bluuebunny/crossref_metadata_2025 huggingface dataset:
Experimental investigation of ducted fan noise control by turbulence grids insertion between propellers and struts
Authors: Wang Ruichen , Ma Zhaokai , Huang Xun
Published: August 2024

The control of turbulence-ingested propeller noise remains a challenging topic for unmanned aerial vehicles and urban air mobility applications. In this work, passive noise control by inserting turbulence grids between a propeller and struts for a ducted fan system is experimentally studied. The 3-bladed, 8 in. diameter propeller is mounted in a short duct downstream of 7 struts, each featuring symmetrical airfoil shapes with a chord length of 30 mm. Two turbulence grid configurations, namely, fully shaded and tip-shaded, are investigated by comparing the spectra and directivity characteristics of the aeroacoustic noise and their aerodynamic performance. Beamforming technology and hot-wire anemometry are employed to explore the fluid mechanics. The results show that at same rotating speed, the fully shaded turbulence grid is more effective in reducing the tonal noise. The overall noise reduction capability for the two cases is similar, and an overall sound pressure level noise reduction of roughly 3 dB is achieved. Due to the blockage effect of the turbulence grid, the fully shaded case bears a 20% thrust loss, while the tip-shaded case has a marginal deficit of thrust. When the rotating speed is adjusted to produce the same thrust of the baseline, the fully shaded case shows an increase in the overall noise, while the tip-shaded case maintains the noise reduction capability. The beamforming results and turbulence intensity measurements show that the propeller tip region has a strong interaction of the turbulence ingestion flow and tip leakage flow where the broadband noise source is dominant.
Quantum chemical package Jaguar: A survey of recent developments and unique features
Authors: Cao Yixiang , Balduf Ty , Beachy Michael D. , Bennett M. Chandler , Bochevarov Art D. , Chien Alan , Dub Pavel A. , Dyall Kenneth G. , Furness James W. , Halls Mathew D. , Hughes Thomas F. , Jacobson Leif D. , Kwak H. Shaun , Levine Daniel S. , Mainz Daniel T. , Moore Kevin B. , Svensson Mats , Videla Pablo E. , Watson Mark A. , Friesner Richard A.
Published: August 2024

This paper is dedicated to the quantum chemical package Jaguar, which is commercial software developed and distributed by Schrödinger, Inc. We discuss Jaguar’s scientific features that are relevant to chemical research as well as describe those aspects of the program that are pertinent to the user interface, the organization of the computer code, and its maintenance and testing. Among the scientific topics that feature prominently in this paper are the quantum chemical methods grounded in the pseudospectral approach. A number of multistep workflows dependent on Jaguar are covered: prediction of protonation equilibria in aqueous solutions (particularly calculations of tautomeric stability and pKa), reactivity predictions based on automated transition state search, assembly of Boltzmann-averaged spectra such as vibrational and electronic circular dichroism, as well as nuclear magnetic resonance. Discussed also are quantum chemical calculations that are oriented toward materials science applications, in particular, prediction of properties of optoelectronic materials and organic semiconductors, and molecular catalyst design. The topic of treatment of conformations inevitably comes up in real world research projects and is considered as part of all the workflows mentioned above. In addition, we examine the role of machine learning methods in quantum chemical calculations performed by Jaguar, from auxiliary functions that return the approximate calculation runtime in a user interface, to prediction of actual molecular properties. The current work is second in a series of reviews of Jaguar, the first having been published more than ten years ago. Thus, this paper serves as a rare milestone on the path that is being traversed by Jaguar’s development in more than thirty years of its existence.
Experiments and gyrokinetic simulations of the nonlinear interaction between spinning magnetized plasma pressure filaments
Authors: Sydora R. D. , Simala-Grant T. , Karbashewski S. , Jimenez F. , Van Compernolle B. , Poulos M. J.
Published: August 2024

A set of experiments using controlled, skin depth-sized plasma pressure filaments in close proximity have been carried out in a large linear magnetized plasma device. Two- and three-filament configurations have been used to determine the scale of cross field nonlinear interaction. When the filaments are separated by a distance of approximately five times the size of a single filament or less, a significant transfer of charge and energy occurs, leading to the generation of inter-filament electric fields. This has the effect of rotating the filaments and influencing the merging dynamics. Nonlinear gyrokinetic simulations using seeded filaments confirm the presence of unstable drift-Alfvén modes driven by the steep electron temperature gradient. When the filaments are within a few collisionless electron skin depths (separations twice the size of a single filament), the unstable perturbations drive the convective mixing of the density and temperature and rearrange the gradients such that they maximize in the region surrounding the filament bundle.
Role of an in-house designed crucible in the fabrication of isotopically enriched 28Si target for an in-beam γ-ray spectroscopy experiment
Authors: Subodh  , S. R. Abhilash , Sharma Madan , Kapil Ashutosh , Singh R. P. , Behera B. R.
Published: August 2024

In the present work, an in-house designed special crucible was developed to fabricate isotopically enriched 28Si targets for a γ-ray spectroscopy experiment. Initially, the crucible was tested with natural Si and then utilized to fabricate isotopically enriched 28Si targets of thickness ∼500 μg/cm2 (∼2.15 μm). The fabricated targets were uniform in thickness and had very little contamination. In addition, one of the fabricated targets was successfully utilized in an in-beam γ-ray spectroscopy experiment. The technique employed in the present work not only facilitates the fabrication of stable and pure targets but also minimizes the wastage of the source material. As a result, these efforts pave the way for future fabrication of low-abundance isotopically enriched nuclear physics targets.
Statistical characterization of high voltage vacuum surface flashover with gapped and ungapped anodes
Authors: Mounho M. , Fuksa C. , Clark R. , Brooks W. , Hopkins M. , Steiner A. , Neuber A. , Stephens J.
Published: August 2024

This manuscript reports the experimental study of a novel vacuum high-voltage (HV) feedthrough geometry with a recessed anode triple junction (ATJ) relevant to large-scale pulsed power systems. It is shown experimentally that introducing a vacuum gap between the insulator–anode interface and recessing the ATJ farther away from the cathode triple junction significantly enhances high voltage (HV) vacuum surface flashover hold-off. The results for “first pulse” and “consecutive pulse” tests are reported. The physical mechanisms contributing to the electrical failure of this feedthrough geometry appear to be unique to this geometry. These findings show the potential to allow for HV vacuum surface flashover geometries with significantly improved electrical characteristics.
A transferable classical force field to describe glyme based lithium solvate ionic liquids
Authors: Carrillo-Bohórquez Orlando , Kuroda Daniel G. , Kumar Revati
Published: August 2024

A non-polarizable force field for lithium (Li+) and bis(trifluoromethanesulfonyl)imide (TFSI−) ions solvated in diglyme at around 0.2 mol fraction salt concentration was developed based on ab initio molecular dynamics (AIMD) simulations and a modified polymer consistent force field model. A force–torque matching based scheme, in conjunction with a genetic algorithm, was used to determine the Lennard-Jones (LJ) parameters of the ion–ion and ion–solvent interactions. This force field includes a partial charge scaling factor and a scaling factor for the 1–4 interactions. The resulting force field successfully reproduces the radial distribution function of the AIMD simulations and shows better agreement compared to the unmodified force field. The new force field was then used to simulate salt solutions with glymes of increasing chain lengths and different salt concentrations. The comparison of the MD simulations, using the new force field, with experimental data at different salt concentrations and AIMD simulations on equimolar concentrations of the triglyme system demonstrates the transferability of the force field parameters to longer glymes and higher salt concentrations. Furthermore, the force field appears to reproduce the features of the experimental x-ray structure factors, suggesting accuracy beyond the first solvation shell, for equimolar salt solutions using both triglyme and tetraglyme as the solvent. Overall, the new force field was found to accurately reproduce the molecular descriptions of LiTFSI-glyme systems not only at various salt concentrations but also with glymes of different chain lengths. Thus, the new force field provides a useful and accurate tool to perform in silico studies of this family of systems at the atomistic level.
Metal-like monoclinic phase and terahertz characteristics in ultrafast phase transition of photoexcited VO2
Authors: Guo Ban Zhen , Shi Yan , Qian Huang Ning , Kui Meng Zan , Chen Zhu Shi
Published: August 2024

Photoexcitation is a powerful way to induce phase transition of strongly correlated materials and dynamically control terahertz (THz) devices integrated with photoinduced phase transition (PIPT) materials. To clarify controversies over the physical mechanism between electronic insulator-metal transition (IMT) and structural phase transition (SPT) of photoexcited vanadium dioxide (VO2), the underlying atomic and electronic state changes during photoinduced monoclinic-to-rutile phase transition are illustrated, and the separation with different thresholds between the quasi-instantaneous IMT and the ultrafast SPT is discovered. Below the SPT threshold, there exist metastable states exhibiting the metal-like monoclinic phases, i.e., the strongest metallicity and weak monoclinic phases, when the bond lengths of the V–V pairs are closest. By analyzing the electronic transport properties of these metal-like monoclinic phases, the THz response of the whole phase transition process can be characterized for first time through the quantum-electromagnetic dispersion modeling method. The THz properties of the practical VO2 film are simulated and the great alignments between the measurements and the simulations verify the proposed analysis method, which provides a powerful exploration path and insights for the theoretical analysis and design verification of PIPT materials and their optoelectronic THz devices.
A nearly complete treatment of the effect of non-adiabaticity on rovibrational energies of H3+ (Part III)
Authors: Jaquet Ralph
Published: August 2024

In this article, significant contributions of non-adiabaticity for the rovibrational bound states up to 25 000 cm−1 and total angular momentum J = 0–20 of H3+ are investigated. A coupled-perturbed full configuration interaction (CP-FCI) treatment is applied to calculate all couplings between electronic states caused by the nuclear motion. These derivative couplings were evaluated up to the second order by means of a perturbation treatment and include all nuclear Cartesian first and second derivatives of the electronic wavefunctions. In particular, the coupling of special derivatives with respect to r and R in the Jacobi coordinate representation is more significant than thought. The perturbation approach is especially optimal for the treatment of weak non-adiabaticity in case of rovibrational energies in H3+ and had not been available before for H3+ or other triatomics. Using exclusively Gaussian basis functions for CP-FCI appears to be sufficient, because explicit correlated wavefunctions are already used for all other potential energy contributions. Our work is an extension of earlier non-adiabatic investigations based on first derivative couplings of electronic states that led to the concept of geometry-dependent effective nuclear masses and which needs only a single potential energy surface for the dynamics. The implementation allows us to include all non-adiabatic effects up to the order of O(μ−2), μ being the reduced nuclear mass. Our treatment works for any isotopologue and for the whole potential energy curve or surface. By this treatment, a further reduction in deviations to experimental data for most rovibrational levels to less than 0.1 cm−1 is possible. For the related transition frequencies, 1366 of 1720 known rovibrational transitions in H3+ have deviations less than 0.1 cm−1 without using any empirically adjustable parameters or optimizing the nuclear mass for a specific transition. For many questionable assignments (deviations >0.3 cm−1) of observed transitions in H3+, a new labeling is proposed.
Implementation of a real-time MSE system
Authors: DiCicco D. S. , Levinton F. M. , Galante M. E.
Published: August 2024

Motional Stark effect polarimetry is a key diagnostic for plasma fusion research since its usage on PBX-M. The MSE diagnostic measures the radial magnetic pitch angle profile in a plasma from a neutral beam by observation of Stark split D-alpha emission from atoms excited by collision with ions and electrons in the plasma. The pitch angle measurement is used with equilibrium reconstruction codes to determine the q-profile for studies of plasma stability, confinement, and transport. Historically, the algorithm was used in a post-processing fashion. The goal of our work was to apply this method in real time and pass the results to the plasma control system computer for real-time equilibrium reconstruction and control.
Prediction and sensitivity analysis of the pressure wave peak value induced by the high-speed train in the long tunnel under a high geothermal environment
Authors: Wang Junyan , Wang Tiantian , Wang Yiping , Wen Chihyung , Zhang Lei , Sun Zhikun
Published: August 2024

Pressure changes outside a train can be transmitted into a carriage when the train is running in the tunnel, seriously affecting passenger comfort. In this paper, the polynomial response surface (PRS) is used to predict the value of the compression wave and obtain the predictive model equations. For the traveling pressure waves, many influencing factors contribute differently to the final pressure wave form and magnitude. In geothermal tunnels, the speed of a high-speed train (V), air temperature of the inner tunnel (T), and atmospheric pressure (P) are the three main influencing parameters. Using a PRS prediction model, the sensitivity of each influencing parameter is analyzed by the Sobol sensitivity method. The result shows that V has the greatest effect on the pressure peak value, and T has the least effect. The initial compressional waves and expansion waves are most and least sensitive to T, respectively. The coupling effect among parameters P, T, and V is relatively small. Using the sensitivity results of the parameters, targeted and reasonable parameter adjustment can effectively relieve the pressure inside and outside the train and improve passenger comfort in geothermal tunnels. These results provide important technical support for the mitigation of pressure waves.
Atomistic simulations of effects of nanostructure on bonding mechanism and mechanical response of direct bonding of (111)-oriented nanotwinned Cu
Authors: Wu Cheng-Da , Liao Chien-Fu
Published: August 2024

Low-temperature, low-pressure Cu-to-Cu direct bonding technology is a promising solution for next-generation high-density interconnects. Previous studies have shown that many properties of nanomaterials are determined by their structural characteristics. Therefore, the effect of the nanostructure (i.e., twin crystal and twin boundary, TB, sizes) on the bonding mechanism and mechanical response of the direct bonding of (111)-oriented nanotwinned Cu (NT-Cu) is studied using molecular dynamics simulations, where TB size means the TB layer thickness in terms of the number of atoms. The simulation results show that NT-Cu with extremely small twin crystals (e.g., 0.625 nm) have poor diffusivity. The number of dislocations induced by plastic deformation increases with increasing twin crystal size during stretching processes, degrading mechanical strength. The strain hardening of bonded NT-Cu with extremely small twin crystals (e.g., 0.625 nm) is dominated by the strong barrier created by a high density of TBs, whereas that with twin crystal sizes of 2.5–10 nm is dominated by dislocation–TB and dislocation–grain boundary interactions. Bonded NT-Cu with 2–6 atoms per TB layer exhibits softening at initial plastic deformation due to the onset of partial collapse of TBs; however, the strength then significantly increases with a further increase in strain due to strain hardening.
Temperature-dependent damping mechanism in ferroelastic-reinforced composites
Authors: Xiang Wenting , Tang Min , Zhu Wenhui , Chai Jingheng , Wu Qi , Zhang Zihan , Guo Xiaoxu , Yang Zheng , Yan Yongke , Geng Liwei D.
Published: August 2024

Phase field modeling and computer simulations were conducted to uncover the fundamental mechanism behind the peak in damping capacity observed in BaTiO3-reinforced composites, considering both insulating and conductive cases. The damping capacity curve obtained from these simulations, which varies with temperature, reveals dual peaks near Tc for both cases. The first peak, labeled Peak I, occurs below Tc and is attributed to temperature-induced domain reorientation. The second peak, labeled Peak II, occurs above Tc and arises from stress-induced phase transitions between paraelastic and ferroelastic states. This transition results in a double-loop strain–stress hysteresis, akin to the polarization-field hysteresis observed in ferroelectric systems at and above Tc. Between Peak I and Peak II, there is a dip in damping capacity just below Tc, caused by the diminished ferroelasticity of BaTiO3 particles near this critical temperature. In composite materials, the dual peaks merge into a single peak due to the heterogeneous nature of Tc, influenced by various factors that either raise or lower Tc. This convergence aligns with experimental observations.
Observation of resilient propagation and free-space skyrmions in toroidal electromagnetic pulses
Authors: Wang Ren , Bao Pan-Yi , Hu Zhi-Qiang , Shi Shuai , Wang Bing-Zhong , Zheludev Nikolay I. , Shen Yijie
Published: August 2024

Toroidal electromagnetic pulses have been recently reported as nontransverse, space-time nonseparable topological excitations of free space. However, their propagation dynamics and topological configurations have not been comprehensively experimentally characterized. In addition, the existing generators were limited in optical and terahertz domains; however, the feasibility and significance of generating such pulses at microwave frequencies have been overlooked. Here, we report that microwave toroidal pulses can be launched by a transient finite-aperture broadband horn antenna emitter, as an electromagnetic counterpart of “air vortex cannon.” Applying this effective generator, we experimentally map the toroidal pulses' topological skyrmionic textures in free space and demonstrate their resilient propagation dynamics, i.e., how that, during propagation, the pulses evolve toward stronger space-time nonseparability and closer proximity to the canonical Hellwarth–Nouchi toroidal pulses. Our work offers a practical opportunity for using topologically robust toroidal pulses as information carriers in high-capacity telecom, cell phone technology, remote sensing, and global positioning, especially where microwave frequencies are predominant.
Sequence and gelation in supramolecular polymers
Authors: Balzer Christopher , Fredrickson Glenn H.
Published: August 2024

Supramolecular polymer networks exhibit unique and tunable thermodynamic and dynamic properties that are attractive for a wide array of applications, such as adhesives, rheology modifiers, and compatibilizers. Coherent states (CS) field theories have emerged as a powerful approach for describing the possibly infinite reaction products that result from associating polymers. Up to this point, CS theories have focused on relatively simple polymer architectures. In this work, we develop an extension of the CS framework to study polymers with reversible bonds distributed along the polymer backbone, opening a broad array of new materials that can be studied with theoretical methods. We use this framework to discern the role of reactive site placement on sol–gel phase behavior, including the prediction of a microstructured gel phase that has not been reported for neutral polymer gels. Our results highlight the subtleties of thermodynamics in supramolecular polymers and the necessity for theories that capture them.
Response to “Comment on ‘Binding Debye–Hückel theory for associative electrolyte solutions’” [J. Chem. Phys. 159, 154503 (2023)]
Authors: Naseri Boroujeni S. , Maribo-Mogensen B. , Liang X. , Kontogeorgis G. M.
Published: August 2024

This Response addresses critiques raised about the Binding Debye–Hückel (BiDH) theory [Naseri Boroujeni et al., J. Chem. Phys. 159, 154503 (2023)] by Simonin and Bernard [J.-P. Simonin and O. Bernard, J. Chem. Phys. 161, 057102 (2024)]. The critiques questioned the foundational framework of the Debye–Hückel (DH) theory, the relevance of ion pairing in primitive model fluids, and the accuracy of the BiDH model compared to mean spherical approximation model. Through a systematic rebuttal, supported by extensive literature review and comparison with Monte Carlo simulation data, this Response addresses these concerns. It demonstrates the efficacy of DH theory in describing real electrolyte solutions, validates the relevance of ion pairing in primitive model fluids, and establishes the BiDH model’s accuracy in describing electrolyte properties.
Study on atomization effect of droplets in venturi reactor with different characteristic parameters
Authors: Lv Chao , Chen Xu-Xin , Zhou Tong , Yang Tao , Zhao Hong-Liang , Liu Yan-Long
Published: August 2024

In the field of preparation of cerium oxide by Venturi jet pyrolysis reactor, the spray pyrolysis process can achieve energy saving and environmental protection. The atomization effect of transverse air flow on the droplet directly affects the morphology of the product, and this research can improve the high value of cerium oxide applications. In this paper, a novel Venturi jet pyrolysis reactor has been developed. The atomization stage in the preparation process was studied by combining experiment and numerical simulation. The results show that the entire atomization process can be divided into primary atomization and secondary atomization. The primary atomization process of the liquid jet consists of columnar fragmentation and surface fragmentation, which are dominated by Rayleigh–Taylor (R-T) instability and Kelvin–Helmholtz (K-H) instability respectively. In the process of atomization of liquid column, the increase in gas velocity helps to promote the atomization. The Sauter mean Diameter value at 35 and 40 m/s gas velocity is the smallest, and the atomization effect of Venturi reactor is the best. With the increase in Weissenberg number (Wi), the crushing mode of droplets in Venturi reactor gradually changes from envelope to envelope—core and further evolves into core-layer. The core-layer crushing effect is the best, and the distribution range of daughter droplets is larger. The crushing state of atomized droplets in Venturi reactor is summarized. When Wi < 12, it is vibration crushing; when 12 < Wi < 30, it is packet crushing; when 30 < Wi < 45; it is pack-core crushing; and when 45 < Wi < 75, it is stamen-layer breakage.
Influence of surface roughness and asymmetry on flow regimes of water and gas in clay nanopores
Authors: Bi Ying , Jia Xiaotian , Hao Youzhi , Qian Jin , Lu Detang
Published: August 2024

The understanding of gas–liquid two-phase flow in rough nanopores is essential for efficient shale gas extraction. In this study, we employed the molecular dynamics simulation to investigate the mechanisms of water–gas two-phase flow in rough shale nanopores using illite clay minerals. To construct rough nanopores, the rough particles are introduced onto smooth wall surfaces, resulting in two types of rough pore structures: symmetric and asymmetric rough nanopores. The simulation results reveal distinct gas cluster shapes during two-phase flow in different rough nanopores: bullet-shaped clusters in smooth channels, bulb-shaped clusters in symmetric rough channels, and wave-like clusters in asymmetric rough channels. Furthermore, the presence of rough particles near the pore walls leads to the formation of three adsorption layers of water molecules. These layers are attributed to the exposed hydroxyl groups on the rough particles. Additionally, the configuration of rough particles influences the formation of low-speed and high-speed flow regions. Comparatively, the velocity of water and methane phases is observed to be higher in asymmetric nanopores than in symmetric nanopores, indicating a greater obstruction effect on fluid flow in symmetric rough channels. The afore-mentioned findings provide valuable insights into the gas–liquid two-phase flow behavior in rough nanopores, which is crucial for optimizing transport and mass transfer processes in nanoscale systems.
Characteristics and performance evaluation of foam in situ generated by microorganisms
Authors: Fu Jian , Liu Yulong , Zhang Cenqian , Wang Chenyue , Feng Qing , Li Xiaonan , Sun Shanshan , She Yuehui , Zhang Fan
Published: August 2024

Foam can effectively improve reservoir heterogeneity, increase gas–liquid flow rate, reduce viscous fingering, and help to improve sweep efficiency. This paper mainly studies the characteristics and performance of microbial foam production, and proposes an enhanced oil recovery method for profile control by in situ microbial foam production. By optimizing the carbon and nitrogen sources of the medium, Pseudomonas aeruginosa PAO1 produced single and double rhamnolipids and biogas composed of N2, CO2, and CH4, and it could also produce foam in high salt, weak acid, and weak alkali environments. Gas injection experiments were carried out using self-produced biogas, the foaming effect is good in the range of gas–liquid ratio 1:1–3:1 and gas injection speed 20–40 ml/min, which was 71.43%–91.25% more than the foam volume produced by CO2 injection, and the foam production was positively correlated with the protein concentration of the foam. In the early stage of incubation, the foam was 20–100 μm in diameter, with high protein concentration and strong foam stability, which slowed down the drainage, polymerization, and disproportionation of the liquid film of the foam system. The foam performance test results show that the foam half-lifetime is long, up to 109 min. Foam culture medium has good viscosity reduction effect, emulsifying properties and less corrosive. The displacement experiment shows that the foam generated in situ by PAO1 in the core has good stability, reproducibility, and profile control performance, which can reduce the permeability of the core to half of the initial permeability and improve the reservoir heterogeneity. Therefore, microbial in situ foam production can be an effective method to enhance oil recovery in heterogeneous reservoirs, which is low cost, low pollution, and simple operation.
Flame and flow dynamics during swirl flame flash-back
Authors: Yu Lijuan , Zhang Junhua , Zhang Chi , Xu Boli , An Qiang
Published: August 2024

Flash-back characteristics of lean-premixed syngas swirl flames were investigated using simultaneous OH planar laser-induced fluorescence and stereoscopic particle image velocimetry at a repetition rate of 10 kHz. The syngas consisted of carbon monoxide, carbon dioxide, and hydrogen. A stable burning condition was first reached. While keeping the flow rates of air and other fuel components fixed, the hydrogen flow rate was increased incrementally until the upstream-propagating flame suddenly flashed from the combustion chamber back into the plenum and quenched. There existed a condition at which appropriate changes in air/fuel flow rates could prevent the flame from irreversible flash-back; these conditions defined the recoverable operation limits. Spectral proper orthogonal decomposition results revealed a transition in flow characteristics from the precessing vortex core instability to Kelvin–Helmholtz (K–H) instability under recoverable conditions with increasing hydrogen, closely related to flow symmetry. A linear trend was observed between the bulk velocities under critical conditions and the corresponding laminar flame speeds, indicating a strong correlation between flow instability transition and flash-back limits.
Dissociation line and driving force for nucleation of the nitrogen hydrate from computer simulation. II. Effect of multiple occupancy
Authors: Torrejón Miguel J. , Algaba Jesús , Blas Felipe J.
Published: August 2024

In this work, we determine the dissociation line of the nitrogen (N2) hydrate by computer simulation using the TIP4P/Ice model for water and the TraPPE force field for N2. This work is the natural extension of Paper I, in which the dissociation temperature of the N2 hydrate has been obtained at 500, 1000, and 1500 bar [Algaba et al., J. Chem. Phys. 159, 224707 (2023)] using the solubility method and assuming single occupancy. We extend our previous study and determine the dissociation temperature of the N2 hydrate at different pressures, from 500 to 4500 bar, taking into account the single and double occupancy of the N2 molecules in the hydrate structure. We calculate the solubility of N2 in the aqueous solution as a function of temperature when it is in contact with a N2-rich liquid phase and when in contact with the hydrate phase with single and double occupancy via planar interfaces. Both curves intersect at a certain temperature that determines the dissociation temperature at a given pressure. We observe a negligible effect of occupancy on the dissociation temperature. Our findings are in very good agreement with the experimental data taken from the literature. We have also obtained the driving force for the nucleation of the hydrate as a function of temperature and occupancy at several pressures. As in the case of the dissociation line, the effect of occupancy on the driving force for nucleation is negligible. To the best of our knowledge, this is the first time that the effect of the occupancy on the driving force for nucleation of a hydrate that exhibits sII crystallographic structure is studied from computer simulation.
Reaction barriers at metal surfaces computed using the random phase approximation: Can we beat DFT in the generalized gradient approximation?
Authors: Oudot B. , Doblhoff-Dier K.
Published: August 2024

Reaction barriers for molecules dissociating on metal surfaces (as relevant to heterogeneous catalysis) are often difficult to predict accurately with density functional theory (DFT). Although the results obtained for several dissociative chemisorption reactions via DFT in the generalized gradient approximation (GGA), in meta-GGA, and for GGA exchange + van der Waals correlation scatter around the true reaction barrier, there is an entire class of dissociative chemisorption reactions for which GGA-type functionals collectively underestimate the reaction barrier. Little is known why GGA-DFT collectively fails in some cases and not in others, and we do not know whether other methods suffer from the same inconsistency. Here, we present barrier heights for dissociative chemisorption reactions obtained from the random phase approximation in the adiabatic-connection fluctuation-dissipation theorem (ACFDT-RPA) and from hybrid functionals with different amounts of exact exchange. By comparing the results obtained for the dissociative chemisorption reaction of H2 on Al(110) (where GGA-DFT collectively underestimates the barrier) and H2 on Cu(111) (where GGA-DFT scatters around the true barrier), we can gauge whether the inconsistent description of the systems persists for hybrid functionals and ACFDT-RPA. We find hybrid functionals to improve the relative description of the two systems, but to fall short of chemical accuracy. ACFDT-RPA improves the results further and leads to chemically accurate barriers for both systems. Together with an analysis of the density of states and the results from selected GGA, meta-GGA, and GGA exchange + van der Waals correlation functionals, these results allow us to discuss possible origins for the inconsistent behavior of GGA-based functionals for molecule–metal reaction barriers.
Energy landscapes for clusters of hexapeptides
Authors: Nicy  , Morgan John W. R. , Wales David J.
Published: August 2024

We present the results for energy landscapes of hexapeptides obtained using interfaces to the Large-scale Atomic/Molecular Massively Parallel Simulator (LAMMPS) program. We have used basin-hopping global optimization and discrete path sampling to explore the landscapes of hexapeptide monomers, dimers, and oligomers containing 10, 100, and 200 monomers modeled using a residue-level coarse-grained potential, Mpipi, implemented in LAMMPS. We find that the dimers of peptides containing amino acid residues that are better at promoting phase separation, such as tyrosine and arginine, have melting peaks at higher temperature in their heat capacity compared to phenylalanine and lysine, respectively. This observation correlates with previous work on the same uncapped hexapeptide monomers modeled using atomistic potential. For oligomers, we compare the variation in monomer conformations with radial distance and observe trends for selected angles calculated for each monomer. The LAMMPS interfaces to the GMIN and OPTIM programs for landscape exploration offer new opportunities to investigate larger systems and provide access to the coarse-grained potentials implemented within LAMMPS.
Electronic dynamics through conical intersections via non-Markovian stochastic Schrödinger equation with complex modes
Authors: Guo Yukai , Gao Xing
Published: August 2024

Conical intersections (CIs) play a crucial role in photochemical reactions, offering an efficient channel for ultrafast non-adiabatic relaxation of excited states. This significantly influences the reaction pathways and the resulting products. In this work, we utilize the non-Markovian stochastic Schrödinger equation with complex modes method to explore the dynamics of electronic transitions through conical intersections (CIs) in pyrazine. The linear vibronic coupling model serves as the foundational framework, incorporating both intra-state and inter-state electron–vibrational interactions. The dynamics of the excited electronic transitions are analyzed across varying strengths of system–bath coupling and different bath relaxation times. The accuracy of this method is demonstrated by comparing its predictions with those from the hierarchical equations of motion method.
Reconstruction of displacement responses of a supertall building during typhoons based on limited field measurements and a physics-informed machine learning model
Authors: Zhou Qi , Li Qiu-Sheng
Published: August 2024

Severe weather conditions during windstorms may result in unavailability of traditional displacement monitoring techniques for civil structures such as supertall buildings. To address this challenge, this paper develops a long short-term memory model with a physics-informed loss function to initially estimate the missing strain responses of structures during typhoons. Subsequently, the missing or unmeasured displacements of structures during typhoons are reconstructed using the estimated missing strain responses and limited field measurements (i.e., acceleration and strain responses), employing a displacement reconstruction method. The proposed methodology is validated using field measurements on a 600 m supertall building during Typhoon Lionrock, demonstrating the effectiveness in accurately reconstructing the missing displacements of the supertall building under typhoon conditions. Finally, the missing displacements of the supertall building during Super Typhoon Saola are reconstructed, and the accuracy of the reconstructed displacements is verified. This paper aims to offer a novel method for displacement reconstructions of supertall buildings during windstorms based on limited monitoring information, enabling real-time structural integrity monitoring while reducing maintenance costs and downtime.
Targeting spectroscopic accuracy for dispersion bound systems from ab initio techniques: Translational eigenstates of Ne@C70
Authors: Panchagnula K. , Graf D. , Johnson E. R. , Thom A. J. W.
Published: August 2024

We investigate the endofullerene system Ne@C70 by constructing a three-dimensional Potential Energy Surface (PES) describing the translational motion of the Ne atom. This is constructed from electronic structure calculations from a plethora of methods, including MP2, SCS-MP2, SOS-MP2, RPA@PBE, and C(HF)-RPA, which were previously used for He@C60 in Panchagnula et al. [J. Chem. Phys. 160, 104303 (2024)], alongside B86bPBE-25X-XDM and B86bPBE-50X-XDM. The reduction in symmetry moving from C60 to C70 introduces a double well potential along the anisotropic direction, which forms a test of the sensitivity and effectiveness of the electronic structure methods. The nuclear Hamiltonian is diagonalized using a symmetrized double minimum basis set outlined in Panchagnula and Thom [J. Chem. Phys. 159, 164308 (2023)], with translational energies having error bars ±1 and ±2 cm−1. We find no consistency between electronic structure methods as they find a range of barrier heights and minima positions of the double well and different translational eigenspectra, which also differ from the Lennard-Jones (LJ) PES given in Mandziuk and Bačić [J. Chem. Phys. 101, 2126–2140 (1994)]. We find that generating effective LJ parameters for each electronic structure method cannot reproduce the full PES nor recreate the eigenstates, and this suggests that the LJ form of the PES, while simple, may not be best suited to describe these systems. Even though MP2 and RPA@PBE performed best for He@C60, due to the lack of concordance between all electronic structure methods, we require more experimental data in order to properly validate the choice.
The effects of supercritical CO2 transient high-pressure impact on coal pore structure characteristics
Authors: Wang Wendi , Ji Huaijun , Hu Shaobin , Liu Xu , Zhang Chenglong
Published: August 2024

The impact of supercritical CO2 transient high-pressure fracturing on coal pore structure is studied here. This examination uses a CO2 fracturing test platform to obtained coal samples at fracturing pressures of 22.6, 26.7, and 30.6 MPa, and we investigated the effects of CO2 transient high-pressure impacts on the pore structure of the coal by means of low-temperature N2 adsorption experiments and CO2 adsorption experiments. The results demonstrate that the specific surface area of the coal samples increased by 60.4%, 200.7%, and 92.6%, and the cumulative total pore volume increased by 56%, 267%, and 77.8% under the pressure impacts of 22.6, 26.7, and 30.6 MPa, with a significant increase in the number of pores. The original pore morphology of coal can be changed by the supercritical CO2 transient high-pressure impact, and the creation of new pores across the whole pore diameter section can be catalyzed. The impact fracturing on the pore structure is mainly attributed to the impact of supercritical CO2 and extraction. The meso-pores and macro-pores of the coal are further expanded by the impact of supercritical CO2, while the micro-pores with chemical properties are primarily modified by the extraction. An impact pressure of 26.7 MPa has a more pronounced effect on the expansion of meso-pores and macro-pores, and its effect on micro-pores is less significant compared to that of the other two fracturing samples. Therefore, it is possible that a specific fracturing pressure can more effectively expand meso-pores and macro-pores while reducing the impact on micro-pores.
Life cycle assessment of greenhouse gas emissions and carbon mitigation methods in probiotic-fed broiler production
Authors: Chin H. W. , Tee T. P. , Tan N. P.
Published: August 2024

Context Livestock production contributes significantly to global anthropogenic greenhouse gas emissions. Probiotic-fed broiler production has been shown to reduce greenhouse emissions in other nations significantly, however, outcomes in Malaysia are unknown. Aims This study assesses the total greenhouse emissions of probiotic-fed broiler production from cradle to farm-gate using an accredited Life Cycle Assessment (LCA) tool, Greenhouse Accounting Framework (GAF). It determines the hotspot of greenhouse emissions and emission intensity of the farm in kg CO2-eq/kg liveweight. Three types of mitigation methods, i.e. selling untreated manure, composting, and conversion into biochar, were compared to identify their effectiveness. Methods The research involves three broiler houses with one production cycle. Fifty-four gas samples and 90 poultry litter samples were collected throughout the production cycle and analysed for the targeted gases – i.e. carbon dioxide, methane, nitrogen and volatile solid composition. Analysis results were used to estimate total greenhouse emissions from the farm using the LCA-GAF model. The mitigation efficiency achieved by selling untreated manure, composting, and biochar production is assessed by estimating the carbon stock mass. Key results A new LCA model based on probiotic-fed broiler production was generated, specifically using data obtained from the experiment. The experimental results indicated that energy consumption, i.e. electricity and fuel, have the highest greenhouse emissions (44%), followed by feed production with 40% of the total 53.51 t CO2-eq/house/cycle in the probiotic-fed broiler farm. The emissions intensity of the farm is 1.57 kg CO2-eq/kg liveweight. Estimates of the mitigation efficiency were compared among untreated manure, biochar, and compost. Conclusions Energy consumption, particularly electricity and fuel, contributed the highest greenhouse emissions in the probiotic-fed broiler production. The strategy of selling untreated poultry litter was the most effective carbon mitigation method. However, due to its adverse environmental and human health impacts, converting poultry litter into biochar is the preferable mitigation option. Implications This study is profound for the poultry industry and environmental sustainability. It highlights the crucial role of energy consumption in greenhouse emissions from the probiotic-fed broiler farm, and the necessity of addressing the environmental impacts. Implementing sustainable agricultural practices could lead to more ecological poultry production, contributing to global efforts in climate change mitigation.
Direct sequencing technologies for bacterial sexually transmitted infections
Authors: Jennison Amy , Pasricha Shivani , Azzato Francesca
Published: August 2024

There is an important role for direct sequencing of patient samples to complement traditional culture-based methods for bacterial sexually transmitted infections (STIs), effectively overcoming limitations posed by fastidious or unculturable pathogens such as Neisseria gonorrhoeae, Treponema pallidum, Mycoplasma genitalium and Chlamydia trachomatis. Metagenomic techniques can enable profiling of antimicrobial resistance (AMR), strain typing and microbiome analysis in the absence of a cultured isolate, contributing critical information to understanding epidemiological trends and guiding targeted therapies. Despite significant advancements, challenges persist, such as cost, bioinformatics complexity and ethical considerations. The paper discusses current applications, technological innovations, and future prospects for integrating metagenomics into routine bacterial STI surveillance, emphasising the need to identify cost and time-effective workflows and enhanced accessibility of genomic data. By addressing these challenges, direct sequencing promises to fill critical gaps in AMR monitoring and pathogen typing, offering new avenues for enhancing public health strategies in combating bacterial STIs worldwide.
Lipid composition of the mussel Mytilus galloprovincialis from the Black Sea: fatty acid-based indices as environmental biomarkers
Authors: Fokina N. N. , Chesnokova I. I.
Published: August 2024

Context Owing to the multiple functions of lipids and fatty acids in organisms, lipid composition can be used as an environmental biomarker of the health status of sentinel organisms in monitoring studies of aquatic ecosystems. Aims To study the lipid profile of the mussel Mytilus galloprovincialis from the Black Sea and to identify lipid compounds as environmental biomarkers. Methods Lipid and fatty acid compositions in the gills and digestive glands of mussels were analysed by chromatography. Key results Membrane-state fatty acid indices in phospholipids were quite stable in all the mussels examined. The fatty acid composition of triacylglycerols is primarily an indicator of the food source for mussels. The selective retention of arachidonic acid as well as the accumulation of non-methylene-interrupted fatty acids in mussels are assumed to be biomarkers of environmental stress. Conclusions The presence of regulatory mechanisms ensuring the stability of the membrane structure was confirmed in all studied mussels. Implications The content of minor phospholipid fractions (namely, phosphatidylinositol and sphingomyelin) and the distribution of some fatty acids and their indices among lipid classes in the gills and digestive glands of M. galloprovincialis can be used in the assessment of the health status of sentinel organisms.
Nutrient and moisture limitations reveal keystone metabolites linking rhizosphere metabolomes and microbiomes
Authors: Baker Nameer R. , Zhalnina Kateryna , Yuan Mengting , Herman Don , Ceja-Navarro Javier A. , Sasse Joelle , Jordan Jacob S. , Bowen Benjamin P. , Wu Liyou , Fossum Christina , Chew Aaron , Fu Ying , Saha Malay , Zhou Jizhong , Pett-Ridge Jennifer , Northen Trent R. , Firestone Mary K.
Published: August 2024

Plants release a wealth of metabolites into the rhizosphere that can shape the composition and activity of microbial communities in response to environmental stress. The connection between rhizodeposition and rhizosphere microbiome succession has been suggested, particularly under environmental stress conditions, yet definitive evidence is scarce. In this study, we investigated the relationship between rhizosphere chemistry, microbiome dynamics, and abiotic stress in the bioenergy crop switchgrass grown in a marginal soil under nutrient-limited, moisture-limited, and nitrogen (N)-replete, phosphorus (P)-replete, and NP-replete conditions. We combined 16S rRNA amplicon sequencing and LC-MS/MS-based metabolomics to link rhizosphere microbial communities and metabolites. We identified significant changes in rhizosphere metabolite profiles in response to abiotic stress and linked them to changes in microbial communities using network analysis. N-limitation amplified the abundance of aromatic acids, pentoses, and their derivatives in the rhizosphere, and their enhanced availability was linked to the abundance of bacterial lineages from Acidobacteria, Verrucomicrobia, Planctomycetes, and Alphaproteobacteria. Conversely, N-amended conditions increased the availability of N-rich rhizosphere compounds, which coincided with proliferation of Actinobacteria. Treatments with contrasting N availability differed greatly in the abundance of potential keystone metabolites; serotonin and ectoine were particularly abundant in N-replete soils, while chlorogenic, cinnamic, and glucuronic acids were enriched in N-limited soils. Serotonin, the keystone metabolite we identified with the largest number of links to microbial taxa, significantly affected root architecture and growth of rhizosphere microorganisms, highlighting its potential to shape microbial community and mediate rhizosphere plant–microbe interactions.