Superconducting Cavity-Based Sensing of Band Gaps in 2D Materials.

The superconducting coplanar waveguide (SCPW) cavity plays an essential role in various areas like superconducting qubits, parametric amplifiers, radiation detectors, and studying magnon-photon and photon-phonon coupling. Despite its wide-ranging applications, the use of SCPW cavities to study various van der Waals 2D materials has been relatively unexplored. The resonant modes of the SCPW cavity exquisitely sense the dielectric environment. In this work, we measure the charge compressibility of bilayer graphene coupled to a half-wavelength SCPW cavity. Our approach provides a means to detect subtle changes in the capacitance of the bilayer graphene heterostructure, which depends on the compressibility of bilayer graphene, manifesting as shifts in the resonant frequency of the cavity. This method holds promise for exploring a wide class of van der Waals 2D materials, including transition metal dichalcogenides (TMDs) and their moiré, where DC transport measurement is challenging.

Physiological effect of prone positioning in mechanically ventilated SARS-CoV-2- infected patients with severe ARDS: An observational study.

Background and Aims: Mechanical ventilation in prone position was associated with a reduction in mortality and increase in arterial oxygenation in acute respiratory distress syndrome (ARDS) patients. However, physiological effects of prone position in COVID ARDS patients are unknown. Material and Methods: In this prospective observational study, data of n = 47 consecutive real time RT- PCR confirmed SARS-CoV-2-infected patients with severe ARDS were included. Respiratory mechanics and oxygenation data of recruited patients were collected before and after prone position. Results: Median (Interquartile range, IQR) age of the recruited patients was 60 (50-67) years and median (IQR) PaO2/FiO2 ratio of 61.2 (54-80) mm Hg with application of median (IQR) positive end expiratory pressure (PEEP) of 12 (10-14) cm H2O before initiation of prone position. Out of those patients, 36 (77%) were prone responders at 16 hours after prone session, evident by increase of PaO2 by at least 20 mm Hg or by 20% as compared to baseline, and 73% patients were sustained responders (after returning to supine position). Plateau airway pressure (p < 0.0001), peak airway pressure (p < 0.0001), and driving pressure (p < 0.0001) were significantly reduced in prone position, and static compliance (p = 0.001), PaO2/FiO2 ratio (p < 0.0001), PaO2 (p = 0.0002), and SpO2 (p = 0.0004) were increased at 4 hours and 16 hours since prone position and also after returning to supine position. Conclusion: In SARS-CoV-2-infected patients, mechanical ventilation in prone position is associated with improvement in lung compliance and oxygenation in almost three-fourth of the patients and persisted in supine position in more than 70% of the patients.

How Useful is Extravascular Lung Water Measurement in Managing Lung Injury in Intensive Care Unit?

CONTEXT: The primary goal of septic shock management is optimization of organ perfusion, often at the risk of overloading the interstitium and causing pulmonary edema. The conventionally used end points of resuscitation do not generally include volumetric parameters such as extravascular lung water index (EVLWI) and pulmonary vascular permeability index (PVPI). AIMS: This study aimed to assess the prognostic value of EVLWI and PVPI by calculating their correlation with the severity of lung injury. SETTINGS AND DESIGN: This prospective observational study included twenty mechanically ventilated critically ill patients with Acute Physiology and Chronic Health Evaluation score (APACHE II) >20. SUBJECTS AND METHODS: EVLWI and PVPI were measured using transpulmonary thermodilution, and simultaneously, PaO2:FiO2 ratio, alveolar-arterial gradient of oxygen (AaDO2), and chest radiograph scores from two radiologists were obtained. STATISTICAL ANALYSIS: The correlation of EVLWI and PVPI with chest radiograph scores, PaO2:FiO2 ratio, and AaDO2 were calculated. The inter-observer agreement between the two radiologists was tested using kappa test. RESULTS: EVLWI and PVPI correlated modestly with PaO2:FiO2 (r = -0.32, P = 0.0004; r = -0.39, P = 0.0001). There was a better correlation of EVLWI and PVPI with PaO2:FiO2 ratio (r = -0.71, P < 0.0001; r = -0.58, P = 0.0001) in the acute respiratory distress syndrome (ARDS) subgroup. The EVLWI values correlated significantly with corresponding chest radiograph scores (r = 0.71, P < 0.0001 for observer 1 and r = 0.68, P < 0.0001 for observer 2). CONCLUSIONS: EVLWI and PVPI may have a prognostic significance in the assessment of lung injury in septic shock patients with ARDS. Further research is required to reveal the usefulness of EVLWI as an end point of fluid resuscitation in the management of septic shock with ARDS.

Computation and Communication Evaluation of an Authentication Mechanism for Time-Triggered Networked Control Systems.

In modern networked control applications, confidentiality and integrity are important features to address in order to prevent against attacks. Moreover, network control systems are a fundamental part of the communication components of current cyber-physical systems (e.g., automotive communications). Many networked control systems employ Time-Triggered (TT) architectures that provide mechanisms enabling the exchange of precise and synchronous messages. TT systems have computation and communication constraints, and with the aim to enable secure communications in the network, it is important to evaluate the computational and communication overhead of implementing secure communication mechanisms. This paper presents a comprehensive analysis and evaluation of the effects of adding a Hash-based Message Authentication (HMAC) to TT networked control systems. The contributions of the paper include (1) the analysis and experimental validation of the communication overhead, as well as a scalability analysis that utilizes the experimental result for both wired and wireless platforms and (2) an experimental evaluation of the computational overhead of HMAC based on a kernel-level Linux implementation. An automotive application is used as an example, and the results show that it is feasible to implement a secure communication mechanism without interfering with the existing automotive controller execution times. The methods and results of the paper can be used for evaluating the performance impact of security mechanisms and, thus, for the design of secure wired and wireless TT networked control systems.

Multiple proton relay routes in the reaction mechanism of RNAP II: assessing the effect of structural model.

RNA polymerase II catalyzes the nucleotidyl transfer reaction for messenger RNA synthesis in eukaryotes. Two crystal structures of this system have been resolved, each with its own defects in the coordination sphere of Mg(2+) (A) resulting from chemical modifications. We have used both structures and also a novel hybrid of the two that allows a better exploration of the parts of configuration space that reflect substrate-enzyme interactions. MD and QM/MM calculations have been performed, the latter with the semiempirical AM1/d-PhoT method, calibrated against density functional theory. Reaction path scans in 1-D provided insights about the role of Mg(2+) (A) which turns out to be more structural than catalytic. In contrast, 1-D scans of the incorporation of the nucleotidyl group yielded barriers that were much too high, necessitating the use of 2-D reaction coordinates. Three different proton acceptors for the initial reaction step were examined. For those models based on the two PDB structures the 2-D scans continued to yield very high barriers, indicating that the reaction is unlikely to proceed from these configurations. On the other hand, two hybrid models, chosen from the early and late parts of a 12 ns molecular dynamics simulation yielded greatly reduced barriers in the range of ∼ 17 to ∼ 27 kcal/mol for the three proton acceptors, as compared to the experimental estimate of 18 kcal/mol. The final step, release of pyrophosphate, was found to be facile. Our overall mechanism involves only active site residues or water without the need for external reactive agents such as the hydroxide ion previously proposed.

Characterization of the divalent metal binding site of bacterial polysaccharide deacetylase using crystallography and quantum chemical calculations.

Peptidoglycan deacetlyase (HP0310, HpPgdA) from the gram-negative pathogen Helicobacter pylori, is the enzyme responsible for a peptidoglycan modification that counteracts the host immune response. In a recent study, we determined the crystallographic structure of the enzyme, which is a homo-tetramer (Shaik et al., PloS One 2011;6:e19207). The metal-binding site, which is essential for the enzyme's catalytic activity, is visible within the structure, but we were unable to identify the nature of the metal itself. In this study, we have obtained a higher-resolution crystal structure of the enzyme, which shows that the ion bound is, in fact, zinc. Analysis of the structure of the four sites, one per monomer, and quantum chemical calculations of models of the site in the presence of different divalent metal ions show an intrinsic preference for zinc, but also significant flexibility of the site so that binding of other ions can eventually occur.

Theoretical modeling of low-energy electronic absorption bands in reduced cobaloximes.

The reduced Co(I) states of cobaloximes are powerful nucleophiles that play an important role in the hydrogen-evolving catalytic activity of these species. In this work we analyze the low-energy electronic absorption bands of two cobaloxime systems experimentally and use a variety of density functional theory and molecular orbital ab initio quantum chemical approaches. Overall we find a reasonable qualitative understanding of the electronic excitation spectra of these compounds but show that obtaining quantitative results remains a challenging task.

A computational study of the mechanism of hydrogen evolution by cobalt(diimine-dioxime) catalysts.

Cobalt(diimine-dioxime) complexes catalyze hydrogen evolution with low overpotentials and remarkable stability. In this study, DFT calculations were used to investigate their catalytic mechanism, to demonstrate that the initial active state was a Co(I) complex and that H2 was evolved in a heterolytic manner through the protonation of a Co(II)-hydride intermediate. In addition, these catalysts were shown to adjust their electrocatalytic potential for hydrogen evolution to the pH value of the solution and such a property was assigned to the presence of a H(+)-exchange site on the oxime bridge. It was possible to establish that protonation of the bridge was directly involved in the H2-evolution mechanism through proton-coupled electron-transfer steps. A consistent mechanistic scheme is proposed that fits the experimentally determined electrocatalytic and electrochemical potentials of cobalt(diimine-dioxime) complexes and reproduces the observed positive shift of the electrocatalytic potential with increasing acidity of the proton source.

Feasibility of anterior temporalis muscle ultrasound for assessing muscle wasting in ICU: a prospective cohort study.

PURPOSE: Skeletal muscle ultrasound is a valuable tool for assessing muscle wasting in ICU. Previous studies on skeletal muscle ultrasound in ICU have been performed on lower limb muscles. The current study is formulated to assess the feasibility and reliability of anterior temporalis (AT) muscle ultrasound for measuring muscle wasting in ICU. METHODS: In this prospective cohort study in 48 critically ill patients with sepsis, muscle layer thicknesses (MLTs) and mean grayscale (GS) values of anterior temporalis muscles and quadriceps femoris (Q) were measured at baseline and serially till 7 days. Correlation was made between baseline and change in MLT and GS values of AT and Q muscle and these parameters were compared between ICU survivors and non survivors. RESULTS: Baseline anterior temporalis MLTs or their longitudinal changes over 7 days did not correlate significantly with the corresponding parameters of quadriceps femoris muscles. The baseline GS values of two muscle groups correlated weakly at baseline, but the change in GS over 7 days showed no correlation. The baseline MLTs of both muscle groups and their longitudinal change over 7 days did not correlate with ICU length of stay. The change in MLT of AT over 7 days was significantly greater in ICU non-survivors compared to survivors. CONCLUSION: Measurement of ultrasonographic muscle layer thickness and grayscale parameters of anterior temporalis muscle did not show good correlation with that of quadriceps muscle.

Combined experimental-theoretical characterization of the hydrido-cobaloxime [HCo(dmgH)2(PnBu3)].

A combined theoretical and experimental approach has been employed to characterize the hydrido-cobaloxime [HCo(dmgH)(2)(PnBu(3))] compound. This complex was originally investigated by Schrauzer et al. [Schrauzer et al., J. Am. Chem. Soc. 1971, 93,1505] and has since been referred to as a key, stable analogue of the hydride intermediate involved in hydrogen evolution catalyzed by cobaloxime compounds [Artero, V. et al. Angew. Chem., Int. Ed. 2011, 50, 7238-7266]. We employed quantum chemical calculations, using density functional theory and correlated RI-SCS-MP2 methods, to characterize the structural and electronic properties of the compound and observed important differences between the calculated (1)H NMR spectrum and that reported in the original study by Schrauzer and Holland. To calibrate the theoretical model, the stable hydrido tetraamine cobalt(III) complex [HCo(tmen)(2)(OH(2))](2+) (tmen = 2,3-dimethyl-butane-2,3-diamine) [Rahman, A. F. M. M. et al. Chem. Commun. 2003, 2748-2749] was subjected to a similar analysis, and, in this case, the calculated results agreed well with those obtained experimentally. As a follow-up to the computational work, the title hydrido-cobaloxime compound was synthesized and recharacterized experimentally, together with the Co(I) derivative, giving results that were in agreement with the theoretical predictions.

Hydrogen bond formation of formamide and N-methylformamide in aqueous solution studied by quantum mechanical charge field-molecular dynamics (QMCF-MD).

The formation of hydrogen-bonds of formamide and "cis"-N-methylformamide in aqueous solution was examined using double zeta HF level Quantum Mechanical Charge Field-Molecular Dynamics (QMCF-MD) simulations. Basic attributes such as structure and dynamics of the solvates and hydrogen-bonds were studied in particular by means of coordination number distributions, mean residence times and radial distribution functions, on which spatial restrictions in the form of planes and cones were applied. Advanced methods of analysis gave detailed information about the sterical environment and the dynamic behavior of strong and weak hydrogen-bonds formed by the residues. The comparison of both molecules over a sampling period of 12 ps provided information on the influence of methylation of the amide function on molecular and hydration properties.

Structural and dynamical aspects of the unsymmetric hydration of Sb(III): an ab initio quantum mechanical charge field molecular dynamics simulation.

An ab initio quantum mechanical charge field molecular dynamics (QMCF MD) simulation was performed to investigate the behavior of the Sb(3+) ion in aqueous solution. The simulation reveals a significant influence of the residual valence shell electron density on the solvation structure and dynamics of Sb(3+). A strong hemidirectional behavior of the ligand binding pattern is observed for the first hydration shell extending up to the second hydration layer. The apparent domain partitioned structural behavior was probed by solvent reorientational kinetics and three-body distribution functions. The three-dimensional hydration space was conveniently segmented such that domains having different properties were properly resolved. The approach afforded a fair isolation of localized solvent structural and dynamical motifs that Sb(3+) seems to induce to a remarkable degree. Most intriguing is the apparent impact of the lone pair electrons on the second hydration shell, which offers insight into the mechanistic aspects of hydrogen bonding networks in water. Such electronic effects observed in the hydration of Sb(3+) can only be studied by applying a suitable quantum mechanical treatment including first and second hydration shell as provided by the QMCF ansatz.

Hydrolysis of tetravalent group IV metal ions: an ab initio simulation study.

Simulations of the tetravalent group IV metal ions, Ge(IV), Sn(IV), and Pb(IV), in aqueous solution were performed using ab initio quantum mechanical charge field molecular dynamics (QMCF MD). The process of hydrolysis, which occurred for each of the metal ions, was analyzed in terms of the time evolution of solvent configuration. Several important factors involved in the initiation of proton dissociation from first shell water molecules are discussed in connection to the nature of proton mobility in aqueous solution.

Hydrolytic conversion of AsO(-3)4 to HAsO(-2)4: a QMCF MD study.

A quantum mechanical charge field molecular dynamics (QMCF MD) study of AsO in water was carried out to gain insight into its conversion from the hydrated anion resulting in OH(-) ions and HAsO, which occurs on the scale of a few hundred femtoseconds. The OH(-) ion undergoes further proton exchange with water molecules, while HAsO is a stable species.

Hydrogen evolution reaction mediated by an all-sulfur trinuclear nickel complex.

We report the synthesis and the characterization of a trinuclear nickel complex. Solid state and solution studies using X-ray diffraction, NMR and UV-vis spectroscopy highlight the square planar geometries around the metal centers and an all-sulfur coordination sphere. It exhibits significant electrocatalytic activity for hydrogen evolution in DMF using Et3NHCl as the proton source. DFT studies suggest that sulfur atoms act as proton relay, as proposed in [NiFe] hydrogenases.

City-Scale Agent-Based Simulators for the Study of Non-pharmaceutical Interventions in the Context of the COVID-19 Epidemic: IISc-TIFR COVID-19 City-Scale Simulation Team.

We highlight the usefulness of city-scale agent-based simulators in studying various non-pharmaceutical interventions to manage an evolving pandemic. We ground our studies in the context of the COVID-19 pandemic and demonstrate the power of the simulator via several exploratory case studies in two metropolises, Bengaluru and Mumbai. Such tools may in time become a common-place item in the tool kit of the administrative authorities of large cities.

Beryllium(II): the strongest structure-forming ion in water? A QMCF MD simulation study.

A quantum mechanical charge field (QMCF) molecular dynamics (MD) simulation including the first and second hydration shells in the QM region has been carried out to describe the structural and dynamical properties of Be(2+) in aqueous solution. In this methodology, the full first and second hydration shells are treated by ab initio quantum mechanics supplemented by a fluctuating electrostatic embedding technique. From the simulation, structural properties were extracted and were found to be in good agreement with previously published experimental and theoretical results. The radial distribution function (RDF) showed the maximum probability of the Be-O bond length at 1.62 A. The first tetrahedrally arranged hydration shell is highly inert with respect to ligand-exchange processes. Application of local-density-corrected three-body correlation analysis showed minor structural influence of the ion beyond the second hydration layer, contrary to the findings of a previous QM/MM MD simulation. The dynamics of the hydrate were studied in terms of ligand mean residence times (MRTs) and the power spectrum of the Be(2+)-O stretching frequency. A comparison of the "classical" QM/MM framework with the QMCF method clearly demonstrated the advantages of the latter, as ambiguities arising from the coupling of the subregions occurring in QM/MM MD simulations did not appear when the QMCF ansatz was applied.

Structure and dynamics of the U4+ ion in aqueous solution: an ab initio quantum mechanical charge field molecular dynamics study.

The structure and dynamics of the stable four-times positively charged uranium(IV) cation in aqueous solution have been investigated by ab initio quantum mechanical charge field (QMCF) molecular dynamics (MD) simulation at the Hartree-Fock double-zeta quantum mechanical level. The QMCF-MD approach enables investigations with the accuracy of a quantum mechanics/molecular mechanics approach without the need for the construction of solute-solvent potentials. Angular distribution functions; radial distribution functions; coordination numbers of the first, second, and third shell (9, 19, and 44, respectively); coordination number distribution functions; tilt- and Theta-angle distribution functions; as well as local density corrected triangle distribution functions have been employed for the evaluation of the hydrated ion's structure. Special attention was paid to the determination of the geometry of the first hydration layer, and the results were compared to experimental large-angle X-ray scattering and extended X-ray absorption fine structure data. The solvent dynamics around the ion were also investigated using mean ligand residence times and related data and, resulting from the unavailability of any experimental data, were compared to ions with similar properties.