Results for “binding modes” — Page 32

DOE OSTI2022

Gapless Higgs mode in the Fulde-Ferrell-Larkin-Ovchinnikov state of a superconductor

We report the Higgs mode associated with amplitude fluctuations of the superconducting gap in uniform superconductors is usually heavy, which makes its excitation and detection difficult. We report on the existence of a gapless Higgs mode in the Fulde-Ferrell-Larkin-Ovchinnikov states. This feature originates from the Goldstone mode associated with translation-symmetry breaking. The existence of the gapless Higgs mode is demonstrated by using both a phenomenological model and microscopic Bardeen-Cooper-Schrieffer (BCS) theory. The gapless Higgs mode can avoid the decay into other low-energy excitations, which renders it stable and detectable.

36 MATERIALS SCIENCE↗

DOE OSTI2019

Fibrillar and Nonfibrillar Amyloid Beta Structures Drive Two Modes of Membrane-Mediated Toxicity

In Alzheimer’s disease, the amyloid-beta peptide (Aβ) is implicated in neuronal toxicity via interactions with the cell membrane. Monomeric Aβ (Aβm) is intrinsically disordered, but it can adopt a range of aggregated conformations with varying toxicities from short fibrillar oligomers (FO), to globular nonfibrillar oligomers (NFO), and full-length amyloid fibrils. NFO is considered to be the most toxic, followed by fibrils, and finally Aβm. To elucidate molecular-level membrane interactions that contribute to their different toxicities, we used liquid surface X-ray scattering and Langmuir trough insertion assays to compare Aβm, FO, and NFO surface activities and interactions with anionic DMPG lipid monolayers at the air/water interface. All Aβ species were highly surface active and rapidly adopted β-sheet rich structures upon adsorption to the air/water interface. Likewise, all Aβ species had affinity for the anionic membrane. Aβm rapidly converted to β-sheet rich assemblies upon binding the membrane, and these aggregated structures of Aβm and FO disrupted hexagonally packed lipid domains and resulted in membrane thinning and instability. In contrast, NFO perturbed membrane structure by extracting lipids from the air/water interface and causing macroscale membrane deformations. Altogether, our results support two models for membrane-mediated Aβ toxicity: fibril-induced reorganization of lipid packing and NFO-induced membrane destabilization and lipid extraction. Here we provide a structural understanding of Aβ neurotoxicity via membrane interactions and aids the effort in understanding early events in Alzheimer’s disease and other neurodegenerative diseases.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2019

XFEL structures of the human MT2 melatonin receptor reveal the basis of subtype selectivity

The human MT 1 and MT 2 melatonin receptors are G-protein-coupled receptors (GPCRs) that help to regulate circadian rhythm and sleep patterns. Drug development efforts have targeted both receptors for the treatment of insomnia, circadian rhythm and mood disorders, and cancer, and MT 2 has also been implicated in type 2 diabetes. Here in this paper we report X-ray free electron laser (XFEL) structures of the human MT 2 receptor in complex with the agonists 2-phenylmelatonin (2-PMT) and ramelteon6 at resolutions of 2.8 Å and 3.3 Å, respectively, along with two structures of function-related mutants: H208 5.46 A (superscripts represent the Ballesteros–Weinstein residue numbering nomenclature7) and N86 2.50 D, obtained in complex with 2-PMT. Comparison of the structures of MT 2 with a published structure of MT 1 reveals that, despite conservation of the orthosteric ligand-binding site residues, there are notable conformational variations as well as differences in [ 3 H]melatonin dissociation kinetics that provide insights into the selectivity between melatonin receptor subtypes. A membrane-buried lateral ligand entry channel is observed in both MT 1 and MT 2 , but in addition the MT 2 structures reveal a narrow opening towards the solvent in the extracellular part of the receptor. We provide functional and kinetic data that support a prominent role for intramembrane ligand entry in both receptors, and suggest that there might also be an extracellular entry path in MT 2 . Our findings contribute to a molecular understanding of melatonin receptor subtype selectivity and ligand access modes, which are essential for the design of highly selective melatonin tool compounds and therapeutic agents.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2021

Twisted bilayer graphene. V. Exact analytic many-body excitations in Coulomb Hamiltonians: Charge gap, Goldstone modes, and absence of Cooper pairing

We find exact analytic expressions for the energies and wave functions of the charged and neutral excitations above the exact ground states (at rational filling per unit cell) of projected Coulomb Hamiltonians in twisted bilayer graphene. Our exact expressions are valid for any form of the Coulomb interaction and any form of A A and A B / B A tunneling. The single charge excitation energy is a convolution of the Coulomb potential with a quantum geometric tensor of the TBG bands. The neutral excitations are (high-symmetry group) magnons, and their dispersion is analytically calculated in terms of the form factors of the active bands in TBG. The two-charge excitation energy and wave functions are also obtained, and a sufficient condition on the graphene eigenstates for obtaining a Cooper pair from Coulomb interactions is obtained. For the actual TBG bands at the first magic angle, we can analytically show that the Cooper pair binding energy is zero in all such projected Coulomb models, implying that either phonons and/or nonzero kinetic energy are needed for superconductivity. Since Vafek and Kang [Phys. Rev. Lett. 125, 257602 (2020)] showed that the kinetic energy bounds on the superexchange energy are less 10 -3 in Coulomb units, the phonon mechanism becomes then very likely. If nonetheless the superconductivity is due to kinetic terms which render the bands nonflat, one prediction of our theory is that the highest T c would not occur at the highest DOS.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2020

Antifungal symbiotic peptide NCR044 exhibits unique structure and multifaceted mechanisms of action that confer plant protection

In the indeterminate nodules of a model legume Medicago truncatula, ~700 nodule-specific cysteine-rich (NCR) peptides with conserved cysteine signature are expressed. NCR peptides are highly diverse in sequence, and some of these cationic peptides exhibit antimicrobial activity in vitro and in vivo. However, there is a lack of knowledge regarding their structural architecture, antifungal activity, and modes of action against plant fungal pathogens. Here, the three-dimensional NMR structure of the 36-amino acid NCR044 peptide was solved. This unique structure was largely disordered and highly dynamic with one four-residue α-helix and one three-residue antiparallel β-sheet stabilized by two disulfide bonds. NCR044 peptide also exhibited potent fungicidal activity against multiple plant fungal pathogens, including Botrytis cinerea and three Fusarium spp. It inhibited germination in quiescent spores of B. cinerea. In germlings, it breached the fungal plasma membrane and induced reactive oxygen species. It bound to multiple bioactive phosphoinositides in vitro. Time-lapse confocal and superresolution microscopy revealed strong fungal cell wall binding, penetration of the cell membrane at discrete foci, followed by gradual loss of turgor, subsequent accumulation in the cytoplasm, and elevated levels in nucleoli of germlings. Spray-applied NCR044 significantly reduced gray mold disease symptoms caused by the fungal pathogen B. cinerea in tomato and tobacco plants, and postharvest products. Our work illustrates the antifungal activity of a structurally unique NCR peptide against plant fungal pathogens and paves the way for future development of this class of peptides as a spray-on fungistat/fungicide.

59 BASIC BIOLOGICAL SCIENCES↗

DOE OSTI2020

Pattern formation in a coupled membrane-bulk reaction-diffusion model for intracellular polarization and oscillations

Reaction-diffusion systems have been widely used to study spatio-temporal phenomena in cell biology, such as cell polarization. Coupled bulk-surface models naturally include compartmentalization of cytosolic and membrane-bound polarity molecules. Here we study the distribution of the polarity protein Cdc42 in a mass-conserved membrane-bulk model, and explore the effects of diffusion and spatial dimensionality on spatio-temporal pattern formation. We first analyze a one-dimensional (1-D) model for Cdc42 oscillations in fission yeast, consisting of two diffusion equations in the bulk domain coupled to nonlinear ODEs for binding kinetics at each end of the cell. In 1-D, our analysis reveals the existence of symmetric and asymmetric steady states, as well as anti-phase relaxation oscillations typical of slow-fast systems. We then extend our analysis to a two-dimensional (2-D) model with circular bulk geometry, for which species can either diffuse inside the cell or become bound to the membrane and undergo a nonlinear reaction-diffusion process. We also consider a nonlocal system of PDEs approximating the dynamics of the 2-D membrane-bulk model in the limit of fast bulk diffusion. In all three model variants we find that mass conservation selects perturbations of spatial modes that simply redistribute mass. In 1-D, only anti-phase oscillations between the two ends of the cell can occur, and in-phase oscillations are excluded. In higher dimensions, no radially symmetric oscillations are observed. Instead, the only instabilities are symmetry-breaking, either corresponding to stationary Turing instabilities, leading to the formation of stationary patterns, or to oscillatory Turing instabilities, leading to traveling and standing waves. Codimension-two Bogdanov—Takens bifurcations occur when the two distinct instabilities coincide, causing traveling waves to slow down and to eventually become stationary patterns. Our work clarifies the effect of geometry and dimensionality on behaviors observed in ma.ss-conserved cell polarity models.

97 MATHEMATICS AND COMPUTING↗

DOE OSTI2019

Structural basis of the atypical activation mechanism of KRAS V14I

RAS regulation and signaling are largely accomplished by direct protein-protein interactions, making RAS protein dynamics a critical determinant of RAS function. In this study, we report a crystal structure of GDP-bound KRAS V14I , a mutated KRAS variant associated with the developmental RASopathy disorder Noonan syndrome (NS), at 1.5–1.6 Å resolution. The structure is notable for revealing a marked extension of switch 1 away from the G-domain and nucleotide-binding site of the KRAS protein. We found that this extension is associated with a loss of the magnesium ion and a tilt in the position of the guanine base because of the additional carbon introduced by the isoleucine substitution. Hydrogen-deuterium exchange MS analysis confirmed that this conformation occurs in solution, but also disclosed a difference in kinetics when compared with KRAS A146T , another RAS mutant that displays a nearly identical conformation in previously reported crystal structures. This conformational change contributed to a high rate of guanine nucleotide-exchange factor (GEF)-dependent and -independent nucleotide exchange and to an increase in affinity for SOS Ras/Rac GEF 1 (SOS1), which appears to be the major mode of activation for this RAS variant. These results highlight a mechanistic connection between KRAS A146T and KRAS V14I that may have implications for the regulation of these variants and for the development of therapeutic strategies to manage KRAS variant-associated disorders.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2016

Phonovoltaic. III. Electron-phonon coupling and figure of merit of graphene:BN

The phonovoltaic cell harvests optical phonons like a photovoltaic harvests photons, that is, a nonequilibrium (hot) population of optical phonons (at temperature $T$ p,O ) more energetic than the band gap produces electron-hole pairs in a $p$-$n$ junction, which separates these pairs to produce power. A phonovoltaic material requires an optical phonon mode more energetic than its band gap and much more energetic than the thermal energy ($E$ p,O $ΔE$ e,g ≫ $k$ B $T$ ) , which relaxes by generating electrons and power (at rate $\dot{γ}$ e-p ) rather than acoustic phonons and heat (at rate $\dot{γ}$ p-p ). Graphene (h-C) is the most promising material candidate: when its band gap is tuned to its optical phonon energy without greatly reducing the electron-phonon (e-p) coupling, it reaches a substantial figure of merit [ $Z$ pV = $ΔE$ e,g $\dot{γ}$ e-p / $E$ p,O ($\dot{γ}$ e-p + $\dot{γ}$ p-p ) ≈ 0.8 ] . A simple tight-binding (TB) model presented here predicts that lifting the sublattice symmetry of graphene in order to open a band gap proscribes the e-p interaction at the band edge, such that $\dot{γ}$ e-p → 0 as $ΔE$ e,g → $E$ p,O . However, ab initio (DFT-LDA) simulations of layered h-C/BN and substitutional h-C:BN reveal that the e-p coupling remains substantial in these asymmetric crystals. Indeed, h-C:BN achieves a high figure of merit ( $Z$ pV ≈ 0.6 ) . At 300 K and for a Carnot limit of 0.5 ( $T$ p,O = 600 K ) , a h-C:BN phonovoltaic can reach an efficiency of η pV ≈ 0.2 , double the thermoelectric efficiency ( $ZT$ ≈ 1) under similar conditions.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

DOE OSTI2025

Single photon emitters in van der Waals solids for quantum photonics: materials, theory and molecular-scale characterization probes

Strong light–matter interactions in two-dimensional layered materials (2D materials) have attracted the interest of researchers from interdisciplinary fields for more than a decade now. A unique phenomenon in some 2D materials is their large exciton binding energies (BEs), increasing the likelihood of exciton survival at room temperature. It is this large BE that mediates the intense light–matter interactions of many of the 2D materials, particularly in their monolayer limit, where the interplay of excitonic phenomena poses a wealth of opportunities for high-performance optoelectronics and quantum photonics. Within quantum photonics, quantum information science (QIS) is growing rapidly, where photons are a promising platform for information processing due to their low-noise properties, excellent modal control, and long-distance propagation. A central element for QIS applications is a single photon emitter (SPE) source, where an ideal on-demand SPE emits exactly one photon at a time into a given spatiotemporal mode. Recently, 2D materials have shown practical appeal for QIS which is directly driven from their unique layered crystalline structure. This structural attribute of 2D materials facilitates their integration with optical elements more easily than the SPEs in conventional three-dimensional solid state materials, such as diamond and SiC. In this review article, we will discuss recent advances made with 2D materials towards their use as quantum emitters, where the SPE emission properties maybe modulated deterministically. Here, the use of unique scanning tunneling microscopy tools for the in-situ generation and characterization of defects is presented, along with theoretical first-principles frameworks and machine learning approaches to model the structure-property relationship of exciton–defect interactions within the lattice towards SPEs. Given the rapid progress made in this area, the SPEs in 2D materials are emerging as promising sources of nonclassical light emitters, well-poised to advance quantum photonics in the future.

2D layered materials↗

DOE OSTI2021

Structural and functional insights into the first Bacillus thuringiensis vegetative insecticidal protein of the Vpb4 fold, active against western corn rootworm

The western corn rootworm (WCR), Diabrotica virgifera virgifera LeConte, is a major maize pest in the United States causing significant economic loss. The emergence of field-evolved resistant WCR to Bacillus thuringiensis (Bt) traits has prompted the need to discover and deploy new insecticidal proteins in transgenic maize. In the current study we determined the crystal structure and mode of action (MOA) of the Vpb4Da2 protein (formerly known as Vip4Da2) from Bt, the first identified insecticidal Vpb4 protein with commercial level control against WCR. The Vpb4Da2 structure exhibits a six-domain architecture mainly comprised of antiparallel β-sheets organized into β-sandwich layers. The amino-terminal domains 1–3 of the protein share structural homology with the protective antigen (PA) PA14 domain and encompass a long β-pore forming loop as in the clostridial binary-toxB module. Domains 5 and 6 at the carboxyl-terminal half of Vpb4Da2 are unique as this extension is not observed in PA or any other structurally-related protein other than Vpb4 homologs. These unique Vpb4 domains adopt the topologies of carbohydrate-binding modules known to participate in receptor-recognition. Functional assessment of Vpb4Da2 suggests that domains 4–6 comprise the WCR receptor binding region and are key in conferring the observed insecticidal activity against WCR. The current structural analysis was complemented by in vitro and in vivo characterizations, including immuno-histochemistry, demonstrating that Vpb4Da2 follows a MOA that is consistent with well-characterized 3-domain Bt insecticidal proteins despite significant structural differences.

59 BASIC BIOLOGICAL SCIENCES↗

NASA NTRS1984

Fastener load tests and retention systems tests for cryogenic wind-tunnel models

A-286 stainless steel screws were tested to determine the tensile load capability and failure mode of various screw sizes and types at both cryogenic and room temperature. Additionally, five fastener retention systems were tested by using A-286 screws with specimens made from the primary metallic alloys that are currently used for cryogenic models. The locking system effectiveness was examined by simple no-load cycling to cryogenic temperatures (-275 F) as well as by dynamic and static loading at cryogenic temperatures. In general, most systems were found to be effective retention devices. There are some differences between the various devices with respect to ease of application, cleanup, and reuse. Results of tests at -275 F imply that the cold temperatures act to improve screw retention. The improved retention is probably the result of differential thermal contraction and/or increased friction (thread-binding effects). The data provided are useful in selecting screw sizes, types, and locking devices for model systems to be tested in cryogenic wind tunnels.

Wallace, J. W.↗

NASA NTRS2016

The IOAG Recommendations on Spacecraft Emergency Cross Support

In 2014, the Inter-agency Operations Advisory Group (IOAG) chartered a multi-agency team effort to study how to best handle spacecraft emergency as part of cross support among network assets. The original intent is to put in place for the first time a process and guidelines to make emergency support as part of a permanent cross-support capability between space agencies. From the perspective of space communications service providers, a few key issues, common to all agencies, concerning the Spacecraft Emergency Cross Support (SECS) have been explored. They are: context of emergency support, provision of emergency support under a cross-support agreement, provision of emergency support with no cross-support agreement, legal and liability issues, response time, support priority, services provided, sustaining emergency support capabilities, and charge for the support. The positions of the various participating agencies with respect to these issues have been collected, analyzed, and finally harmonized to form the recommended IOAG positions. A central challenge most communications service providers are facing is that since the spacecraft emergency is an unplanned critical event, it typically requires fast response to the emergency call, hence lacking an international standard process for the operational interfaces seems to exacerbate the difficulty in providing SECS. For reducing the response time, i.e. from the time of accepting a request for SECS to the readiness for support, it is recommended that a “cross-support emergency system” be established by IOAG member agencies. Along with it, the IOAG core services, just-in-time ground communications line, cross support service management (CSSM), and standard operations procedures (SOP) for operational interfaces form the basic foundation of the “cross support emergency system”. Of the above, new to the cross support conducted thus far in the IOAG community is the concept of the SOP specifically for the interfaces between the service provider and service user during the SECS. Use cases, salient features, and definition of the key operational activities/tasks relevant to the interfaces are addressed by the effort. Underpinning such a system is the availability of the RF license granted by the local authority, at national and/or regional level, for a given ground station to communicate with and track the spacecraft in emergency mode at the uplink and downlink frequencies assigned to that spacecraft. That means it is critical for the IOAG member agencies to obtain a priori all-band licenses (for the entire X-band or S-band) for some, if not all, of their ground stations that are most capable of or likely to provide SECS. It is also recommended that certain prior arrangements be made with the relevant local licensing authorities for a process that will allow expedited authorization to transmit/receive signals to/from the declared spacecraft over the declared ground stations specifically and solely for the emergency case. Our analysis of the SECS has also uncovered a few fundamental programmatic issues. Recognizing any IOAG positions reached on these issues do not necessarily lead to any binding authority, it is recommended that they, along with those key attributes of the cross support emergency system, be explicitly stated as multi-agency guidelines to guide the implementation and provision of the SECS. The paper will present the results of the working group on Spacecraft Emergency Cross Support and, in particular, its findings, products and recommendations. It will also identify the next steps of this work that may include the production of some international standards as an extension of this work, or the process to make this emergency system usable by other spacecraft operators beyond the space agencies.

Tai, Wallace S.↗

NASA NTRS2016

The IOAG Recommendations on Spacecraft Emergency Cross Support

In 2014, the Inter-agency Operations Advisory Group (IOAG) chartered a multi-agency team effort to study how to best handle spacecraft emergency as part of cross support among network assets. The original intent is to put in place for the first time a process and guidelines to make emergency support as part of a permanent cross-support capability between space agencies. From the perspective of space communications service providers, a few key issues, common to all agencies, concerning the Spacecraft Emergency Cross Support (SECS) have been explored. They are: context of emergency support, provision of emergency support under a cross-support agreement, provision of emergency support with no cross-support agreement, legal and liability issues, response time, support priority, services provided, sustaining emergency support capabilities, and charge for the support. The positions of the various participating agencies with respect to these issues have been collected, analyzed, and finally harmonized to form the recommended IOAG positions. A central challenge most communications service providers are facing is that since the spacecraft emergency is an unplanned critical event, it typically requires fast response to the emergency call, hence lacking an international standard process for the operational interfaces seems to exacerbate the difficulty in providing SECS. For reducing the response time, i.e. from the time of accepting a request for SECS to the readiness for support, it is recommended that a “cross-support emergency system” be established by IOAG member agencies. Along with it, the IOAG core services, just-in-time ground communications line, cross support service management (CSSM), and standard operations procedures (SOP) for operational interfaces form the basic foundation of the “cross support emergency system”. Of the above, new to the cross support conducted thus far in the IOAG community is the concept of the SOP specifically for the interfaces between the service provider and service user during the SECS. Use cases, salient features, and definition of the key operational activities/tasks relevant to the interfaces are addressed by the effort. Underpinning such a system is the availability of the RF license granted by the local authority, at national and/or regional level, for a given ground station to communicate with and track the spacecraft in emergency mode at the uplink and downlink frequencies assigned to that spacecraft. That means it is critical for the IOAG member agencies to obtain a priori all-band licenses (for the entire X-band or S-band) for some, if not all, of their ground stations that are most capable of or likely to provide SECS. It is also recommended that certain prior arrangements be made with the relevant local licensing authorities for a process that will allow expedited authorization to transmit/receive signals to/from the declared spacecraft over the declared ground stations specifically and solely for the emergency case. Our analysis of the SECS has also uncovered a few fundamental programmatic issues. Recognizing any IOAG positions reached on these issues do not necessarily lead to any binding authority, it is recommended that they, along with those key attributes of the cross support emergency system, be explicitly stated as multi-agency guidelines to guide the implementation and provision of the SECS. The paper will present the results of the working group on Spacecraft Emergency Cross Support and, in particular, its findings, products and recommendations. It will also identify the next steps of this work that may include the production of some international standards as an extension of this work, or the process to make this emergency system usable by other spacecraft operators beyond the space agencies.

Tai, Wallace S.↗

DOE OSTI2016

Diverse Cd{sup II} coordination complexes derived from bromide isophthalic acid binding with auxiliary N-donor ligands

The coordination characteristics of 4-bromoisophthalic acid (4-Br-H{sub 2}ip) have been investigated in a series of Cd{sup II}-based frameworks. Hydrothermal reactions of Cd{sup II} salts and 4-Br-H{sub 2}ip together with flexible or semiflexible N-donor auxiliary ligands resulted in the formation of four three-dimensional coordination complexes with diverse structures: (Cd(bix){sub 0.5}(bix){sub 0.5}(4-Br-ip)]·H{sub 2}O){sub n} (1), [Cd(bbi){sub 0.5}(bbi){sub 0.5}(4-Br-ip)]{sub n} (2), ([Cd(btx){sub 0.5}(4-Br-ip)(H{sub 2}O)]·0.5CH{sub 3}OH·H{sub 2}O){sub n} (3) and ([Cd(bbt){sub 0.5}(4-Br-ip)(H{sub 2}O)]·3·5H{sub 2}O){sub n} (4). These compounds were characterized by elemental analyses, IR spectra, single-crystal and powder X-ray diffraction. They displayed diverse structures depending on the configuration of the 4-connected metal node, the coordination mode of the 4-Br-H{sub 2}ip, the coordination ability and conformationally flexibility of the N-donor auxiliary. Compound 1 exhibits 3-fold interpenetrated 6{sup 6} topology and compound 2 has a 4{sup 12} topology. Compounds 3–4 have similar 3D pillar-layered structures based on 3,4-connected binodal net with the Schläfli symbol of (4·3{sup 8}). The thermal stabilities and photoluminescence properties of them were discussed in detail. - Graphical abstract: Four 3D Cd{sup II} coordination complexes on the basis of 4-bromoisophthalic acid (4-Br-H{sub 2}ip) and two types of flexible (bbi, bbt) and semiflexible (bix, btx) N-donor ligands are prepared. They displayed diverse topology structures of 6{sup 6} (1), 4{sup 12} (2) and 4·3{sup 8} (3−4), depending on the configuration of the 4-connected metal node, the coordination mode of the 4-Br-H{sub 2}ip, the coordination ability and conformationally flexibility of the N-donor auxiliary ligand. - Highlights: • Four 3D Cd{sup II} coordination complexes based on 4-Br-H{sub 2}ip and flexible/semiflexible N-donor ligands have been synthesized. • They displayed diverse topology structures of 6{sup 6} for 1, 4{sup 12} for 2 and 4·3{sup 8} for 3–4. • The structural diversity depends on the configuration of 4-Br-H{sub 2}ip and the coordination behaviors of the auxiliary ligand.

36 MATERIALS SCIENCE↗

DOE OSTI2025

Magnet-superconductor hybrid quantum systems: a materials platform for topological superconductivity

Magnet–superconductor hybrid (MSH) systems have recently emerged as one of the most significant developments in condensed matter physics. This has generated, in the last decade, a steadily rising interest in the understanding of their unique properties. They have been proposed as one of the most promising platforms for the establishment of topological superconductivity, which holds high potential for application in future quantum information technologies. Their emergent electronic properties stem from the exchange interaction between the magnetic moments and the superconducting condensate. Given the atomic-level origin of such interaction, it is of paramount importance to investigate new magnet–superconductor hybrids at the atomic scale. In this regard, scanning tunneling microscopy (STM) and spectroscopy are playing a crucial role in the race to unveil the fundamental origin of the unique properties of MSH systems, with the aim to discover new hybrid quantum materials capable of hosting topologically non-trivial unconventional superconducting phases. In particular, the combination of STM studies with tight-binding model calculations have represented, so far, the most successful approach to unveil and explain the emergent electronic properties of MSHs. The scope of this review is to offer a broad perspective on the field of MSHs from an atomic-level investigation point-of-view. The focus is on discussing the link between the magnetic ground state hosted by the hybrid system and the corresponding emergent superconducting phase. This is done for MSHs with both one-dimensional (atomic chains) and two-dimensional (atomic lattices and thin films) magnetic systems proximitized to conventional s-wave superconductors. We present a systematic categorization of the experimentally investigated systems with respect to defined experimentally accessible criteria to verify or falsify the presence of topological superconductivity and Majorana edge modes. The discussion will start with an introduction to the physics of Yu–Shiba–Rusinov bound states at magnetic impurities on superconducting surfaces. This will be used as a base for the discussion of magnetic atomic chains on superconductors, distinguishing between ferromagnetic, antiferromagnetic and non-collinear magnetic ground states. A similar approach will be used for the discussion of magnetic thin film islands on superconductors. Given the vast number of publications on the topic, we limit ourselves to discuss works which are most relevant to the search for topological superconductivity.

Majorana states↗

DOE OSTI2017

A Markov State-based Quantitative Kinetic Model of Sodium Release from the Dopamine Transporter

Here, the dopamine transporter (DAT) belongs to the neurotransmitter:sodium symporter (NSS) family of membrane proteins that are responsible for reuptake of neurotransmitters from the synaptic cleft to terminate a neuronal signal and enable subsequent neurotransmitter release from the presynaptic neuron. The release of one sodium ion from the crystallographically determined sodium binding site Na2 had been identified as an initial step in the transport cycle which prepares the transporter for substrate translocation by stabilizing an inward-open conformation. We have constructed Markov State Models (MSMs) from extensive molecular dynamics simulations of human DAT (hDAT) to explore the mechanism of this sodium release. Our results quantify the release process triggered by hydration of the Na2 site that occurs concomitantly with a conformational transition from an outward-facing to an inward-facing state of the transporter. The kinetics of the release process are computed from the MSM, and transition path theory is used to identify the most probable sodium release pathways. An intermediate state is discovered on the sodium release pathway, and the results reveal the importance of various modes of interaction of the N-terminus of hDAT in controlling the pathways of release.

60 APPLIED LIFE SCIENCES↗

DOE OSTI2017

Structures of the peptide-modifying radical SAM enzyme SuiB elucidate the basis of substrate recognition

Posttranslational modification of ribosomally synthesized peptides provides an elegant means for the production of biologically active molecules known as RiPPs (ribosomally synthesized and posttranslationally modified peptides). Although the leader sequence of the precursor peptide is often required for turnover, the exact mode of recognition by the modifying enzymes remains unclear for many members of this class of natural products. In this report, we have used X-ray crystallography and computational modeling to examine the role of the leader peptide in the biosynthesis of a homolog of streptide, a recently identified peptide natural product with an intramolecular lysine–tryptophan cross-link, which is installed by the radical S -adenosylmethionine (SAM) enzyme, StrB. We present crystal structures of SuiB, a close ortholog of StrB, in various forms, including apo SuiB, SAM-bound SuiB, and a complex of SuiB with SAM and its peptide substrate, SuiA. Although the N-terminal domain of SuiB adopts a typical RRE (RiPP recognition element) motif, which has been implicated in precursor peptide recognition, we observe binding of the leader peptide in the catalytic barrel rather than the N-terminal domain. Computational simulations support a mechanism in which the leader peptide guides posttranslational modification by positioning the cross-linking residues of the precursor peptide within the active site. Together the results shed light onto binding of the precursor peptide and the associated conformational changes needed for the formation of the unique carbon–carbon cross-link in the streptide family of natural products.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

DOE OSTI2022

Crystal structure of active CDK4-cyclin D and mechanistic basis for abemaciclib efficacy

Despite the biological and therapeutic relevance of CDK4/6 for the treatment of HR+, HER2- advanced breast cancer, the detailed mode of action of CDK4/6 inhibitors is not completely understood. Of particular interest, phosphorylation of CDK4 at T172 (pT172) is critical for generating the active conformation, yet no such crystal structure has been reported to date. We describe here the x-ray structure of active CDK4-cyclin D3 bound to the CDK4/6 inhibitor abemaciclib and discuss the key aspects of the catalytically-competent complex. Furthermore, the effect of CDK4/6 inhibitors on CDK4 T172 phosphorylation has not been explored, despite its role as a potential biomarker of CDK4/6 inhibitor response. We show mechanistically that CDK4/6i stabilize primed (pT172) CDK4-cyclin D complex and selectively displace p21 in responsive tumor cells. Stabilization of active CDK4-cyclin D1 complex can lead to pathway reactivation following alternate dosing regimen. Consequently, sustained binding of abemaciclib to CDK4 leads to potent cell cycle inhibition in breast cancer cell lines and prevents rebound activation of downstream signaling. Overall, our study provides key insights demonstrating that prolonged treatment with CDK4/6 inhibitors and composition of the CDK4/6-cyclin D complex are both critical determinants of abemaciclib efficacy, with implications for this class of anticancer therapy.

60 APPLIED LIFE SCIENCES↗