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"Rey, S"
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Site-selectively generated photon emitters in monolayer MoS2 via local helium ion irradiation
Quantum light sources in solid-state systems are of major interest as a basic ingredient for integrated quantum photonic technologies. The ability to tailor quantum emitters via site-selective defect engineering is essential for realizing scalable architectures. However, a major difficulty is that defects need to be controllably positioned within the material. Here, we overcome this challenge by controllably irradiating monolayer MoS
2
using a sub-nm focused helium ion beam to deterministically create defects. Subsequent encapsulation of the ion exposed MoS
2
flake with high-quality hBN reveals spectrally narrow emission lines that produce photons in the visible spectral range. Based on ab-initio calculations we interpret these emission lines as stemming from the recombination of highly localized electron–hole complexes at defect states generated by the local helium ion exposure. Our approach to deterministically write optically active defect states in a single transition metal dichalcogenide layer provides a platform for realizing exotic many-body systems, including coupled single-photon sources and interacting exciton lattices that may allow the exploration of Hubbard physics.
Light emitters can be induced in transition metal dichalcogenides by defect engineering, but challenges remain in their controlled spatial positioning. Here, the authors irradiate monolayer MoS
2
with a sub-nm focused helium ion beam to deterministically create defects, and obtain spectrally narrow emission lines that produce photons in the visible spectral range
Journal Article
Performance efficient macromolecular mechanics via sub-nanometer shape based coarse graining
Dimensionality reduction via coarse grain modeling is a valuable tool in biomolecular research. For large assemblies, ultra coarse models are often knowledge-based, relying on a priori information to parameterize models thus hindering general predictive capability. Here, we present substantial advances to the shape based coarse graining (SBCG) method, which we refer to as SBCG2. SBCG2 utilizes a revitalized formulation of the topology representing network which makes high-granularity modeling possible, preserving atomistic details that maintain assembly characteristics. Further, we present a method of granularity selection based on charge density Fourier Shell Correlation and have additionally developed a refinement method to optimize, adjust and validate high-granularity models. We demonstrate our approach with the conical HIV-1 capsid and heteromultimeric cofilin-2 bound actin filaments. Our approach is available in the Visual Molecular Dynamics (VMD) software suite, and employs a CHARMM-compatible Hamiltonian that enables high-performance simulation in the GPU-resident NAMD3 molecular dynamics engine.
Here the authors report SBCG2 an update to the neural network based, Shape-Based Coarse Graining (SBCG) approach for creating coarse grained molecular topologies with atomistic detail. They show how SBCG2 can reduce the computational costs of simulating very large assemblies like the HIV-1 capsid allowing simulation on commodity hardware.
Journal Article
Macroscopic strings as heavy quarks: Large-N gauge theory and anti-de Sitter supergravity
We study some aspects of Maldacena's large-N correspondence between \\({\\cal N}=4\\) superconformal gauge theory on the D3-brane and maximal supergravity on AdS\\(_5 \\times S_5\\) by introducing macroscopic strings as heavy (anti-) quark probes. The macroscopic strings are semi-infinite Type IIB strings ending on a D3-brane world-volume. We first study deformation and fluctuation of D3-branes when a macroscopic BPS string is attached. We find that both dynamics and boundary conditions agree with those for the macroscopic string in anti-de Sitter supergravity. As a by-product we clarify how Polchinski's Dirichlet and Neumann open string boundary conditions arise dynamically. We then study the non-BPS macroscopic string–anti-string pair configuration as a physical realization of a heavy quark Wilson loop. We obtain the \\(Q \\bar Q\\) static potential from the supergravity side and find that the potential exhibits non-analyticity of the square-root branch cut in the 't Hooft coupling parameter. We put forward non-analyticity as a prediction for large-N gauge theory in the strong 't Hooft coupling limit. By turning on the Ramond–Ramond zero-form potential, we also study the \\(\\theta\\) vacuum angle dependence of the static potential. We finally discuss the possible dynamical realization of the heavy N-prong string junction and of the large-N loop equation via a local electric field and string recoil thereof. Throughout comparisons of the AdS–CFT correspondence, we find that a crucial role is played by “geometric duality” between the UV and IR scales in directions perpendicular to the D3-brane and parallel ones, explaining how the AdS\\(_5\\) spacetime geometry emerges out of four-dimensional gauge theory at strong coupling.
Journal Article
Integration of hypoxic HIF-α signaling in blood cancers
Hypoxia (low O
2
) is a fundamental microenvironmental determinant of bone marrow (BM) pathophysiology. Recent data from molecular and clinical studies indicate that hematopoiesis and leukemogenesis are dependent upon hypoxia-inducible factors (HIFs), a family of essential transcriptional activators mediating the metazoan hypoxic response. In blood cancers, the synergism between HIF overexpression and stabilization within the hypoxic BM microenvironment promotes disease progression, therapy resistance and relapse. In this review, we will summarize current advances in the understanding of HIF signaling in blood cancers and its translational implications for hypoxic-targeted therapy.
Journal Article
Strontium-doped hydroxyapatite polysaccharide materials effect on ectopic bone formation
Previous studies performed using polysaccharide-based matrices supplemented with hydroxyapatite (HA) particles showed their ability to form in subcutaneous and intramuscular sites a mineralized and osteoid tissue. Our objectives are to optimize the HA content in the matrix and to test the combination of HA with strontium (Sr-HA) to increase the matrix bioactivity. First, non-doped Sr-HA powders were combined to the matrix at three different ratios and were implanted subcutaneously for 2 and 4 weeks. Interestingly, matrices showed radiolucent properties before implantation. Quantitative analysis of micro-CT data evidenced a significant increase of mineralized tissue formed ectopically with time of implantation and allowed us to select the best ratio of HA to polysaccharides of 30% (w/w). Then, two Sr-substitution of 8% and 50% were incorporated in the HA powders (8Sr-HA and 50Sr-HA). Both Sr-HA were chemically characterized and dispersed in matrices. In vitro studies performed with human mesenchymal stem cells (MSCs) demonstrated the absence of cytotoxicity of the Sr-doped matrices whatever the amount of incorporated Sr. They also supported osteoblastic differentiation and activated the expression of one late osteoblastic marker involved in the mineralization process i.e. osteopontin. In vivo, subcutaneous implantation of these Sr-doped matrices induced osteoid tissue and blood vessels formation.
Journal Article
Molecular architecture and conservation of an immature human endogenous retrovirus
The human endogenous retrovirus K (HERV-K) is the most recently acquired endogenous retrovirus in the human genome and is activated and expressed in many cancers and amyotrophic lateral sclerosis. We present the immature HERV-K capsid structure at 3.2 Å resolution determined from native virus-like particles using cryo-electron tomography and subtomogram averaging. The structure shows a hexamer unit oligomerized through a 6-helix bundle, which is stabilized by a small molecule analogous to IP6 in immature HIV-1 capsid. The HERV-K immature lattice is assembled via highly conserved dimer and trimer interfaces, as detailed through all-atom molecular dynamics simulations and supported by mutational studies. A large conformational change mediated by the linker between the N-terminal and the C-terminal domains of CA occurs during HERV-K maturation. Comparison between HERV-K and other retroviral immature capsid structures reveals a highly conserved mechanism for the assembly and maturation of retroviruses across genera and evolutionary time.
The hexagonal immature capsid lattice of human endogenous retrovirus K is determined at 3.2 Å resolution, which is an assembly of small molecule-stabilized hexamers via dimer and trimer interfaces, a highly conserved mechanism among retroviruses.
Journal Article
Structural basis for HIV-1 capsid adaption to a deficiency in IP6 packaging
Inositol hexakisphosphate (IP6) promotes HIV-1 assembly by stabilizing the immature Gag lattice and becomes enriched within virions, where it is required for mature capsid assembly. Previously, we identified Gag mutants that package little IP6 yet assemble particles, though they are non-infectious due to defective capsid formation. Here, we report a compensatory mutation, G225R, in the C-terminus of capsid protein (CA) that restores capsid assembly and infectivity in these IP6-deficient mutants. G225R also enhances in vitro assembly of CA into capsid-like particles at far lower IP6 concentrations than required for wild-type CA. CryoEM structures of G225R CA hexamers and lattices at 2.7 Å resolution reveal that the otherwise disordered C-terminus becomes structured, stabilizing hexamer-hexamer interfaces. Molecular dynamics simulations support this mechanism. These findings uncover how HIV-1 can adapt to IP6 deficiency and highlight a previously unrecognized structural role of the CA C-terminus, while offering tools for capsid-related studies.
IP6 is a critical host cofactor for HIV-1 assembly and infectivity. In this study, the authors uncover the structural basis by which HIV-1 adapts to a deficiency in IP6 packaging through a G225R mutation at the C-terminus of the capsid protein.
Journal Article
Release of methane from a volcanic basin as a mechanism for initial Eocene global warming
A 200,000-yr interval of extreme global warming marked the start of the Eocene epoch about 55 million years ago. Negative carbon- and oxygen-isotope excursions in marine and terrestrial sediments show that this event was linked to a massive and rapid (∼10,000 yr) input of isotopically depleted carbon
1
,
2
. It has been suggested previously that extensive melting of gas hydrates buried in marine sediments may represent the carbon source
3
,
4
and has caused the global climate change. Large-scale hydrate melting, however, requires a hitherto unknown triggering mechanism. Here we present evidence for the presence of thousands of hydrothermal vent complexes identified on seismic reflection profiles from the Vøring and Møre basins in the Norwegian Sea. We propose that intrusion of voluminous mantle-derived melts in carbon-rich sedimentary strata in the northeast Atlantic may have caused an explosive release of methane—transported to the ocean or atmosphere through the vent complexes—close to the Palaeocene/Eocene boundary. Similar volcanic and metamorphic processes may explain climate events associated with other large igneous provinces such as the Siberian Traps (∼250 million years ago) and the Karoo Igneous Province (∼183 million years ago).
Journal Article