Comprehensive Comparison and Critical Assessment of RNA-Specific Force Fields

Molecular dynamics simulations play a pivotal role in elucidating the dynamic behaviors of RNA structures, offering a valuable complement to traditional methods such as nuclear magnetic resonance or X-ray. Despite this, the current precision of RNA force fields lags behind that of protein force fields. In this work, we systematically compared the performance of four RNA force fields (ff99bsc0χOL3, AMBERDES, ff99OL3_CMAP1, AMBERMaxEnt) across diverse RNA structures. Our findings highlight significant challenges in maintaining stability, particularly with regard to cross-strand and cross-loop hydrogen bonds. Furthermore, we observed the limitations in accurately describing the conformations of nonhelical structural motif, terminal nucleotides, and also base pairing and base stacking interactions by the tested RNA force fields. The identified deficiencies in existing RNA force fields provide valuable insights for subsequent force field development. Concurrently, these findings offer recommendations for selecting appropriate force fields in RNA simulations.

Long-term outcomes following hospital admission for COVID-19 versus seasonal influenza: a cohort study

BACKGROUND

Previous comparative analyses of people admitted to hospital for COVID-19 versus influenza evaluated the risk of death, hospital readmission, and a narrow set of health outcomes up to 6 months following infection. We aimed to do a comparative evaluation of both acute and long-term risks and burdens of a comprehensive set of health outcomes following hospital admission for COVID-19 or seasonal influenza.

METHODS

For this cohort study we used the health-care databases of the US Department of Veterans Affairs to analyse data from 81 280 participants admitted to hospital for COVID-19 between March 1, 2020, and June 30, 2022, and 10 985 participants admitted to hospital for seasonal influenza between Oct 1, 2015, and Feb 28, 2019. Participants were followed up for up to 18 months to comparatively evaluate risks and burdens of death, a prespecified set of 94 individual health outcomes, ten organ systems, overall burden across all organ systems, readmission, and admission to intensive care. Inverse probability weighting was used to balance the baseline characteristics. Cox and Poisson models were used to generate estimates of risk on both the relative scale and absolute scale as the event rate and disability-adjusted life-years (DALYs) per 100 persons.

FINDINGS

Over 18 months of follow-up, compared to seasonal influenza, the COVID-19 group had an increased risk of death (hazard ratio [HR] 1·51 [95% CI 1·45-1·58]), corresponding to an excess death rate of 8·62 (95% CI 7·55-9·44) per 100 persons in the COVID-19 group versus the influenza group. Comparative analyses of 94 prespecified health outcomes showed that COVID-19 had an increased risk of 68·1% (64 of 94) pre-specified health outcomes; seasonal influenza was associated with an increased risk of 6·4% (six of 94) pre-specified health outcomes, including three out of four pre-specified pulmonary outcomes. Analyses of organ systems showed that COVID-19 had a higher risk across all organ systems except for the pulmonary system, the risk of which was higher in seasonal influenza. The cumulative rates of adverse health outcomes across all organ systems were 615·18 (95% CI 605·17-624·88) per 100 persons in COVID-19 and 536·90 (527·38-544·90) per 100 persons in seasonal influenza, corresponding to an excess rate of 78·72 (95% CI 66·15-91·24) per 100 persons in COVID-19. The total number of DALYs across all organ systems were 287·43 (95% CI 281·10-293·59) per 100 persons in the COVID-19 group and 242·66 (236·75, 247·67) per 100 persons in the seasonal influenza group, corresponding to 45·03 (95% CI 37·15-52·90) higher DALYs per 100 persons in COVID-19. Decomposition analyses showed that in both COVID-19 and seasonal influenza, there was a higher burden of health loss in the post-acute than the acute phase; and comparatively, except for the pulmonary system, COVID-19 had a higher burden of health loss across all other organ systems than seasonal influenza in both the acute and post-acute phase. Compared to seasonal influenza, COVID-19 also had an increased risk of hospital readmission (excess rate 20·50 [95% CI 16·10-24·86] per 100 persons) and admission to intensive care (excess rate 9·23 [6·68-11·82] per 100 persons). The findings were consistent in analyses comparatively evaluating risks in seasonal influenza versus COVID-19 by individuals' respective vaccination status and in those admitted to hospital during the pre-delta, delta, and omicron eras.

INTERPRETATION

Although rates of death and adverse health outcomes following hospital admission for either seasonal influenza or COVID-19 are high, this comparative analysis shows that hospital admission for COVID-19 was associated with higher long-term risks of death and adverse health outcomes in nearly every organ system (except for the pulmonary system) and significant cumulative excess DALYs than hospital admission for seasonal influenza. The substantial cumulative burden of health loss in both groups calls for greater prevention of hospital admission for these two viruses and for greater attention to the care needs of people with long-term health effects due to either seasonal influenza or SARS-CoV-2 infection.

FUNDING

US Department of Veterans Affairs.

Influence of the Magnetic Tip on Heterodimers in Electron Spin Resonance Combined with Scanning Tunneling Microscopy

Investigating the quantum properties of individual spins adsorbed on surfaces by electron spin resonance combined with scanning tunneling microscopy (ESR-STM) has shown great potential for the development of quantum information technology on the atomic scale. A magnetic tip exhibiting high spin polarization is critical for performing an ESR-STM experiment. While the tip has been conventionally treated as providing a static magnetic field in ESR-STM, it was found that the tip can exhibit bistability, influencing ESR spectra. Ideally, the ESR splitting caused by the magnetic interaction between two spins on a surface should be independent of the tip. However, we found that the measured ESR splitting of a metal atom-molecule heterodimer can be tip-dependent. Detailed theoretical analysis reveals that this tip-dependent ESR splitting is caused by a different interaction energy between the tip and each spin of the heterodimer. Our work provides a comprehensive reference for characterizing tip features in ESR-STM experiments and highlights the importance of employing a proper physical model when describing the ESR tip, in particular, for heterospin systems.

Molecular dynamics simulations reveal the inhibition mechanism of Cdc42 by RhoGDI1

Cell division control protein 42 homolog (Cdc42), which controls a variety of cellular functions including rearrangements of the cell cytoskeleton, cell differentiation and proliferation, is a potential cancer therapeutic target. As an endogenous negative regulator of Cdc42, the Rho GDP dissociation inhibitor 1 (RhoGDI1) can prevent the GDP/GTP exchange of Cdc42 to maintain Cdc42 into an inactive state. To investigate the inhibition mechanism of Cdc42 through RhoGDI1 at the atomic level, we performed molecular dynamics (MD) simulations. Without RhoGDI1, Cdc42 has more flexible conformations, especially in switch regions which are vital for binding GDP/GTP and regulators. In the presence of RhoGDI1, it not only can change the intramolecular interactions of Cdc42 but also can maintain the switch regions into a closed conformation through extensive interactions with Cdc42. These results which are consistent with findings of biochemical and mutational studies provide deep structural insights into the inhibition mechanisms of Cdc42 by RhoGDI1. These findings are beneficial for the development of novel therapies targeting Cdc42-related cancers.

Molnupiravir and risk of post-acute sequelae of covid-19: cohort study

OBJECTIVE

To examine whether treatment with the antiviral agent molnupiravir during the first five days of SARS-CoV-2 infection is associated with reduced risk of post-acute adverse health outcomes.

DESIGN

Cohort study.

SETTING

US Department of Veterans Affairs.

PARTICIPANTS

229 286 participants who tested positive for SARS-CoV-2 between 5 January 2022 and 15 January 2023, had at least one risk factor for progression to severe covid-19, and survived the first 30 days after testing positive were enrolled. 11 472 participants received a prescription for molnupiravir within five days of the positive test result and 217 814 received no covid-19 antiviral or antibody treatment (no treatment group).

MAIN OUTCOME MEASURES

Risks of post-acute sequelae of SARS-CoV-2 (PASC, defined based on a prespecified set of 13 post-acute sequelae), post-acute death, post-acute hospital admission, and each individual post-acute sequela between the molnupiravir group and no treatment group were examined after application of inverse probability weighting to balance the treatment and no treatment groups. Post-acute outcomes were ascertained from 30 days after the first SARS-CoV-2 positive test result until end of follow-up. Risks on the relative scale (relative risk or hazard ratio) and absolute scale (absolute risk reduction at 180 days) were estimated.

RESULTS

Compared with no treatment, molnupiravir use within five days of a positive SARS-CoV-2 test result was associated with reduced risk of PASC (relative risk 0.86 (95% confidence interval 0.83 to 0.89); absolute risk reduction at 180 days 2.97% (95% confidence interval 2.31% to 3.60%)), post-acute death (hazard ratio 0.62 (0.52 to 0.74); 0.87% (0.62% to 1.13%)), and post-acute hospital admission (0.86 (0.80 to 0.93); 1.32% (0.72% to 1.92%)). Molnupiravir was associated with reduced risk of eight of the 13 post-acute sequelae: dysrhythmia, pulmonary embolism, deep vein thrombosis, fatigue and malaise, liver disease, acute kidney injury, muscle pain, and neurocognitive impairment. Molnupiravir was also associated with reduced risk of PASC in people who had not received a covid-19 vaccine, had received at one or two vaccine doses, and had received a booster dose, and in people with primary SARS-CoV-2 infection and reinfection.

CONCLUSIONS

In people with SARS-CoV-2 infection and at least one risk factor for progression to severe covid-19, compared with no treatment, molnupiravir use within five days of infection was associated with reduced risk of PASC in people who had not received a covid-19 vaccine, had received one or two vaccine doses, and had received a booster dose, and in those with primary SARS-CoV-2 infection and reinfection. Among people at high risk of progression to severe covid-19, molnupiravir use within five days of SARS-CoV-2 infection may be a viable approach to reduce the risk of PASC.

Research and Evaluation of the Allosteric Protein-Specific Force Field Based on a Pre-Training Deep Learning Model

Allosteric modulators are important regulation elements that bind the allosteric site beyond the active site, leading to the changes in dynamic and/or thermodynamic properties of the protein. Allosteric modulators have been a considerable interest as potential drugs with high selectivity and safety. However, current experimental methods have limitations to identify allosteric sites. Therefore, molecular dynamics simulation based on empirical force field becomes an important complement of experimental methods. Moreover, the precision and efficiency of current force fields need improvement. Deep learning and reweighting methods were used to train allosteric protein-specific precise force field (named APSF). Multiple allosteric proteins were used to evaluate the performance of APSF. The results indicate that APSF can capture different types of allosteric pockets and sample multiple energy-minimum reference conformations of allosteric proteins. At the same time, the efficiency of conformation sampling for APSF is higher than that for ff14SB. These findings confirm that the newly developed force field APSF can be effectively used to identify the allosteric pocket that can be further used to screen potential allosteric drugs based on these pockets.

Association of Treatment With Nirmatrelvir and the Risk of Post-COVID-19 Condition

Importance

Post-COVID-19 condition (PCC), also known as long COVID, affects many individuals. Prevention of PCC is an urgent public health priority.

Objective

To examine whether treatment with nirmatrelvir in the acute phase of COVID-19 is associated with reduced risk of PCC.

Design, Setting, and Participants

This cohort study used the health care databases of the US Department of Veterans Affairs (VA) to identify patients who had a SARS-CoV-2 positive test result between January 3, 2022, and December 31, 2022, who were not hospitalized on the day of the positive test result, who had at least 1 risk factor for progression to severe COVID-19 illness, and who had survived the first 30 days after SARS-CoV-2 diagnosis. Those who were treated with oral nirmatrelvir within 5 days after the positive test (n = 35 717) and those who received no COVID-19 antiviral or antibody treatment during the acute phase of SARS-CoV-2 infection (control group, n = 246 076) were identified.

Exposures

Treatment with nirmatrelvir or receipt of no COVID-19 antiviral or antibody treatment based on prescription records.

Main Outcomes and Measures

Inverse probability weighted survival models were used to estimate the association of nirmatrelvir (vs control) with post-acute death, post-acute hospitalization, and a prespecified panel of 13 post-acute COVID-19 sequelae (components of PCC) and reported in relative scale as relative risk (RR) or hazard ratio (HR) and in absolute scale as absolute risk reduction in percentage at 180 days (ARR).

Results

A total of 281 793 patients (mean [SD] age, 61.99 [14.96]; 242 383 [86.01%] male) who had a positive SARS-CoV-2 test result and had at least 1 risk factor for progression to severe COVID-19 illness were studied. Among them, 246 076 received no COVID-19 antiviral or antibody treatment during the acute phase of SARS-CoV-2 infection, and 35 717 received oral nirmatrelvir within 5 days after the positive SARS-CoV-2 test result. Compared with the control group, nirmatrelvir was associated with reduced risk of PCC (RR, 0.74; 95% CI, 0.72-0.77; ARR, 4.51%; 95% CI, 4.01-4.99), including reduced risk of 10 of 13 post-acute sequelae (components of PCC) in the cardiovascular system (dysrhythmia and ischemic heart disease), coagulation and hematologic disorders (pulmonary embolism and deep vein thrombosis), fatigue and malaise, acute kidney disease, muscle pain, neurologic system (neurocognitive impairment and dysautonomia), and shortness of breath. Nirmatrelvir was also associated with reduced risk of post-acute death (HR, 0.53; 95% CI, 0.46-0.61); ARR, 0.65%; 95% CI, 0.54-0.77), and post-acute hospitalization (HR, 0.76; 95% CI, 0.73-0.80; ARR, 1.72%; 95% CI, 1.42-2.01). Nirmatrelvir was associated with reduced risk of PCC in people who were unvaccinated, vaccinated, and boosted, and in people with primary SARS-CoV-2 infection and reinfection.

Conclusions and Relevance

This cohort study found that in people with SARS-CoV-2 infection who had at least 1 risk factor for progression to severe disease, treatment with nirmatrelvir within 5 days of a positive SARS-CoV-2 test result was associated with reduced risk of PCC across the risk spectrum in this cohort and regardless of vaccination status and history of prior infection; the totality of findings suggests that treatment with nirmatrelvir during the acute phase of COVID-19 may reduce the risk of post-acute adverse health outcomes.

Activation Mechanism of RhoA Caused by Constitutively Activating Mutations G14V and Q63L

RhoA, a member of Rho GTPases, regulates myriad cellular processes. Abnormal expression of RhoA has been implicated in various diseases, including cancers, developmental disorders and bacterial infections. RhoA mutations G14V and Q63L have been reported to constitutively activate RhoA. To figure out the mechanisms, in total, 1.8 μs molecular dynamics (MD) simulations were performed here on RhoA^WT and mutants G14V and Q63L in GTP-bound forms, followed by dynamic analysis. Both mutations were found to affect the conformational dynamics of RhoA switch regions, especially switch I, shifting the whole ensemble from the wild type's open inactive state to different active-like states, where T37 and Mg²⁺ played important roles. In RhoA^G14V, both switches underwent thorough state transition, whereas in RhoA^Q63L, only switch I was sustained in a much more closed conformation with additional hydrophobic interactions introduced by L63. Moreover, significantly decreased solvent exposure of the GTP-binding site was observed in both mutants with the surrounding hydrophobic regions expanded, which furnished access to water molecules required for hydrolysis more difficult and thereby impaired GTP hydrolysis. These structural and dynamic differences first suggested the potential activation mechanism of RhoA^G14V and RhoA^Q63L. Together, our findings complemented the understanding of RhoA activation at the atomic level and can be utilized in the development of novel therapies for RhoA-related diseases.

Exciton Transfer at Heterointerfaces of MoS2 Monolayers and Fluorescent Molecular Aggregates

Integration of distinct materials to form heterostructures enables the proposal of new functional devices based on emergent physical phenomena beyond the properties of the constituent materials. The optical responses and electrical transport characteristics of heterostructures depend on the charge and exciton transfer (CT and ET) at the interfaces, determined by the interfacial energy level alignment. In this work, heterostructures consisting of aggregates of fluorescent molecules (DY1) and 2D semiconductor MoS₂ monolayers are fabricated. Photoluminescence spectra of DY1/MoS₂ show quenching of the DY1 emission and enhancement of the MoS₂ emission, indicating a strong electronic interaction between these two materials. Nanoscopic mappings of the light-induced contact potential difference changes rule out the CT process at the interface. Using femtosecond transient absorption spectroscopy, the rapid interfacial ET process from DY1 aggregates to MoS₂ and a fourfold extension of the exciton lifetime in MoS₂ are elucidated. These results suggest that the integration of 2D inorganic semiconductors with fluorescent molecules can provide versatile approaches to engineer the physical characteristics of materials for both fundamental studies and novel optoelectronic device applications.

Spin-Selective Hole-Exciton Coupling in a V-Doped WSe2 Ferromagnetic Semiconductor at Room Temperature

While valley polarization with strong Zeeman splitting is the most prominent characteristic of two-dimensional (2D) transition metal dichalcogenide (TMD) semiconductors under magnetic fields, enhancement of the Zeeman splitting has been demonstrated by incorporating magnetic dopants into the host materials. Unlike Fe, Mn, and Co, V is a distinctive dopant for ferromagnetic semiconducting properties at room temperature with large Zeeman shifting of band edges. Nevertheless, little known is the excitons interacting with spin-polarized carriers in V-doped TMDs. Here, we report anomalous circularly polarized photoluminescence (CPL) in a V-doped WSe₂ monolayer at room temperature. Excitons couple to V-induced spin-polarized holes to generate spin-selective positive trions, leading to differences in the populations of neutral excitons and trions between left and right CPL. Using transient absorption spectroscopy, we elucidate the origin of excitons and trions that are inherently distinct for defect-mediated and impurity-mediated trions. Ferromagnetic characteristics are further confirmed by the significant Zeeman splitting of nanodiamonds deposited on the V-doped WSe₂ monolayer.

Coherent Spin Control of Single Molecules on a Surface

Control of single electron spins constitutes one of the most promising platforms for spintronics, quantum sensing, and quantum information processing. Utilizing single molecular magnets as their hosts establishes an interesting framework since their molecular structure is highly flexible and chemistry-based large-scale synthesis directly provides a way toward scalability. Here, we demonstrate coherent spin manipulation of single molecules on a surface, which we control individually using a scanning tunneling microscope in combination with electron spin resonance. We previously found that iron phthalocyanine (FePc) molecules form a spin-1/2 system when placed on an insulating thin film of magnesium oxide (MgO). Performing Rabi oscillation and Hahn echo measurements, we show that the FePc spin can be coherently manipulated with a phase coherence time T₂^Echo of several hundreds of nanoseconds. Tunneling current-dependent measurements demonstrate that interaction with the tunneling electrons is the dominating source of decoherence. In addition, we perform Hahn echo measurements on small self-assembled arrays of FePc molecules. We show that, despite additional intermolecular magnetic coupling, spin resonance and T₂^Echo are much less perturbed by T₁ spin flip events of neighboring spins than by the tunneling current. This will potentially allow for individual addressable molecular spins in self-assemblies and with application for quantum information processing.

Electron spin resonance of single iron phthalocyanine molecules and role of their non-localized spins in magnetic interactions

Electron spin resonance (ESR) spectroscopy is a crucial tool, through spin labelling, in investigations of the chemical structure of materials and of the electronic structure of materials associated with unpaired spins. ESR spectra measured in molecular systems, however, are established on large ensembles of spins and usually require a complicated structural analysis. Recently, the combination of scanning tunnelling microscopy with ESR has proved to be a powerful tool to image and coherently control individual atomic spins on surfaces. Here we extend this technique to single coordination complexes-iron phthalocyanines (FePc)-and investigate the magnetic interactions between their molecular spin with either another molecular spin (in FePc-FePc dimers) or an atomic spin (in FePc-Ti pairs). We show that the molecular spin density of FePc is both localized at the central Fe atom and also distributed to the ligands (Pc), which yields a strongly molecular-geometry-dependent exchange coupling.

Electronic structures and optical characteristics of fluorescent pyrazinoquinoxaline assemblies and Au interfaces

Understanding the excitonic processes at the interfaces of fluorescent π-conjugated molecules and metal electrodes is important for both fundamental studies and emerging applications. Adsorption configurations of molecules on metal surfaces significantly affect the physical characteristics of junctions as well as molecules. Here, the electronic structures and optical properties of molecular assemblies/Au interfaces were investigated using scanning probe and photoluminescence microscopy techniques. Scanning tunneling microscopy images and tunneling conductance spectra suggested that the self-assembled molecules were physisorbed on the Au surface. Visible-range photoluminescence studies showed that Au thin films modified the emission spectra and reduced the lifetime of excitons. Surface potential maps, obtained by Kelvin probe force microscopy, could visualize electron transfer from the molecules to Au under illumination, which could explain the decreased lifetime of excitons at the molecule/Au interface.

Engineering atomic-scale magnetic fields by dysprosium single atom magnets

Atomic scale engineering of magnetic fields is a key ingredient for miniaturizing quantum devices and precision control of quantum systems. This requires a unique combination of magnetic stability and spin-manipulation capabilities. Surface-supported single atom magnets offer such possibilities, where long temporal and thermal stability of the magnetic states can be achieved by maximizing the magnet/ic anisotropy energy (MAE) and by minimizing quantum tunnelling of the magnetization. Here, we show that dysprosium (Dy) atoms on magnesium oxide (MgO) have a giant MAE of 250 meV, currently the highest among all surface spins. Using a variety of scanning tunnelling microscopy (STM) techniques including single atom electron spin resonance (ESR), we confirm no spontaneous spin-switching in Dy over days at ≈ 1 K under low and even vanishing magnetic field. We utilize these robust Dy single atom magnets to engineer magnetic nanostructures, demonstrating unique control of magnetic fields with atomic scale tunability.

Probing Magnetism in Artificial Metal-Organic Complexes Using Electronic Spin Relaxometry

Single spins are considered as a versatile candidate for miniaturizing information devices down to the nanoscale. To engineer the spin's properties, metal-organic frameworks provide a promising route which in turn requires thorough understanding of the metal-molecule interaction. Here, we investigate the magnetic robustness of a single iron (Fe) atom in artificially built Fe-tetracyanoethylene (TCNE) complexes by using low-temperature scanning tunneling microscopy (STM). We find that the magnetic anisotropy and spin relaxation dynamics of the Fe atom within the complexes remain unperturbed in comparison to well-isolated Fe atoms. Density functional theory (DFT) calculations support our experimental findings, suggesting that the 3d orbitals of the Fe atom remain largely undisturbed while the 4s and 4p orbitals are rearranged in the process of forming a complex. To precisely determine the location of the spin center within the complex, we utilize STM-based spin relaxometry, mapping out the spatial dependence of spin relaxation with subnanometer resolution. Our work suggests that the magnetic properties of atoms can remain unchanged while being embedded in a weakly bound molecular framework.

Tuning Single-Atom Electron Spin Resonance in a Vector Magnetic Field

Spin resonance of single spin centers bears great potential for chemical structure analysis, quantum sensing, and quantum coherent manipulation. Essential for these experiments is the presence of a two-level spin system whose energy splitting can be chosen by applying a magnetic field. In recent years, a combination of electron spin resonance (ESR) and scanning tunneling microscopy (STM) has been demonstrated as a technique to detect magnetic properties of single atoms on surfaces and to achieve sub-microelectronvolts energy resolution. Nevertheless, up to now the role of the required magnetic fields has not been elucidated. Here, we perform single-atom ESR on individual Fe atoms adsorbed on magnesium oxide (MgO) using a two-dimensional vector magnetic field as well as the local field of the magnetic STM tip in a commercially available STM. We show how the ESR amplitude can be greatly improved by optimizing the magnetic fields, revealing in particular an enhanced signal at large in-plane magnetic fields. Moreover, we demonstrate that the stray field from the magnetic STM tip is a versatile tool. We use it here to drive the electron spin more efficiently and to perform ESR measurements at constant frequency by employing tip-field sweeps. Lastly, we show that it is possible to perform ESR using only the tip field, under zero external magnetic field, which promises to make this technique available in many existing STM systems.

Tuning the Exchange Bias on a Single Atom from 1 mT to 10 T

Shrinking spintronic devices to the nanoscale ultimately requires localized control of individual atomic magnetic moments. At these length scales, the exchange interaction plays important roles, such as in the stabilization of spin-quantization axes, the production of spin frustration, and creation of magnetic ordering. Here, we demonstrate the precise control of the exchange bias experienced by a single atom on a surface, covering an energy range of 4 orders of magnitude. The exchange interaction is continuously tunable from milli-eV to micro-eV by adjusting the separation between a spin-1/2 atom on a surface and the magnetic tip of a scanning tunneling microscope. We seamlessly combine inelastic electron tunneling spectroscopy and electron spin resonance to map out the different energy scales. This control of exchange bias over a wide span of energies provides versatile control of spin states, with applications ranging from precise tuning of quantum state properties, to strong exchange bias for local spin doping. In addition, we show that a time-varying exchange interaction generates a localized ac magnetic field that resonantly drives the surface spin. The static and dynamic control of the exchange interaction at the atomic scale provides a new tool to tune the quantum states of coupled-spin systems.

On-orbit radiometric calibration of Suomi NPP VIIRS reflective solar bands using the Moon and solar diffuser

Radiometric calibration of the Suomi National Polar-orbiting Partnership Visible Infrared Imaging Radiometer Suite (VIIRS) reflective solar bands relies mainly on the onboard solar diffuser (SD) observations. The SD reflectance degrades over time due to the exposure to solar ultraviolet radiation. The uncertainties embedded in characterizing the SD bidirectional reflectance distribution function (BRDF) directly affect the accuracy of sensor radiometric calibration coefficients, such as F-factors, which are proxies of detector gain. The Moon-based radiometric calibration provides an independent way of validating and correcting the SD-based calibration. This study focuses on the comparison of the long-term SD F-factors with lunar F-factors by using two independent lunar irradiance models, i.e., Miller and Turner (MT) model and the Global Space-based Inter-Calibration System Implementation of ROLO (GIRO) model. To monitor the long-term detector response changes, the lunar F-factor differences are matched to the SD F-factors by applying the best fit scaling factors. Overall, the two lunar F-factors agree well, within 2% of one sigma standard deviation in the reflective solar bands compared to the SD F-factors. The lifetime standard deviations of difference between the GIRO-based lunar and SD F-factors show better long-term match than that of MT-based lunar F-factors. The GIRO-based lunar F-factors show increasing differences over time in comparison with the SD F-factors especially for bands M1 to M4, which indicates the underestimation of the VIIRS detector degradation by SD F-factors for these bands. Using standard SD calibration method and the GIRO-based lunar model, long-term difference between the lunar and SD F-factors shows there are 1.6%, 1.3%, 1.0%, and 0.9% increases in lunar F-factor trend for bands M1 to M4 at the end of year 2015. To mitigate these time-dependent biases, NOAA Ocean Color (OC) group and NASA VIIRS characterization support team (VCST) developed lunar correction methods and applied them to their specific products. However, the amounts of band-dependent lunar corrections are not consistent between these two teams, especially in the short-wavelength bands from M1 to M4, depending on the versions of lunar models and SD F-factor calculation algorithms. Using the standard SD F-factor algorithm and the multi-agency endorsed GIRO model, we derived lunar correction factors based on the quadratic fits between the SD and lunar F-factors. The differences with the NOAA OC group and NASA VCST team are compared and described in this study.

Enhanced quantum coherence in exchange coupled spins via singlet-triplet transitions

Manipulation of spin states at the single-atom scale underlies spin-based quantum information processing and spintronic devices. These applications require protection of the spin states against quantum decoherence due to interactions with the environment. While a single spin is easily disrupted, a coupled-spin system can resist decoherence by using a subspace of states that is immune to magnetic field fluctuations. Here, we engineered the magnetic interactions between the electron spins of two spin-1/2 atoms to create a "clock transition" and thus enhance their spin coherence. To construct and electrically access the desired spin structures, we use atom manipulation combined with electron spin resonance (ESR) in a scanning tunneling microscope. We show that a two-level system composed of a singlet state and a triplet state is insensitive to local and global magnetic field noise, resulting in much longer spin coherence times compared with individual atoms. Moreover, the spin decoherence resulting from the interaction with tunneling electrons is markedly reduced by a homodyne readout of ESR. These results demonstrate that atomically precise spin structures can be designed and assembled to yield enhanced quantum coherence.

Probing quantum coherence in single-atom electron spin resonance

Spin resonance of individual spin centers allows applications ranging from quantum information technology to atomic-scale magnetometry. To protect the quantum properties of a spin, control over its local environment, including energy relaxation and decoherence processes, is crucial. However, in most existing architectures, the environment remains fixed by the crystal structure and electrical contacts. Recently, spin-polarized scanning tunneling microscopy (STM), in combination with electron spin resonance (ESR), allowed the study of single adatoms and inter-atomic coupling with an unprecedented combination of spatial and energy resolution. We elucidate and control the interplay of an Fe single spin with its atomic-scale environment by precisely tuning the phase coherence time T₂ using the STM tip as a variable electrode. We find that the decoherence rate is the sum of two main contributions. The first scales linearly with tunnel current and shows that, on average, every tunneling electron causes one dephasing event. The second, effective even without current, arises from thermally activated spin-flip processes of tip spins. Understanding these interactions allows us to maximize T₂ and improve the energy resolution. It also allows us to maximize the amplitude of the ESR signal, which supports measurements even at elevated temperatures as high as 4 K. Thus, ESR-STM allows control of quantum coherence in individual, electrically accessible spins.

Engineering the Eigenstates of Coupled Spin-1/2 Atoms on a Surface

Quantum spin networks having engineered geometries and interactions are eagerly pursued for quantum simulation and access to emergent quantum phenomena such as spin liquids. Spin-1/2 centers are particularly desirable, because they readily manifest coherent quantum fluctuations. Here we introduce a controllable spin-1/2 architecture consisting of titanium atoms on a magnesium oxide surface. We tailor the spin interactions by atomic-precision positioning using a scanning tunneling microscope (STM) and subsequently perform electron spin resonance on individual atoms to drive transitions into and out of quantum eigenstates of the coupled-spin system. Interactions between the atoms are mapped over a range of distances extending from highly anisotropic dipole coupling to strong exchange coupling. The local magnetic field of the magnetic STM tip serves to precisely tune the superposition states of a pair of spins. The precise control of the spin-spin interactions and ability to probe the states of the coupled-spin network by addressing individual spins will enable the exploration of quantum many-body systems based on networks of spin-1/2 atoms on surfaces.

Atomic-scale sensing of the magnetic dipolar field from single atoms

Spin resonance provides the high-energy resolution needed to determine biological and material structures by sensing weak magnetic interactions. In recent years, there have been notable achievements in detecting and coherently controlling individual atomic-scale spin centres for sensitive local magnetometry. However, positioning the spin sensor and characterizing spin-spin interactions with sub-nanometre precision have remained outstanding challenges. Here, we use individual Fe atoms as an electron spin resonance (ESR) sensor in a scanning tunnelling microscope to measure the magnetic field emanating from nearby spins with atomic-scale precision. On artificially built assemblies of magnetic atoms (Fe and Co) on a magnesium oxide surface, we measure that the interaction energy between the ESR sensor and an adatom shows an inverse-cube distance dependence (r^-3.01±0.04). This demonstrates that the atoms are predominantly coupled by the magnetic dipole-dipole interaction, which, according to our observations, dominates for atom separations greater than 1 nm. This dipolar sensor can determine the magnetic moments of individual adatoms with high accuracy. The achieved atomic-scale spatial resolution in remote sensing of spins may ultimately allow the structural imaging of individual magnetic molecules, nanostructures and spin-labelled biomolecules.

Electron paramagnetic resonance of individual atoms on a surface

We combined the high-energy resolution of conventional spin resonance (here ~10 nano-electron volts) with scanning tunneling microscopy to measure electron paramagnetic resonance of individual iron (Fe) atoms placed on a magnesium oxide film. We drove the spin resonance with an oscillating electric field (20 to 30 gigahertz) between tip and sample. The readout of the Fe atom's quantum state was performed by spin-polarized detection of the atomic-scale tunneling magnetoresistance. We determine an energy relaxation time of T1 ≈ 100 microseconds and a phase-coherence time of T2 ≈ 210 nanoseconds. The spin resonance signals of different Fe atoms differ by much more than their resonance linewidth; in a traditional ensemble measurement, this difference would appear as inhomogeneous broadening.

[A disulfiram-alcohol reaction after inhalation of a salbutamol aerosol: a plausible interaction?]

An asthmatic patient (male, aged 47) being treated for his alcohol dependence complained of experiencing mild symptoms of disulfiram-alcohol reaction after using of pressurised metered-dose inhaler containing ethanol. It has been reported in the literature that the disulfiram-alcohol reaction may occur after a patient has been exposed to only minimal amounts of ethanol. This is why, in daily practice, physicians are generally reluctant to prescribe preparations containing ethanol and why they usually switch patients to an alternative. However, close evaluation of the biopharmaceutical and pharmacokinetic aspects of ethanol suggests that subjective disulfiram-alcohol reactions following the use of inhalers containing ethanol cannot be explained rationally from a clinical pharmacological perspective.

Estrogen via estrogen receptor beta partially inhibits mandibular condylar cartilage growth

OBJECTIVE

Temporomandibular joint (TMJ) diseases predominantly afflict women, suggesting a role for female hormones in the disease process. However, little is known about the role of estrogen receptor (ER) signaling in regulating mandibular condylar cartilage growth. Therefore, the goal of this study was to examine the effects of altered estrogen levels on the mandibular condylar cartilage in wild type (WT) and ER beta Knockout (KO) mice.

MATERIALS AND METHODS

21-day-old female WT (n = 37) and ER beta KO mice (n = 36) were either sham operated or ovariectomized, and treated with either placebo or estradiol. The mandibular condylar cartilage was evaluated by histomorphometry, proliferation was analyzed by double ethynyl-2'-deoxyuridine/bromodeoxyuridine (EdU/BrdU) labeling, and assays on gene and protein expression of chondrocyte maturation markers were performed.

RESULTS

In WT mice, ovariectomy caused a significant increase in mandibular condylar cartilage cell numbers, a significant increase in Sox9 expression and a significant increase in proliferation compared with sham operated WT mice. In contrast, ovariectomy did not cause any of these effects in the ER beta KO mice. Estrogen replacement treatment in ovariectomized WT mice caused a significant decrease in ER alpha expression and a significant increase in Sost expression compared with ovariectomized mice treated with placebo. Estrogen replacement treatment in ovariectomized ER beta KO mice caused a significant increase in Col2 expression, no change in ER alpha expression, and a significant increase in Sost expression.

CONCLUSION

Estrogen via ER beta inhibits proliferation and ER alpha expression while estrogen independent of ER beta induces Col2 and Sost expression.

Building blocks for studies of nanoscale magnetism: adsorbates on ultrathin insulating Cu2N

Scanning tunneling microscopy and spectroscopy were performed to study transition metal adatoms (Fe, Co, Cu) and individual metal-dithiol complexes on insulating Cu2N islands. Adsorption of metal adatoms on Cu2N is surprisingly complex and in the case of Fe, we find two distinct adsorption states for each of two distinct adsorption sites. Connection of these metal adatoms to dithiol molecules was pursued to model a single molecule junction, with the aim of understanding further details about the nature of metal/molecule electrical contact. Pronounced changes in local density of states, magnetic anisotropy and Kondo interactions were observed for Co adatoms connected to dithiol molecules. These results illustrate some of the challenges and opportunities for STM studies of nanoscale magnetism in complex systems.

National genetic evaluation (system) of hanwoo (korean native cattle)

Hanwoo (Also known as Korean native cattle; Bos taurus coreanae) have been used for transportation and farming for a long time in South Korea. It has been about 30 yrs since Hanwoo improvement began in earnest as beef cattle for meat yield. The purpose of this study was to determine the trend of improvement as well as to estimate genetic parameters of the traits being used for seedstock selection based on the data collected from the past. Hanwoo proven bulls in South Korea are currently selected through performance and progeny tests. National Hanwoo genetic evaluations are implemented with yearling weight (YW), carcass weight (CW), eye muscle area (EMA), backfat thickness (BF) and marbling score (MS). Yearling weights and MS are used for selecting young bulls, and EMA, BF, and MS are used for selecting proven bulls. One individual per testing room was used for performance tests, and five individuals per room for progeny tests. Individuals tested were not allowed to graze pasture, but there was enough space for them to move around in the testing room. Feeds including roughages and minerals were fed ad libitum, and concentrates were provided at the rate of about 1.8% of individual weight. Overall means of the traits were 352.8±38.56 kg, 335.09±44.61 kg, 77.85±8.838 cm², 8.6±3.7 mm and 3.293±1.648 for YW, CW, EMA, BF and MS. Heritabilities estimated in this study were 0.30, 0.30, 0.42, 0.50 and 0.63 in YW, CW, EMA, BF and MS, respectively, which are similar to results from previous research. Yearling weight was 315.54 kg in 1998, and had increased to 355.06 kg in 2011, resulting in about 40 kg of improvement over 13 yrs. YW and CW have improved remarkably over the past 15 yrs. Breeding values between 1996 and 2000 decreased or did not change much, but have moved in a desirable direction since 2001. These improvements correspond with the substantial increase in use of animal models since the late 1990s in Korea. Hanwoo testing programs have practically contributed to the improvement in aspects of quality and quantity. In sum, the current selection system is good enough to accommodate circumstances where fewer sires are used on many more cows. Although progeny tests take longer and cost more, they seem to be appropriate under the circumstances of the domestic market with its higher requirement for better meat quality. Consequently, accumulative data collection, genetic evaluation model development, revision of selection indices, as well as cooperation among farms, associations, National Agricultural Cooperative Federation, universities, research institutes, and government agencies must be applied to the Hanwoo selection program. All these efforts will assist the domestic market to secure a competitive position against imported beef under Free Trade Agreement trade system and will provide farmers with higher profits as well as the public with a higher quality of beef.

Beat note stabilization of mode-locked lasers for quantum information processing

We stabilize a chosen radio frequency beat note between two optical fields derived from the same mode-locked laser pulse train in order to coherently manipulate quantum information. This scheme does not require access or active stabilization of the laser repetition rate. We implement and characterize this external lock, in the context of two-photon stimulated Raman transitions between the hyperfine ground states of trapped 171Yb(+) quantum bits.

Optimal quantum control of multimode couplings between trapped ion qubits for scalable entanglement

We demonstrate entangling quantum gates within a chain of five trapped ion qubits by optimally shaping optical fields that couple to multiple collective modes of motion. We individually address qubits with segmented optical pulses to construct multipartite entangled states in a programmable way. This approach enables high-fidelity gates that can be scaled to larger qubit registers for quantum computation and simulation.

Magnetism in single metalloorganic complexes formed by atom manipulation

The magnetic properties of molecular structures can be tailored by chemical synthesis or bottom-up assembly at the atomic scale. We used scanning tunneling microscopy to study charge and spin transfer in individual complexes of transition metals with the charge acceptor, tetracyanoethylene (TCNE). The complexes were formed on a thin insulator, Cu2N on Cu(100), by manipulation of individual atoms and molecules. The Cu2N layer decouples the complexes from Cu electron density, enabling direct imaging of the TCNE molecular orbitals as well as spin-flip inelastic electron tunneling spectroscopy. Results were obtained at low temperature down to 1 K and in magnetic fields up to 7 T in order to resolve splitting of spin states in the complexes. We also performed spin-polarized density functional theory calculations to compare with the experimental data. Our results indicate that charge transfer to TCNE leads to a change in spin magnitude, Kondo resonance, and magnetic anisotropy for the metal atoms.

A circuit analysis of an in situ tunable radio-frequency quantum point contact

A detailed analysis of the tunability of a radio-frequency quantum point contact setup using a C - LCR circuit is presented. We calculate how the series capacitance influences resonance frequency and charge-detector resistance for which matching is achieved as well as the voltage and power delivered to the load. Furthermore, we compute the noise contributions in the system and compare our findings with measurements taken with an etched quantum point contact. While our considerations mostly focus on our specific choice of matching circuit, the discussion of the influence of source-to-load power transfer on the signal-to-noise ratio is valid generally.

Association of coronary artery calcium score and vascular dysfunction in long-term hemodialysis patients

Long-term hemodialysis patients are prone to an exceptionally high burden of cardiovascular disease and mortality. The novel temperature-based technology of digital thermal monitoring (DTM) of vascular reactivity appears associated with the severity of coronary artery disease in asymptomatic population. We hypothesized that in hemodialysis patients, the DTM and coronary artery calcium (CAC) score have a gradient association that follows that of subjects without kidney disease. We examined the cross-sectional DTM-CAC associations in a group of long-term hemodialysis patients, and their 1:1 matched normal counterpart. Area under the curve for temperature (TMP-AUC), the surrogate of the DTM index of vascular function, was assessed after a 5-minute arm-cuff reactive hyperemia test. Coronary calcium score was measured via electron beam computed tomography or multidetector computed tomography scan. We studied 105 randomly recruited hemodialysis patients (age: 58 ± 13 years, 47% men) and 105 age- and gender-matched controls. In hemodialysis patients vs. controls, TMP-AUC was significantly worse (114 ± 72 vs. 143 ± 80, P = 0.001) and CAC score was higher (525 ± 425 vs. 240 ± 332, P < 0.001). Hemodialysis patients were 14 times more likely to have CAC score >1000 as compared with controls. After adjustment for known confounders, the relative risk for case vs. control for each standard deviation decrease in TMP-AUC was 1.46 (95% confidence interval: 1.12-1.93, P = 0.007). Vascular reactivity measured via the novel DTM technology is incrementally worse across CAC scores in hemodialysis patients, in whom both measures are even worse than their age- and gender-matched controls. The DTM technology may offer a convenient and radiation-free approach to risk-stratify hemodialysis patients.

Graphite patterning in a controlled gas environment

Although a number of methods using scanning probe lithography to pattern graphene have already been introduced, the fabrication of real devices still faces limitations. We report graphite patterning using scanning probe lithography with control of the gas environment. Patterning processes using scanning probe lithography of graphite or graphene are normally performed in air because water molecules forming the meniscus between the tip and the sample mediate the etching reaction. This water meniscus, however, may prevent uniform patterning due to its strong surface tension or large contact angle on surfaces. To investigate this side effect of water, our experiment was performed in a chamber where the gas environment was controlled with methyl alcohol, oxygen or isopropanol gases. We found that methyl alcohol facilitates graphite etching, and a line width as narrow as 3 nm was achieved as methyl alcohol also contains an oxygen atom which gives rise to the required oxidation. Due to its low surface tension and highly adsorptive behavior, methyl alcohol has advantages for a narrow line width and high speed etching conditions.