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77 records · Page 5

Dimension-free path-integral molecular dynamics without preconditioning

Convergence with respect to imaginary-time discretization (i.e., the number of ring-polymer beads) is an essential part of any path-integral-based molecular dynamics (MD) calculation. However, an unfortunate property of existing non-preconditioned numerical integration schemes for path-integral molecular dynamics—including essentially all existing ring-polymer molecular dynamics (RPMD) and thermostatted RPMD (T-RPMD) methods—is that for a given MD time step, the overlap between the exact ring-polymer Boltzmann–Gibbs distribution and that sampled using MD becomes zero in the infinite-bead limit. This has clear implications for hybrid Metropolis Monte Carlo/MD sampling schemes, and it also causes the divergence with bead number of the primitive path-integral kinetic-energy expectation value when using standard RPMD or T-RPMD. We show that these and other problems can be avoided through the introduction of “dimension-free” numerical integration schemes for which the sampled ring-polymer position distribution has non-zero overlap with the exact distribution in the infinite-bead limit for the case of a harmonic potential. Most notably, we introduce the BCOCB integration scheme, which achieves dimension freedom via a particular symmetric splitting of the integration time step and a novel implementation of the Cayley modification [R. Korol et al., J. Chem. Phys. 151, 124103 (2019)] for the free ring-polymer half-steps. More generally, we show that dimension freedom can be achieved via mollification of the forces from the external physical potential. The dimension-free path-integral numerical integration schemes introduced here yield finite error bounds for a given MD time step, even as the number of beads is taken to infinity; these conclusions are proven for the case of a harmonic potential and borne out numerically for anharmonic systems that include liquid water. The numerical results for BCOCB are particularly striking, allowing for nearly three-fold increases in the stable time step for liquid water with respect to the Bussi–Parrinello (OBABO) and Leimkuhler (BAOAB) integrators, while introducing negligible errors in the calculated statistical properties and absorption spectrum. Importantly, the dimension-free, non-preconditioned integration schemes introduced here preserve ergodicity and global second-order accuracy, and they remain simple, black-box methods that avoid additional computational costs, tunable parameters, or system-specific implementations.

Korol, Roman (ORCID:0000000193076351)↗

FOXM1-activated SIRT4 inhibits NF-κB signaling and NLRP3 inflammasome to alleviate kidney injury and podocyte pyroptosis in diabetic nephropathy

Highlights: • FOXM1 is downregulated in kidney tissues of patients with DN. • Overexpression of FOXM1 alleviates kidney injury in DN modeled mice. • Overexpression of FOXM1 reduces pyroptosis of HG-treated podocytes. • FOXM1 activates SIRT4 to inhibit the NFκB pathway and the NLRP3 inflammasome. • Downregulation of SIRT4 blocks the protective roles of FOXM1 in podocytes and mice. Forkhead box M1 (FOXM1) has been reported to play a protective role against acute kidney injury by driving tubular regeneration. This study aims to probe the function of FOXM1 in diabetic nephropathy (DN) and the molecules involved. FOXM1 was poorly expressed in DN-diseased kidney tissues. A murine model of DN was established, and podocytes cells (MPC5) were treated with high-glucose (HG) for in vitro studies. FOXM1 overexpression improved kidney function and reduced pathological changes in mice, and it increased the expression of the podocyte marker Nephrin in kidney tissues. In vitro, FOXM1 increased viability and reduced pyroptosis of the HG-treated MPC5 cells, and it elevated the expression of the podocyte marker Nephrin whereas reduced the expression of pyroptosis-related NLRP3 inflammasome and cleaved caspase 1. FOXM1 bound to the promoter of sirtuin 4 (SIRT4) to induce transcriptional activation. Downregulation of SIRT4 blocked the protective roles of FOXM1 both in vivo and in vitro. Phosphorylation of nuclear factor-kappa B (NF-κB) in HG-treated cells was suppressed by FOXM1 but restored after SIRT4 inhibition. In conclusion, this study suggested that FOXM1 transcriptionally activates SIRT4 and inhibits NF-κB signaling and the NLRP3 inflammasome to alleviate kidney injury and podocyte pyroptosis in DN.

60 APPLIED LIFE SCIENCES↗

Performance of the A-01 Constructed Wetland over 20 Years

The A-01 wetland treatment system (WTS) was designed to remove metals from the effluent at the A-01 National Pollution Discharge Elimination System (NPDES) outfall at the Savannah River Site, Aiken, SC. The A-01 effluent flows from a retention basin to a splitter box, where it is distributed to four pairs of cells in series before discharge to a stream. Each treatment cell is a one-acre wetland that contains Schoenoplectus californicus (giant bulrush) and has a nominal 24-hour retention time. The purpose of this research was to investigate metal removal, distribution and retention in the A-01 WTS over a period of 20 years. During 20 years of operation, systematic water and sediment sampling validated the wetlands' performance. After passage through the treatment cells, Cu concentrations were well below permit limits (22 pg L -1 ) during all years of operation, often falling below 10 pg L -1 . Cu removal has been consistent over time, averaging about 80% despite large changes in influent Cu concentrations. Most divalent metals were rapidly removed from the water and held in the sediments shortly after the water entered the treatment wetlands. Average removal of Pb from water by the wetland system was 67 and 74%, respectively, in 2004, and 2020. Comparable values for Zn were 52 and 65%, respectively. Generally, the highest concentrations of Cu, Pb, and Zn were found in the sediment from the first cell in each pair of cells suggesting that most of the Cu, Pb, and Zn in the A-01 effluent was bound to the sediment quickly. Diffusive gradients in thin films (DGT) measurements of Cu and Zn in the sediments were much lower than bulk sediment concentrations. These results suggest that most of the Cu and Zn in the A-01 WTS sediments was not bioavailable, hence not toxic to aquatic organisms, as a likely consequence of adsorption to sediment particles and complexation with organic and inorganic substances.

12 MANAGEMENT OF RADIOACTIVE AND NON-RADIOACTIVE W↗

Earth as a transducer for dark-photon dark-matter detection

We propose the use of the Earth as a transducer for ultralight dark-matter detection. In particular, we point out a novel signal of kinetically mixed dark-photon dark matter: a monochromatic oscillating magnetic field generated at the surface of the Earth. Similar to the signal in a laboratory experiment in a shielded box (or cavity), this signal arises because the lower atmosphere is a low-conductivity air gap sandwiched between the highly conductive interior of the Earth below and ionosphere or interplanetary medium above. At low masses (frequencies) the signal in a laboratory detector is usually suppressed by the size of the detector multiplied by the dark-matter mass. Crucially, in our case the suppression is by the radius of the Earth, and not by the (much smaller) height of the atmosphere. We compute the size and global vectorial pattern of our magnetic field signal, which enables sensitive searches for this signal using unshielded magnetometers dispersed over the surface of the Earth. In principle, the signal we compute exists for any dark photon in the mass range 10 –21 eV ≲ m A' ≲ 3 × 10 –14 eV . We summarize the results of our companion paper [M. A. Fedderke et al., Search for dark-photon dark matter in the SuperMAG geomagnetic field dataset, arXiv:2108.08852], in which we detail such a search using a publicly available dataset from the SuperMAG Collaboration: we report no robust signal candidates and so place constraints in the (more limited) dark-photon dark-matter mass range 2 × 10 –18 eV ≲ m A' ≲ 7 × 10 –17 eV (corresponding to frequencies 6 × 10 –4 Hz ≲ f ≲ 2 × 10 –2 Hz). These constraints are complementary to existing astrophysical bounds. Future searches for this signal may improve the sensitivity over a wide range of ultralight dark-matter candidates and masses.

79 ASTRONOMY AND ASTROPHYSICS↗

Barium ion sensing with IPG K + molecular probes

Fluorophores covalently bound to azacrown ether ionophores can be assembled into sensitive turn-on chemosensors. The size specificity and electron-rich nature of the ionophore's binding domain contribute to both selectivity and strong turn-on fluorescence sensing by various mechanisms when properly constructed. Aza-18-crown-6 ethers are quite selective for binding to K + and Ba 2+ , yet the more electron-withdrawing dicationic nature of barium imposes a larger electronic effect on turn-on fluorescent sensors. Barium chemosensors can be important for measuring soluble Ba 2+ in drinking water and have gained recent attention for their potential to enhance the detection of rare events in xenon decay. Here we quantify the capability of three chemosensors, marketed for biologically useful K + sensing, as effective probes for Ba 2+ ions. Here, we present measurements from bulk spectrofluorometry to characterize the system in aqueous solutions and demonstrate the usefulness of these species for low-background single-ion fluorescence microscopy, revealing new candidates for Ba 2+ sensing.

Miller, R. L. [Department of Chemistry and Biochem↗