experimental studies have found the capacity of enhancing the heat storage property of the molten carbonate by doping ZnO nanoparticles. However, it has been rarely reported to conduct simulations of ZnO/molten carbonate nanofluids, and the underlying mechanism of how ZnO nanoparticles enhance the heat transfer and storage capacity has less been explored. In this study, molecular dynamics (MD) simulation has been used to investigate the heat transfer and storage properties of a molten K2CO3 nanofluid containing ZnO nanoparticles. It was found that as the nanoparticle mass ratio in molten salt based nanofluids rises, their specific heat capacity initially increases but subsequently diminishes. The specific heat capacity peaks when the ZnO mass ratio is at 1 wt%, resulting in an increase of 17.83 % compared with the base salt. The thermal conductivity in nanofluids based on molten salt increases with the increasing of ZnO mass ratio. Multi-perspective analysis of the mechanism how ZnO nanoparticles enhance the thermal energy storage performance of molten salt, including the microstructural analysis, number density, vibrational density of state, and heat flow decomposition, is conducted. In addition, results of the number density illustrates that a compressed layer of K+ is formed surrounding the ZnO nanoparticles, and the change in the potential energy leads to an increasing heat capacity. Analysis of the heat flow decomposition suggests that the enhanced nonbonded interaction is the main reason for the improvement of thermal conductive performance in the nanofluids based on molten salt. The findings in the present study provide a new perspective of how ZnO nanoparticles enhance the thermophysical properties of molten salts.

Three prime repair exonuclease 1 preferentially degrades the integration-incompetent HIV-1 DNA through favorable kinetics, thermodynamic, structural, and conformational properties

HIV-1 integration into the human genome is dependent on 3’-processing of the viral DNA. Recently, we reported that the cellular Three Prime Repair Exonuclease 1 (TREX1) enhances HIV-1 integration by degrading the unprocessed viral DNA, while the integration-competent 3’-processed DNA remained resistant. Here, we describe the mechanism by which the 3’-processed HIV-1 DNA resists TREX1-mediated degradation. Our kinetic studies revealed that the rate of cleavage (kcat) of the 3’-processed DNA was significantly lower (approximately 2-2.5-fold) than the unprocessed HIV-1 DNA by TREX1. The kcat values of human TREX1 for the processed U5 and U3 DNA substrates were 3.8 s-1 and 4.5 s-1, respectively. In contrast, the unprocessed U5 and U3 substrates were cleaved at 10.2 s-1 and 9.8 s-1, respectively. The efficiency of degradation (kcat/Km) of the 3’-processed DNA (U5-70.2 and U3-28.05 pM-1s-1) was also significantly lower than the unprocessed DNA (U5-103.1 and U3-65.3 pM-1s-1). Furthermore, the binding affinity (Kd) of TREX1 was markedly lower (∼ 2-fold) for the 3’-processed DNA compared to the unprocessed DNA. Molecular docking and dynamics studies revealed distinct conformational binding modes of TREX1 with the 3’-processed and unprocessed HIV-1 DNA. Particularly, the unprocessed DNA was favorably positioned in the active site with polar interactions with the catalytic residues of TREX1. Additionally, a stable complex was formed between TREX1 and the unprocessed DNA compared the 3’-processed DNA. These results pinpoint the mechanism by which TREX1 preferentially degrades the integration-incompetent HIV-1 DNA and reveal the unique structural and conformational properties of the integration-competent 3’-processed HIV-1 DNA.

Use of Pharmacophore Modeling, 3D-atom-based QSAR, ADMET, Docking, and Molecular Dynamics Studies for the Development of Psoralen-based Derivatives as Antifungal Agents

Background:: The mortality and morbidity rates in patients caused by fungi are ex-tremely high. 3-4 % of species of fungi like Candida and Aspergillus are responsible for >99% of invasive fungal infections. Aim:: The goal of the current work was to use several In-silico methods, such as Pharmacophore modeling and 3D-QSAR, to design New chemical entities (NCEs) that have antifungal activity. Material & Method:: A dataset of 40 Psoralen derivatives was taken from available literature, and then, the pharmacophore hypothesis and 3D-QSAR model development were generated using Schrodinger 2023-1 software. After designing a library of 36 compounds, they were sub-jected to ADMET prediction. Screened compounds from the ADMET study were docked with 14 alpha demethylase CYP51 (PDB ID: 3LD6) using Schrödinger software. Molecular dynam-ics (MD) simulation studies were performed on PDB-3LD6 using Desmond-v7.2. Results & Discussion:: The top-ranked hypothesis, AHRRR_1, was taken into consideration when designing the library of potential NCEs.In order to check the drug likeliness of the com-pounds, all 36 designed NCEs were subjected to ADMET prediction using the QikProp tool. The majority of compounds have a good partition coefficient index (less than five). Qplog HERG value was found to be less, making them safer and less toxic. C- 4, 6, 9, 13, 15, 22, 24, 27, 31, and 33 have shown compliance with Lipinski’s rule with zero violations. Compounds C-9, C-13, C-22, C-24, and C-27 have shown better docking scores than the standard Ketocon-azole. Compounds C-9, 24, and 27 have shown a greater number of hydrophobic and hydrogen bond interactions in comparison with the other compounds. Compounds 9, 24, and 27 showed good stability after 100ns molecular simulation simulations. result: The top ranked hypothesis AHRRR_1 was taken into consideration when designing the library of potential NCE's.In order to check the drug likeliness of the compounds, all 36 designed NCE's were subjected to ADMET prediction using QikProp tool. The majority of compounds have good partition coefficient index (less than five), and Qplog HERG value was found to be less, making them safer and less toxic.C- 4, 6, 9, 13, 15, 22, 24, 27, 31, 33 have shown compliance to Lipinski’s rule with zero violations. The majority of the compounds had greater binding affinity than the standard Ketoconazole. Three compounds C-9, 24 and 27 have the good hydrophobic and hydrogen bonding interactions required for antifungal activity.The Compounds 9, 24 and 27 showed good stability after 100ns molecular simulation simulations. Conclusion:: In the current work, the application of insilico methods such as pharmacophore hypothesis, 3D QSAR, ADMET study, docking, and simulation studies have helped to optimize Psoralen pharmacophore for potential antifungal activity. Therefore, the outcomes of the present study could provide insights into the discovery of new potential alpha demethylase inhibitors with improved selectivity and activity against fungal infections. other: Nil

Nanoscale insights into NASH under high-velocity fluids erosion: A molecular dynamics study

The poor durability of geopolymer is a major factor hindering its application, and erosion from high-velocity fluids exacerbates this drawback. This study aimed to characterize the microstructural features of geopolymer under high-velocity fluids erosion and investigate the influence of harmful ions on erosion damage. Models of geopolymer/water solution and geopolymer/NaCl solution were constructed to simulate the erosion of geopolymer by high-velocity fluids. The results indicated that under high-velocity fluids erosion, most of the atoms on the surface of the geopolymer experienced leaching, indicating destruction of the substrate. Additionally, water molecules in solution were able to form hydrogen bonds to the substrate surface, accelerating its degradation. Under NaCl solution erosion, Na ions interacted with the exposed bridging oxygen in the geopolymer, and ion exchange occurred between Na ions and the substrate, making the substrate more unstable and leaching more pronounced. The findings of this study provide nanoscale insights into the erosion resistance of geopolymer that could guide the development of new erosion-resistant materials and methods.

Fluctuation covariance-based study of roll-streak dynamics in Poiseuille flow turbulence

Fluctuation covariance-based study of roll-streak dynamics in Poiseuille flow turbulence

Investigating emodin derivatives against SARS-CoV-2 found in medicinal herbs

SARS-CoV-2 continues to mutate and circulate at alarming levels around the world and is exemplified by the emergence of the new variant JN.1. The emergence of novel SARS-CoV variants underscores the urgency for the development of new drugs. Phytochemicals, known for their safety and efficacy, have been widely used to address various ailments. This study aims at identifying the anti-SARS-CoV potential of emodin, a bioactive anthraquinone, and its derivatives. Key proteins, including hemagglutinin-esterase (HE), papain-like protease (PLpro), major protease (3CLpro), non-structural protein (nsp3) and spike protein(S) of SARS-CoV, were used as protein targets for the virtual screening of 110 emodin derivatives (ED) and remdesivir a proven antiviral drug. Among the 110 derivatives, ED21, ED25, ED5 inhibited HE, 3CLpro and S protein, respectively. ED29 inhibited both PLpro and nsp3 with high binding affinity. Similar receptor binding sites were occupied by remdesivir and emodin derivatives. These emodin derivatives are bound to similar amino acids in receptors as compared to remdesivir. Further dynamic simulations studies with ED21-HE, ED25-3CLpro, ED5-S, ED29-PLpro and ED29-nsp3 complexes showed all of them are stable with minimum root mean square deviation (RMSD), root mean square fluctuation (RMSF), solvent-accessible surface area (SASA) and radius of gyration (Rg) and are comparable to APO protein. All the ligands accepted Lipinski's rule of five. Absorption, distribution, metabolism, excretion, and toxicity (ADMET) analysis revealed only ED21 and ED5 as promising druglike candidates that can have high therapeutic value and no side effects. These in-silico findings contribute to the development of potent SARS-CoV-2 inhibitors, potentially advancing the quest for effective antiviral drugs.

Novel Carbazoles as AChE Inhibitors: Synthesis, Molecular Docking and Dynamic Simulation Studies

Novel Carbazoles as AChE Inhibitors: Synthesis, Molecular Docking and Dynamic Simulation Studies

Clinical Implications of Fat Grafting in the Posterior Calf: A Dynamic Cadaver-based Study.

Intramuscular fat grafting in extremity muscles, especially the gastrocnemius, has become increasingly popular. However, while safety in truncal muscle fat grafting has been well-studied, research on extremity muscles is lacking. This study aims to explore the anatomy of the gastrocnemius muscle and adjacent structures concerning intramuscular and subcutaneous recipient sites. Additionally, it seeks to analyze pressure/volume relationships and fat migration patterns during posterior calf grafting. Eight cadaveric lower extremities were examined. A prosection was performed to better understand the vascular complex as it exists about the gastrocnemius. Ultrasound-guided fat injections were then performed into both the subcutaneous and intramuscular layers; dynamic pressures were measured with a manometer. Lastly, dyed-injectate was injected subcutaneously to better elucidate subcutaneous anatomy. Anatomic prosection demonstrated the proximity of the gastrocnemius muscle to the popliteal venous system which arborized (>1mm) intramuscularly. In the three specimens that underwent intramuscular fat grafting, the peak intramuscular pressures plateaued at 21mmHg (19.5-23mmHg); there was no observed extra-fascial migration of the injectate. With subcutaneous injectate into one specimen, pressures in the subcutaneous space increased (125mmHg) with additional injectate (240cc) while pressures in the intramuscular space remained relatively constant (4mmHg). Intramuscular gastrocnemius fat grafting should be done with caution: its proximity to critical veins and sustained increased intramuscular pressures following grafting increases risk of embolus and thrombosis, respectively. Subcutaneous injection may be safer in that increased pressures are not communicated to deep structures. Lastly, we present a novel description of posterior calf subcutaneous compartments that may better allow surgeons to direct and predict subcutaneous injectate.

Molecular dynamics study on nanodust removal strategies from nanotrench structures

The process of removing nanodust adhering to nanostructured surfaces is important for improving yield and sustainability in manufacturing fields that utilize the structural characteristics of patterns. In this study, we computationally proposed a method to remove nanodust from a trench-shaped Si substrate using an atomic force microscopy tip. A molecular system is thus constructed in which a Si substrate with a trench structure, a cylindrical C tip, and a spherical Cu nanoparticle coexist. By moving the C tip in a specific direction and pushing it into direct contact with the Cu nanoparticle, the interaction force between the Cu and the sidewall of the Si substrate can be substantially reduced. In particular, moving the C tip in a direction parallel to the pattern can effectively push nanodust away while minimizing damage to the Si substrate. The damage experienced by the substrate during the process was comprehensively evaluated using the von Mises stress, adhesion energy, contact area, and strain energy density developed by the axial stress components. The suitability of this method was systematically evaluated based on the diameter of the Cu nanoparticle and its position relative to the C tip. For each case, the maximum strain energy experienced at the edge of the trench structure was quantified, which suggests appropriate nanoparticle removal process conditions from a structural perspective. The strategy can be potentially used as a repair method for semiconductor production components, such as pellicles and hard masks.

Properties of radiation-induced point defects in austenitic steels: a molecular dynamics study

Austenitic steels are recognized as excellent structural materials for pressurized water reactors due to their outstanding mechanical properties and radiation resistance. However, compared to the widely studied FeCrNi series of steels, little is known about the radiation resistance of FeCrNiMn steel. In this study, the generation and evolution of radiation-induced defects in FeCrNiMn steel were investigated by molecular dynamics simulations. The results showed that more defect atoms were produced in the thermal spike stage, but fewer defects survived at the end of the cascades in FeCrNiMn compared to pure Fe. Point defect properties were analyzed by molecular statics, and the formation energies of defects in FeCrNiMn were lower than those of pure Fe, while the migration energies were higher. Compared to FeCrNi, FeCrNiMn had smaller migration energies and a larger overlap of vacancy and interstitial migration energies. The low vacancy formation energies and widely overlapping migration energies suggested that the number of point defects in the thermal spike stage was higher, but the possibility of recombination was greater. Additionally, Mn exhibited the smallest interstitial formation energies and migration energies. The difference in defect migration energies revealed that vacancy and interstitial defects migrate through different alloy constituent elements. This study revealed the underlying mechanism for the excellent irradiation resistance of FeCrNiMn.

Dynamic Column Studies of Multicomponent PFAS Sequestration Facilitated by Four Contrasting Injectable Adsorbent Suspensions and Associated PFAS Release in Simulated Groundwater

Dynamic Column Studies of Multicomponent PFAS Sequestration Facilitated by Four Contrasting Injectable Adsorbent Suspensions and Associated PFAS Release in Simulated Groundwater

Directional solidification of Cu with dispersed W nanoparticles: A molecular dynamics study in the context of additive manufacturing

Directional solidification, resulting in the development of columnar grains, is prevalent in laser-additive manufacturing of metal parts. The addition of grain refiners or inoculants enables the control of the nucleation process and columnar-to-equiaxed transition. In this study, we applied molecular dynamics simulations to investigate the directional solidification in liquid copper inoculated with tungsten nanoparticles. The interaction of the solidification front with inert nanoparticles resulted in either their engulfment in the Cu matrix or their pinning by grain boundaries. Analysis of the forces acting on the nanoparticles and the temperature field provides conditions for engulfment, determining the feasibility of copper matrix composites. By global cooling reflecting the thermal dynamics characteristics of additive manufacturing, a columnar-to-equiaxed transition can be captured at the nanoscale, with heterogeneous nucleation occurring at the nanoparticle surfaces. The conditions for the onset of heterogeneous nucleation were assessed on the basis of nanoparticle size and interpreted in terms of classical nucleation theory. Our results highlight the critical role of W-nanoparticle wetting by Cu solid grains in increasing grain refinement efficiency and suppression of columnar growth in additive manufacturing.

Structural insights into the role of deleterious mutations at the dimeric interface of Toll-like receptor interferon-β related adaptor protein.

Toll-like receptors (TLRs) are major players in the innate immune system-recognizing pathogens and differentiating self/non-self components of immunity. These proteins are present either on the plasma membrane or endosome and recognize pathogens at their extracellular domains. They are characterized by a single transmembrane helix and an intracellular toll-interleukin-1 receptor (TIR) domain. Few TIRs directly invoke downstream signaling, while others require other TIR domains of adaptors like TIR domain-containing adaptor-inducing interferon-β (TRIF) and TRIF-related adaptor molecule (TRAM). On recognizing pathogenic lipopolysaccharides, TLR4 dimerises and interacts with the intracellular TRAM dimer through the TIR domain to recruit a downstream signaling adaptor (TRIF). We have performed an in-depth study of the structural effect of two mutations (P116H and C117H) at the dimeric interface of the adaptor TRAM, which are known to abrogate downstream signaling. We modeled the structure and performed molecular dynamics studies in order to decipher the structural basis of this effect. We observed that these mutations led to an increased radius of gyration of the complex and resulted in several changes to the interaction energy values when compared against the wild type (WT) and positive control mutants. We identified highly interacting residues as hubs in the WT dimer, and a few such hubs that were lost in the mutant dimers. Changes in the protein residue path, hampering the information flow between the crucial A86/E87/D88/D89 and T155/S156 sites, were observed for the mutants. Overall, we show that such residue changes can have subtle but long-distance effects, impacting the signaling path allosterically.

Hour-Long, Kilohertz Sampling Rate Three-Dimensional Single-Virus Tracking in Live Cells Enabled by StayGold Fluorescent Protein Fusions.

A viral infection process covers a large range of spatiotemporal scales. Tracking the viral infection process with fluorescent labels over long durations while maintaining a fast sampling rate requires bright and highly photostable labels. StayGold is a recently identified green fluorescent protein that has a greater photostability and higher signal intensity under identical illumination conditions compared to existing fluorescence protein variants. Here, StayGold protein fusions were used to generate virus-like particles (StayGold-VLPs) to achieve hour-long 3D single-virus tracking (SVT) with 1000 localizations per second (kHz sampling rate) in live cells. The expanded photon budget from StayGold protein fusions prolonged the tracking duration, facilitating a comprehensive study of viral trafficking dynamics with high temporal resolution over long time scales. The development of StayGold-VLPs presents a simple and general VLP labeling strategy for better performance in SVT, enabling exponentially more information to be collected from single trajectories and allowing for the future possibility of observing the entire life cycle of a single virus.

Visualizing Dynamic Single Atom Catalysis.

Many industrial chemical processes, including for producing fuels, foods, pharmaceuticals, chemicals and environmental controls, employ heterogeneous solid state catalysts at elevated temperatures in gas or liquid environments. Dynamic reactions at the atomic level play a critical role in catalyst stability and functionality. In situ visualization and analysis of atomic-scale processes in real time under controlled reaction environments can provide important insights into practical frameworks to improve catalytic processes and materials. This review focuses on innovative real time in situ electron microscopy (EM)methods, including recent progress in analytical insitu environmental (scanning) transmission EM (E(STEM), incorporating environmental scanning TEM (ESTEM) and environmental transmission EM (ETEM), with single atom resolution for visualizing and analysing dynamic single atom catalysis under controlled flowing gas reaction environments. ESTEM studies of single atom dynamics of reactions, and of sintering deactivation, contribute to a better-informed understanding of the yield and stability of catalyst operations. Advances in in situ technologies, including gas and liquid sample holders, nanotomography, and higher voltages, as well as challenges and opportunities in tracking reacting atoms, are highlighted. The findings show that the understanding and application of fundamental processes in catalysis can be improved, with valuable economic, environmental, and societal benefits.

Molecular dynamics study of the temperature dependence of viscosity and thermal conductivity of molten salts FLiNaK and FLiNaK with LaF3 or NdF3

In this work, the temperature dependence of the viscosity and thermal conductivity of molten systems FLiNaK and FLiNaK-MeF3 (Me = La, Nd) was studied using the molecular dynamics method with Born-Mayer-Huggins potential. The dependencies were obtained in the temperature range of 800 < T < 1020 K, as well as for the concentration of lanthanide fluoride additives up to 15 mol.%. The temperature behavior of these kinetic properties is explained based on an MD model of dynamic ionic connectivity. The main contribution to the connectivity of pure FLiNaK ions is made by Li-F ion pairs, and in the presence of LaF3 and NdF3 dissolved in the salt mixture, the connectivity in the system is supplemented by ion pairs formed by lanthanides with fluorine. Both viscosity and thermal conductivity decrease with increasing temperature and rise when lanthanide trifluorides are added to the molten salt.

An N-terminal acidic β-sheet domain is responsible for the metal-accumulation properties of amyloid-β protofibrils: a molecular dynamics study

The influence of metal ions on the structure of amyloid-β\\documentclass[12pt]{minimal} \\usepackage{amsmath} \\usepackage{wasysym} \\usepackage{amsfonts} \\usepackage{amssymb} \\usepackage{amsbsy} \\usepackage{mathrsfs} \\usepackage{upgreek} \\setlength{\\oddsidemargin}{-69pt} \\begin{document}$$\\beta $$\\end{document} (Aβ) protofibril models was studied through molecular dynamics to explore the molecular mechanisms underlying metal-induced Aβ aggregation relevant in Alzheimer’s disease (AD). The models included 36-, 48-, and 188-mers of the Aβ42 sequence and two disease-modifying variants. Primary structural effects were observed at the N-terminal domain, as it became susceptible to the presence of cations. Specially when β-sheets predominate, this motif orients N-terminal acidic residues toward one single face of the β-sheet, resulting in the formation of an acidic region that attracts cations from the media and promotes the folding of the N-terminal region, with implications in amyloid aggregation. The molecular phenotype of the protofibril models based on Aβ variants shows that the AD-causative D7N mutation promotes the formation of N-terminal β-sheets and accumulates more Zn2+, in contrast to the non-amyloidogenic rodent sequence that hinders the β-sheets and is more selective for Na+ over Zn2+ cations. It is proposed that forming an acidic β-sheet domain and accumulating cations is a plausible molecular mechanism connecting the elevated affinity and concentration of metals in Aβ fibrils to their high content of β-sheet structure at the N-terminal sequence.Graphic abstract

Mid-infrared computational temporal ghost imaging

Ghost imaging in the time domain allows for reconstructing fast temporal objects using a slow photodetector. The technique involves correlating random or pre-programmed probing temporal intensity patterns with the integrated signal measured after modulation by the temporal object. However, the implementation of temporal ghost imaging necessitates ultrafast detectors or modulators for measuring or pre-programming the probing intensity patterns, which are not available in all spectral regions especially in the mid-infrared range. Here, we demonstrate a frequency downconversion temporal ghost imaging scheme that enables to extend the operation regime to arbitrary wavelengths regions where fast modulators and detectors are not available. The approach modulates a signal with temporal intensity patterns in the near-infrared and transfers the patterns to an idler via difference-frequency generation in a nonlinear crystal at a wavelength where the temporal object can be retrieved. As a proof-of-concept, we demonstrate computational temporal ghost imaging in the mid-infrared with operating wavelength that can be tuned from 3.2 to 4.3 μm. The scheme is flexible and can be extended to other regimes. Our results introduce new possibilities for scan-free pump-probe imaging and the study of ultrafast dynamics in spectral regions where ultrafast modulation or detection is challenging such as the mid-infrared and THz regions.

Product-specific reaction kinetics in continuous uniform supersonic flows probed by chirped-pulse microwave spectroscopy.

Experimental studies of the products of elementary gas-phase chemical reactions occurring at low temperatures (<50K) are very scarce, but of importance for fundamental studies of reaction dynamics, comparisons with high-level quantum dynamical calculations, and, in particular, for providing data for the modeling of cold astrophysical environments, such as dense interstellar clouds, the atmospheres of the outer planets, and cometary comae. This study describes the construction and testing of a new apparatus designed to measure product branching fractions of elementary bimolecular gas-phase reactions at low temperatures. It combines chirped-pulse Fourier transform millimeter wave spectroscopy with continuous uniform supersonic flows and high repetition rate laser photolysis. After a comprehensive description of the apparatus, the experimental procedures and data processing protocols used for signal recovery, the capabilities of the instrument are explored by the study of the photodissociation of acrylonitrile and the detection of two of its photoproducts, HC3N and HCN. A description is then given of a study of the reactions of the CN radical with C2H2 at 30K, detecting the HC3N product, and with C2H6 at 10K, detecting the HCN product. A calibration of these two products is finally attempted using the photodissociation of acrylonitrile as a reference process. The limitations and possible improvements in the instrument are discussed in conclusion.

A systematic study of carbon clustering dynamics for explosives

ABSTRACT The carbon clustering mechanism of insensitive explosive is investigated by molecular dynamics. We find that the free carbon gas aggregates to form flexible chain, and the chain changes to graphite-phase particle. A set of thermodynamic properties for carbon clusters are calculated, and five clustering mechanisms are investigated, including the nucleation, deposition, sublimation, diffusion and phase transition effects. We use chemical reaction model to describe the free carbon aggregation, use diffusion/impaction model to describe the deposition/growing process, use heterogeneous equilibrium condition to evaluate the sublimation rate, use Shaw's model to describe the Smoluchowski coagulation and use Arrhenius model to describe the phase transition rate. Based on the microscopic properties, the detonation wave of explosive is simulated by finite difference method. A set of detonation properties are calculated, and the meso-structure of slow reaction zone is obtained.