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At least 1,117 records · Page 62

Identification of a ligand binding hot spot and structural motifs replicating aspects of tyrosyl-DNA phosphodiesterase I (TDP1) phosphoryl recognition by crystallographic fragment cocktail screening

Tyrosyl DNA-phosphodiesterase I (TDP1) repairs type IB topoisomerase (TOP1) cleavage complexes generated by TOP1 inhibitors commonly used as anticancer agents. TDP1 also removes DNA 3' end blocking lesions generated by chain-terminating nucleosides and alkylating agents, and base oxidation both in the nuclear and mitochondrial genomes. Combination therapy with TDP1 inhibitors is proposed to synergize with topoisomerase targeting drugs to enhance selectivity against cancer cells exhibiting deficiencies in parallel DNA repair pathways. A crystallographic fragment screening campaign against the catalytic domain of TDP1 was conducted to identify new lead compounds. Crystal structures revealed two fragments that bind to the TDP1 active site and exhibit inhibitory activity against TDP1. These fragments occupy a similar position in the TDP1 active site as seen in prior crystal structures of TDP1 with bound vanadate, a transition state mimic. Using structural insights into fragment binding, several fragment derivatives have been prepared and evaluated in biochemical assays. These results demonstrate that fragment-based methods can be a highly feasible approach toward the discovery of small-molecule chemical scaffolds to target TDP1, and for the first time, we provide co-crystal structures of small molecule inhibitors bound to TDP1, which could serve for the rational development of medicinal TDP1 inhibitors.

Lountos, George T.↗

Aspects of the Domain-Wall Standard Model

Abstract In the “Domain-Wall Standard Model,” all the Standard Model (SM) fields are localized in certain domains in a non-compact 5D space-time. While the SM is realized as a 4D effective theory at low energies, the model involves Kaluza–Klein (KK) modes of the SM particles. In this paper we introduce two simple solvable examples which lead to domain-wall configurations for the SM particles and their KK-modes. Based on the examples, we address a variety of phenomenologies of the Domain-Wall SM, such as the KK-mode gauge boson phenomenology at the Large Hadron Collider (LHC), the effect of the KK-mode SM fermions on Higgs boson phenomenology, and the KK-mode fermion search at the LHC with its decay into a corresponding SM fermion and a Nambu–Goldstone boson associated with a spontaneous breaking of the translational invariance in the 5th dimension. We also propose a simple unified picture of localizing all the SM fields.

Physics↗

New scaling and nuclear structure aspects in heavy-ion fusion reactions

Three new behaviors have been found in comparisons of fusion cross sections for different collision systems. root (1) Replacing the energy E with a scaling one, E scal = (E-V g )/($\sqrt{2}$W g ), is successful for washing out the Coulomb interaction in the spectra of fusion cross sections, where V g and W g are barrier height and width of the single-Gaussian barrier distribution model. (2) In a representation of σE vs the scaling energy, E scal , all data sets display in parallel. Here, the ratio for sigma E from any two fusion systems over the whole range is a constant value. That behavior is also studied in another representation, in which the data sets display as parallel horizontal lines for any heavy-ion fusion system. (3) The constant ratio value is the ratio of parameter products, $R^2_gW_g$, of the two systems; where R g is the barrier radius obtained in the single-Gaussian barrier distribution model. Moreover, when comparing neighboring collision systems at the same E scal , the ratio of sigma is near a constant value within a few percent over the whole range. Thus a quantitative comparison for the fusion enhancement for neighboring systems is developed. The present finding could be beneficial for predicting unmeasured fusion cross sections.

Jiang, C. L. [Argonne National Laboratory (ANL), A↗

Aspects of the normal state resistivity of cuprate superconductors

Planar normal state resistivity data taken from three families of cuprate superconductors are compared here with theoretical calculations from the recent extremely correlated Fermi liquid theory (ECFL). The two hole doped cuprate materials LSCO and BSLCO and the electron doped material LCCO have yielded rich data sets at several densities δ and temperatures T, thereby enabling a systematic comparison with theory. The recent ECFL resistivity calculations for the highly correlated t-t'-J model by us give the resistivity for a wide set of model parameters. After using X-ray diffraction and angle resolved photoemission data to fix parameters appearing in the theoretical resistivity, only one parameter, the magnitude of the hopping t, remains undetermined. For each data set, the slope of the experimental resistivity at a single temperature-density point is sufficient to determine t, and hence the resistivity on absolute scale at all remaining densities and temperatures. This procedure is demonstrated to give a fair account of the entire data.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Prediction of superconductivity and topological aspects in single-layer β -Bi 2 Pd

Topological superconductors, characterized by topologically nontrivial states residing in a superconducting gap, are a recently discovered class of materials having Majorana fermions. The interplay of superconductivity and topological states gives rise to opportunities for achieving such topological superconductors in condensed matter systems. Up to now, several single-material topological superconductors in this form have been theoretically predicted and experimentally confirmed. Here, using the first-principles calculations, we study the superconducting single-layer β-Bi 2 Pd. In this work, the electronic density of states near Fermi level of this monolayer are dominated by the Bi-p and Pd-d orbitals, forming a two-band Fermi surface with multiclass sheets. The presence of soft phonon bands, in cooperation with the electron susceptibility, accounts for electron-phonon superconductivity of single-layer β-Bi 2 Pd. With the centrosymmetric structure, single-layer β-Bi 2 Pd possesses a continuous gap over the whole Brillouin zone and topological Dirac-like states at its one-dimensional boundary. The present findings would lead to the expectation of one-dimensional topological superconductivity and Majorana bound states in a monolayer candidate of β-Bi 2 Pd with intrinsic full-gap superconductivity.

36 MATERIALS SCIENCE↗

Nonperturbative aspects of the electromagnetic pion form factor at high energies

The structure of hadronic form factors at high energies and their deviations from perturbative quantum chromodynamics provide insight on nonperturbative dynamics. Using an approach that is consistent with dispersion relations, we construct a model that simultaneously accounts for the pion wave function, gluonic exchanges, and quark Reggeization. In particular, we find that quark Reggeization can be investigated at high energies by studying scaling violation of the form factor.

Form factors↗

Aspects of gravitational portals and freeze-in during reheating

We conduct a systematic investigation of freeze-in during reheating while taking care to include both direct and indirect production of dark matter (DM) via gravitational portals and inflaton decay. Direct production of DM can occur via gravitational scattering of the inflaton, while indirect production occurs through scattering in the Standard Model radiation bath. We consider two main contributions to the radiation bath during reheating. The first, which may dominate at the onset of the reheating process, is produced via gravitational scattering of the inflaton. The second (and more standard contribution) comes from inflaton decay. We consider a broad class of DM production rates parametrized as R χ ∝ T n + 6 / Λ n + 2 , and inflaton potentials with a power-law form V ( ϕ ) ∝ ϕ k about the minimum. We find the relic density produced by freeze-in for each contribution to the Standard Model bath for arbitrary k and n , and compare these with the DM density produced gravitationally by inflaton scattering. We find that freeze-in production from the gravitationally produced radiation bath can exceed that of the conventional decay bath and account for the observed relic density provided that m χ > T RH , with additional k - and n -dependent constraints. For each freeze-in interaction considered, we also find m χ - and T RH -dependent limits on the beyond the Standard Model scale, Λ , for which gravitational production will exceed ordinary freeze-in production. Published by the American Physical Society 2025

Henrich, Stephen E. (ORCID:0000000323669519)↗

Nuclear structure aspects of spin-independent WIMP scattering off xenon

We study the structure factors for spin-independent WIMP scattering off xenon based on state-of-the-art large-scale shell-model calculations, which are shown to yield a good spectroscopic description of all experimentally relevant isotopes. Our results are based on the leading scalar one-body currents only. At this level and for the momentum transfers relevant to direct dark matter detection, the structure factors are in very good agreement with the phenomenological Helm form factors used to give experimental limits for WIMP- nucleon cross sections. In contrast to spin-dependent WIMP scattering, the spin-independent channel, at the one-body level, is less sensitive to nuclear structure details. In addition, we explicitly show that the structure factors for inelastic scattering are suppressed by ∼10 −4 compared to the coherent elastic scattering response. Here, this implies that the detection of inelastic scattering will be able to discriminate clearly between spin- independent and spin-dependent scattering. Finally, we provide fits for all calculated structure factors.

Vietze, L.↗