Em Ab Research Articles

How Many-Body Correlations andαClustering ShapeHe6

The Borromean $^6$He nucleus is an exotic system characterized by two `halo' neutrons orbiting around a compact $^4$He (or $\alpha$) core, in which the binary subsystems are unbound. The simultaneous reproduction of its small binding energy and extended matter and point-proton radii has been a challenge for {\em ab initio} theoretical calculations based on traditional bound-state methods. Using soft nucleon-nucleon interactions based on chiral effective field theory potentials, we show that supplementing the model space with $^4$He+$n$+$n$ cluster degrees of freedom largely solves this issue. We analyze the role played by the $\alpha$-clustering and many-body correlations, and study the dependence of the energy spectrum on the resolution scale of the interaction.

Electronic and magnetic properties of single-layerMPX3metal phosphorous trichalcogenides

We systematically investigate the electronic structure and magnetic properties of two dimensional (2D) MPX$_3$ (M= V, Cr, Mn, Fe, Co, Ni, Cu, Zn, and X = S, Se, Te) transition metal chacogenophosphates to examine their potential role as single-layer van der Waals materials that exhibit magnetic order. Our {\em ab initio} calculations predict that most of these single-layer materials are antiferromagnetic semiconductors. The band gaps of the antiferromagnetic states decrease as the atomic number of the chalcogen atom increases (from S to Se, Te), leading in some cases to half-metallic ferromagnetic states or to non-magnetic metallic states. We find that the phase transition from antiferromagnetic semiconductor to ferromagnetic half-metal can be controlled by gating or by strain engineering. The sensitive interdependence we find between magnetic, structural, and electronic properties establishes the potential of this 2D materials class for applications in spintronics.

Optical absorption and conductivity in quasi-two-dimensional crystals from first principles: Application to graphene

This paper gives a theoretical formulation of the electromagnetic response of the quasi-two-dimensional (Q2D) crystals suitable for investigation of optical activity and polariton modes. The response to external electromagnetic field is described by current-current response tensor $\Pi_{\mu\nu}$ calculated by solving the Dyson equation in the random phase approximation (RPA), where current-current interaction is mediated by the photon propagator $D_{\mu\nu}$. The irreducible current-current response tensor $\Pi^0_{\mu\nu}$ is calculated from the {\em ab initio} Kohn-Sham (KS) orbitals. The accuracy of $\Pi^0_{\mu\nu}$ is tested in the long wavelength limit where it gives correct Drude dielectric function and conductivity. The theory is applied to the calculation of optical absorption and conductivity in pristine and doped single layer graphene and successfully compared with previous calculations and measurements.

Ab initio calculations of reactions with light nuclei

An {\em ab initio} (i.e., from first principles) theoretical framework capable of providing a unified description of the structure and low-energy reaction properties of light nuclei is desirable to further our understanding of the fundamental interactions among nucleons, and provide accurate predictions of crucial reaction rates for nuclear astrophysics, fusion-energy research, and other applications. In this contribution we review {\em ab initio} calculations for nucleon and deuterium scattering on light nuclei starting from chiral two- and three-body Hamiltonians, obtained within the framework of the {\em ab initio} no-core shell model with continuum. This is a unified approach to nuclear bound and scattering states, in which square-integrable energy eigenstates of the $A$-nucleon system are coupled to $(A-a)+a$ target-plus-projectile wave functions in the spirit of the resonating group method to obtain an efficient description of the many-body nuclear dynamics both at short and medium distances and at long ranges.

Structural Basis for Antibody Recognition of Lipid A: INSIGHTS TO POLYSPECIFICITY TOWARD SINGLE-STRANDED DNA

Septic shock is a leading cause of death, and it results from an inflammatory cascade triggered by the presence of microbial products in the blood. Certain LPS from Gram-negative bacteria are very potent inducers and are responsible for a high percentage of septic shock cases. Despite decades of research, mAbs specific for lipid A (the endotoxic principle of LPS) have not been successfully developed into a clinical treatment for sepsis. To understand the molecular basis for the observed inability to translate in vitro specificity for lipid A into clinical potential, the structures of antigen-binding fragments of mAbs S1-15 and A6 have been determined both in complex with lipid A carbohydrate backbone and in the unliganded form. The two antibodies have separate germ line origins that generate two markedly different combining-site pockets that are complementary both in shape and charge to the antigen. mAb A6 binds lipid A through both variable light and heavy chain residues, whereas S1-15 utilizes exclusively the variable heavy chain. Both antibodies bind lipid A such that the GlcN-O6 attachment point for the core oligosaccharide is buried in the combining site, which explains the lack of LPS recognition. Longstanding reports of polyspecificity of anti-lipid A antibodies toward single-stranded DNA combined with observed homology of S1-15 and A6 and the reports of several single-stranded DNA-specific mAbs prompted the determination of the structure of S1-15 in complex with single-stranded DNA fragments, which may provide clues about the genesis of autoimmune diseases such as systemic lupus erythematosus, thyroiditis, and rheumatic autoimmune diseases.

Erratum: Radioimmunotherapy of human tumours

Nature Reviews Cancer 15, 347–360 (2015) Nai-Kong V. Cheung and Steven M. Larson have now declared competing interests that were not stated in the version of this article that was originally published. The following competing interests statement has now been added to the online version: “S.M.L. has ownership interest (including patents) in nanoparticle constructs of C-DOTs, use of mAB A33, and small molecular radio label drugs in Dasatinib and the HSP 90 inhibitor PUH71 and kinetics of immunoPET localization to tumours.

Designing Isoelectronic Counterparts to Layered Group V Semiconductors.

In analogy to III-V compounds, which have significantly broadened the scope of group IV semiconductors, we propose a class of IV-VI compounds as isoelectronic counterparts to layered group V semiconductors. Using ab initio density functional theory, we study yet unrealized structural phases of silicon monosulfide (SiS). We find the black-phosphorus-like α-SiS to be almost equally stable as the blue-phosphorus-like β-SiS. Both α-SiS and β-SiS monolayers display a significant, indirect band gap that depends sensitively on the in-layer strain. Unlike 2D semiconductors of group V elements with the corresponding nonplanar structure, different SiS allotropes show a strong polarization either within or normal to the layers. We find that SiS may form both lateral and vertical heterostructures with phosphorene at a very small energy penalty, offering an unprecedented tunability in structural and electronic properties of SiS-P compounds.

Unified description of ^{6}Li structure and deuterium-^{4}He dynamics with chiral two- and three-nucleon forces.

We provide a unified abinitio description of the ^{6}Li ground state and elastic scattering of deuterium (d) on ^{4}He (α) using two- and three-nucleon forces from chiral effective field theory. We analyze the influence of the three-nucleon force and reveal the role of continuum degrees of freedom in shaping the low-lying spectrum of ^{6}Li. The calculation reproduces the empirical binding energy of ^{6}Li, yielding an asymptotic D- to S-state ratio of the ^{6}Li wave function in the d+α configuration of -0.027, in agreement with a determination from ^{6}Li-^{4}He elastic scattering, but overestimates the excitation energy of the 3^{+} state by 350keV. The bulk of the computed differential cross section is in good agreement with data. These results endorse the application of the present approach to the evaluation of the ^{2}H(α,γ)^{6}Li radiative capture, responsible for the big-bang nucleosynthesis of ^{6}Li.

Relative stability and local curvature analysis in carbon nanotori

We introduce a concise formalism to characterize nanometer-sized tori based on carbon nanotubes and to determine their stability by combining {\em ab initio} density functional calculations with a continuum elasticity theory approach that requires only shape information. We find that the high strain energy in nanotori containing only hexagonal rings is significantly reduced in nanotori containing also other polygons. Our approach allows to determine local curvature and link it to local strain energy, which is correlated with local stability and chemical reactivity.

Phase coexistence and metal-insulator transition in few-layer phosphorene: a computational study.

Based on ab initio density functional calculations, we propose γ-P and δ-P as two additional stable structural phases of layered phosphorus besides the layered α-P (black) and β-P (blue) phosphorus allotropes. Monolayers of some of these allotropes have a wide band gap, whereas others, including γ-P, show a metal-insulator transition caused by in-layer strain or changing the number of layers. An unforeseen benefit is the possibility to connect different structural phases at no energy cost. This becomes particularly valuable in assembling heterostructures with well-defined metallic and semiconducting regions in one contiguous layer.

Interrelation of superconductivity and magnetism in FeSe1−xTex compounds. Pressure effects

The effect of isotropic pressures P up to 5 kbar on the superconducting transition temperature Tc of the FeSe1−xTex system (x = 0, 0.85, 0.88, 0.90) is studied. For the first time, a change in the sign of the effect of pressure on Tc on going from FeSe to the tellurium-rich alloys is observed. This makes it possible to specify more precisely the form of the dependence of the pressure derivative dTc/dP on composition in this system. This dependence is compared with first principles calculations of the electron structure and magnetism of FeSe, FeTe, and FeSe0.5Te0.5 as functions of pressure, as well as with our earlier experimental data on the effect of pressure on the magnetic susceptibility of the normal state in FeSe and FeTe. This comparison is indicative of a competitive interrelationship between superconductivity and magnetism in tellurium rich FeSe1−xTex compounds.

Coronal lines and the importance of deep-core–valence correlation in Ag-like ions

We report on large-scale and critically evaluated {\em ab initio} MCDHF calculations of the wavelength of the "coronal", M1 transition $4f\ ^2\mathrm{F}_{5/2}^o-^2\mathrm{F}_{7/2}^o$ in Ag-like ions. The transition between these two fine structure levels, which makes up the ground term for $Z \ge 62$ in the isoelectronic sequence, has recently been observed in Yb$^{23+}$ and W$^{27+}$, where the latter could be of great importance for fusion plasma diagnostics. We present recommended values for all members of the sequence between $Z = 50$ and $94$, which are supported by excellent agreement with values from recent experiments. The importance of including core-valence correlation with the $n=3$ shell in the theoretical model is emphasized. The results show close to spectroscopic accuracy for these forbidden lines.

Interplay of growth mode and thermally induced spin accumulation in epitaxialAl/Co2TiSi/AlandAl/Co2TiGe/Alcontacts

The feasibility of thermally driven spin injectors built from half-metallic Heusler alloys inserted between aluminum leads was investigated by means of {\em ab initio} calculations of the thermodynamic equilibrium and electronic transport. We have focused on two main issues and found that: (i) the interface between Al and the closely lattice-matched Heusler alloys of type Co$_2$Ti$Z$ ($Z=$ Si or Ge) is stable under various growth conditions; and (ii) the conventional and spin-dependent Seebeck coefficients in such heterojunctions exhibit a strong dependence on both the spacer and the atomic composition of the Al/Heusler interface. The latter quantity gives a measure of the spin accumulation and varies between $+8$~$\mu$V/K and $-3$~$\mu$V/K near $300$~K, depending on whether a Ti-Ge or a Co-Co plane makes the contact between Al and Co$_2$TiGe in the trilayer. Our results show that it is in principle possible to tailor the spin-caloric effects by a targeted growth control of the samples.

Functional characterization of two scFv-Fc antibodies from an HIV controller selected on soluble HIV-1 Env complexes: a neutralizing V3- and a trimer-specific gp41 antibody.

HIV neutralizing antibodies (nAbs) represent an important tool in view of prophylactic and therapeutic applications for HIV-1 infection. Patients chronically infected by HIV-1 represent a valuable source for nAbs. HIV controllers, including long-term non-progressors (LTNP) and elite controllers (EC), represent an interesting subgroup in this regard, as here nAbs can develop over time in a rather healthy immune system and in the absence of any therapeutic selection pressure. In this study, we characterized two particular antibodies that were selected as scFv antibody fragments from a phage immune library generated from an LTNP with HIV neutralizing antibodies in his plasma. The phage library was screened on recombinant soluble gp140 envelope (Env) proteins. Sequencing the selected peptide inserts revealed two major classes of antibody sequences. Binding analysis of the corresponding scFv-Fc derivatives to various trimeric and monomeric Env constructs as well as to peptide arrays showed that one class, represented by monoclonal antibody (mAb) A2, specifically recognizes an epitope localized in the pocket binding domain of the C heptad repeat (CHR) in the ectodomain of gp41, but only in the trimeric context. Thus, this antibody represents an interesting tool for trimer identification. MAb A7, representing the second class, binds to structural elements of the third variable loop V3 and neutralizes tier 1 and tier 2 HIV-1 isolates of different subtypes with matching critical amino acids in the linear epitope sequence. In conclusion, HIV controllers are a valuable source for the selection of functionally interesting antibodies that can be selected on soluble gp140 proteins with properties from the native envelope spike.

Accurate tight-binding models for theπbands of bilayer graphene

We derive an {\em ab initio} $\pi$-band tight-binding model for $AB$ stacked bilayer graphene based on maximally localized Wannier wave functions (MLWFs) centered on the carbon sites, finding that both intralayer and interlayer hopping is longer in range than assumed in commonly used phenomenological tight-binding models. Starting from this full tight-binding model, we derive two effective models that are intended to provide a convenient starting point for theories of $\pi$-band electronic properties by achieving accuracy over the full width of the $\pi$-bands, and especially at the Dirac points, in models with a relatively small number of hopping parameters. The simplified models are then compared with phenomenological Slonczewski-Weiss-McClure type tight-binding models in an effort to clarify confusions that exists in the literature concerning tight-binding model parameter signs.

Periodicity of the time-dependent Kohn-Sham equation and the Floquet theorem

The Floquet theorem allows one to reformulate periodic time-dependent problems such as the interaction of a many-body system with a laser field in terms of time-independent, field-dressed states, also known as Floquet states. If this was possible for density-functional theory as well, one could reduce in such cases time-dependent density-functional theory to a time-independent Floquet density-functional theory. We analyze under which conditions the Floquet theorem is applicable in a density-functional framework. By employing numerical ab initio solutions of the interacting time-dependent Schr\"odinger equation with time-periodic external potentials we show that the exact effective potential in the corresponding Kohn-Sham equation is not unconditionally periodic. Whenever several Floquet states in the interacting system are involved in a physical process the corresponding Hartree-exchange-correlation potential is not periodic with the external frequency only. Using an analytically solvable example we demonstrate that, in general, the periodicity of the time-dependent Kohn-Sham Hamiltonian cannot be restored by choosing a different initial state. Only if the external periodic potential is sufficiently weak such that the initial state of the interacting system evolves adiabatically to a single, field-dressed state, the resulting Kohn-Sham system admits the application of the Floquet theorem.

No-Core Shell Model Analysis of Light Nuclei

The fundamental description of both structural properties and reactions of light nuclei in terms of constituent protons and neutrons interacting through nucleon-nucleon and three-nucleon forces is a long-sought goal of nuclear theory. I will briefly present a promising technique, built upon the {\em ab initio} no-core shell model, which emerged recently as a candidate to reach such a goal: the no-core shell model/resonating-group method. This approach, capable of describing simultaneously both bound and scattering states in light nuclei, complements a microscopic cluster technique with the use of two-nucleon realistic interactions, and a microscopic and consistent description of the nucleon clusters. I will discuss applications to light nuclei binary scattering processes and fusion reactions that power stars and Earth based fusion facilities, such as the deuterium-$^3$He fusion, and outline the progress toward the inclusion of the three-nucleon force into the formalism and the treatment of three-body clusters.

Early patterning of cloned mouse embryos contributes to post-implantation development

Several research groups have suggested that the embryonic–abembryonic (Em–Ab) axis in the mouse can be predicted by the first cleavage plane of the early embryo. Currently, it is not known whether this early patterning occurs in cloned embryos produced by nuclear transfer and whether it affects development to term. In this work, the relationship between the first cleavage plane and the Em–Ab axis was determined by the labeling of one blastomere in cloned mouse embryos at the 2-cell stage, followed by ex-vivo tracking until the blastocyst stage. The results demonstrate that approximately half of the cloned blastocysts had an Em–Ab axis perpendicular to the initial cleavage plane of the 2-cell stage. These embryos were classified as “orthogonal” and the remainder as “deviant”. Additionally, we report here that cloned embryos were significantly more often orthogonal than their naturally fertilized counterparts and overexpressed Sox2. Orthogonal cloned embryos demonstrated a higher rate of post-implantation embryonic development than deviant embryos, but cloned pups did not all survive. These results reveal that the angular relationship between the Em–Ab axis and the first cleavage plane can influence later development and they support the hypothesis that proper early patterning of mammalian embryos is required after nuclear transfer.

Targeting malignant B cells with an immunotoxin against ROR1

The selective cell surface expression of receptor tyrosine kinase-like orphan receptor 1 (ROR1) in chronic lymphocytic leukemia (CLL) and mantle cell lymphoma (MCL) has made ROR1 a novel and promising target for therapeutic monoclonal antibodies (mAbs). Four mouse mAbs generated by hybridoma technology exhibited specific binding to human ROR1. Epitope mapping studies showed that two mAbs (2A2 and 2D11) recognized N-terminal epitopes in the extracellular region of ROR1 and the other two (1A1 and 1A7) recognized C-terminal epitopes. A ROR1- immunotoxin (BT-1) consisting of truncated Pseudomonas exotoxin A (PE38) and the VH and VL fragments of 2A2-IgG was made recombinantly. Both 2A2-IgG and BT-1 showed dose-dependent and selective binding to primary CLL and MCL cells and MCL cell lines. Kinetic analyses revealed 0.12-nM (2A2-IgG) to 65-nM (BT-1) avidity/affinity to hROR1, depicting bivalent and monovalent interactions, respectively. After binding to cell surface ROR1, 2A2-IgG and BT-1 were partially internalized by primary CLL cells and MCL cell lines, and BT-1 induced profound apoptosis of ROR1-expressing MCL cell lines in vitro (EC50 = 16 pM–16 nM), but did not affect ROR1-negative cell lines. Our data suggest that ROR1-immunotoxins such as BT-1 could serve as targeted therapeutic agents for ROR1-expressing B cell malignancies and other cancers.

Frequency Metrology of Helium around 1083 nm and Determination of the Nuclear Charge Radius

We measure the absolute frequency of seven out of the nine allowed transitions between the 2 (3)S and 2 (3)P hyperfine manifolds in a metastable (3)He beam by using an optical frequency comb synthesizer-assisted spectrometer. The relative uncertainty of our measurements ranges from 1×10(-11) to 5×10(-12), which is, to our knowledge, the most precise result for any optical ^{3}He transition to date. The resulting 2 (3)P-2 (3)S centroid frequency is 276,702,827,204.8(2.4) kHz. Comparing this value with the known result for the (4)He centroid and performing ab initio QED calculations of the (4)He-(3)He isotope shift, we extract the difference of the squared nuclear charge radii δr(2) of (3)He and (4)He. Our result for δr(2)=1.074(3) fm(2) disagrees by about 4σ with the recent determination [R. van Rooij et al., Science 333, 196 (2011)].