The dynamics of copper intercalated molybdenum ditelluride

Layered transition metal dichalcogenides are emerging as key materials in nanoelectronics and energy applications. Predictive models to understand their growth, thermomechanical properties and interactions with metals are needed in order to accelerate their incorporation into commercial products. Interatomic potentials enable large-scale atomistic simulations at the device level, beyond the range of applications of first principle methods. We present a ReaxFF reactive force field to describe molybdenum ditelluride and its interactions with copper. We optimized the force field parameters to describe the properties of layered MoTe2 in various phases, the intercalation of Cu atoms and clusters within its van der Waals gap, including a proper description of energetics, charges and mechanical properties. The training set consists of an extensive set of first principle calculations computed from density functional theory. We use the force field to study the adhesion of a single layer MoTe2 on a Cu(111) surface and the results are in good agreement with density functional theory, even though such structures were not part of the training set. We characterized the mobility of the Cu ions intercalated into MoTe2 under the presence of an external electric fields via molecular dynamics simulations. The results show a significant increase in drift velocity for electric fields of approximately 0.4 V/A and that mobility increases with Cu ion concentration.Comment: 21 pages, 9 Figure

Molecular dynamic simulation of tip-polymer interaction in tapping-mode atomic force microscopy

We present a molecular dynamic study of the interaction between an amorphous silica tip (SiO_2) and an amorphous poly-(methyl-methacrylate) substrate under conditions relevant for tapping-mode atomic force microscopy. To capture the actual dynamics of the tip, we use the dynamic contact simulation method [Kim et al., J. Appl. Phys. 112, 094325 (2012)]. We obtain force-displacement relationships both for neat polymer substrates and a sample with a sub-surface nanotube and extract the local stiffness and energy dissipation per cycle. The simulations capture non-trivial aspects of the interaction that originate from the viscoelastic nature of the polymer including an increase in repulsive interaction force during approach with tip velocity and an increase in adhesion during retraction with decreasing tip velocity. Scans of local stiffness and dissipation over the samples reveal intrinsic variability in the amorphous polymer but also the effect of local surface topography on the extracted properties as well as the ability of the method to detect a sub-surface nanotube. This insight and quantitative data should be valuable to interpret the results of atomic force microscopy studies

Black hole mass estimates in quasars - A comparative analysis of high- and low-ionization lines

The inter-line comparison between high- and low-ionization emission lines has yielded a wealth of information on the quasar broad line region (BLR) structure and dynamics, including perhaps the earliest unambiguous evidence in favor of a disk + wind structure in radio-quiet quasars. We carried out an analysis of the CIV 1549 and Hbeta line profiles of 28 Hamburg-ESO high luminosity quasars and of 48 low-z, low luminosity sources in order to test whether the high-ionization line CIV 1549 width could be correlated with Hbeta and be used as a virial broadening estimator. We analyze intermediate- to high-S/N, moderate resolution optical and NIR spectra covering the redshifted CIV and H$\beta$ over a broad range of luminosity log L ~ 44 - 48.5 [erg/s] and redshift (0 - 3), following an approach based on the quasar main sequence. The present analysis indicates that the line width of CIV 1549 is not immediately offering a virial broadening estimator equivalent to H$\beta$. At the same time a virialized part of the BLR appears to be preserved even at the highest luminosities. We suggest a correction to FWHM(CIV) for Eddington ratio (using the CIV blueshift as a proxy) and luminosity effects that can be applied over more than four dex in luminosity. Great care should be used in estimating high-L black hole masses from CIV 1549 line width. However, once corrected FWHM(CIV) values are used, a CIV-based scaling law can yield unbiased MBH values with respect to the ones based on H$\beta$ with sample standard deviation ~ 0.3 dex.Comment: 43 pages, 15 Figures, submitted to A&

Experimental observation of the Bogoliubov transformation for a Bose-Einstein condensed gas

Phonons with wavevector $q/\hbar$ were optically imprinted into a Bose-Einstein condensate. Their momentum distribution was analyzed using Bragg spectroscopy with a high momentum transfer. The wavefunction of the phonons was shown to be a superposition of +q and -q free particle momentum states, in agreement with the Bogoliubov quasiparticle picture.Comment: 4 pages, 3 figures, please take postscript version for the best version of Fig

Quantum damping of position due to energy measurements

Quantum theory for measurements of energy is introduced and its consequences for the average position of monitored dynamical systems are analyzed. It turns out that energy measurements lead to a localization of the expectation values of other observables. This is manifested, in the case of position, as a damping of the motion without classical analogue. Quantum damping of position for an atom bouncing on a reflecting surface in presence of a homogeneous gravitational field is dealt in detail and the connection with an experiment already performed in the classical regime is studied. We show that quantum damping is testable provided that the same measurement strength obtained in the experimental verification of the quantum Zeno effect in atomic spectroscopy [W. M. Itano et al., Phys. Rev. A {\bf 41}, 2295 (1990)] is made available.Comment: 19 pages + 4 figures available upon request; Plain REVTeX; To be published in Phys. Rev.

A protocol for identifying the binding sites of small molecules on the cystic fibrosis transmembrane conductance regulator (CFTR) protein

We describe a protocol to identify the binding site(s) for a drug called ivacaftor that potentiates the CFTR chloride channel. We use photoaffinity probes-based on the structure of ivacaftor-to covalently modify the CFTR protein at the region that constitutes the drug binding site(s). We define the methods for photo-labeling CFTR, its membrane extraction, and enzymatic digestion using trypsin. We then describe the experimental methods to identify the modified peptides by using mass spectrometry. For complete details on the use and execution of this protocol, please refer to Laselva et al. (2021)

Functional integral treatment of some quantum nondemolition systems

In the scheme of a quantum nondemolition (QND) measurement, an observable is measured without perturbing its evolution. In the context of studies of decoherence in quantum computing, we examine the `open' quantum system of a two-level atom, or equivalently, a spin-1/2 system, in interaction with quantum reservoirs of either oscillators or spins, under the QND condition of the Hamiltonian of the system commuting with the system-reservoir interaction. For completeness, we also examine the well-known non-QND spin-Bose problem. For all these many-body systems, we use the methods of functional integration to work out the propagators. The propagators for the QND Hamiltonians are shown to be analogous to the squeezing and rotation operators, respectively, for the two kinds of baths considered. Squeezing and rotation being both phase space area-preserving canonical transformations, this brings out an interesting connection between the energy-preserving QND Hamiltonians and the homogeneous linear canonical transformations.Comment: 16 pages, no figure

Stage-Specific Generation of Human Pluripotent Stem Cell Derived Lung Models to Measure CFTR Function

Human embryonic stem cells (ES) and induced pluripotent stem cells (iPSC) are powerful tools that have the potential to generate in vitro human lung epithelial cells. However, challenges in efficiency and reproducibility remain in utilizing the cells for therapy discovery platforms. Here, we optimize our previously published protocols to efficiently generate three developmental stages of the lung model (fetal lung epithelial progenitors, fLEP; immature airway epithelial spheroid, AES; air-liquid interface culture, ALI), and demonstrate its potential for cystic fibrosis (CF) drug discovery platforms. The stepwise approach directs differentiation from hPSC to definitive endoderm, anterior ventral foregut endoderm, and fetal lung progenitor cells. The article also describes the generation of immature airway epithelial spheroids in Matrigel with epithelial cells sorted by a magnetic-activated cell sorting system, and the generation of adult-like airway epithelia through air-liquid interface conditions. We demonstrate that this optimized procedure generates remarkably higher cystic fibrosis transmembrane conductance regulator (CFTR) expression and function than our previous method, and thus is uniquely suitable for CF research applications. © 2022 The Authors. Current Protocols published by Wiley Periodicals LLC. Basic Protocol 1: hESC/hiPSC differentiation to fetal lung progenitors Basic Protocol 2: Formation of airway epithelial spheroids Alternate Protocol 1: Cryopreservation of airway epithelial spheroids Basic Protocol 3: Differentiation and maturation in air-liquid interface culture Alternate Protocol 2: Differentiation and maturation of epithelial progenitors from airway epithelial spheroids in ALI culture

Bogoliubov spectrum and Bragg spectroscopy of elongated Bose-Einstein condensates

The behavior of the momentum transferred to a trapped Bose-Einstein condensate by a two-photon Bragg pulse reflects the structure of the underlying Bogoliubov spectrum. In elongated condensates, axial phonons with different number of radial nodes give rise to a multibranch spectrum which can be resolved in Bragg spectroscopy, as shown by Steinhauer {\it et al.} [Phys. Rev. Lett. {\bf 90}, 060404 (2003)]. Here we present a detailed theoretical analysis of this process. We calculate the momentum transferred by numerically solving the time dependent Gross-Pitaevskii equation. In the case of a cylindrical condensate, we compare the results with those obtained by linearizing the Gross-Pitaevskii equation and using a quasiparticle projection method. This analysis shows how the axial-phonon branches affect the momentum transfer, in agreement with our previous interpretation of the observed data. We also discuss the applicability of this type of spectroscopy to typical available condensates, as well as the role of nonlinear effects.Comment: 8 pages, 7 figures, minor changes, typos correcte

Narrow-line Seyfert 1s: what is wrong in a name?

Narrow-line Seyfert 1s (NLSy1s) are an ill-defined class. Work done over the past 20 years as well as recent analyses show a continuity in properties (e.g., Balmer line profiles, blueshifts of high-ionization lines) between sources with FWHM above and below 2000 km/s, the defining boundary of NLSy1s. This finding alone suggests that comparisons between samples of NLSy1s and rest of broad-line AGNs are most likely biased. NLSy1s can be properly contextualized by their location on the quasar main sequence originally defined by Sulentic et al 2000. At one end, NLSy1s encompass sources with strong FeII emission and associated with high Eddington ratio that hold the promise of becoming useful distance indicators; at the other end, at least some of them are sources with broad profiles seen face-on. Any rigid FWHM limit gives rise to some physical ambiguity, as the FWHM of low-ionization lines depends in a complex way on mass, Eddington ratio, orientation, and luminosity. In addition, if the scaling derived from luminosity and virial dynamics applies to the broad line regions, NLSy1s at luminosity higher than 1E47 erg/s become physically impossible. Therefore, in a broader context, a proper subdivision of two distinct classes of AGNs and quasars may be achieved by the distinction between Pop. A and B with boundary at = 4000 km/s in samples at z < 1, or on the basis of spectrophotometric properties which may ultimately be related to differences in accretion modes if high-luminosity quasars are considered.Comment: Contribution presented at the meeting Revisiting narrow-line Seyfert 1 galaxies and their place in the Universe, held at the Padova Botanical Garden, Italy, on 9-13 April 201