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At least 217 records · Page 12

PERKS: a Locality-Optimized Execution Model for Iterative Memory-bound GPU Applications

Iterative memory-bound solvers commonly occur in HPC codes. Typical GPU implementations have a loop on the host side that invokes the GPU kernel as much as time/algorithm steps there are. The termination of each kernel implicitly acts the barrier required after advancing the solution every time step. We propose an execution model for running memory-bound iterative GPU kernels: PERsistent KernelS (PERKS). In this model, the time loop is moved inside persistent kernel, and device-wide barriers are used for synchronization. We then reduce the traffic to device memory by caching subset of the output in each time step in the unused registers and shared memory. PERKS can be generalized to any iterative solver: they largely independent of the solver's implementation. We explain the design principle of PERKS and demonstrate effectiveness of PERKS for a wide range of iterative 2D/3D stencil benchmarks (geomean speedup of 2.12x for 2D stencils and 1.24x for 3D stencils over state-of-art libraries), and a Krylov subspace conjugate gradient solver (geomean speedup of 4.86x in smaller SpMV datasets from SuiteSparse and 1.43x in larger SpMV datasets over a state-of-art library). All PERKS-based implementations available at: https://github.com/neozhang307/PERKS.

Zhang, Lingqi↗

A numerical study of bounds in the correlations of fractional quantum Hall states

We numerically compute the guiding center static structure factor \bar S(k) S ‾ ( k ) of various fractional quantum Hall (FQH) states to \mathcal{O}(k\ell)^6 𝒪 ( k ℓ ) 6 where k k is the wavenumber and \ell ℓ is the magnetic length. Employing density matrix renormalization group on an infinite cylinder of circumference L_y L y , we study the two-dimensional limit using L_y/\xi \gg 1 L y / ξ ≫ 1 , where \xi ξ is the correlation length. The main findings of our work are: 1) the ground states that deviate away from the ideal conformal block wavefunctions, do not saturate the Haldane bound, and 2) the coefficient of O(k\ell)^6 O ( k ℓ ) 6 term appears to be bounded above by a value predicted by field theories proposed in the literature. The first finding implies that the graviton mode is not maximally chiral for experimentally relevant FQH states.

Kumar, Prashant (ORCID:0000000258002768)↗

Root Influences on Mobilization and Export of Mineral-bound Soil Organic Matter

Biogeochemical cycles within mountainous watersheds are key regulators of ecosystem carbon storage and downstream nutrient loadings, and they have shown to be particularly vulnerable to climate change impacts. Increasing temperature and persistent droughts have already dramatically changed vegetation cover across the mountainous western US, with unknown consequences for soil carbon and nutrient cycles belowground. What remains elusive is to what extent associated changes in root-soil interactions may mobilize the vast pool of organic matter (OM) that has been stabilized by associations with minerals for centuries or millennia. Although plant root-driven OM mobilization from minerals may be a central control on carbon loss and nutrient export, such mechanisms are currently missing from conceptual and numerical models. The overall objective of this Exploratory Project is to identify the biogeochemical mechanisms by which roots destabilize mineral-associated organic matter (MAOM) and the cumulative impact on carbon and nutrient fate. To accomplish this goal, we integrated well-controlled laboratory experiments with in-field measurements and a scalable modeling approach. First, we conducted model system experiments to assess the vulnerability of MAOM to exudate-mediated mechanisms. Our results show that common root exudates effectively destabilize MAOM not only through direct, ligand-driven mobilization mechanisms, but also indirect, microbially-mediated mechanisms relying on secondary metabolites and enzymes. We further found that OM bound to poorly crystalline Fe and Al (hydr)oxides is more vulnerable to exudate-induced destabilization than OM bound to more crystalline phases, particularly in response to direct, ligand-promoted mechanisms. These findings demonstrate that the stability of MAOM is not just a function of their inherent properties, but also will depend in large parts on the ability of plant roots and microbes to produce exudates capable of triggering suitable mobilization mechanisms. We further employed a well-controlled rhizobox approach, combining advanced microsensor and mass spectrometry techniques, to resolve spatiotemporal variations in the composition and availability of exudates along single growing roots of grasses. Our results show that the composition of functionally relevant exudate compounds varies at extremely short time scales, seemingly shifting from ligands such as aromatic acids around root tips to less reactive metabolites such as amino acids around mature root segments. These results suggest a prevalence of direct MAOM mobilization mechanisms around the root tip, while indirect MAOM mobilization strategies may dominate around more mature root segments. Additionally, we utilized microsensor measurements in rhizoboxes to parameterize a rhizosphere (hydro)biogeochemistry reactive transport model (eSTOMP-ROOTS). The resulting model was used to assess how root exudations affects the stability of MAOM. Model simulations show that diel pulses of root exudation are strong enough to cause oscillations in biogeochemical conditions—particularly in pH, oxygen concentrations, and microbial activity— that repeatedly disrupt MAOM. Finally, we assessed field-scale impacts of root-driven MAOM destabilization over short and long time scales. A combination of in-field incubations and field-based characterizations showed that MAOM may not only be vulnerable to seasonal variations in root activity, but also to root-driven weathering over pedogenic time scales. In sum, results from our Exploratory Award highlight the strong control plant roots exert on MAOM mobilization and, thus, on the potential for carbon and nutrient export from watersheds.

54 ENVIRONMENTAL SCIENCES↗

The Inducible Accumulation of Cell Wall-Bound p -Hydroxybenzoates Is Involved in the Regulation of Gravitropic Response of Poplar

Lignin in Populus species is acylated with p-hydroxybenzoate. Monolignol p-hydroxybenzoyltransferase 1 (PHBMT1) mediates p-hydroxybenzoylation of sinapyl alcohol, eventually leading to the modification of syringyl lignin subunits. Angiosperm trees upon gravistimulation undergo the re-orientation of their growth along with the production of specialized secondary xylem, i.e., tension wood (TW), that generates tensile force to pull the inclined stem or leaning branch upward. Sporadic evidence suggests that angiosperm TW contains relatively a high percentage of syringyl lignin and lignin-bound p-hydroxybenzoate. However, whether such lignin modification plays a role in gravitropic response remains unclear. By imposing mechanical bending and/or gravitropic stimuli to the hybrid aspens in the wild type (WT), lignin p-hydroxybenzoate deficient, and p-hydroxybenzoate overproduction plants, we examined the responses of plants to gravitropic/mechanical stress and their cell wall composition changes. We revealed that mechanical bending or gravitropic stimulation not only induced the overproduction of crystalline cellulose fibers and increased the relative abundance of syringyl lignin, but also significantly induced the expression of PHBMT1 and the increased accumulation of p-hydroxybenzoates in TW. Furthermore, we found that although disturbing lignin-bound p-hydroxybenzoate accumulation in the PHBMT1 knockout and overexpression (OE) poplars did not affect the major chemical composition shifts of the cell walls in their TW as occurred in the WT plants, depletion of p-hydroxybenzoates intensified the gravitropic curving of the plantlets in response to gravistimulation, evident with the enhanced stem secant bending angle. By contrast, hyperaccumulation of p-hydroxybenzoates mitigated gravitropic response. These data suggest that PHBMT1-mediated lignin modification is involved in the regulation of poplar gravitropic response and, likely by compromising gravitropism and/or enhancing autotropism, negatively coordinates the action of TW cellulose fibers to control the poplar wood deformation and plant growth.

59 BASIC BIOLOGICAL SCIENCES↗

The Structure of Maltooctaose-Bound Escherichia coli Branching Enzyme Suggests a Mechanism for Donor Chain Specificity

Glycogen is the primary storage polysaccharide in bacteria and animals. It is a glucose polymer linked by α-1,4 glucose linkages and branched via α-1,6-linkages, with the latter reaction catalyzed by branching enzymes. Both the length and dispensation of these branches are critical in defining the structure, density, and relative bioavailability of the storage polysaccharide. Key to this is the specificity of branching enzymes because they define branch length. Herein, we report the crystal structure of the maltooctaose-bound branching enzyme from the enterobacteria E. coli. The structure identifies three new malto-oligosaccharide binding sites and confirms oligosaccharide binding in seven others, bringing the total number of oligosaccharide binding sites to twelve. In addition, the structure shows distinctly different binding in previously identified site I, with a substantially longer glucan chain ordered in the binding site. Using the donor oligosaccharide chain-bound Cyanothece branching enzyme structure as a guide, binding site I was identified as the likely binding surface for the extended donor chains that the E. coli branching enzyme is known to transfer. Furthermore, the structure suggests that analogous loops in branching enzymes from a diversity of organisms are responsible for branch chain length specificity. Together, these results suggest a possible mechanism for transfer chain specificity involving some of these surface binding sites.

59 BASIC BIOLOGICAL SCIENCES↗

Removal of Non-Specifically Bound Proteins Using Rayleigh Waves Generated on ST-Quartz Substrates

Label-free biosensors are plagued by the issue of non-specific protein binding which negatively affects sensing parameters such as sensitivity, selectivity, and limit-of-detection. In the current work, we explore the possibility of using the Rayleigh waves in ST-Quartz devices to efficiently remove non-specifically bound proteins via acoustic streaming. A coupled-field finite element (FE) fluid structure interaction (FSI) model of a surface acoustic wave (SAW) device based on ST-Quartz substrate in contact with a liquid loading was first used to predict trends in forces related to SAW-induced acoustic streaming. Based on model predictions, it is found that the computed SAW body force is sufficient to overcome adhesive forces between particles and a surface while lift and drag forces prevent reattachment for a range of SAW frequencies. We further performed experiments to validate the model predictions and observe that the excitation of Rayleigh SAWs removed non-specifically bound (NSB) antigens and antibodies from sensing and non-sensing regions, while rinsing and blocking agents were ineffective. An amplified RF signal applied to the device input disrupted the specific interactions between antigens and their capture antibody as well. ST-quartz allows propagation of Rayleigh and leaky SH-SAW waves in orthogonal directions. Thus, the results reported here could allow integration of three important biosensor functions on a single chip, i.e., removal of non-specific binding, mixing, and sensing in the liquid phase.

59 BASIC BIOLOGICAL SCIENCES↗

Tight Bound on the Neutron Star Radius with Quasiperiodic Oscillations in Short Gamma-Ray Bursts

Abstract Quasiperiodic oscillations (QPOs) have been recently discovered in the short gamma-ray bursts (GRBs) 910711 and 931101B. Their frequencies are consistent with those of the quasiradial and quadrupolar oscillations of binary neutron star (BNS) merger remnants, as obtained in numerical relativity simulations. These simulations reveal quasi-universal relations between the remnant oscillation frequencies and the tidal coupling constant of the binaries. Under the assumption that the observed QPOs are due to these postmerger oscillations, we use the frequency–tide relations in a Bayesian framework to infer the source redshift, as well as the chirp mass and the binary tidal deformability of the BNS progenitors for GRBs 910711 and 931101B. We further use this inference to estimate bounds on the mass–radius relation for neutron stars. By combining the estimates from the two GRBs, we find a 68% credible range R 1.4 = 12.4 8 − 0.40 + 0.41 km for the radius of a neutron star with mass M = 1.4 M ⊙ , which is one of the tightest bounds to date.

Guedes, Victor↗

Upper Bound on Parity Breaking Scale for Doublet WIMP Dark Matter

We consider weakly interacting massive particle (WIMP) dark matter in a Parity solution to the strong CP problem. The WIMP phenomenology can be drastically affected by the presence of Parity partners of the WIMP and electroweak gauge bosons. We focus on a Parity extension of $SU(2)_L$-doublet fermion dark matter, identify the viable parameter space, and derive the predictions of the theory. We find that the Parity symmetry breaking scale is bounded from above, with the bound given by $25-60$ TeV, depending on whether or not dark matter and its Parity partner coannihilate with each other. The High-Luminosity Large Hadron Collider, future colliders, and direct and indirect detection experiments can probe the parameter space further, with correlated signal rates.

Baldwin, Matthew J. [Chicago U.; Chicago U., KICP]↗

Quantum information processing with majorana bound states in superconducting circuits

In a weak link of two s-wave superconductors (SCs) coupled via a time-reversal-invariant (TRI) topological superconducting (TSC) island, a Josephson current can flow due to Cooper pairs tunneling in and out of spatially separated Majorana Kramers pairs (MKPs), which are doublets of Majorana bound states (MBSs). The sign of the resulting Josephson current is fixed by the joint parity of the four Majorana bound states that make up the MKPs on the TSC island. This parity-controlled Josephson effect can be used as a read-out mechanism for the joint parity in Majorana-based quantum computing. For a TSC island with four terminals, the SC leads can address a Majorana superconducting qubit (MSQ) formed by the charge ground states of the TSC island's terminals. Cooper pair splitting enables single-qubit operations, qubit read-out, as well as two-qubit entangling gates. Hence, TSC islands between SC leads may provide an alternative approach to superconducting quantum computation.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Bounded Universal Droop Control to Enable the Operation of Power Inverters Under Some Abnormal Conditions and Maintain Voltage and Frequency Within Predetermined Ranges

The universal droop control (UDC) can be applied to power inverters having an impedance angle between -pi/2 rad and pi/2 rad to achieve voltage and frequency regulation and accurate proportional power sharing without the need of knowing the type or value of impedance. However, there is an increasing need for voltage and frequency regulation within predetermined ranges even under some abnormal conditions, such as overloading, sensor faults, and large set-point changes, etc. In this paper, a bounded nonlinear dynamics is introduced into the UDC to ensure that the voltage and frequency can always stay within predetermined ranges under normal and some abnormal conditions, up to hardware limits when current protection needs to be triggered. As a result, the proposed controller can extend the operational range of power inverters in terms of voltage and frequency regulation to cover different scenarios. More importantly, the ranges for both voltage and frequency can be chosen independently from each other. Since the original structure of the UDC is kept in the proposed controller, the properties of the UDC, such as without the need of knowing the type or value of impedance, are well maintained. Furthermore, the closed-loop stability of the system is established via the Lyapunov method. Extensive simulation and experimental results are presented to validate the effectiveness of the proposed controller.

14 SOLAR ENERGY↗

Half‐Integer Topological Charge Polarization of Quasi‐Dirac Bound States in the Continuum

Abstract The non‐trivial polarization topology of bound states in the continuum (BICs) provides new strategies in nanophotonics. The polarization topology depends on the geometric parameters and energy‐momentum dispersion of the system and can be engineered to add specific functionalities for light molding. Herein, such a possibility is investigated by studying the topology of the polarization states associated with the optical field radiated by BICs when Dirac‐cone‐degeneracy is lifted. The opening of a pseudogap in the Dirac cone dispersion of square‐lattice dielectric photonic crystal slabs is achieved by tuning the slab thickness. First, the emergence of half‐integer topological charges without the requirement of BIC annihilation is theoretically shown, which instead occurs when in‐plane inversion symmetry is broken. Then, using spin‐to‐orbital angular momentum conversion, the theory of half‐integer topological charges mediated by BICs is demonstrated and experimentally proved. The same device is able to give rise to vortices with different orbital angular momentum depending on the way it is illuminated, thus improving the potential of optical multiplexing. In addition, the additive character of the topology‐induced phase‐vortex generation is finally demonstrated for both integer and half‐integer charges using also vortex states as input beams, which is of relevance for information delivery.

36 MATERIALS SCIENCE↗

Molecularly Imprinted Polymer Sensor Empowered by Bound States in the Continuum for Selective Trace-Detection of TGF-beta

The integration of advanced materials and photonic nanostructures can lead to enhanced biodetection capabilities, crucial in clinical scenarios and point-of-care diagnostics, where simplified strategies are essential. Herein, a molecularly imprinted polymer (MIP) photonic nanostructure is demonstrated, which selectively binding to transforming growth factor-beta (TGF-β), in which the sensing transduction is enhanced by bound states in the continuum (BICs). The MIP operating as a synthetic antibody matrix and coupled with BIC resonance, enhances the optical response to TGF-β at imprinted sites, leading to an augmented detection capability, thoroughly evaluated through spectral shift and optical lever analogue readout. The validation underscores the MIP-BIC sensor capability to detect TGF-β in spiked saliva, achieving a limit of detection of 10 fM and a resolution of 0.5 pM at physiological concentrations, with a precision of two orders of magnitude above discrimination threshold in patients. The MIP tailored selectivity is highlighted by an imprinting factor of 52, showcasing the sensor resistance to interference from other analytes. The MIP-BIC sensor architecture streamlines the detection process eliminating the need for complex sandwich immunoassays and demonstrates the potential for high-precision quantification. This positions the system as a robust tool for biomarker detection, especially in real-world diagnostic scenarios.

77 NANOSCIENCE AND NANOTECHNOLOGY↗

Lines of Bound States in the Continuum in Monodisperse Microsphere Structures

Incorporating epitaxially grown active semiconductor media into self-assembled microsphere crystals has remained a major challenge as the curved geometry of the spheres is incompatible with conventional planar growth and patterning techniques. As a result, active photonic devices based on such self-assembled structures, which have other desirable properties such as enabling the rapid assembly of large area systems, have been elusive. Here, we numerically demonstrate an alternative route to creating high-Q resonances in microsphere-based nanophotonic assemblies compatible with standard optical gain materials. We show that close-packed layers of monodisperse microspheres can exhibit symmetry bandgaps, regardless of their layer stacking order. Thus, this microsphere environment can be used to create lines of bound states in the continuum (BICs) of an embedded slab made of active material. Using a realistic ZnS@SiO 2 (core-shell) architecture and sphere diameters compatible with scalable colloidal assembly, we predict sharp spectral features in angle-resolved transmission that trace these lines of BICs and persist in the presence of some fabrication disorder. Altogether, in enabling the integration of unpatterned epitaxial gain slabs with large-area colloidal microsphere assemblies, this approach opens a practical path toward active, dynamically reconfigurable photonic devices that leverage BIC physics for narrow-linewidth lasing and enhanced light–matter interactions.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Improved Bounds for Burning Fence Graphs

Graph burning studies how fast a contagion, modeled as a set of fires, spreads in a graph. The burning process takes place in synchronous, discrete rounds. In each round, a fire breaks out at a vertex, and the fire spreads to all vertices that are adjacent to a burning vertex. Additionally, the burning number of a graph G is the minimum number of rounds necessary for each vertex of G to burn. We consider the burning number of the \(m \times n\) Cartesian grid graphs, written \(G_{m,n}\) . For \(m = \omega (\sqrt{n})\) , the asymptotic value of the burning number of \(G_{m,n}\) was determined, but only the growth rate of the burning number was investigated in the case \(m = O(\sqrt{n})\) , which we refer to as fence graphs. We provide new explicit bounds on the burning number of fence graphs \(G_{c\sqrt{n},n}\) , where \(c > 0\) .

79 ASTRONOMY AND ASTROPHYSICS↗

Resolving SPARC–HSA binding kinetics with an ultrasensitive photonic sensor based on bound states in the continuum

Secreted protein acidic and rich in cysteine (SPARC) is critical in cell-matrix interactions and tissue remodeling. It influences tumor progression through its affinity for human serum albumin (HSA) - the most abundant plasma protein, which also plays a crucial role in drug delivery. Strong molecular binding leads to a dissociation constant KD in the nanomolar range. Thus, determining KD requires detecting sub-nanomolar concentrations with ultrasensitive methods. This may be crucial for elucidating the nature of SPARC-HSA binding, as their interaction remains a subject of debate. Capturing these interactions accurately requires a platform capable of resolving rapid binding kinetics at extremely low analyte concentrations. In this work, we report on a microfluidics-integrated photonic nanostructure that supports bound states in the continuum (BICs) and is optimized for studying the fast kinetics of high-affinity protein-protein interactions. The unprecedented capability of detecting sub-nanomolar concentrations allows quantifying KD between SPARC and HSA beyond the state of the art. We leverage an all-dielectric photonic crystal slab (PhCS) sustaining two BIC branches arising from gapped Dirac cone dispersion. HSA is covalently immobilized on the PhCS bonded to a PDMS microfluidic chamber. SPARC dissociation is carried out using PBS buffer (pH 7.4), ensuring complete protein release through precise control of the flow rate and continuous spectral monitoring of the BICs. The measured KD=8.2±0.8 nM confirms the strong affinity of SPARC for HSA. This study highlights the potential of BIC-based sensing as a versatile tool for investigating protein interactions. These results also have implications for the optimization of drug delivery systems and cancer treatment strategies.

Albumin↗

Continuously bounds-preserving discontinuous Galerkin methods for hyperbolic conservation laws

For finite element approximations of transport phenomena, it is often necessary to apply a form of limiting to ensure that the discrete solution remains well-behaved and satisfies physical constraints. However, these limiting procedures are typically performed at discrete nodal locations, which is not sufficient to ensure the robustness of the scheme when the solution must be evaluated at arbitrary locations (e.g., for adaptive mesh refinement, remapping in arbitrary Lagrangian–Eulerian solvers, overset meshes, etc.). In this work, a novel limiting approach for discontinuous Galerkin methods is presented which ensures that the solution is continuously bounds-preserving (i.e., across the entire solution polynomial) for any arbitrary choice of basis, approximation order, and mesh element type. Through a modified formulation for the constraint functionals, the proposed approach requires only the solution of a single spatial scalar minimization problem per element for which a highly efficient numerical optimization procedure is presented. Here, the efficacy of this approach is shown in numerical experiments by enforcing continuous constraints in high-order unstructured discontinuous Galerkin discretizations of hyperbolic conservation laws, ranging from scalar transport with maximum principle preserving constraints to compressible gas dynamics with positivity-preserving constraints.

97 MATHEMATICS AND COMPUTING↗

Reduced Order Modeling conditioned on monitored features for response and error bounds estimation in engineered systems

Reduced Order Models (ROMs) form essential tools across engineering domains by virtue of their function as surrogates for computationally intensive digital twinning simulators. Although purely data-driven methods are available for ROM construction, schemes that allow to retain a portion of the physics tend to enhance the interpretability and generalization of ROMs. However, physics-based techniques can adversely scale when dealing with nonlinear systems that feature parametric dependencies. This study introduces a generative physics-based ROM that is suited for nonlinear systems with parametric dependencies and is additionally able to provide numerical error bounds associated with the respective estimates. A main contribution of this work is the conditioning of these parametric ROMs to features that can be derived from monitoring measurements, feasibly in an online fashion. This is contrary to most existing ROM schemes, which remain restricted to the prescription of the physics-based, and usually a priori unknown, system parameters. Our work utilizes conditional Variational Autoencoders to continuously map the required reduction bases to a feature vector extracted from limited output measurements, while additionally allowing for a probabilistic assessment of the ROM-estimated Quantities of Interest. An auxiliary task using a neural network-based parametrization of suitable probability distributions is introduced to re-establish the link with physical model parameters. We verify the proposed scheme on a series of simulated case studies incorporating effects of geometric and material nonlinearity under parametric dependencies related to system properties and input load characteristics.

Conditional VAEs↗

Enhanced Second and Third Harmonic Generations in Metasurfaces Enabled through Point Group Design and Accidental Bound States in the Continuum

Here, we investigate enhanced second‑ and third‑harmonic generation (SHG and THG) in GaAs metasurfaces by combining electromagnetic point‑group designs with accidental bound states in the continuum (BICs). Using group theory, we predict the existence, suppression, and polarization selection rules of SHG and THG for metasurfaces belonging to the D 2h and C 2v point groups. In D 2h metasurfaces, inversion symmetry suppresses SHG while enabling polarization‑selective THG, which is strongly enhanced near accidental BICs with ultrahigh Q‑factors approaching 107. By breaking inversion symmetry to form C 2v metasurfaces through the introduction of nanogaps, SHG is now allowed and is dramatically enhanced near accidental BICs. Importantly, accidental BICs preserve polarization selection rules while providing a robust parameter range for high‑Q resonances, in contrast to quasi‑BICs induced by symmetry breaking. Our results demonstrate that the combination of point‑group theory and accidental‑BIC engineering offers a predictive and robust route toward highly efficient nonlinear metasurfaces.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗