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For presentation at PCCC-7 - Post Carbon Capture Conference2023, Pittsburgh, PA, September 25-27, 2023.
ABSTRACT The first paper in this series showed that quantum chromodynamic axion dark matter, as a highly correlated Bose fluid, contains extra-classical physics on cosmological scales. The source of the derived extra-classical physics is exchange–correlation interactions induced by the constraints of symmetric particle exchange and interaxion correlations from self-gravitation. The paper also showed that the impact of extra-classical physics on early structure formation is marginal, as the exchange–correlation interaction is inherently non-linear. This paper continues the study of axion structure formation into the non-linear regime, considering the case of full collapse and virialization. The N-body method is chosen to study the collapse, and its algorithms are derived for a condensed Bose fluid. Simulations of isolated gravitational collapse are performed for both Bose and cold dark matter fluids using a prototype N-body code. Unique Bose structures are found to survive even the most violent collapses. Bose post-collapse features include dynamical changes to global structures, creation of new broad sub-structures, violations of classical binding energy conditions, and new fine structures. Effective models of the novel structures are constructed and possibilities for their observation are discussed.
Isopropyl 3-deoxy-α-D-ribo-hexopyranoside (isopropyl 3-deoxy-α-D-glucopyranoside), C 9 H 18 O 5 , (I), crystallizes from a methanol–ethyl acetate solvent mixture at room temperature in a 4C1 chair conformation that is slightly distorted towards the C5 S C1 twist-boat form. A comparison of the structural parameters in (I), methyl α-D-glucopyranoside, (II), α-D-glucopyranosyl-(1→4)-D-glucitol (maltitol), (III), and 3-deoxy-α-D-ribo-hexopyranose (3-deoxy-α-D-glucopyranose), (IV), shows that most endocyclic and exocyclic bond lengths, valence bond angles and torsion angles in the aldohexopyranosyl rings are more affected by anomeric configuration, aglycone structure and/or the conformation of exocyclic substituents, such as hydroxymethyl groups, than by monodeoxygenation at C3. The structural effects observed in the crystal structures of (I)–(IV) were confirmed though density functional theory (DFT) calculations in computed structures (I) c –(IV) c . Exocyclic hydroxymethyl groups adopt the gauche–gauche (gg) conformation (H5 anti to O6) in (I) and (III), and the gauche–trans (gt) conformation (C4 anti to O6) in (II) and (IV). The O-glycoside linkage conformations in (I) and (III) resemble those observed in disaccharides containing β-(1→4) linkages.
A series of compounds based on the macrocyclic ligand cyclohexanocucurbit[6]uril (Cy6Q[6]) with formulas (Ln(H{sub 2}O){sub 6}Cy6Q[6])·2(CdCl{sub 4})·H{sub 3}O·xH{sub 2}O [isomorphous with Ln=La (1), Ce (2), Pr (3) and Nd (4), x=11 (1), 11 (2), 10 (3) and 11 (4)], (Sm(H{sub 2}O){sub 5}Cy6Q[6])·2(CdCl{sub 4})·H{sub 3}O·10H{sub 2}O (5) and (Ln(H{sub 2}O){sub 5}(NO{sub 3})@Cy6Q[6])·2(CdCl{sub 4})·2H{sub 3}O·xH{sub 2}O [isomorphous with Ln=Gd (6), Tb (7) and Dy (8), x=8 (6), 6 (7) and 6 (8)], have been successfully synthesized by the self-assembly of Cy6Q[6] with the corresponding lanthanide nitrate under hydrochloric acid aqueous solution in the presence of CdCl{sub 2}. Single-crystal X-ray diffraction analyses revealed that compounds 1–8 all crystallize in monoclinic space group P2{sub 1}/c, and display 1D coordination polymer structures. The lanthanide contraction effect on the structures of 1–8 has also been investigated and discussed in detail. In contrast, the reaction of Cy6Q[6] with the Ho(NO){sub 3}, Tm(NO){sub 3}, Yb(NO){sub 3} under the same conditions resulted in the compounds 9–11 with formulas Cy6Q[6]·2(CdCl{sub 4})·2H{sub 3}O·xH{sub 2}O [isomorphous with x=10 (9), 10 (10), and 9 (11)], in which no lanthanide cations are observed. The structural difference of these compounds indicates that the Cy6Q[6] may be used in the separation of lanthanide cations. - Graphical abstract: The reaction of cyclohexanocucurbit[6]uril with lanthanide ions (La{sup 3+}, Ce{sup 3+}, Pr{sup 3+}, Nd{sup 3+}, Sm{sup 3+}, Gd{sup 3+}, Tb{sup 3+}, Dy{sup 3+}, Ho{sup 3+}, Tm{sup 3+} and Yb{sup 3+}) under hydrochloric acid in the presence of CdCl{sub 2} resulted in eleven compounds, which demonstrate interesting lanthanide contraction effect and provide a means of separating lanthanide ions. - Highlights: • Eleven compounds of the Ln{sup 3+} with the Cy6Q[6] were synthesized and described. • Compounds 1-8 demonstrate interesting lanthanide contraction effect. • In solid-state structures of compounds 9-11, no lanthanide ions were observed. • This study provides a means of separating lanthanides cations.
A major open topic in cuprates is the interplay between the lattice and electronic dynamics and the importance of their coupling to the mechanism of high-temperature superconductivity (HTSC). As evidenced by extended x-ray absorption fine structure (EXAFS) experiments, anharmonic structural effects are correlated with the charge dynamics and the transition to a superconducting phase in different HTSC compounds. Here, in this paper, we describe how structural anharmonic effects can be coupled to electronic and lattice dynamics in cuprate systems by performing the exact diagonalization of a prototype anharmonic many-body Hamiltonian on a relevant 6-atom cluster and show that the EXAFS results can be understood as a Kuramoto synchronization transition between coupled internal quantum tunneling of polarons associated with the two-site distribution of the copper–apical oxygen (Cu-O ap ) pair in the dynamic structure. The transition is driven by the anharmonicity of the lattice vibrations and promotes the pumping of charge, initially stored at the apical oxygen reservoirs, into the copper-oxide plane. Simultaneously, a finite projection of the internal quantum tunneling polaron extends to the copper–planar oxygen (Cu-O pl ) pair. All these findings allow an interpretation based on an effective quantum-mechanical triple-well potential associated with the oxygen sites of the 6-atom cluster, which accurately represents the phase synchronization of apical oxygens and lattice-assisted charge transfer to the CuO 2 plane.
EGAN-3F (Equivariant Graph Attention Network - 3D Conformers & Feature Fusion) presents an innovative approach for predicting binding affinity between small molecules and protein targets, a fundamental task in drug discovery. Traditional structure-based methods often depend on protein-ligand complex structures obtained from crystallography or molecular docking. In contrast, ligand-only machine learning models using 1D or 2D representations such as SMILES have been developed to predict binding affinity without structural information about the target; however, their accuracy is often limited due to the lack of 3D ligand information. EGAN-3F addresses this limitation by integrating spatially aware graph learning with traditional descriptor-based features. We systematically investigate how combining 2D and 3D molecular representations enhances binding affinity prediction from SMILES strings. This approach underscores the importance of modeling conformational diversity and incorporating chemically meaningful descriptors to improve predictive accuracy. The key innovation of EGAN-3F lies in its ability to achieve robust ligand-based binding affinity predictions without requiring protein-ligand complex structures, effectively bridging the gap between purely structural and ligand-only modeling paradigms.
The origin of the near-infrared photoluminescence (PL) from thiolate-protected gold nanoclusters (Au NCs, <2 nm) has long been controversial, and the exact mechanism for the enhancement of quantum yield (QY) in many works remains elusive. Meanwhile, based upon the sole steady-state PL analysis, it is still a major challenge for researchers to map out a definitive relationship between the atomic structure and the PL property and understand how the Au(0) kernel and Au(I)–S surface contribute to the PL of Au NCs. Herein, we provide a paradigm study to address the above critical issues. By using a correlated series of “mono-cuboctahedral kernel” Au NCs and combined analyses of steady-state, temperature-dependence, femtosecond transient absorption, and Stark spectroscopy measurements, we have explicitly mapped out a kernel-origin mechanism and clearly elucidate the surface–structure effect, which establishes a definitive atomic-level structure–emission relationship. A ~100-fold enhancement of QY is realized via suppression of two effects: (i) the ultrafast kernel relaxation and (ii) the surface vibrations. Furthermore the new insights into the PL origin, QY enhancement, wavelength tunability, and structure–property relationship constitute a major step toward the fundamental understanding and structural-tailoring-based modulation and enhancement of PL from Au NCs.
Cellulose is typically characterized as a mixture of crystalline and amorphous material. A large part of the general understanding of the chemical, biochemical and physical properties of cellulosic materials is thought to depend on the consequences of the ratio of these components. For example, amorphous materials are said to be more reactive and have less tensile strength but comprehensive understanding and definitive analysis remain elusive. Ball milling has been used for decades to increase the ratio of amorphous material. The present work used 13 techniques to follow the changes in cotton fibers (nearly pure cellulose) after ball milling for 15, 45 and 120 min. X-ray diffraction results were analyzed with the Rietveld method; DNP (dynamic nuclear polarization) natural abundance 2D NMR studies in the next paper in this issue assisted with the interpretation of the 1D analyses in the present work. A conventional NMR model’s paracrystalline and inaccessible crystallite surfaces were not needed in the model used for the DNP studies. Sum frequency generation (SFG) spectroscopy also showed profound changes as the cellulose was decrystallized. Optical microscopy and field emission-scanning electron microscopy results showed the changes in particle size; molecular weight and carbonyl group analyses by gel permeation chromatography confirmed chemical changes. Specific surface areas and pore sizes increased. Fourier transform infrared (FTIR) and Raman spectroscopy also indicated progressive changes; some proposed indicators of crystallinity for FTIR were not in good agreement with our results. Thermogravimetric analysis results indicated progressive increase in initial moisture content and some loss in stability. Although understanding of structural changes as cellulose is amorphized by ball milling is increased by this work, continued effort is needed to improve agreement between the synchrotron and laboratory X-ray methods used herein and to provide physical interpretation of the SFG results.
Nuclear quantum effects (NQEs) have a significant influence on the hydrogen bonds in water and aqueous solutions and have thus been the topic of extensive studies. However, the microscopic origin and the corresponding temperature dependence of NQEs have been elusive and still remain the subject of ongoing discussion. Previous x-ray scattering investigations indicate that NQEs on the structure of water exhibit significant temperature dependence. Here, by performing wide-angle x-ray scattering of H 2 O and D 2 O droplets at temperatures from 275 K down to 240 K, we determine the temperature dependence of NQEs on the structure of water down to the deeply supercooled regime. The data reveal that the magnitude of NQEs on the structure of water is temperature independent, as the structure factor of D 2 O is similar to H 2 O if the temperature is shifted by a constant 5 K, valid from ambient conditions to the deeply supercooled regime. Analysis of the accelerated growth of tetrahedral structures in supercooled H 2 O and D 2 O also shows similar behavior with a clear 5 K shift. The results indicate a constant compensation between NQEs delocalizing the proton in the librational motion away from the bond and in the OH stretch vibrational modes along the bond. In conclusion, this is consistent with the fact that only the vibrational ground state is populated at ambient and supercooled conditions.
Optical extinction spectra calculated via multisphere T-matrices for nanoparticles with different concentrations of metals and different architectures (core–shell, inverse core–shell, or alloy) are considered. A method is proposed for determination of architecture of nanoparticles (core–shell or alloy) from only data on the position of plasmon resonance and composition of components. The use of an optical spectrum fitting technique to the spectra of monodisperse noninteracting bimetallic nanoparticles with a predetermined structure appeared to be effective for the determination of the internal structure of nanoparticles, except large nanoparticles with a radius of more than 60 nm containing less than ∼25% silver atoms.
Transition-metal oxyhydroxides such as CoOOH are promising low-cost electrocatalysts for the selective electrooxidation of organic molecules, yet the influence of ubiquitous transition-metal impurities on their performance and durability remains poorly understood. Here, we experimentally probed the individual and synergistic electrochemical and structural effects of Ni and Mn incorporations into model CoOOH electrocatalysts toward an efficient benzyl alcohol oxidation reaction (BAOR). Comprehensive electrochemical, microscopic, and spectroscopic analyses reveal that Ni incorporation enhances charge-transfer kinetics and overall activity through the formation of catalytically active Ni 3+ sites, whereas Mn exhibited a more complex but interesting role. At the early stages of operation, Mn 4+ acts as a stabilizing surface layer that mitigates catalyst degradation but partially blocks Co sites before they undergo gradual leaching. The concurrent incorporation of both Ni and Mn yields a trimetallic 2NMC@NF electrocatalyst that integrates the activity benefits of Ni with the stability conferred by Mn, achieving 92.9% benzyl alcohol conversion and 91.4% Faradaic efficiency after 24 h at 1.5 V vs RHE. These findings elucidate how trace Ni and Mn impurities, often introduced from electrolytes or external sources, can modulate the lattice and electronic structure of CoOOH, offering a design strategy for enhancing both activity and long-term stability in electrocatalytic organic oxidation.
The Effective Field Theory of Large-Scale Structure (EFTofLSS) provides a consistent perturbative framework for describing the statistical distribution of cosmological large-scale structure. In a previous EFTofLSS calculation that involved the one-loop power spectra and tree-level bispectra, it was shown that the k-reach of the prediction for biased tracers is comparable for all investigated masses if suitable higher-derivative biases, which are less suppressed for more massive tracers, are added. However, it is possible that the non-linear biases grow faster with tracer mass than the linear bias, implying that loop contributions could be the leading correction to the bispectra. To check this, we include the one-loop contributions in a fit to numerical data in the limit of strongly enhanced higher-order biases. Here, we show that the resulting one-loop power spectra and higher-derivative plus leading one-loop bispectra fit the two- and three-point functions respectively up to k≃0.19 h Mpc -1 and ksime 0.14 h Mpc -1 at the percent level. We find that the higher-order bias coefficients are not strongly enhanced, and we argue that the gain in perturbative reach due to the leading one-loop contributions to the bispectra is relatively small. Thus, we conclude that higher-derivative biases provide the leading correction to the bispectra for tracers of a very wide range of masses.
The Effective Field Theory of Large-Scale Structure is a formalism that allows us to predict the clustering of Cosmological Large-Scale Structure in the mildly non-linear regime in an accurate and reliable way. In this paper, after validating our technique against several sets of numerical simulations, we perform the analysis for the cosmological parameters of the DR12 BOSS data. We assume Λ CDM, a fixed value of the baryon/dark-matter ratio, Ω b /Ω c , and of the tilt of the primordial power spectrum, n s , and no significant input from numerical simulations. By using the one-loop power spectrum multipoles, we measure the primordial amplitude of the power spectrum, A s , the abundance of matter, Ω m , and the Hubble parameter, H 0 , {to about 13% , 3.2% and 3.2% respectively, obtaining ln (10 10 A s )=2.72± 0.13 , 0Ω m =0.309± 0.01 , H 0 =68.5± 2.2 km/(s Mpc) at 68% confidence level. If we then add a CMB prior on the sound horizon, the error bar on H 0 is reduced to 1.6% .} These results are a substantial qualitative and quantitative improvement with respect to former analyses, and suggest that the EFTofLSS is a powerful instrument to extract cosmological information from Large-Scale Structure.
The mutation of SARS-CoV-2 influences viral function as residue replacements affect both physiochemical properties and folding conformations. Although a large amount of data on SARS-CoV-2 is available, the investigation of how viral functions change in response to mutations is hampered by a lack of effective structural analysis. Here, we exploit the advances of protein structure fingerprint technology to study the folding conformational changes induced by mutations. With integration of both protein sequences and folding conformations, the structures are aligned for SARS-CoV to SARS-CoV-2, including Alpha variant (lineage B.1.1.7) and Delta variant (lineage B.1.617.2). The results showed that the virus evolution with change in mutational positions and physicochemical properties increased the affinity between spike protein and ACE2, which plays a critical role in coronavirus entry into human cells. Additionally, these structural variations impact vaccine effectiveness and drug function over the course of SARS-CoV-2 evolution. The analysis of structural variations revealed how the coronavirus has gradually evolved in both structure and function and how the SARS-CoV-2 variants have contributed to more severe acute disease worldwide.
Abstract Photoinduced structural changes (PSC) is one of the fundamental excited‐state dynamic processes, and yet often very challenging to distinguish from competing electronic excited‐state relaxation channels having similar or even comparable timescales. Here, we report a detailed study on the PSC of a pyrazolate bridged platinum(II) binuclear complex, BFPtPZ (C^NPt(μ‐pz′) 2 PtC^N, C^N=2‐(2,4‐difluorophenyl)pyridine, pz′=pyrazolate), a molecular butterfly, using time‐correlated single photon counting measurements at different wavelengths and sample temperatures. Analysis of the results obtained using dichloromethane (DCM) and ethylene carbonate (EC) as solvents enabled us to reveal an unexpected, strong solvent effect on the PSC processes. We show that a rapid PSC process with a characteristic timescale of 323 ps is observed in DCM, which leads to an excitation equilibrium between the ligand center/metal‐to‐ligand charge transfer ( 3 LC/MLCT) and metal‐metal‐to‐ligand charge transfer ( 3 MMLCT) triplet states. The subsequent relaxation from these electronic states to the ground state takes place in several nanoseconds. In contrast, the corresponding PSC process in EC appears slow at all temperatures studied in our experiments and showed no sign of such excitation equilibrium. The observed solvent effect is found to arise from distinct solvent properties including their viscosities and polarities as well as the peculiar electronic excited‐states of the butterfly‐like molecules with charge transfer character.
It is a serial/parallel code for fast electron beam longitudinal forward or backward tracking through an electron linear accelerator. This codes includes longitudinal space-charge effect, structure and resistive wall wakefields, and longitudinal coherent synchrotron radiation effect. To use it as a parallel code, please comment out the "use mpistub" in BeamBunch.f90, rename mpif.h as mpif.hh, and use the Makefile_parallel as Makefile.