Em Ab Research Articles

Characterization of Two Highly Specific Monoclonal Antibodies Targeting the Glycan Loop of the Zika Virus Envelope Protein.

Zika virus (ZIKV) is an emerging flavivirus associated with several neurological diseases such as Guillain-Barré syndrome in adults and microcephaly in newborn children. Its distribution and mode of transmission (via Aedes aegypti and Aedes albopictus mosquitoes) collectively cause ZIKV to be a serious concern for global health. High genetic homology of flaviviruses and shared ecology is a hurdle for accurate detection. Distinguishing infections caused by different viruses based on serological recognition can be misleading as many anti-flavivirus monoclonal antibodies (mAbs) discovered to date are highly cross-reactive, especially those against the envelope (E) protein. To provide more specific research tools, we produced ZIKV E directed hybridoma cell lines and characterized two highly ZIKV-specific mAb clones (mAbs A11 and A42) against several members of the Flavivirus genus. Epitope mapping of mAb A11 revealed glycan loop specificity in Domain I of the ZIKV E protein. The development of two highly specific mAbs targeting the surface fusion protein of ZIKV presents a significant advancement in research capabilities as these can be employed as essential tools to enhance our understanding of ZIKV identification on infected cells ex vivo or in culture.

Reduced-density-matrix-based ab initio cavity quantum electrodynamics

A reduced-density-matrix (RDM)-based approach to {\em ab initio} cavity quantum electrodynamics (QED) is developed. The expectation value of the Pauli-Fierz Hamiltonian is expressed in terms of one- and two-body electronic and photonic RDMs, and the elements of these RDMs are optimized directly in polynomial time by semidefinite programming techniques, without knowledge of the full wave function. QED generalizations of important ensemble $N$-representability conditions are derived and enforced in this procedure. The resulting approach is applied to the description of classic ground-state strong electron correlation problems, augmented by the presence of ultrastrong light-matter coupling. First, we assess cavity-induced changes to the singlet-triplet energy gap of the linear oligoacene series; for a heptacene molecule, this gap can change by as much as 1.9 kcal mol$^{-1}$ (or 15\%) when the molecule is aligned along the cavity mode polarization axis. We also explore the metal-insulator transition in linear hydrogen chains and demonstrate that strong electron-photon interactions increase the insulating character of these systems under all coupling strengths considered.

Unusual electric polarization behavior in elemental quasi-two-dimensional allotropes of selenium

We investigate tunable electric polarization and electronic structure of quasi-two-dimensional (quasi-2D) allotropes of selenium, which are formed from their constituent one-dimensional (1D) structures through an inter-chain interaction facilitated by the multi-valence nature of Se. Our em ab initio calculations reveal that different quasi-2D Se allotropes display different types of electric polarization, including ferroelectric (FE) polarization normal to the chain direction in alpha and delta allotropes, non-collinear ferrielectric (FiE) polarization along the chain axis in tau-Se, and anti-ferroelectric (AFE) polarization in eta-Se. The magnitude and direction of the polarization can be changed by a previously unexplored rotation of the constituent chains. In that case, an in-plane polarization direction may change to out-of-plane in alpha-Se and delta-Se, flip its direction, and even disappear in tau-Se. Also, the band gap may be reduced and changed from indirect to direct by rotating the constituent chains about their axes in these quasi-2D Se allotropes.

Elasticity of two-dimensional ferroelectrics across their paraelectric phase transformation

The mechanical behavior of two-dimensional (2D) materials across 2D phase changes is unknown, and the finite temperature ($T$) elasticity of paradigmatic SnSe monolayers -- ferroelectric 2D materials turning paraelectric as their unit cell (u.c.) turns from a rectangle onto a square -- is described here in a progressive manner. To begin with, their zero$-T$ {\em elastic energy landscape} gives way to (Boltzmann-like) averages from which the elastic behavior is determined. These estimates are complemented with results from the strain-fluctuation method, which employs the energy landscape or {\em ab initio} molecular dynamics (MD) data. Both approaches capture the coalescence of elastic moduli $\langle C_{11}(T)\rangle=\langle C_{22}(T)\rangle$ due to the structural transformation. The broad evolution and sudden changes of elastic parameters $\langle C_{11}(T)\rangle$, $\langle C_{22}(T)\rangle$, and $\langle C_{12}(T)\rangle$ of these atomically-thin phase-change membranes establishes a heretofore overlooked connection among 2D materials and soft matter.

Testing the Green's function coupled cluster singles and doubles impurity solver on real materials within the framework of self-energy embedding theory

We apply the Green's function coupled cluster singles and doubles (GFCCSD) impurity solver to realistic impurity problems arising for strongly correlated solids within the self-energy embedding theory (SEET) framework. We describe the details of our GFCC solver implementation, investigate its performance, and highlight potential advantages and problems on examples of impurities created during the self-consistent SEET for antiferromagnetic MnO and paramagnetic SrMnO$_{3}$. GFCCSD provides satisfactory descriptions for weakly and moderately correlated impurities with sizes that are intractable by existing accurate impurity solvers such as exact diagonalization (ED). However, our data also shows that when correlations become strong, the singles and doubles approximation used in GFCC could lead to instabilities in searching for the particle number present in impurity problems. These instabilities appears especially severe when the impurity size gets larger and multiple degenerate orbitals with strong correlations are present. We conclude that to fully check the reliability of GFCCSD results and use them in fully {\em ab initio} calculations in the absence of experiments, a verification from a GFCC solver with higher order excitations is necessary.

Deep learning of accurate force field of ferroelectric HfO2

The discovery of ferroelectricity in HfO$_2$-based thin films opens up new opportunities for using this silicon-compatible ferroelectric to realize low-power logic circuits and high-density non-volatile memories. The functional performances of ferroelectrics are intimately related to their dynamic responses to external stimuli such as electric fields at finite temperatures. Molecular dynamics is an ideal technique for investigating dynamical processes on large length and time scales, though its applications to new materials is often hindered by the limited availability and accuracy of classical force fields. Here we present a deep neural network-based interatomic force field of HfO$_2$ learned from {\em ab initio} data using a concurrent learning procedure. The model potential is able to predict structural properties such as elastic constants, equation of states, phonon dispersion relationships, and phase transition barriers of various hafnia polymorphs with accuracy comparable with density functional theory calculations. The validity of this model potential is further confirmed by the reproduction of experimental sequences of temperature-driven ferroelectric-paraelectric phase transitions of HfO$_2$ with isobaric-isothermal ensemble molecular dynamics simulations. We suggest a general approach to extend the model potential of HfO$_2$ to related material systems including dopants and defects.

Metastable piezoelectric group-IV monochalcogenide monolayers with a buckled honeycomb structure

Twelve two-dimensional group-IV monochalcogenide monolayers (SiS, SiSe, SiTe, GeS, GeSe, GeTe, SnS, SnSe, SnTe, PbS, PbSe, and PbTe) with a buckled honeycomb atomistic structure--belonging to symmetry group P3m1--and an out-of-plane intrinsic electric polarization are shown to be metastable by three independendent methods. First, we uncover a coordination-preserving structural transformation from the low-buckled honeycomb structure onto the lower-energy Pnm2$_1$ (or Pmmn for PbS, PbSe, and PbTe) phase to estimate {\em energy barriers} $E_B$ that must be overcome during such structural transformation. Using the curvature of the local minima and $E_B$ as inputs to Kramers escape formula, large escape times are found, implying the structural metastability of the buckled honeycomb phase (nevertheless, and with the exception of PbS and PbSe, these phases display escape times ranging from 700 years to multiple times the age of the universe, and can be considered "stable" for practical purposes only in that relative sense). The second demonstration is provided by phonon dispersion relations that include the effect of long-range Coulomb forces and display no negative vibrational modes. The third and final demonstration of structural metastability is furnished by room-temperature {\em ab initio} molecular dynamics for selected compounds. The magnitude of the electronic band gap evolves with chemical composition. Different from other binary two-dimensional compounds such as transition metal dichalcogenide monolayers and hexagonal boron nitride monolayers which only develop an in-plane piezoelectric response, the twelve group-IV monochalcogenide monolayers with a buckled honeycomb structure also display out-of-plane piezoelectric properties.

Anomalous thermoelectricity at the two-dimensional structural transition of SnSe monolayers

SnSe monolayers experience a temperature induced two-dimensional Pnm2$_1 \to$ P4/nmm structural transformation precipitated by the softening of vibrational modes. The standard theoretical treatment of thermoelectricity---which relies on a zero temperature phonon dispersion and on a zero temperature electronic structure---is incapable of describing thermoelectric phenomena induced by structural transformations. Relying on structural data obtained from {\em ab initio} molecular dynamics calculations that is utilized in a non-standard way to inform of electronic and vibrational transport coefficients, the present work establishes a general route to understand thermoelectricity across phase transitions. Similar to recent experimental observations pointing to an overestimated thermoelectric figure of merit $ZT$ past the transition temperature, our work indicates a smaller $ZT$ when compared to its value predicted by the standard paradigm. Its decrease is related to the dramatic changes in the electrical conductivity and lattice thermal conductivity as the structural transformation ensues. Though exemplified on a SnSe monolayer, the method does not have any built-in assumptions concerning dimensionality, and thus applicable to arbitrary thermoelectric materials in one, two, and three dimensions.

A compact SPR biosensor device for the rapid and efficient monitoring of gluten-free diet directly in human urine.

Celiac disease (CD) is a chronic autoimmune disorder induced in genetically susceptible individuals by the ingestion of gluten from wheat, rye, barley, or certain varieties of oats. A careful diet follow-up is necessary to avoid health complications associated with long-term gluten intake by the celiac patients. Small peptides (GIP, gluten immunogenic peptides) derived from gluten digestion, which are excreted in the urine and feces, have emerged as promising biomarkers to monitor gluten intake. We have implemented a simple and sensitive label-free point-of-care (POC) device based on surface plasmon resonance for the direct detection of these biomarkers in urine. The assay employs specific monoclonal antibodies and has been optimized for the detection of the 33-mer α2-gliadin, known as the main immunogenic peptide of wheat gluten, and for the detection of GIP. Direct detection in undiluted urine has been accomplished by using biosensing chips containing a robust and stable biorecognition layer, obtained after carefully optimizing the biofunctionalization protocol. Excellent limits of detection have been reached (1.6-4.0ngmL-1 using mAb G12 and A1, respectively), which ensures the detection of gluten peptides even when the gluten intake is around the maximum tolerable amount in the digestive tract (< 50mg) for celiac individuals. No sample pretreatment, extraction, or dilution is required, and the analysis takes less than 15min. The assays have excellent reproducibility' as demonstrated by measuring spiked urine samples containing the same target concentration using different biofunctionalized chips prepared and stored at different periods of time (i.e., CV% of 3.58% and 11.30%, for G12- and A1-based assays, respectively). The assay has been validated with real samples. These features pave the way towards an end-user easy-to-handle biosensor device for the rapid monitoring of gluten-free diet (GFD) and follow-up of the health status in celiac patients.

Carrier- and strain-tunable intrinsic magnetism in two-dimensional MAX3 transition metal chalcogenides

We present a density functional theory study of the carrier-density and strain dependence of magnetic order in two-dimensional (2D) MAX$_3$ (M= V, Cr, Mn, Fe, Co, Ni; A= Si, Ge, Sn, and X= S, Se, Te) transition metal trichalcogenides. Our {\em ab initio} calculations show that this class of compounds includes wide and narrow gap semiconductors and metals and half-metals, and that most of these compounds are magnetic. Although antiferromagnetic order is most common, ferromagnetism is predicted in MSiSe$_3$ for M= Mn, Ni, in MSiTe$_3$ for M= V, Ni, in MnGeSe$_3$, in MGeTe$_3$ for M=Cr, Mn, Ni, in FeSnS$_3$, and in MSnTe$_3$ for M= V, Mn, Fe. Among these compounds CrGeTe$_3$ and VSnTe$_3$ are ferromagnetic semiconductors. Our calculations suggest that the competition between antiferromagnetic and ferromagnetic order can be substantially altered by strain engineering, and in the semiconductor case also by gating. The associated critical temperatures can be substantially enhanced by means of carrier doping and strains.

Pump-driven normal-to-excitonic insulator transition: Josephson oscillations and signatures of BEC-BCS crossover in time-resolved ARPES

We consider a ground-state wide-gap band insulator turning into a nonequilibrium excitonic insulator (NEQ-EI) upon visiting properly selected and physically relevant highly excited states. The NEQ-EI phase, characterized by self-sustained oscillations of the complex order parameter, neatly follows from a Nonequilibrium Green's Function treatment on the Konstantinov-Perel' contour. We present the first {\em ab initio} band structure of LiF, a ground-state bulk insulator, in different NEQ-EI states and show that these states can be generated by currently available pump pulses. We highlight two general features of time-resolved ARPES spectra: (1) during the pump-driving the excitonic spectral structure undergoes a convex-to-concave shape transition and {\em concomitantly} the state of the system goes through a BEC-BCS crossover; (2) attosecond pulses shone after the pump-driving at different times $t_{\rm delay}$ generate a photocurrent which {\em oscillates} in $t_{\rm delay}$ with a pump-tunable frequency -- we show that this phenomenon is similar to the AC response of an exotic Josephson junction.

Clinical efficacy of leuprorelin combined with mifepristone in the treatment of endometriosis

Objective To observe the clinical efficacy of leuprorelin combined with mifepristone in the treatment of endometriosis. Methods From September 2014 to September 2016, 168 cases of endometriosis were selected in the research.The patients were divided into the control group and the research group according to the random number table method, with 84 patients in each group.All patients underwent laparoscopic endometrial debridement with fertility preservation.The control group was treated with mifepristone, while the study group was treated with combination of leuprorelin and mifepristone.The incidence of adverse drug reactions during treatment was observed, the levels of serum E2, LH, FSH, EmAb and CA125 were detected before and after treatment, the curative effect after treatment was evaluated, and the recurrence and pregnancy of endometriosis within 12 months after treatment were followed. Results During the treatment, the incidence rate of adverse drug reactions in the study group(17/84, 20.24%) had no statistically significant difference compared with the control group (13/84, 15.48%) (χ2=0.649, P=0.420). The levels of serum estradiol (E2), luteinizing hormone (LH), follicle stimulating hormone (FSH), anti-endometrial antibody (EmAb) and carbohydrate antigen 125 (CA125) in the two groups were significantly lower than those before treatment (t=17.694, 13.271, 7.943, 4.315, 10.029, 7.952, 14.231, 10.610, 27.953, 22.436, all P<0.001), and the indicators in the study group were significantly lower than those in the control group (t=5.217, 3.859, 3.526, 4.337, 6.048, all P<0.001). The total effective rate of the study group (96.43%) was significantly higher than that of the control group (83.33%) (χ2=7.919, P=0.005). Within 12 months after treatment, the recurrence rate of endometriosis in the study group (2.38%) was significantly lower than that of the control group (15.48%), while the rate of pregnancy (48.81%) was significantly higher than that of the control group(27.38%), there were statistically significant differences between the two groups (χ2=8.858, 8.178; P=0.003, 0.004). Conclusion Compared with leuprorelin treatment alone, leuprorelin combined with mifepristone can significantly reduce the serum levels of E2, LH, FSH, EmAb and CA125 in patients with endometriosis, and improve the overall treatment of endometriosis, reduce recurrence, promote pregnancy, and has high safety. Key words: Endometriosis; Estradiol; Luteinizing hormone; Follicle stimulating hormone, human; Leuprorelin; Mifepristone

Theoretical study of the electron structure of superheavy elements with an open 6d shell: Sg, Bh, Hs, and Mt

We use recently developed efficient versions of the configuration interaction method to perform {\em ab initio} calculations of the spectra of superheavy elements seaborgium (Sg, $Z=106$), bohrium (Bh, $Z=107$), hassium (Hs, $Z=108$) and meitnerium (Mt, $Z=109$). We calculate energy levels, ionization potentials, isotope shifts and electric dipole transition amplitudes. Comparison with lighter analogs reveals significant differences caused by strong relativistic effects in superheavy elements. Very large spin-orbit interaction distinguishes subshells containing orbitals with a definite total electron angular momentum $j$. This effect replaces Hund's rule holding for lighter elements.

Structure and Electronic Properties of Transition-Metal/Mg Bimetallic Clusters at Realistic Temperatures and Oxygen Partial Pressures

Composition, atomic structure, and electronic properties of TM$_x$Mg$_y$O$_z$ clusters (TM = Cr, Ni, Fe, Co, $x+y \leq 3$) at realistic temperature $T$ and partial oxygen pressure $p_{\textrm{O}_2}$ conditions are explored using the {\em ab initio} atomistic thermodynamics approach. The low-energy isomers of the different clusters are identified using a massively parallel cascade genetic algorithm at the hybrid density-functional level of theory. On analyzing a large set of data, we find that the fundamental gap E$_\textrm{g}$ of the thermodynamically stable clusters are strongly affected by the presence of Mg-coordinated O$_2$ moieties. In contrast, the nature of the transition metal does not play a significant role in determining E$_\textrm{g}$. Using E$_\textrm{g}$ of a cluster as a descriptor of its redox properties, our finding is against the conventional belief that the transition metal plays the key role in determining the electronic and therefore chemical properties of the clusters. High reactivity may be correlated more strongly with oxygen content in the cluster than with any specific TM type.

Absence of superconductivity in iron polyhydrides at high pressures

Recently, C. M. P\'epin \textit{et al.} [Science \textbf{357}, 382 (2017)] reported the formation of several new iron polyhydrides FeH$_x$ at pressures in the megabar range, and spotted FeH$_5$, which forms above 130 GPa, as a potential high-\tc \ superconductor, because of an alleged layer of dense metallic hydrogen. Shortly after, two studies by A.~Majumdar \textit{et al.} [Phys. Rev. B \textbf{96}, 201107 (2017)] and A.~G.~Kvashnin \textit{et al.} [J. Phys. Chem. C \textbf{122}, 4731 (2018)] based on {\em ab initio} Migdal-Eliashberg theory seemed to independently confirm such a conjecture. We conversely find, on the same theoretical-numerical basis, that neither FeH$_5$ nor its precursor, FeH$_3$, shows any conventional superconductivity and explain why this is the case. We also show that superconductivity may be attained by transition-metal polyhydrides in the FeH$_3$ structure type by adding more electrons to partially fill one of the Fe--H hybrid bands (as, e.g., in NiH$_3$). Critical temperatures, however, will remain low because the $d$--metal bonding, and not the metallic hydrogen, dominates the behavior of electrons and phonons involved in the superconducting pairing in these compounds.

Development and characterization of a human monoclonal antibody targeting the N-terminal region of hepatitis C virus envelope glycoprotein E1

Monoclonal antibodies (mAbs) targeting the hepatitis C virus (HCV) envelope have been raised mainly against envelope protein 2 (E2), while the antigenic epitopes of envelope protein 1 (E1) are not fully identified. Here we describe the detailed characterization of a human mAb, designated A6, generated from an HCV genotype 1b infected patient. ELISA results showed reactivity of mAb A6 to full-length HCV E1E2 of genotypes 1a, 1b and 2a. Epitope mapping identified a region spanning amino acids 230–239 within the N-terminal region of E1 as critical for binding. Antibody binding to this epitope was not conformation dependent. Neutralization assays showed that mAb A6 lacks neutralizing capacity and does not interfere with the activity of known neutralizing antibodies. In summary, mAb A6 is an important tool to study the structure and function of E1 within the viral envelope, a crucial step in the development of an effective prophylactic HCV vaccine.

Automation methodologies and large-scale validation for GW : Towards high-throughput GW calculations

The search for new materials, based on computational screening, relies on methods that accurately predict, in an automatic manner, total energy, atomic-scale geometries, and other fundamental characteristics of materials. Many technologically important material properties directly stem from the electronic structure of a material, but the usual workhorse for total energies, namely density-functional theory, is plagued by fundamental shortcomings and errors from approximate exchange-correlation functionals in its prediction of the electronic structure. At variance, the $GW$ method is currently the state-of-the-art {\em ab initio} approach for accurate electronic structure. It is mostly used to perturbatively correct density-functional theory results, but is however computationally demanding and also requires expert knowledge to give accurate results. Accordingly, it is not presently used in high-throughput screening: fully automatized algorithms for setting up the calculations and determining convergence are lacking. In this work we develop such a method and, as a first application, use it to validate the accuracy of $G_0W_0$ using the PBE starting point, and the Godby-Needs plasmon pole model ($G_0W_0^\textrm{GN}$@PBE), on a set of about 80 solids. The results of the automatic convergence study utilized provides valuable insights. Indeed, we find correlations between computational parameters that can be used to further improve the automatization of $GW$ calculations. Moreover, we find that $G_0W_0^\textrm{GN}$@PBE shows a correlation between the PBE and the $G_0W_0^\textrm{GN}$@PBE gaps that is much stronger than that between $GW$ and experimental gaps. However, the $G_0W_0^\textrm{GN}$@PBE gaps still describe the experimental gaps more accurately than a linear model based on the PBE gaps.

Chemical and Electronic Repair Mechanism of Defects in MoS2 Monolayers

Using ab initio density functional theory calculations, we characterize changes in the electronic structure of MoS2 monolayers introduced by missing or additional adsorbed sulfur atoms. We furthermore identify the chemical and electronic function of substances that have been reported to reduce the adverse effect of sulfur vacancies in quenching photoluminescence and reducing electronic conductance. We find that thiol-group-containing molecules adsorbed at vacancy sites may reinsert missing sulfur atoms. In the presence of additional adsorbed sulfur atoms, thiols may form disulfides on the MoS2 surface to mitigate the adverse effect of defects.

Clustering according to urolithin metabotype explains the interindividual variability in the improvement of cardiovascular risk biomarkers in overweight-obese individuals consuming pomegranate: A randomized clinical trial.

The pomegranate lipid-lowering properties remain controversial, probably due to the interindividual variability in polyphenol (ellagitannins) metabolism. We aimed at investigating whether the microbially derived ellagitannin-metabolizing phenotypes, i.e. urolithin metabotypes A, (UM-A), B (UM-B), and 0 (UM-0), influence the effects of pomegranate extract (PE) consumption on 18 cardiovascular risk biomarkers in healthy overweight-obese individuals. A double-blind, crossover, dose-response, randomized, placebo-controlled trial was conducted. The study (POMEcardio) consisted of two test phases (dose-1 and dose-2, lasting 3 weeks each) and a 3-week washout period between each phase. Forty-nine participants (BMI > 27 kg/m2 ) daily consumed one (dose-1, 160 mg phenolics/day) or four (dose-2, 640 mg phenolics/day) PE or placebo capsules. Notably, UM-B individuals showed the highest baseline cardiovascular risk. After dose-2, total cholesterol (-15.5 ± 3.7%), LDL-cholesterol (-14.9 ± 2.1%), small LDL-cholesterol (-47 ± 7%), non-HDL-cholesterol (-11.3 ± 2.5%), apolipoprotein-B (-12 ± 2.2%), and oxidized LDL-cholesterol -24 ± 2.5%) dose dependently decreased (P < 0.05) but only in UM-B subjects. These effects were partially correlated with urolithin production and the increase in Gordonibacter levels. Three (50%) nonproducers (UM-0) became producers following PE consumption. UM clustering suggests a personalized effect of ellagitannin-containing foods and could explain the controversial pomegranate benefits. Research on the specific role of urolithins and the microbiota associated with each UM is warranted.

First-principles approach to excitons in time-resolved and angle-resolved photoemission spectra

We show that any {\em quasi-particle} or GW approximation to the self-energy does not capture excitonic features in time-resolved (TR) photoemission spectroscopy. In this work we put forward a first-principles approach and propose a feasible diagrammatic approximation to solve this problem. We also derive an alternative formula for the TR photocurrent which involves a single time-integral of the lesser Green's function. The diagrammatic approximation applies to the {\em relaxed} regime characterized by the presence of quasi-stationary excitons and vanishing polarization. The main distinctive feature of the theory is that the diagrams must be evaluated using {\em excited} Green's functions. As this is not standard the analytic derivation is presented in detail. The final result is an expression for the lesser Green's function in terms of quantities that can all be calculated {\em ab initio}. The validity of the proposed theory is illustrated in a one-dimensional model system with a direct gap. We discuss possible scenarios and highlight some universal features of the exciton peaks. Our results indicate that the exciton dispersion can be observed in TR {\em and} angle-resolved photoemission.