12,117 results on '"Alexandrova, A."'
Search Results
2. $^{229}\mathrm{ThF}_4$ thin films for solid-state nuclear clocks
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Zhang, Chuankun, von der Wense, Lars, Doyle, Jack F., Higgins, Jacob S., Ooi, Tian, Friebel, Hans U., Ye, Jun, Elwell, R., Terhune, J. E. S., Morgan, H. W. T., Alexandrova, A. N., Tan, H. B. Tran, Derevianko, Andrei, and Hudson, Eric R.
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Physics - Atomic Physics ,Nuclear Experiment ,Physics - Optics ,Quantum Physics - Abstract
After nearly fifty years of searching, the vacuum ultraviolet $^{229}$Th nuclear isomeric transition has recently been directly laser excited [1,2] and measured with high spectroscopic precision [3]. Nuclear clocks based on this transition are expected to be more robust [4,5] than and may outperform [6,7] current optical atomic clocks. They also promise sensitive tests for new physics beyond the standard model [5,8,9]. In light of these important advances and applications, a dramatic increase in the need for $^{229}$Th spectroscopy targets in a variety of platforms is anticipated. However, the growth and handling of high-concentration $^{229}$Th-doped crystals [5] used in previous measurements [1-3,10] are challenging due to the scarcity and radioactivity of the $^{229}$Th material. Here, we demonstrate a potentially scalable solution to these problems by demonstrating laser excitation of the nuclear transition in $^{229}$ThF$_4$ thin films grown with a physical vapor deposition process, consuming only micrograms of $^{229}$Th material. The $^{229}$ThF$_4$ thin films are intrinsically compatible with photonics platforms and nanofabrication tools for integration with laser sources and detectors, paving the way for an integrated and field-deployable solid-state nuclear clock with radioactivity up to three orders of magnitude smaller than typical \thor-doped crystals [1-3,10]. The high nuclear emitter density in $^{229}$ThF$_4$ also potentially enables quantum optics studies in a new regime. Finally, we describe the operation and present the estimation of the performance of a nuclear clock based on a defect-free ThF$_4$ crystal., Comment: 15 pages, 3 figures
- Published
- 2024
3. Radiative Decay of the $^{229m}$Th Nuclear Clock Isomer in Different Host Materials
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Pineda, S. V., Chhetri, P., Bara, S., Elskens, Y., Casci, S., Alexandrova, A. N., Au, M., Athanasakis-Kaklamanakis, M., Bartokos, M., Beeks, K., Bernerd, C., Claessens, A., Chrysalidis, K., Cocolios, T. E., Correia, J. G., De Witte, H., Elwell, R., Ferrer, R., Heinke, R., Hudson, E. R., Ivandikov, F., Kudryavtsev, Yu., Köster, U., Kraemer, S., Laatiaoui, M., Lica, R., Merckling, C., Morawetz, I., Morgan, H. W. T., Moritz, D., Pereira, L. M. C., Raeder, S., Rothe, S., Schaden, F., Scharl, K., Schumm, T., Stegemann, S., Terhune, J., Thirolf, P. G., Tunhuma, S. M., Bergh, P. Van Den, Van Duppen, P., Vantomme, A., Wahl, U., and Yue, Z.
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Nuclear Experiment - Abstract
A comparative vacuum ultraviolet spectroscopy study conducted at ISOLDE-CERN of the radiative decay of the $^{229m}$Th nuclear clock isomer embedded in different host materials is reported. The ratio of the number of radiative decay photons and the number of $^{229m}$Th embedded are determined for single crystalline CaF$_2$, MgF$_2$, LiSrAlF$_6$, AlN, and amorphous SiO$_2$. For the latter two materials, no radiative decay signal was observed and an upper limit of the ratio is reported. The radiative decay wavelength was determined in LiSrAlF$_6$ and CaF$_2$, reducing its uncertainty by a factor of 2.5 relative to our previous measurement. This value is in agreement with the recently reported improved values from laser excitation.
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- 2024
4. Aperiodic fragments in periodic solids: Eliminating the need for supercells and background charges in electronic structure calculations of defects
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Lavroff, Robert H., Kats, Daniel, Maschio, Lorenzo, Bogdanov, Nikolay, Alavi, Ali, Alexandrova, Anastassia N., and Usvyat, Denis
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Physics - Chemical Physics ,Condensed Matter - Materials Science ,Condensed Matter - Strongly Correlated Electrons - Abstract
To date, computational methods for modeling defects (vacancies, adsorbates, etc.) rely on periodic supercells in which the defect is far enough from its repeated image such that they can be assumed non-interacting. Defects in real solids, however, can be spaced microns or more apart, whereas affordable supercells for density functional theory calculations are no wider than a few nanometers. The relative proximity and periodic repetition of the defect's images may lead to unphysical artifacts, especially if the defect is charged and/or open-shell. Furthermore, to avoid divergence of the periodic electrostatics, a compensating background charge must be introduced if the defect is charged. Even if post-hoc corrections are used, this is a source of unquantifiable error and, in some cases, renders energies useless. In this communication, we introduce an embedding formalism such that a pristine, primitive unit cell may be used for the periodic mean field, after which atoms may be moved or charged within an embedded fragment. This fragment can then be treated with a post-Hartree Fock method to capture important electron correlations pertaining to the defect. By eliminating the need for compensating background charges and periodicity of the defect, we circumvent all associated unphysicalities and numerical issues. Furthermore, the primitive cell calculations drastically reduce computational expense compared to supercell approaches. This method is size-intensive with respect to energy differences and can be routinely applied even to multireference defects, localized excited states, etc. using a variety of fragment solvers. In examining with this approach bond-breaking in a fluorine-substituted graphane monolayer, a difficult testing ground for condensed-phase electronic structure methods, we observe key aspects of the dissociation pathway, specifically a covalent-to-ionic avoided crossing., Comment: This manuscript has not yet been submitted to a journal
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- 2024
5. Elucidating ultranarrow 2F7/2 to 2F5/2 absorption in ytterbium(iii) complexes.
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Li, Barry, Dickerson, Claire, Shin, Ashley, Zhao, Changling, Shen, Yi, He, Yongjia, Diaconescu, Paula, Alexandrova, Anastassia, and Caram, Justin
- Abstract
Achieving ultranarrow absorption linewidths in the condensed phase enables optical state preparation of specific non-thermal states, a prerequisite for quantum-enabled technologies. The 4f orbitals of lanthanide(iii) complexes are often referred to as atom-like, reflecting their isolated nature, and are promising substrates for the optical preparation of specific quantum states. To better understand the photophysical properties of 4f states and assess their potential for quantum applications, theoretical building blocks are required for rapid screening. In this study, an atomic-level perturbative calculation (i.e., spin-orbit crystal field, SOCF) is applied to various Yb(iii) complexes to investigate their linear absorption and emission through a fitting mechanism of their experimentally determined transition energies and oscillator strengths. In particular, the optical properties of (thiolfan)YbCl(THF) (thiolfan = 1,1-bis(2,4-di-tert-butyl-6-thiomethylenephenoxy)ferrocene), a recently reported complex with an ultranarrow optical linewidth, are computed and compared to those of other Yb(iii) compounds. Through a transition energy sampling study, major contributors to the optical linewidth are identified. We observe particularly isolated f-f transitions and narrow linewidths, which we attribute to two distinct factors. Firstly, the ultra-high atomic similarity of the orbitals involved in the optical transition, along with the presence of an anisotropic crystal field, collectively contribute to the observed narrow transitions. Secondly, we note highly correlated excited-ground energy fluctuations that serve to greatly suppress inhomogeneous line-broadening. This article illustrates how SOCF can be used as a low-cost method to probe the influence of crystal field environment on the optical properties of Yb(iii) complexes to assist the development of novel lanthanide series quantum materials.
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- 2024
6. Directed Evolution of Protoglobin Optimizes the Enzyme Electric Field
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Chaturvedi, Shobhit S, Vargas, Santiago, Ajmera, Pujan, and Alexandrova, Anastassia N
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Chemical Sciences ,Bioengineering ,Biotechnology ,General Chemistry ,Chemical sciences ,Engineering - Abstract
To unravel why computational design fails in creating viable enzymes, while directed evolution (DE) succeeds, our research delves into the laboratory evolution of protoglobin. DE has adapted this protein to efficiently catalyze carbene transfer reactions. We show that the previously proposed enhanced substrate access and binding alone cannot account for increased yields during DE. The 3D electric field in the entire active site is tracked through protein dynamics, clustered using the affinity propagation algorithm, and subjected to principal component analysis. This analysis reveals notable changes in the electric field with DE, where distinct field topologies influence transition state energetics and mechanism. A chemically meaningful field component emerges and takes the lead during DE and facilitates crossing the barrier to carbene transfer. Our findings underscore intrinsic electric field dynamic's influence on enzyme function, the ability of the field to switch mechanisms within the same protein, and the crucial role of the field in enzyme design.
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- 2024
7. H and CO Co-Induced Roughening of Cu Surface in CO2 Electroreduction Conditions
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Zhang, Zisheng, Gee, Winston, Sautet, Philippe, and Alexandrova, Anastassia N
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Macromolecular and Materials Chemistry ,Chemical Sciences ,General Chemistry ,Chemical sciences ,Engineering - Abstract
The dynamic restructuring of Cu has been observed under electrochemical conditions, and it has been hypothesized to underlie the unique reactivity of Cu toward CO2 electroreduction. Roughening is one of the key surface phenomena for Cu activation, whereby numerous atomic vacancies and adatoms form. However, the atomic structure of such surface motifs in the presence of relevant adsorbates has remained elusive. Here, we explore the chemical space of Cu surface restructuring under coverage of CO and H in realistic electroreduction conditions, by combining grand canonical DFT and global optimization techniques, from which we construct a potential-dependent grand canonical ensemble representation. The regime of intermediate and mixed CO and H coverage─where structures exhibit some elevated surface Cu─is thermodynamically unfavorable yet kinetically inevitable. Therefore, we develop a quasi-kinetic Monte Carlo simulation to track the system's evolution during a simulated cathodic scan. We reveal the evolution path of the system across coverage space and identify the accessible metastable structures formed along the way. Chemical bonding analysis is performed on the metastable structures with elevated Cu*CO species to understand their formation mechanism. By molecular dynamics simulations and free energy calculations, the surface chemistry of the Cu*CO species is explored, and we identify plausible mechanisms via which the Cu*CO species may diffuse or dimerize. This work provides rich atomistic insights into the phenomenon of surface roughening and the structure of involved species. It also features generalizable methods to explore the chemical space of restructuring surfaces with mixed adsorbates and their nonequilibrium evolution.
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- 2024
8. Fermiology and transport properties of the proposed topological crystalline insulator SrAg4Sb2
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Green, J, Emmanouilidou, Eve, Morgan, Harry W. T., Laderer, William T., Hu, Chaowei, Loera, Jonathan, Alexandrova, Anastassia N., and Ni, Ni
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Condensed Matter - Materials Science - Abstract
Compared to time-reversal symmetry-protected Z2 topological insulators and Dirac/Weyl semimetals, there are significantly fewer candidates for topological crystalline insulators. SrAg4Sb2 is predicted to exhibit topological crystalline insulator behavior when considering spin-orbit coupling. In this study, we systematically investigate single crystals of SrAg4Sb2 using electrical transport and magnetic torque measurements, along with first-principles calculations. Our transport data reveals its compensated semimetal nature with a magnetoresistance up to around 700% at 2 K and 9 T. Analysis of de Haas-van Alphen oscillations uncovers a Fermi surface consisting of three distinct Fermi pockets with light effective masses. Comparison between the three-dimensional fermiology obtained from our oscillation data and the first-principles calculations demonstrates excellent agreement. This confirms the accuracy of the calculations, which indicate a band inversion centered at the {\Gamma} point and identify the existence of nontrivial tube and needle hole Fermi pockets at {\Gamma}, alongside one trivial diamond electron pocket at the T point in the Brillouin zone. Furthermore, symmetry and topology analysis results in two potential sets of topological invariants, suggesting the emergence of two-dimensional gapless Dirac surface states either on the ab planes or on both the ab planes and mirror planes, protected by crystal symmetries. Therefore, SrAg4Sb2 emerges as a promising candidate topological crystalline insulator., Comment: 9 pages, 5 figures
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- 2024
9. Laser excitation of the $^{229}$Th nuclear isomeric transition in a solid-state host
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Elwell, R., Schneider, Christian, Jeet, Justin, Terhune, J. E. S., Morgan, H. W. T., Alexandrova, A. N., Tan, H. B. Tran, Derevianko, Andrei, and Hudson, Eric R.
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Physics - Atomic Physics ,Nuclear Experiment - Abstract
LiSrAlF$_6$ crystals doped with $^{229}$Th are used in a laser-based search for the nuclear isomeric transition. Two spectroscopic features near the nuclear transition energy are observed. The first is a broad excitation feature that produces red-shifted fluorescence that decays with a timescale of a few seconds. The second is a narrow, laser-linewidth-limited spectral feature at $148.38219(4)_{\textrm{stat}}(20)_{\textrm{sys}}$ nm ($2020407.3(5)_{\textrm{stat}}(30)_{\textrm{sys}}$ GHz) that decays with a lifetime of $568(13)_{\textrm{stat}}(20)_{\textrm{sys}}$ s. This feature is assigned to the excitation of the $^{229}$Th nuclear isomeric state, whose energy is found to be $8.355733(2)_{\textrm{stat}}(10)_{\textrm{sys}}$ eV in $^{229}$Th:\thor:LiSrAlF$_6$., Comment: Submitted to Physical Review Letters on March 25, 2024
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- 2024
10. Towards a theory of steady-state solidification process with a quasi-equilibrium two-phase region
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Makoveeva, Eugenya V., Koroznikova, Irina E., Glebova, Alexandra E., Ivanov, Alexander A., Alexandrova, Irina V., Bulycheva, Svetlana V., Alexandrov, Dmitri V., and Toropova, Liubov V.
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- 2024
- Full Text
- View/download PDF
11. Identification of a Single Plasma Parcel during a Parker Solar Probe-Solar Orbiter radial alignment
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Berriot, Etienne, Démoulin, Pascal, Alexandrova, Olga, Zaslavsky, Arnaud, and Maksimovic, Milan
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Astrophysics - Solar and Stellar Astrophysics ,Physics - Space Physics - Abstract
Configurations where two spacecraft, such as Parker Solar Probe (PSP) and Solar Orbiter (SolO), are radially aligned provide opportunities to study the evolution of a single solar wind parcel during so called plasma line-ups. The most critical part of such studies is arguably the identification of what can be considered a same plasma crossing both spacecraft. We present here a method that allowed us to find what we believe to be the same plasma parcel passing through PSP ($\sim 0.075$ au) and SolO ($\sim 0.9$ au) after their radial alignment the 29/04/2021. We started by modeling the plasma propagation in order to get a first estimation of the plasma line-up intervals. The identification of the same density structure (with a crossing duration $\sim 1.5$ h) passing through the two spacecraft allows to precise and confirm this estimation. Our main finding is how stable the density structure is, remaining well recognizable from PSP to SolO despite its $\sim 137$ hours journey in the inner heliosphere. We moreover found that the studied slow solar wind plasma parcel undergone a significant acceleration (from $\sim 200$ to $\sim 300$ km/s) during its propagation., Comment: 12 pages, 9 figures, submitted to Astronomy and Astrophysics (A&A) - Revised version after referee report
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- 2024
- Full Text
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12. Fermiology and transport properties of the candidate topological crystalline insulator SrAg4Sb2
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Green, J, Emmanouilidou, Eve, Morgan, Harry WT, Laderer, William T, Hu, Chaowei, Loera, Jonathan, Alexandrova, Anastassia N, and Ni, Ni
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Quantum Physics ,Physical Sciences ,Condensed Matter Physics ,Macromolecular and materials chemistry ,Materials engineering ,Condensed matter physics - Published
- 2024
13. Repurposing mebendazole against triple-negative breast cancer CNS metastasis
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Rodrigues, Adrian J, Chernikova, Sophia B, Wang, Yuelong, Trinh, Thy TH, Solow-Cordero, David E, Alexandrova, Ludmila, Casey, Kerriann M, Alli, Elizabeth, Aggarwal, Abhishek, Quill, Tyler, Koegel, Ashley K, Feldman, Brian J, Ford, James M, and Hayden-Gephart, Melanie
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Biomedical and Clinical Sciences ,Oncology and Carcinogenesis ,Breast Cancer ,Neurosciences ,Cancer ,Women's Health ,2.1 Biological and endogenous factors ,5.1 Pharmaceuticals ,Triple Negative Breast Neoplasms ,Animals ,Humans ,Drug Repositioning ,Female ,Mebendazole ,Mice ,Mice ,Nude ,Mice ,Inbred BALB C ,Cell Movement ,Xenograft Model Antitumor Assays ,Cell Line ,Tumor ,Central Nervous System Neoplasms ,Cell Proliferation ,Breast cancer ,Leptomeningeal disease ,Drug repurposing ,Oncology & Carcinogenesis ,Oncology and carcinogenesis - Abstract
PurposeTriple-negative breast cancer (TNBC) often metastasizes to the central nervous system (CNS) and has the highest propensity among breast cancer subtypes to develop leptomeningeal disease (LMD). LMD is a spread of cancer into leptomeningeal space that speeds up the disease progression and severely aggravates the prognosis. LMD has limited treatment options. We sought to test whether the common anti-helminthic drug mebendazole (MBZ) may be effective against murine TNBC LMD.MethodsA small-molecule screen involving TNBC cell lines identified benzimidazoles as potential therapeutic agents for further study. In vitro migration assays were used to evaluate cell migration capacity and the effect of MBZ. For in vivo testing, CNS metastasis was introduced into BALB/c athymic nude mice through internal carotid artery injections of brain-tropic MDA-MB-231-BR or MCF7-BR cells. Tumor growth and spread was monitored by bioluminescence imaging and immunohistochemistry. MBZ was given orally at 50 and 100 mg/kg doses. MBZ bioavailability was assayed by mass spectrometry.ResultsBioinformatic analysis and migration assays revealed higher migratory capacity of TNBC compared to other breast cancer subtypes. MBZ effectively slowed down migration of TNBC cell line MDA-MB-231 and its brain tropic derivative MDA-MB-231-BR. In animal studies, MBZ reduced leptomeningeal spread, and extended survival in brain metastasis model produced by MDA-MB-231-BR cells. MBZ did not have an effect in the non-migratory MCF7-BR model.ConclusionsWe demonstrated that MBZ is a safe and effective oral agent in an animal model of TNBC CNS metastasis. Our findings are concordant with previous efforts involving MBZ and CNS pathology and support the drug's potential utility to slow down leptomeningeal spread.
- Published
- 2024
14. Chemical bonding dictates drastic critical temperature difference in two seemingly identical superconductors.
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Lavroff, Robert H, Munarriz, Julen, Dickerson, Claire E, Munoz, Francisco, and Alexandrova, Anastassia N
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Physical Sciences ,Chemical Sciences ,Physical Chemistry ,Condensed Matter Physics ,borides ,chemical bonding ,electron–phonon coupling ,superconductivity - Abstract
Though YB6 and LaB6 share the same crystal structure, atomic valence electron configuration, and phonon modes, they exhibit drastically different phonon-mediated superconductivity. YB6 superconducts below 8.4 K, giving it the second-highest critical temperature of known borides, second only to MgB2. LaB6 does not superconduct until near-absolute zero temperatures (below 0.45 K), however. Though previous studies have quantified the canonical superconductivity descriptors of YB6's greater Fermi-level (Ef) density of states and higher electron-phonon coupling (EPC), the root of this difference has not been assessed with full detail of the electronic structure. Through chemical bonding, we determine low-lying, unoccupied 4f atomic orbitals in lanthanum to be the key difference between these superconductors. These orbitals, which are not accessible in YB6, hybridize with π B-B bonds and bring this π-system lower in energy than the σ B-B bonds otherwise at Ef. This inversion of bands is crucial: the optical phonon modes we show responsible for superconductivity cause the σ-orbitals of YB6 to change drastically in overlap, but couple weakly to the π-orbitals of LaB6. These phonons in YB6 even access a crossing of electronic states, indicating strong EPC. No such crossing in LaB6 is observed. Finally, a supercell (the M k-point) is shown to undergo Peierls-like effects in YB6, introducing additional EPC from both softened acoustic phonons and the same electron-coupled optical modes as in the unit cell. Overall, we find that LaB6 and YB6 have fundamentally different mechanisms of superconductivity, despite their otherwise near-identity.
- Published
- 2024
15. Thermodynamic Equilibrium versus Kinetic Trapping: Thermalization of Cluster Catalyst Ensembles Can Extend Beyond Reaction Time Scales
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Poths, Patricia, Vargas, Santiago, Sautet, Philippe, and Alexandrova, Anastassia N
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Inorganic Chemistry ,Organic Chemistry ,Chemical Engineering ,Industrial biotechnology ,Organic chemistry ,Physical chemistry - Published
- 2024
16. Understanding the Adiabatic Evolution of Surface States in Tetradymite Topological Insulators under Electrochemical Conditions
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Weng, Guorong, Laderer, William, and Alexandrova, Anastassia N
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Physical Sciences ,Condensed Matter Physics ,Affordable and Clean Energy ,Chemical Sciences ,Chemical sciences ,Physical sciences - Abstract
Nontrivial surface states in topological materials have emerged as exciting targets for surface chemistry research. In particular, topological insulators have been used as electrodes in electrocatalytic reactions. Herein, we investigate the robustness of the topological surface states and band topology under electrochemical conditions, specifically in the presence of an electric double layer. First-principles band structure calculations are performed on the electrified (111) surfaces of Bi2Te3, Bi2Se3, and Sb2Te3 using an implicit electrolyte model. Our results demonstrate the adiabatic evolution of the surface states upon surface charging. Under oxidizing potentials, the surface states are shifted upward in energy, preserving the Dirac point on the surface and the band inversion in the bulk. Conversely, under reduced potentials, hybridization is observed between the surface and bulk states, suggesting a likely breakdown of topological protection. The position of the Fermi level, which dictates the working states in catalytic reactions, should ideally be confined within the bulk bandgap. This requirement defines a potential window for the effective application of topological electrocatalysis.
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- 2024
17. Role of Oxidizing Conditions in the Dispersion of Supported Platinum Nanoparticles Explored by Ab Initio Modeling
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Salcedo, Agustin, Alexandrova, Anastassia N, Loffreda, David, and Michel, Carine
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Chemical Sciences ,Physical Chemistry ,Nanotechnology ,Bioengineering ,Engineering ,Technology ,Chemical sciences - Published
- 2024
18. Platinum Surface Water Orientation Dictates Hydrogen Evolution Reaction Kinetics in Alkaline Media.
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Shah, Aamir Hassan, Zhang, Zisheng, Wan, Chengzhang, Wang, Sibo, Zhang, Ao, Wang, Laiyuan, Alexandrova, Anastassia N, Huang, Yu, and Duan, Xiangfeng
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Chemical Sciences ,General Chemistry ,Chemical sciences ,Engineering - Abstract
The fundamental understanding of sluggish hydrogen evolution reaction (HER) kinetics on a platinum (Pt) surface in alkaline media is a topic of considerable debate. Herein, we combine cyclic voltammetry (CV) and electrical transport spectroscopy (ETS) approaches to probe the Pt surface at different pH values and develop molecular-level insights into the pH-dependent HER kinetics in alkaline media. The change in HER Tafel slope from ∼110 mV/decade in pH 7-10 to ∼53 mV/decade in pH 11-13 suggests considerably enhanced kinetics at higher pH. The ETS studies reveal a similar pH-dependent switch in the ETS conductance signal at around pH 10, suggesting a notable change of surface adsorbates. Fixed-potential calculations and chemical bonding analysis suggest that this switch is attributed to a change in interfacial water orientation, shifting from primarily an O-down configuration below pH 10 to a H-down configuration above pH 10. This reorientation weakens the O-H bond in the interfacial water molecules and modifies the reaction pathway, leading to considerably accelerated HER kinetics at higher pH. Our integrated studies provide an unprecedented molecular-level understanding of the nontrivial pH-dependent HER kinetics in alkaline media.
- Published
- 2024
19. Improved Numerical Model of Motion of Artificial Satellites of the Moon and its Application in Research Features of the Dynamics of Circumlunar Objects
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Popandopulo, N. A., Alexandrova, A. G., Kucheryavchenko, N. A., Bordovitsyna, T. V., and Krasavin, D. S.
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- 2024
- Full Text
- View/download PDF
20. Dynamics of crystals in metastable liquids with applications to the growth of polypeptide hormones
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Alexandrov, Dmitri V., Ivanov, Alexander A., Alexandrova, Irina V., and Makoveeva, Eugenya V.
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- 2024
- Full Text
- View/download PDF
21. Extending the large molecule limit: The role of Fermi resonance in developing a quantum functional group
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Zhu, Guo-Zhu, Lao, Guanming, Dickerson, Claire E., Caram, Justin R., Campbell, Wesley C., Alexandrova, Anastassia N., and Hudson, Eric R.
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Physics - Chemical Physics - Abstract
Polyatomic molecules equipped with optical cycling centers (OCCs), enabling continuous photon scattering during optical excitation, are exciting candidates for advancing quantum information science. However, as these molecules grow in size and complexity the interplay of complex vibronic couplings on optical cycling becomes a critical, but relatively unexplored consideration. Here, we present an extensive exploration of Fermi resonances in large OCC-containing molecules, surpassing the constraints of harmonic approximation. High-resolution dispersed laser-induced fluorescence and excitation spectroscopy reveal Fermi resonances in calcium and strontium phenoxides and their derivatives. This resonance manifests as vibrational coupling leading to intensity borrowing by combination bands near optically active harmonic bands. The resulting additional vibration-changing decays require more repumping lasers for effective optical cycling. To mitigate these effects, we explore altering vibrational energy level spacing through substitutions on the phenyl ring or changes in the OCC itself. While the complete elimination of vibrational coupling in complex molecules remains challenging, our findings underscore the potential for significant mitigation, opening new avenues for optimizing optical cycling in large polyatomic molecules., Comment: 8 pages, 4 figures, 1 table, SI (15 pages)
- Published
- 2023
22. Single molecule superradiance for optical cycling
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Dickerson, Claire E., Alexandrova, Anastassia N., Narang, Prineha, and Philbin, John P.
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Physics - Optics - Abstract
Herein, we show that single molecules containing multiple optical cycling centers (CaO moieties) can exhibit superradiant phenomena. We demonstrate the accuracy of the Frenkel exciton model at describing these superradiant states via comparisons to high-level electronic structure methods. We then rationally design molecules with superradiant properties optimized for laser cooling. Lastly, we demonstrate how multi-photon superradiant phenomena can occur in these novel molecular systems.
- Published
- 2023
23. Competing Intermolecular and Molecule–Surface Interactions: Dipole–Dipole-Driven Patterns in Mixed Carborane Self-Assembled Monolayers
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White, Katherine E, Avery, Erin M, Cummings, Edison, Hong, Zixiang, Langecker, Jens, Vetushka, Aliaksei, Dušek, Michal, Macháček, Jan, Višnák, Jakub, Endres, Jan, Bastl, Zdeněk, Mete, Ersen, Alexandrova, Anastassia N, Baše, Tomáš, and Weiss, Paul S
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Chemical Sciences ,Physical Chemistry ,Engineering ,Materials ,Chemical sciences - Published
- 2024
24. A new look at the architecture and dynamics of the Hydra nerve net.
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Keramidioti, Athina, Schneid, Sandra, Busse, Christina, Cramer von Laue, Christoph, Bertulat, Bianca, Salvenmoser, Willi, Hess, Martin, Alexandrova, Olga, Glauber, Kristine, Steele, Robert, Hobmayer, Bert, Holstein, Thomas, and David, Charles
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Hydra ,developmental biology ,gap junction ,innexin ,nerve bundles ,nerve net ,neuroscience ,Animals ,Hydra ,Nerve Net ,Neurons ,Neurites ,Cnidaria - Abstract
The Hydra nervous system is the paradigm of a simple nerve net. Nerve cells in Hydra, as in many cnidarian polyps, are organized in a nerve net extending throughout the body column. This nerve net is required for control of spontaneous behavior: elimination of nerve cells leads to polyps that do not move and are incapable of capturing and ingesting prey (Campbell, 1976). We have re-examined the structure of the Hydra nerve net by immunostaining fixed polyps with a novel antibody that stains all nerve cells in Hydra. Confocal imaging shows that there are two distinct nerve nets, one in the ectoderm and one in the endoderm, with the unexpected absence of nerve cells in the endoderm of the tentacles. The nerve nets in the ectoderm and endoderm do not contact each other. High-resolution TEM (transmission electron microscopy) and serial block face SEM (scanning electron microscopy) show that the nerve nets consist of bundles of parallel overlapping neurites. Results from transgenic lines show that neurite bundles include different neural circuits and hence that neurites in bundles require circuit-specific recognition. Nerve cell-specific innexins indicate that gap junctions can provide this specificity. The occurrence of bundles of neurites supports a model for continuous growth and differentiation of the nerve net by lateral addition of new nerve cells to the existing net. This model was confirmed by tracking newly differentiated nerve cells.
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- 2024
25. H‑Induced Restructuring on Cu(111) Triggers CO Electroreduction in an Acidic Electrolyte
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Cheng, Dongfang, Alexandrova, Anastassia N, and Sautet, Philippe
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Chemical Sciences ,Physical Chemistry ,Physical Sciences ,Chemical sciences ,Physical sciences - Abstract
In acidic conditions, the electroreduction of CO or CO2 (noted CO(2)RR) on metal surfaces is conventionally hindered by intense competition with the hydrogen evolution reaction (HER). In this study, we present first-principles calculations of a mechanism wherein the formation of H-induced Cu adatoms on Cu(111) serves as a pivotal trigger for CORR in acidic environments. Through an analysis of the grand canonical surface state population, we elucidate that these newly formed adatoms create an array of active sites essential for both CO adsorption and subsequent reduction. Our ensemble-based kinetic models unveil the role of adatoms, enhancing the HER while simultaneously initiating CORR. Notably, the cumulative activity of the HER and CORR is contingent upon the combination of various surface states, with their individual contributions varying based on the electrode potential and pH. The interplay between surface state dynamics and electrochemical activity sheds new light on the potential-dependent nature of the active site and reaction kinetics governing CORR on Cu(111) in acidic media.
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- 2024
26. Extending the Large Molecule Limit: The Role of Fermi Resonance in Developing a Quantum Functional Group
- Author
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Zhu, Guo-Zhu, Lao, Guanming, Dickerson, Claire E, Caram, Justin R, Campbell, Wesley C, Alexandrova, Anastassia N, and Hudson, Eric R
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Quantum Physics ,Chemical Sciences ,Physical Chemistry ,Physical Sciences ,Atomic ,Molecular and Optical Physics ,Chemical sciences ,Physical sciences - Abstract
Polyatomic molecules equipped with optical cycling centers (OCCs), enabling continuous photon scattering during optical excitation, are exciting candidates for advancing quantum information science. However, as these molecules grow in size and complexity, the interplay of complex vibronic couplings on optical cycling becomes a critical but relatively unexplored consideration. Here, we present an extensive exploration of Fermi resonances in large-scale OCC-containing molecules using high-resolution dispersed laser-induced fluorescence and excitation spectroscopy. These resonances manifest as vibrational coupling leading to intensity borrowing by combination bands near optically active harmonic bands, which require additional repumping lasers for effective optical cycling. To mitigate these effects, we explore altering the vibrational energy level spacing through substitutions on the phenyl ring or changes in the OCC itself. While the complete elimination of vibrational coupling in complex molecules remains challenging, our findings highlight significant mitigation possibilities, opening new avenues for optimizing optical cycling in large polyatomic molecules.
- Published
- 2024
27. Hardening in Tungsten Tetraboride with the Addition of Carbon, Zirconium, and Silicon: Intrinsic vs Extrinsic Effects
- Author
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Akopov, Georgiy, Hu, Shanlin, Shumilov, Kirill D, Hamilton, Spencer G, Pangilinan, Lisa E, Mehmedović, Zerina, Yin, Hang, Robinson, Paul J, Roh, Inwhan, Kavner, Abby, Alexandrova, Anastassia N, Tolbert, Sarah H, and Kaner, Richard B
- Subjects
Inorganic Chemistry ,Chemical Sciences ,Engineering ,Materials ,Chemical sciences - Abstract
Alloys of tungsten tetraboride (WB4) with the addition of C and Si were prepared by arc-melting of the constituent elements. The phase purity was established by powder X-ray diffraction (PXRD) and surface morphology by scanning electron microscopy (SEM) analysis. Vickers hardness measurements showed hardness enhancement for alloys with a nominal composition of (W0.98Si0.02):11.6B and (W0.95C0.05):11.6B of 52.2 ± 3.0 and 50.5 ± 2.5 GPa, respectively, compared to 41.2 ± 1.4 GPa for pure WB4. (W0.92Zr0.08):11.6B was determined in previous work to have a hardness of 55.9 ± 2.8 GPa. Bulk moduli were calculated following analysis of high-pressure radial diffraction data and were determined to be 329 ± 4 (K0′ = 2) and 390 ± 9 (K0′ = 0.6) GPa for 8 atom % Zr and 5 atom % C-doping, respectively, compared to 326-339 GPa for pure WB4. Computational analysis was used to determine the dopant positions in the crystal structure, and it was found that Zr primarily substitutes W in the 2c position, Si substitutes for the entire B3 trimers, and C inserts in the Bhex-layer. The hardness enhancement in the case of Zr-doping is attributed primarily to extrinsic hardness effects (nanograin morphology), in the case of C─to intrinsic effects (interlayer bond strengthening), and in the intermediate case of Si─to both intrinsic and extrinsic effects (bond strengthening and fine surface morphology).
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- 2024
28. δ‐bonding and spin‐orbit coupling make SrAg4Sb2 a topological insulator
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Morgan, HWT, Laderer, WT, and Alexandrova, AN
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Chemical Sciences ,Topology ,Bond theory ,Transition metals ,Intermetallic phases ,Ab initio calculations ,General Chemistry ,Chemical sciences - Abstract
Bonding interactions and spin-orbit coupling in the topological insulator SrAg4 Sb2 are investigated using DFT with orbital projection analysis. Ag-Ag delta bonding is a key ingredient in the topological insulating state because the 4dxy+4dx2-y2${4d_{xy} + 4d_{x^2 - y^2 } }$ delta antibonding band forms a band inversion with the 5 s sigma bonding band. Spin-orbit coupling is required to lift d orbital degeneracies and lower the antibonding band enough to create the band inversion. These bonding effects are enabled by a longer-than-covalent Ag-Ag distance in the crystal lattice, which might be a structural characteristic of other transition metal based topological insulators. A simplified model of the topological bands is constructed to capture the essence of the topological insulating state in a way that may be engineered in other materials.
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- 2023
29. Nature of Zirconia on a Copper Inverse Catalyst Under CO2 Hydrogenation Conditions
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Kumari, Simran, Alexandrova, Anastassia N, and Sautet, Philippe
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Macromolecular and Materials Chemistry ,Chemical Sciences ,General Chemistry ,Chemical sciences ,Engineering - Abstract
The growing concern over the escalating levels of anthropogenic CO2 emissions necessitates effective strategies for its conversion to valuable chemicals and fuels. In this research, we embark on a comprehensive investigation of the nature of zirconia on a copper inverse catalyst under the conditions of CO2 hydrogenation to methanol. We employ density functional theory calculations in combination with the Grand Canonical Basin Hopping method, enabling an exploration of the free energy surface including a variable amount of adsorbates within the relevant reaction conditions. Our focus centers on a model three-atom Zr cluster on a Cu(111) surface decorated with various OH, O, and formate ligands, noted Zr3Ox (OH)y (HCOO)z/Cu(111), revealing major changes in the active site induced by various reaction parameters such as the gas pressure, temperature, conversion levels, and CO2/H2 feed ratios. Through our analysis, we have unveiled insights into the dynamic behavior of the catalyst. Specifically, under reaction conditions, we observe a large number of composition and structures with similar free energy for the catalyst, with respect to changing the type, number, and binding sites of adsorbates, suggesting that the active site should be regarded as a statistical ensemble of diverse structures that interconvert.
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- 2023
30. Does gut microbiota dysbiosis impact the metabolic alterations of hydrogen sulfide and lanthionine in patients with chronic kidney disease?
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Yuselys Garcia-Martinez, Elena Alexandrova, Valerio Iebba, Carlo Ferravante, Michelle Spinelli, Gianluigi Franci, Angela Amoresano, Alessandro Weisz, Francesco Trepiccione, Margherita Borriello, Diego Ingrosso, and Alessandra F. Perna
- Subjects
Chronic kidney disease ,Hemodialysis ,Kidney transplant ,Gut microbiota ,Dysbiosis ,Hydrogen sulfide (H2S) ,Microbiology ,QR1-502 - Abstract
Abstract Background Chronic Kidney Disease (CKD) is characterized by a methionine-related metabolic disorder involving reduced plasma levels of hydrogen sulfide (H2S) and increased lanthionine. The gut microbiota influences methionine metabolism, potentially impacting sulfur metabolite dysfunctions in CKD. We evaluated whether gut microbiota dysbiosis contributes to H2S and lanthionine metabolic alterations in CKD. Methods The gut microbiota of 88 CKD patients (non-dialysis, hemodialysis, and transplant patients) and 26 healthy controls were profiled using 16 S-amplicon sequencing. H2S and lanthionine concentrations were measured in serum and fecal samples using the methylene blue method and LC-MS/MS, respectively. Results The CKD population exhibited a tenfold increase in serum lanthionine associated with kidney dysfunction. Despite lanthionine retention, hemodialysis and transplant patients had significantly lower serum H2S than healthy controls. Fecal H2S levels were not altered or related to bloodstream H2S concentrations. Conversely, fecal lanthionine was significantly increased in CKD compared to healthy controls and associated with kidney dysfunction. Microbiota composition varied among CKD groups and healthy controls, with the greatest dissimilarity observed between hemodialysis and transplant patients. Changes relative to the healthy group included uneven Ruminococcus gnavus distribution (higher in transplant patients and lower in non-dialysis CKD patients), reduced abundance of the short-chain fatty acid-producing bacteria Alistipes indistinctus and Coprococcus eutactus among transplant patients, and depleted Streptococcus salivarius in non-dialysis CKD patients. A higher abundance of Methanobrevibacter smithii, Christensenella minuta, and Negativibacillus massiliensis differentiated hemodialysis patients from controls. No correlation was found between differentially abundant species and the metabolic profile that could account for the H2S and lanthionine alterations observed. Conclusions The metabolic deregulation of H2S and lanthionine observed in the study was not associated with alterations in the gut microbiota composition in CKD patients. Further research on microbial sulfur pathways may provide a better understanding of the role of gut microbiota in maintaining H2S and lanthionine homeostasis.
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- 2024
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31. The emergence of the PRC as the largest shipbuilding power in the world (1949–2019)
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Alexandrova M.V. and Mustafaeva E.Dzh.
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prc ,shipbuilding ,shipbuilding industry ,foreign technologies ,ship export ,excess capacity ,mergers and acquisitions ,high added value ,South Asia. Southeast Asia. East Asia ,KN ,Bibliography. Library science. Information resources ,History of Asia ,DS1-937 - Abstract
Shipbuilding is a typical strategic industry and, due to its high importance, is known as a complex one. The authors, based on foreign primary sources, for the first time in Russian scientific literature explore the path that the shipbuilding industry of the PRC has taken from “emergence from nothing” to the position in the largest shipbuilding country in the world, i.e. five main stages of development. The article describes the key steps taken towards the formation of the industry, both at the level of the creation of ministries and departments, and at the level of the emergence and development of scientific centers. The important government documents related to maintaining and stimulating the development of shipbuilding are studied in sufficient detail. The authors analyze the achievements and weaknesses of the modern Chinese shipbuilding industry. It is shown how China gradually rose to a leading position in the world shipbuilding from stage to stage, and what efforts were made by the state along this path.
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- 2024
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32. The concept of choosing a Xiaomi Corporation’s company name
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Alexandrova A.D.
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china ,xiaomi corporation ,branding ,symbol ,company name ,rice ,South Asia. Southeast Asia. East Asia ,KN ,Bibliography. Library science. Information resources ,History of Asia ,DS1-937 - Abstract
The article is dedicated to the reasons and process of choosing a company name in Xiaomi Corporation, whicn can be translated as “A small grain of rice”. Unlike many Chinese companies, Xiaomi Corporation’s choice of name was associated not only with a marketing move that would allow the company to successfully enter the international market and stand out from other brands, but also with the desire to demonstrate “its history”, which, by using certain symbols, would reflect such significant aspects of Chinese culture as respect for traditions, connection with historical memory, etc. The experience of Xiaomi Corporation shows how strongly traditions and history can influence modern ideas about the creation and development of a brand.
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- 2024
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33. Electronic Structure and Vibrational Stability of Copper-substituted Lead Apatite (LK-99)
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Cabezas-Escares, J., Barrera, N. F., Lavroff, R. H., Alexandrova, A. N., Cardenas, C., and Munoz, F.
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Condensed Matter - Superconductivity ,Condensed Matter - Materials Science - Abstract
Two recent preprints in the physics archive (arXiv) have called attention as they claim experimental evidence that a Cu-substituted apatite material (dubbed LK-99) exhibits superconductivity at room temperature and pressure. If this proves to be true, LK-99 will be a ``holy grail" of superconductors. In this work, we used Density Functional Theory (DFT+U) calculations to elucidate some key features of the electronic structure of LK-99. We find two different phases of this material: (i) a hexagonal lattice featuring metallic half-filled and spin-split bands, a nesting of the Fermi surface, a remarkably large electron-phonon coupling, but this lattice is vibrationally unstable. (ii) a triclinic lattice, with the Cu and surrounding O distorted. This lattice is vibrationally stable and its bands correspond to an insulator. In a crystal, the Cu atoms should oscillate between equivalent triclinic positions, with an average close to the hexagonal positions. We discuss the electronic structure expected from these fluctuations and if it is compatible with superconductivity.
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- 2023
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34. Embedded coherent structures from MHD to sub-ion scales in turbulent solar wind at 0.17 au
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Vinogradov, Alexander, Alexandrova, Olga, Démoulin, Pascal, Artemyev, Anton, Maksimovic, Milan, Mangeney, André, Vasiliev, Alexei, Petrukovich, Anatoly, and Bale, Stuart
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Astrophysics - Solar and Stellar Astrophysics ,Physics - Plasma Physics ,Physics - Space Physics - Abstract
We study intermittent coherent structures in solar wind magnetic turbulence from MHD to kinetic plasma scales using Parker Solar Probe data during its first perihelion (at 0.17 au), when the satellite was in the Alfv\'enic slow wind of 340 km/s. The coherent structures are energetic events localized in time and covering wide range of scales. We detect them using Morlet wavelets. For the first time, we apply a multi-scale analyses in physical space to study these structures. At MHD scales within the inertial range, times scales $\tau \in (1, 10^{2} )$ s, we find (i) current sheets including switchback boundaries and (ii) Alfv\'en vortices. Within these events, there are embedded structures at smaller scales: typically Alfv\'en vortices at ion scales, $\tau \in (0.08, 1)$ s, and a compressible vortices at sub-ion scales, $\tau \in (8,80)$ ms. The number of coherent structures grows toward smaller scales: we observe about $\sim 200$ events during 5 h time interval at MHD scales, $\sim 10^{3}$ events ai ion scales and $\sim 10^{4}$ events at sub-ion scales. In general, there are multiple structures of ion and sub-ion scales embedded within one MHD structure. There are also examples of ion and sub-ion scales structures outside of MHD structures. To quantify the relative importance of different type of structures, we do a statistical comparison of the observed structures with the expectations of models of the current sheets and vortices. This comparison is based on amplitude anisotropy of magnetic fluctuations within the structures. The results show the dominance of Alfv\'en vortices at all scales in contrast to the widespread view of dominance of current sheets. This means that Alfv\'en vortices are important building blocs of solar wind turbulence., Comment: Revised version of the article, accepted for publication in Astrophysical Journal, 30 pages, 15 figures
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- 2023
35. HelioSwarm: A Multipoint, Multiscale Mission to Characterize Turbulence
- Author
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Klein, Kristopher G., Spence, Harlan, Alexandrova, Olga, Argall, Matthew, Arzamasskiy, Lev, Bookbinder, Jay, Broeren, Theodore, Caprioli, Damiano, Case, Anthony, Chandran, Benjamin, Chen, Li-Jen, Dors, Ivan, Eastwood, Jonathan, Forsyth, Colin, Galvin, Antoinette, Genot, Vincent, Halekas, Jasper, Hesse, Michael, Hine, Butler, Horbury, Tim, Jian, Lan, Kasper, Justin, Kretzschmar, Matthieu, Kunz, Matthew, Lavraud, Benoit, Contel, Olivier Le, Mallet, Alfred, Maruca, Bennett, Matthaeus, William, Niehof, Jonathan, O'Brian, Helen, Owen, Christopher, Retino, Alessandro, Reynolds, Christopher, Roberts, Owen, Schekochihin, Alexander, Skoug, Ruth, Smith, Charles, Smith, Sonya, Steinberg, John, Stevens, Michael, Szabo, Adam, TenBarge, Jason, Torbert, Roy, Vasquez, Bernard, Verscharen, Daniel, Whittlesey, Phyllis, Wickizer, Brittany, Zank, Gary, and Zweibel, Ellen
- Subjects
Physics - Plasma Physics ,Astrophysics - Solar and Stellar Astrophysics ,Physics - Space Physics - Abstract
HelioSwarm (HS) is a NASA Medium-Class Explorer mission of the Heliophysics Division designed to explore the dynamic three-dimensional mechanisms controlling the physics of plasma turbulence, a ubiquitous process occurring in the heliosphere and in plasmas throughout the universe. This will be accomplished by making simultaneous measurements at nine spacecraft with separations spanning magnetohydrodynamic and sub-ion spatial scales in a variety of near-Earth plasmas. In this paper, we describe the scientific background for the HS investigation, the mission goals and objectives, the observatory reference trajectory and instrumentation implementation before the start of Phase B. Through multipoint, multiscale measurements, HS promises to reveal how energy is transferred across scales and boundaries in plasmas throughout the universe., Comment: Submitted to Space Science Reviews, 60 pages, 15 figures, 2 videos
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- 2023
36. Probing the limits of optical cycling in a predissociative diatomic molecule
- Author
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Sun, Qi, Dickerson, Claire E., Dai, Jinyu, Pope, Isaac M., Cheng, Lan, Neuhauser, Daniel, Alexandrova, Anastassia N., Mitra, Debayan, and Zelevinsky, Tanya
- Subjects
Physics - Atomic Physics ,Condensed Matter - Quantum Gases - Abstract
Molecular predissociation is the spontaneous, nonradiative bond breaking process that can occur upon excitation. In the context of laser cooling, predissociation is an unwanted consequence of molecular structure that limits the ability to scatter a large number of photons required to reach the ultracold regime. Unlike rovibrational branching, predissociation is irreversible since the fragments fly apart with high kinetic energy. Of particular interest is the simple diatomic molecule, CaH, for which the two lowest electronically excited states used in laser cooling lie above the dissociation threshold of the ground potential. In this work, we present measurements and calculations that quantify the predissociation probabilities affecting the cooling cycle. The results allow us to design a laser cooling scheme that will enable the creation of an ultracold and optically trapped cloud of CaH molecules. In addition, we use the results to propose a two-photon pathway to controlled dissociation of the molecules, in order to gain access to their ultracold fragments, including hydrogen., Comment: 16 pages, 4 figures
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- 2023
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37. Tracking Active Phase Behavior on Boron Nitride during the Oxidative Dehydrogenation of Propane Using Operando X‑ray Raman Spectroscopy
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Cendejas, Melissa C, Mellone, Oscar A Paredes, Kurumbail, Unni, Zhang, Zisheng, Jansen, Jacob H, Ibrahim, Faysal, Dong, Son, Vinson, John, Alexandrova, Anastassia N, Sokaras, Dimosthenis, Bare, Simon R, and Hermans, Ive
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Engineering ,Chemical Sciences ,Physical Chemistry ,General Chemistry ,Chemical sciences - Abstract
Hexagonal boron nitride (hBN) is a highly selective catalyst for the oxidative dehydrogenation of propane (ODHP) to propylene. Using a variety of ex situ characterization techniques, the activity of the catalyst has been attributed to the formation of an amorphous boron oxyhydroxide surface layer. The ODHP reaction mechanism proceeds via a combination of surface mediated and gas phase propagated radical reactions with the relative importance of both depending on the surface-to-void-volume ratio. Here we demonstrate the unique capability of operando X-ray Raman spectroscopy (XRS) to investigate the oxyfunctionalization of the catalyst under reaction conditions (1 mm outer diameter reactor, 500 to 550 °C, P = 30 kPa C3H8, 15 kPa O2, 56 kPa He). We probe the effect of a water cofeed on the surface of the activated catalyst and find that water removes boron oxyhydroxide from the surface, resulting in a lower reaction rate when the surface reaction dominates and an enhanced reaction rate when the gas phase contribution dominates. Computational description of the surface transformations at an atomic-level combined with high precision XRS spectra simulations with the OCEAN code rationalize the experimental observations. This work establishes XRS as a powerful technique for the investigation of light element-containing catalysts under working conditions.
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- 2023
38. From random to rational: improving enzyme design through electric fields, second coordination sphere interactions, and conformational dynamics.
- Author
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Chaturvedi, Shobhit, Bím, Daniel, Christov, Christo, and Alexandrova, Anastassia
- Abstract
Enzymes are versatile and efficient biological catalysts that drive numerous cellular processes, motivating the development of enzyme design approaches to tailor catalysts for diverse applications. In this perspective, we investigate the unique properties of natural, evolved, and designed enzymes, recognizing their strengths and shortcomings. We highlight the challenges and limitations of current enzyme design protocols, with a particular focus on their limited consideration of long-range electrostatic and dynamic effects. We then delve deeper into the impact of the protein environment on enzyme catalysis and explore the roles of preorganized electric fields, second coordination sphere interactions, and protein dynamics for enzyme function. Furthermore, we present several case studies illustrating successful enzyme-design efforts incorporating enzyme strategies mentioned above to achieve improved catalytic properties. Finally, we envision the future of enzyme design research, spotlighting the challenges yet to be overcome and the synergy of intrinsic electric fields, second coordination sphere interactions, and conformational dynamics to push the state-of-the-art boundaries.
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- 2023
39. Coenzyme Q10 trapping in mitochondrial complex I underlies Lebers hereditary optic neuropathy.
- Author
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Sadun, Alfredo, Fuller, Jack, Sadun, Lorenzo, Ajmera, Pujan, Alexandrova, Anastassia, and Barnes, Steven
- Subjects
Coenzyme Q10 ,blinding genetic disease ,mitochondria ,molecular dynamics simulation ,quantum electron tunneling ,Humans ,Optic Atrophy ,Hereditary ,Leber ,Reactive Oxygen Species ,Electron Transport Complex I ,Alanine - Abstract
How does a single amino acid mutation occurring in the blinding disease, Lebers hereditary optic neuropathy (LHON), impair electron shuttling in mitochondria? We investigated changes induced by the m.3460 G>A mutation in mitochondrial protein ND1 using the tools of Molecular Dynamics and Free Energy Perturbation simulations, with the goal of determining the mechanism by which this mutation affects mitochondrial function. A recent analysis suggested that the mutations replacement of alanine A52 with a threonine perturbs the stability of a region where binding of the electron shuttling protein, Coenzyme Q10, occurs. We found two functionally opposing changes involving the role of Coenzyme Q10. The first showed that quantum electron transfer from the terminal Fe/S complex, N2, to the Coenzyme Q10 headgroup, docked in its binding pocket, is enhanced. However, this positive adjustment is overshadowed by our finding that the mobility of Coenzyme Q10 in its oxidized and reduced states, entering and exiting its binding pocket, is disrupted by the mutation in a manner that leads to conditions promoting the generation of reactive oxygen species. An increase in reactive oxygen species caused by the LHON mutation has been proposed to be responsible for this optic neuropathy.
- Published
- 2023
40. Does gut microbiota dysbiosis impact the metabolic alterations of hydrogen sulfide and lanthionine in patients with chronic kidney disease?
- Author
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Garcia-Martinez, Yuselys, Alexandrova, Elena, Iebba, Valerio, Ferravante, Carlo, Spinelli, Michelle, Franci, Gianluigi, Amoresano, Angela, Weisz, Alessandro, Trepiccione, Francesco, Borriello, Margherita, Ingrosso, Diego, and Perna, Alessandra F.
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- 2024
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- View/download PDF
41. Combined analysis of genome-wide DNA methylome and transcriptome reveals the first epigenetic-based antibiotic-resistance mechanism in Acinetobacter baumannii
- Author
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Brancaccio, Rosario Nicola, Folliero, Veronica, Di Rosa, Domenico, Dell’Annunziata, Federica, Alexandrova, Elena, Smal, Marharyta, Giurato, Giorgio, Boccia, Giovanni, Panetta, Vittorio, Greco, Rita, Weisz, Alessandro, Rizzo, Francesca, and Franci, Gianluigi
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- 2024
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42. Small non-coding RNA transcriptomic profiling in adult and fetal human brain
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Smal, Marharyta, Memoli, Domenico, Alexandrova, Elena, Di Rosa, Domenico, D’Agostino, Ylenia, Russo, Fabio, Giurato, Giorgio, Nassa, Giovanni, Tarallo, Roberta, Weisz, Alessandro, and Rizzo, Francesca
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- 2024
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43. Dynamics of pulmonary mucosal cytotoxic CD8 T-cells in people living with HIV under suppressive antiretroviral therapy
- Author
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Alexandrova, Yulia, Yero, Alexis, Olivenstein, Ronald, Orlova, Marianna, Schurr, Erwin, Estaquier, Jerome, Costiniuk, Cecilia T., and Jenabian, Mohammad-Ali
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- 2024
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44. Primus Inter PARES: First among equals—practical strategies for young adult PAtient RESearch partners (PARES) by young adult PARES
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Rao, Sandy, Dimitropoulos, Gina, Jardine, Rae, Quickstad, Julien, Satam, Laetitia, Qureshi, Mohammad, Bui, Thyra, Todorova, Antoaneta Alexandrova, Tumaneng, Ysabelle, Suthakaran, Abitha, Dalley, Kaiden, Smith, Stacie, and Patten, Scott B.
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- 2024
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45. Preorganization of Langmuir Monolayers of Crown-Substituted 1,8-Naphthalimide to Enhance the Efficiency of Silver Ion Binding at Interfaces
- Author
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Alexandrova, A. V., Panchenko, P. A., and Selektor, S. L.
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- 2024
- Full Text
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46. Retrospective Estimation of Potential Mobility of Artificial Radionuclides (60Co, 137Сs, 152Eu, 154Eu) in Bottom Sediments of the Yenisei River
- Author
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Zotina, T. A., Alexandrova, Yu. V., Chuguevsky, A. V., and Melgunov, M. S.
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- 2024
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47. Probiotic Lactobacilli Ameliorate Antibiotic-Induced Cognitive and Behavioral Impairments in Mice
- Author
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Dina Yarullina, Vera Novoselova, Anastasia Alexandrova, Alisa Arslanova, Olga Yakovleva, Ilnar Shaidullov, Yury Nikolaev, Galina El-Registan, Vladimir Kudrin, and Guzel Sitdikova
- Subjects
antibiotics ,probiotics ,lactobacilli ,mice ,gut dysbiosis ,microbiota ,Microbiology ,QR1-502 - Abstract
Increasing evidence suggests that the gut microbiota, through the “microbiota–gut–brain axis”, can regulate anxiety, mood, and cognitive abilities such as memory and learning processes. Consistently with this, treatments altering the gut microbiota, such as antibiotics and probiotics, may influence brain function and impact behavior. The mechanisms that underlie the interplay between the intestinal microbiota and the brain have been intensively studied. We aimed to investigate the effects of two probiotic lactobacilli strains, Lacticaseibacillus rhamnosus 12L and Lactiplantibacillus plantarum 8PA3, on behavioral disorders in mice induced by a two-week parenteral treatment with broad-spectrum antibiotics. On completion of the treatment, the mice were subjected to behavioral tests, including the open field test (OFT), novel object recognition test (ORT), and T-maze test. Antibiotic-treated mice demonstrated anxiety-related behavior, decreased cognition, and retarded exploratory activity that were ameliorated by the administration of probiotics. As was determined by high-performance liquid chromatography (HPLC), both tested strains produced serotonin and its metabolite 5-hydroxyindoleacetic acid (5-HIAA), as well as dopamine, which was further metabolized into norepinephrine by L. plantarum 8PA3 and epinephrine by L. rhamnosus 12L. Moreover, these lactobacilli were found to harbor catecholamines and 3,4-dihydroxyphenylacetic acid (DOPAC) in their biomass when grown on MRS broth. Additionally, L. plantarum 8PA3 and L. rhamnosus 12L were able to impact oxidative stress via H2O2 production and antioxidant activity, as determined in this study by the ferrous oxidation–xylenol orange (FOX) assay and the 2,2-diphenyl-1-picrylhydrazyl (DPPH) free radical scavenging assay, respectively. The results obtained in this study support the role of probiotics as a promising therapeutic for neurological disorders. However, more investigations are required to confirm the clinical significance of this finding.
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- 2024
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48. Optical and Morphological Characterization of Nanoscale Oxides Grown in Low-Energy H+-Implanted c-Silicon
- Author
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Anna Szekeres, Sashka Alexandrova, Mihai Anastasescu, Hermine Stroescu, Mariuca Gartner, and Peter Petrik
- Subjects
low-energy H+ ion implantation of c-Si ,dry oxidation of H+-implanted silicon ,UV–vis–IR spectroscopic ellipsometry ,electroreflectance spectroscopy ,AFM imaging ,Physics ,QC1-999 ,Microscopy ,QH201-278.5 ,Microbiology ,QR1-502 ,Chemistry ,QD1-999 - Abstract
Nanoscale oxides grown in c-silicon, implanted with low-energy (2 keV) H+ ions and fluences ranging from 1013 cm−2 to 1015 cm−2 by RF plasma immersion implantation (PII), have been investigated. The oxidation of the implanted Si layers proceeded in dry O2 at temperatures of 700 °C, 750 °C and 800 °C. The optical characterization of the formed Si/SiOx structures was conducted by electroreflectance (ER) and spectroscopic ellipsometric (SE) measurements. From the ER and SE spectra analysis, the characteristic energy bands of direct electron transitions in Si are elaborated. The stress in dependence on hydrogenation conditions is considered and related to the energy shifts of the Si interband transitions around 3.4 eV. Silicon oxides, grown on PII Si at a low H+ fluence, have a non-stoichiometric nature, as revealed by IR-SE spectra analysis, while with an increasing H+ fluence in the PII Si substrates and/or the subsequent oxidation temperature the stoichiometric Si-O4 units in the oxides become predominant. The development of surface morphology is studied by atomic force microscopy (AFM) imaging. Oxidation of the H+-implanted Si surface region flattens out the surface pits created on the Si surface by H+ implants. Based on the evaluation of the texture index and mean fractal dimension, the isotropic and self-similar character of the studied surfaces is emphasized.
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- 2024
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49. THE LOW SERUM FERRITIN AS AN INDICATOR OF INADEQUATE NUTRITION IN INTERNATIONAL-LEVEL FEMALE SWIMMER
- Author
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Lubomir Petrov, Mihail Kachaunov, and Albena Alexandrova
- Subjects
swimmers ,iron status ,hematological status ,hormones ,sports achievements ,Sports ,GV557-1198.995 - Abstract
Introduction: Iron deficiency is a common feature in athletes, and optimizing iron levels may become a contributing factor to improved athletic performance. Purpose: This study aimed to evaluate body iron stores and their relationship with sports performance. It also sought correlations between the swimmers’ hematological, hormonal, anthropometric, and functional status and their sports achievements. Methodology: The research involved 19 athletes (11 women and 8 men) from the Bulgarian national swimming team. They were tested for maximal aerobic capacity on a cycle ergometer and had blood samples taken to determine iron status and hematological and hormonal markers. Their swimming achievements (Swimming points) were evaluated as a percentage of the world records in the respective discipline. Results: There were statistically significant differences between the female and male swimmers for Unbound Iron Binding Capacity (UIBC) and ferritin. A higher UIBC in women indicated lower iron levels in them. Among female swimmers, five had ferritin levels below 40 ng/mL. In women, a highly reliable correlation between the Swimming points and ferritin concentration (r = .68) was observed. All male swimmers had ferritin values above 40 ng/mL, and there was no reliable correlation between ferritin concentration and Swimming points, probably because ferritin was in the optimal range and is no longer a significant performance factor. Conclusions: In swimmers, the optimal serum ferritin concentration is probably in the range of 40–90 ng/mL. Many female swimmers have a relative iron deficiency with sub-optimal ferritin values. In competitive female swimmers, low ferritin level is an indicator of both iron deficiency and inadequate diet. It can be expected that an adequate nutritional regime in athletes with low ferritin values will lead both to the replenishment of iron stores and to an increase in muscle mass and, ultimately, to an improvement in sports performance.
- Published
- 2024
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50. Small non-coding RNA transcriptomic profiling in adult and fetal human brain
- Author
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Marharyta Smal, Domenico Memoli, Elena Alexandrova, Domenico Di Rosa, Ylenia D’Agostino, Fabio Russo, Giorgio Giurato, Giovanni Nassa, Roberta Tarallo, Alessandro Weisz, and Francesca Rizzo
- Subjects
Science - Abstract
Abstract Small non-coding RNAs (sncRNAs) make up ~1% of the transcriptome; nevertheless, they play significant roles in regulating cellular processes. Given the complexity of the central nervous system, sncRNAs likely hold particular importance in the human brain. In this study, we provide sncRNA transcriptomic profiles in a range of adult and prenatal brain regions, with a focus on piRNAs, due to their underexplored expression in somatic cells and tissue-specific nature. Using the WIND workflow, which combines two detection methods, we found 1333 (731 miRNAs, 249 piRNAs, 285 snoRNAs, and 68 other sncRNAs) and 1445 unique sncRNAs (770 miRNAs, 307 piRNAs, 289 snoRNAs, and 79 other sncRNAs) in developing and adult brains, respectively. Significant variations were found upon comparison of fetal and adult brain groups, with 82 miRNAs, 17 piRNAs, and 70 snoRNAs enriched in fetal brains and 22 miRNAs, 11 piRNAs in adult brains. This dataset represents a valuable resource for exploring the sncRNA roles in brain function, their involvement in neurological diseases, and the molecular mechanisms behind brain region interactions.
- Published
- 2024
- Full Text
- View/download PDF
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