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Results for “transition state”
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Visualization and modeling of inhibition of IL-1β and TNF-α mRNA transcription at the single-cell level
Abstract IL-1β and TNF-α are canonical immune response mediators that play key regulatory roles in a wide range of inflammatory responses to both chronic and acute conditions. Here we employ an automated microscopy platform for the analysis of messenger RNA (mRNA) expression of IL-1β and TNF-α at the single-cell level. The amount of IL-1β and TNF-α mRNA expressed in a human monocytic leukemia cell line (THP-1) is visualized and counted using single-molecule fluorescent in-situ hybridization (smFISH) following exposure of the cells to lipopolysaccharide (LPS), an outer-membrane component of Gram-negative bacteria. We show that the small molecule inhibitors MG132 (a 26S proteasome inhibitor used to block NF-κB signaling) and U0126 (a MAPK Kinase inhibitor used to block CCAAT-enhancer-binding proteins C/EBP) successfully block IL-1β and TNF-α mRNA expression. Based upon this single-cell mRNA expression data, we screened 36 different mathematical models of gene expression, and found two similar models that capture the effects by which the drugs U0126 and MG132 affect the rates at which the genes transition into highly activated states. When their parameters were informed by the action of each drug independently, both models were able to predict the effects of the combined drug treatment. From our data and models, we postulate that IL-1β is activated by both NF-κB and C/EBP, while TNF-α is predominantly activated by NF-κB. Our combined single-cell experimental and modeling efforts show the interconnection between these two genes and demonstrates how the single-cell responses, including the distribution shapes, mean expression, and kinetics of gene expression, change with inhibition.
Efficient crystal structure materials as reactive sorbent for the CO 2 and CH 4 adsorption and storage
The efficient dirubidium cobalt bis(dihydrogendiphosphate) dihydrate compound is successfully synthesized in a solution and used as a reactive sorbent for the CO 2 and CH 4 gases adsorption and storage. A crystal of this Rb 2 Co(H 2 P 2 O 7 ) 2 ·2H 2 O compound has been isolated and characterized by single X-ray diffraction analysis and was found to crystallize in the triclinic system (P$\overline{1}$) with the cell parameters (Å): 6.980(1), 7.370(1), 7.816(1), 81.74(1), 70.35(1), 86.34(1); V = 374.68(9) Å3, Z = 2. The crystal-packing consists of a three-dimensional framework made upon corners and edges sharing of [RbO 7 ], [H 2 P 2 O 7 ] and [CoO 6 ] entities, furthermore linked by a network of H-bonds. The UV–Vis spectroscopy revealed usual transitions between the ground state 4T1g and the upper levels 4T2g, 4A2g and 4T1g (P). Moreover, the CO 2 and CH 4 gases sorption measurements were successfully performed at two different temperatures (25 and 45 °C) and various pressures ranging from vacuum to 50 bar. Our results show that rate of CO 2 and CH 4 capturing was 3.10 mmol/g and 2.35 mmol/g at temperature 25 °C and pressure 50 bar, respectively. This compound showed a clear potential for CO 2 /CH 4 adsorption and storage thereby paving the way towards its exploration and adaptation for capturing and collecting carbon dioxide and greenhouse gases from the air, and their conversion into hydrocarbon fuels using existing mature technologies. We have also conducted density functional theory calculations to study the CO 2 and CH 4 adsorption properties of Rb 2 Co(H 2 P 2 O 7 ) 2 ·2H 2 O. The simulation results show enhanced adsorption of both types of molecules on the surface of the material.
Impact of CuInP 2 S 6 –metal interfaces on the stabilization of polar phases and polarization switching
The multifunctionality of two-dimensional ferroelectric CuInP 2 S 6 (CIPS) arises from the existence of multiple polar phases combined with a high ionic conductivity that facilitates polarization switching in unusual ways. The van der Waals (vdW) layered structure provides ultrathin flakes and ideal interfaces to integrate with other materials for microelectronics and neuromorphic elements. However, device integration necessitates metal contacts to read, write, or transmit signals. In this work, we find that different types of metal–CIPS interfaces strongly impact the stabilization of specific polar phases and the field-induced transitions between the polarization states. Cu electrodes initially suppress the piezoresponse, whereas, at CIPS–Ag interfaces, the electromechanical signal is increased. Under electric fields, the Cu electrodes, Ag electrodes and surrounding CIPS surfaces can show distinct switching behavior as different phases and polarization orientations are stabilized. These findings highlight that metal–CIPS interfaces provide the opportunity to optimize functional material properties.
Intercalated chalcogenides Fe 1/4 TaS 2 and Fe 1/3 TaS 2 under extreme pressure—temperature conditions
Intercalation is an important strategy for enhancing functionality in complex chalcogenides. This is because layered materials can be endowed with intriguing properties by filling the van der Waals gap with various ions and molecules, which, in addition to their unique chemistry, break symmetry in new ways. In order to explore the properties of intercalated metal dichalcogenides under extreme pressure-temperature conditions, we combine diamond anvil cell techniques, Raman scattering spectroscopy, magnetic susceptibility, and first-principles calculations to reveal the pressure–temperature phase diagram of Fe 1/3 TaS 2 . This system hosts a compression-driven structural phase transition to a polar state as well as remnant charge density wave signatures deriving from the host lamella of the 2H-parent compound. We also explore the role of different A-site patterns and determine that, by comparison, Fe 1/4 TaS 2 is soft and flexible due to the lower metal density inside the van der Waals gap. These findings open the door to entirely new states of matter with exciting property combinations, including metallicity, polarity, chirality, and altermagnetism – depending upon the conditions – that can support a wide range of spintronics and phononics applications.
Towards controlling the reversibility of anionic redox in transition metal oxides for high-energy Li-ion positive electrodes
Transition metal d-states and oxygen p-states overlap and oxygen lattice integrity dictates the oxygen redox reversibility in metal substituted Li 2 RuO 3 positive electrodes for Li-ion batteries.
Advanced spectroscopic studies of (PPh 4 ) 2 [Co(N 3 ) 4 ], a field-induced single-ion magnet
The high-spin Co II complex (PPh 4 ) 2 [Co(N 3 ) 4 ] (Co-N 3 )has been investigated using advanced spectroscopic techniques [far-IR magneto-spectroscopy (FIRMS), high-frequency and high-field EPR (HFEPR), and inelastic neutron scattering (INS)] to study its zero-field-splitting (ZFS), giving spin-Hamiltonian (SH) parameters. The analysis of multi-frequency HFEPR reveals the easy-axis anisotropy with a D value of −10.39(5) cm −1 and a rhombic ratio (E/D) of 0.21(1). The magnetic properties have also been probed by direct-current (DC) magnetometry, suggesting minor differences in anisotropy from the previously reported polymorph (Co-N 3 ′). Ligand-field theory (LFT) analysis indicates that the structures of Co-N 3 and Co-N 3 ′ are closer to D 2d symmetry than other symmetries considered. Alternate-current (AC) susceptibility reveals slow magnetic relaxation under an applied field, indicating that Co-N 3 is a field-induced single-ion magnet (SIM). Here, while both Co-N 3 and Co-N 3 ′ were studied by DC magnetometry, one unusual aspect of the current work on Co-N 3 is that advanced spectroscopies HFEPR, FIRMS, and INS were used to directly observe transitions between ZFS split states, giving accurate SH parameters.
A practical guide for crystal growth of van der Waals layered materials
This Tutorial provides an overview of the techniques that are most commonly utilized to grow bulk van der Waals crystals. The materials discussed were selected to highlight various challenges that are often encountered during crystal growth. Additionally, in relatively equal parts, the text covers melt-based techniques, vapor transport growths, and the characterization of crystal quality with an emphasis on structural and chemical homogeneities. Furthermore, pertinent details are given regarding the growth and characterization of many specific compounds, with examples mostly drawn from our own research, and an effort is made to highlight cases where the growths offer a particular lesson or the conditions have a significant impact on the crystal’s physical properties. A primary goal is to motivate more researchers to grow crystals by providing general descriptions and considerations for different growth techniques and equipment while sharing some of our own lessons learned and best practices for the growth and characterization of layered van der Waals crystals. The Tutorial is not written solely for aspiring crystal growers, however, because any researcher who collaborates with a crystal grower can benefit from having a greater understanding and appreciation of the processes of crystal growth and materials development.
Charge transfer rate constants for the carotenoid-porphyrin-C 60 molecular triad dissolved in tetrahydrofuran: The spin-boson model vs the linearized semiclassical approximation
Charge transfer rate constants were calculated for the carotenoid-porphyrin-C 60 (CPC 60 ) molecular triad dissolved in explicit tetrahydrofuran. The calculation was based on mapping the all-atom anharmonic Hamiltonian of this system onto the spin-boson Hamiltonian. The mapping was based on discretizing the spectral density from the time correlation function of the donor–acceptor potential energy gap, as obtained from all-atom molecular dynamics simulations. Different spin-boson Hamiltonians were constructed for each of the possible transitions between the three excited electronic states in two different triad conformations. The rate constants of three possible transitions were calculated via the quantum-mechanically exact Fermi’s golden rule (FGR), as well as a progression of more approximate expressions that lead to the classical Marcus expression. The advantage of the spin-boson approach is that once the mapping is established, the quantum-mechanically exact FGR and the hierarchy of approximations are known in closed form. The classical Marcus charge transfer rate constants obtained with the spin-boson Hamiltonians were found to reproduce those obtained from all-atom simulations with the linearized semiclassical approximation, thereby confirming the equivalence of the two approaches for this system. Furthermore, within the spin-boson Hamiltonian, we also found that the quantum-mechanically exact FGR rate constants were significantly enhanced compared to the classical Marcus theory rate constants for two out of three transitions in one of the two conformations under consideration. The results confirm that mapping to the spin-boson model can yield accurate predictions for charge transfer rate constants in a system as complex as CPC 60 dissolved in tetrahydrofuran.
Prediction of chlorine and fluorine crystal structures at high pressure using symmetry driven structure search with geometric constraints
The high-pressure properties of fluorine and chlorine are not yet well understood because both are highly reactive and volatile elements, which have made conducting diamond anvil cell and x-ray diffraction experiments a challenge. Here, we use ab initio methods to search for stable crystal structures of both elements at megabar pressures. We demonstrate how symmetry and geometric constraints can be combined to efficiently generate crystal structures that are composed of diatomic molecules. Furthermore, our algorithm extends the symmetry driven structure search method by adding constraints for the bond length and the number of atoms in a molecule while still maintaining generality. As a method of validation, we have tested our approach for dense hydrogen and reproduced the known molecular structures of Cmca-12 and Cmca-4. We apply our algorithm to study chlorine and fluorine in the pressure range of 10 GPa–4000 GPa while considering crystal structures with up to 40 atoms per unit cell. We predict chlorine to follow the same series of phase transformations as elemental iodine from Cmca to Immm to Fm3¯m, but at substantially higher pressures. We predict fluorine to transition from a C2/c to Cmca structure at 70 GPa, to a novel orthorhombic and metallic structure with P42/mmc symmetry at 2500 GPa, and finally to its cubic analog form with Pm3¯n symmetry at 3000 GPa.
Uncertainty Quantification for a Multi-phase Carbon Equation of State Model
Many physics models have tunable parameters that are calibrated by matching the model output to experimental or calculated data. However, given that calibration data often contain uncertainty and that different model parameter sets might result in a very similar simulated output for a finite calibration data set, it is advantageous to provide an ensemble of parameter sets that are consistent with the calibration data. Uncertainty quantification (UQ) provides a means to generate such an ensemble in a statistically rigorous fashion. In this work, we perform UQ for a multi-phase equation of state (EOS) model for carbon containing the diamond, graphite, and liquid phases. We use a Bayesian framework for the UQ and introduce a novel strategy for including phase diagram information in the calibration. The method is highly general and accurately reproduces the calibration data without any material-specific prior knowledge of the EOS model parameters.
Acoustic properties, elasticity, and equation of state of glycerol under pressure
Herein we employed high-pressure Brillouin scattering to study the pressure dependencies of acoustic modes of glycerol up to 14 GPa at 300 K. We observed longitudinal acoustic velocities and transverse acoustic velocities for the first time from 5 to 14 GPa. The results allow the determination of a complete set of elastic properties and an accurate determination of the pressure–volume (P–V) equation of state (EOS). EOS parameters, K 0 = 14.9 ± 1.8 GPa and K' 0 = 5.6 ± 0.5, were determined from fits to the data from ambient pressure to 14 GPa. Direct volume measurements of the P–V EOS are consistent with those determined by Brillouin scattering. A deviation from a Cauchy-like relationship for elastic properties was observed, and the pressure dependencies of the photoelastic constants and relaxation times were documented from 5 to 14 GPa. These results have broad implications for glass-forming liquids, viscoelastic theory, and mode coupling theory.
Photo-induced electron paramagnetic resonance: A means to identify defects and the defect level throughout the bandgap of ultrawide bandgap semiconductors
Ultrawide bandgap semiconductors (UWBGs) provide great promise for optical devices operating in the near to deep ultraviolet, and recently they have become a viable semiconducting material for high power electronics. From the power grid to electronic vehicles, the intention is to replace massively awkward components with the convenience of a solid state electronic “chip.” Unfortunately, the challenges faced by wide bandgap electronic materials, such as GaN and SiC, increase as the bandgap increases. A point defect, for example, can take on more charge states and energy configurations. This perspective describes a method to investigate the many charge states and their associated transitions—photo-induced electron paramagnetic resonance (photo-EPR) spectroscopy. Although not new to the study of defects in semiconductors, photo-EPR studies can probe the entire ultrawide bandgap given the appropriate light source for excitation. Examples provided here cover specific defects in UWBGs, AlN, and Ga2O3. The discussion also reminds us how the rapid pace of discovery surrounding this newest class of semiconductors is due, in part, to fundamental research studies of the past, some as far back as a century ago and some based on very different materials systems.
Time-reversal symmetry breaking in the Fe-chalcogenide superconductors
Significance In the Fe-chalcogenide superconductors, topology, superconductivity, and magnetism all come together to provide a platform for a range of exotic quantum phenomena. Topology and superconductivity can interact to give topological superconductivity capable of supporting Majorana fermions that could prove to be the basis of future qubit technology. The large spin–orbit interaction associated with the topological phenomena combined with magnetism can potentially result in the quantum anomalous Hall effect although the superconductivity will work against such. It is important that we understand the relevant roles of the different phenomena. Here we provide evidence of time-reversal symmetry breaking and associated mass acquisition in a topological surface state at the superconducting transition, an observation highly suggestive of the formation of surface ferromagnetism.
Band-selective gap opening by a C 4 -symmetric order in a proximity-coupled heterostructure Sr 2 VO 3 FeAs
Significance Heterostructures of correlated electronic systems offer versatile platforms for various types of quantum phases and their transitions. A common wisdom states that the proximity coupling between constituent layers plays a secondary role, because it is much weaker than the intralayer interactions. In this work, we present a counterexample of the belief. Namely, the proximity coupling between localized spins and itinerant electrons stabilizes an exotic electronic state with band-selective gap opening whose observation is done in a correlated heterostructure Sr 2 VO 3 FeAs. Our finding highlights that the proximity coupling can be an effective knob for exotic phases in correlated heterostructures.
Colloidal superionic conductors
Nanoparticles with highly asymmetric sizes and charges that self-assemble into crystals via electrostatics may exhibit behaviors reminiscent of those of metals or superionic materials. Here, we use coarse-grained molecular simulations with underdamped Langevin dynamics to explore how a binary charged colloidal crystal reacts to an external electric field. As the field strength increases, we find transitions from insulator (ionic state), to superionic (conductive state), to laning, to complete melting (liquid state). In the superionic state, the resistivity decreases with increasing temperature, which is contrary to metals, yet the increment decreases as the electric field becomes stronger. Additionally, we verify that the dissipation of the system and the fluctuation of charge currents obey recently developed thermodynamic uncertainty relation. Our results describe charge transport mechanisms in colloidal superionic conductors.
Elastocaloric evidence for a multicomponent superconductor stabilized within the nematic state in Ba(Fe 1− x Co x ) 2 As 2
The iron-based high-$T_c$ superconductors (SCs) exhibit rich phase diagrams with intertwined phases, including magnetism, nematicity, and superconductivity. The superconducting $T_c$ in many of these materials is maximized in the regime of strong nematic fluctuations, making the role of nematicity in influencing the superconductivity a topic of intense research. Here, in this study, we use the AC elastocaloric effect (ECE) to map out the phase diagram of Ba(Fe 1− x Co x ) 2 As 2 near optimal doping. The ECE signature at $T_c$ on the overdoped side, where superconductivity condenses without any nematic order, is quantitatively consistent with other thermodynamic probes that indicate a single-component superconducting state. In contrast, on the slightly underdoped side, where superconductivity condenses within the nematic phase, ECE reveals a second thermodynamic transition proximate to and below $T_c$. We rule out magnetism and reentrant tetragonality as the origin of this transition and find that our observations strongly suggest a phase transition into a multicomponent superconducting state. This implies the existence of a subdominant pairing instability that competes strongly with the dominant $s^±$ instability. Our results highlight the significant role of nematic order in determining the pairing symmetry close to optimal doping in this extensively studied iron-based SC, while also demonstrating the power of ECE in uncovering strain-tuned phase diagrams of quantum materials.
Static compression of rare earth metal holmium to 282;#8197;GPa
Abstract not provided