Bounding Computation and Complexity for Reactive Transport on Supercomputers: A Perspective from Nuclear Waste Repository Performance Assessment.
Abstract not provided.
Hammond, Glenn Edward↗
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Structures, activity and mechanism of the Type IIS restriction endonuclease PaqCI
Abstract Type IIS restriction endonucleases contain separate DNA recognition and catalytic domains and cleave their substrates at well-defined distances outside their target sequences. They are employed in biotechnology for a variety of purposes, including the creation of gene-targeting zinc finger and TAL effector nucleases and DNA synthesis applications such as Golden Gate assembly. The most thoroughly studied Type IIS enzyme, FokI, has been shown to require multimerization and engagement with multiple DNA targets for optimal cleavage activity; however, details of how it or similar enzymes forms a DNA-bound reaction complex have not been described at atomic resolution. Here we describe biochemical analyses of DNA cleavage by the Type IIS PaqCI restriction endonuclease and a series of molecular structures in the presence and absence of multiple bound DNA targets. The enzyme displays a similar tetrameric organization of target recognition domains in the absence or presence of bound substrate, with a significant repositioning of endonuclease domains in a trapped DNA-bound complex that is poised to deliver the first of a series of double-strand breaks. PaqCI and FokI share similar structural mechanisms of DNA cleavage, but considerable differences in their domain organization and quaternary architecture, facilitating comparisons between distinct Type IIS enzymes.
59 BASIC BIOLOGICAL SCIENCES↗
Elucidating the Structure of the Eu‐EDTA Complex in Solution at Various Protonation States
Abstract Ethylenediaminetetraacetic acid (EDTA), which has two amine and four carboxylate protonation sites, forms stable complexes with lanthanide ions. This work analyzes the coordination structure, in atomic resolution, of the Eu 3+ ion complexed with EDTA in all its protonation states in aqueous solution. Eu‐EDTA complexes were modeled using classical molecular dynamics (MD) simulations using force field parameters optimized with ab initio molecular dynamics (AIMD) simulations. Structures from the MD simulations were used to predict extended X‐ray absorption fine structure (EXAFS) spectra and compared with EXAFS measurements of the Eu 3+ aqua ion and Eu‐EDTA complexes at pH 3 and 11. This work details how Eu‐EDTA complex coordination structures change with increasing protonation of the EDTA ligand in the complex, from the tightly bound unprotonated complex to the unbinding of the fully protonated EDTA ligand from the Eu 3+ ion as both become solvated by water. Agreement between predicted and measured EXAFS spectra supports the findings from simulation.
Chemistry↗
A Stochastic Quasi-Newton Method in the Absence of Common Random Numbers
We present Q-SASS, a quasi-Newton method for unconstrained stochastic optimization that does not rely on common random numbers. Most existing quasi-Newton approaches leverage common random numbers to construct second-order updates. However, motivated by challenges in variational quantum algorithms—where such coordination is not possible—we consider the setting in which function values and gradients are accessible only through noisy probabilistic zeroth- and first-order oracles, and no common random numbers can be exploited. We derive high-probability tail bounds on the iteration complexity of our algorithm for nonconvex, convex, and strongly convex (more generally, those satisfying the PL condition) objective functions. Finally, we demonstrate the empirical benefits of our quasi-Newton updating scheme on both synthetic and quantum chemistry problems.
Complexity bound↗
A log-barrier Newton-CG method for bound constrained optimization with complexity guarantees
Abstract We describe an algorithm based on a logarithmic barrier function, Newton’s method and linear conjugate gradients that seeks an approximate minimizer of a smooth function over the non-negative orthant. We develop a bound on the complexity of the approach, stated in terms of the required accuracy and the cost of a single gradient evaluation of the objective function and/or a matrix-vector multiplication involving the Hessian of the objective. The approach can be implemented without explicit calculation or storage of the Hessian.
O’Neill, Michael↗
Testing Classical Properties from Quantum Data
Many properties of Boolean functions can be tested far more efficiently than the function itself can be learned. However, this dramatic advantage often disappears when testers are limited to random samples of ƒ instead of adaptively chosen queries to f. In this work we investigate the quantum version of this restriction: quantum algorithms that test properties of a Boolean function f solely from copies of either the function state |ƒ⟩ ∝ ∑ x |x, ƒ(x)⟩ or the phase state |(-1) ƒ ⟩ ∝ ∑ x (-1) ƒ(x) |x⟩. For monotonicity, symmetry, and triangle-freeness, we show passive quantum testers are unboundedly or super-polynomially better than their classical passive testing counterparts. They are competitive with classic query -based testers in each case. Our new testers use techniques beyond quantum Fourier sampling, and it turns out this is necessary: we show a certain class of bent functions can be tested from 𝒪(1) function states but has a sample complexity lower bound of 2 Ω(n) for any tester relying exclusively on Fourier and classical samples. Our passive quantum testers are competitive with classical query -based testers, but this isn't universal: we exhibit a testing problem that can be solved from 𝒪(1) classical queries but requires Ω(2 n/2 ) function state copies. The Forrelation problem provides a separation of the same magnitude in the opposite direction, so we conclude that quantum data and classical queries are "maximally incomparable" resources for testing. We also begin the study of lower bounds for testing from quantum data. For quantum monotonicity testing, we prove that the ensembles of [Goldreich et al., 2000; Black, 2024], which give exponential lower bounds for classical sample-based testing, do not yield any nontrivial lower bounds for testing from quantum data. New insights specific to quantum data will be required for proving copy complexity lower bounds for testing in this model.
Boolean Functions↗
Charged Bosons Made of Fermions in Bilayer Structures with Strong Metallic Screening
Two-dimensional monolayer structures of transition metal dichalogenides (TMDs) have been shown to allow many higher-order excitonic bound states, including trions (charged excitons), biexcitons (excitonic molecules), and charged biexcitons. Here, we report here experimental evidence and the theoretical basis for a new bound excitonic complex, consisting of two free carriers bound to an exciton in a bilayer structure. Our experimental measurements on structures made using two different materials show a new spectral line at the predicted energy with two different TMD materials (MoSe 2 and WSe 2 ) with both n- and p-doping, if and only if all the required theoretical conditions for this complex are fulfilled, in particular, only in the presence of a parallel metal layer that significantly screens the repulsive interaction between the like-charge carriers. Because these four-carrier bound states are charged bosons, they could eventually be the basis for a new path to superconductivity without Cooper pairing.
75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗
Non-destructive simulation of node defects in additively manufactured lattice structures
Additive Manufacturing (AM), commonly referred to as 3D printing, offers the ability to not only fabricate geometrically complex lattice structures but parts in which lattice topologies in-fill volumes bounded by complex surface geometries. However, current AM processes produce defects on the strut and node elements which make up the lattice structure. This creates an inherent difference between the as-designed and as-fabricated geometries, which negatively affects predictions (via numerical simulation) of the lattice’s mechanical performance. Although experimental and numerical analysis of an AM lattice’s bulk structure, unit cell and struts have been performed, there exists almost no research data on the mechanical response of the individual as-manufactured lattice node elements. Here we propose a methodology that, for the first time, allows non-destructive quantification of the mechanical response of node elements within an as-manufactured lattice structure. A custom-developed tool is used to extract and classify each individual node geometry from micro-computed tomography scans of an AM fabricated lattice. Voxel-based finite element meshes are generated for numerical simulation and the mechanical response distribution is compared to that of the idealised computer-aided design model. The method demonstrates compatibility with Uncertainty Quantification methods that provide opportunities for efficient prediction of a population of nodal responses from sampled data. Overall, the non-destructive and automated nature of the node extraction and response evaluation is promising for its application in qualification and certification of additively manufactured lattice structures.
36 MATERIALS SCIENCE↗
Near-optimal ground state preparation
Preparing the ground state of a given Hamiltonian and estimating its ground energy are important but computationally hard tasks. However, given some additional information, these problems can be solved efficiently on a quantum computer. We assume that an initial state with non-trivial overlap with the ground state can be efficiently prepared, and the spectral gap between the ground energy and the first excited energy is bounded from below. With these assumptions we design an algorithm that prepares the ground state when an upper bound of the ground energy is known, whose runtime has a logarithmic dependence on the inverse error. When such an upper bound is not known, we propose a hybrid quantum-classical algorithm to estimate the ground energy, where the dependence of the number of queries to the initial state on the desired precision is exponentially improved compared to the current state-of-the-art algorithm proposed in [Ge et al. 2019]. These two algorithms can then be combined to prepare a ground state without knowing an upper bound of the ground energy. We also prove that our algorithms reach the complexity lower bounds by applying it to the unstructured search problem and the quantum approximate counting problem.
97 MATHEMATICS AND COMPUTING↗
Molecular model of TFIIH recruitment to the transcription-coupled repair machinery
Transcription-coupled repair (TCR) is a vital nucleotide excision repair sub-pathway that removes DNA lesions from actively transcribed DNA strands. Binding of CSB to lesion-stalled RNA Polymerase II (Pol II) initiates TCR by triggering the recruitment of downstream repair factors. Yet it remains unknown how transcription factor IIH (TFIIH) is recruited to the intact TCR complex. Combining existing structural data with AlphaFold predictions, we build an integrative model of the initial TFIIH-bound TCR complex. We show how TFIIH can be first recruited in an open repair-inhibited conformation, which requires subsequent CAK module removal and conformational closure to process damaged DNA. In our model, CSB, CSA, UVSSA, elongation factor 1 (ELOF1), and specific Pol II and UVSSA-bound ubiquitin moieties come together to provide interaction interfaces needed for TFIIH recruitment. STK19 acts as a linchpin of the assembly, orienting the incoming TFIIH and bridging Pol II to core TCR factors and DNA. Molecular simulations of the TCR-associated CRL4CSA ubiquitin ligase complex unveil the interplay of segmental DDB1 flexibility, continuous Cullin4A flexibility, and the key role of ELOF1 for Pol II ubiquitination that enables TCR. Collectively, these findings elucidate the coordinated assembly of repair proteins in early TCR.
Paul, Tanmoy↗
Theoretical study of the HCS + –H 2 van der Waals complex: potential energy surface, rovibrational bound states, and rotationally inelastic collisional cross sections
An accurate ground-state intermolecular potential energy surface (PES) was calculated for the HCS + –H 2 complex. The surface was constructed from 3023 ab initio energies, computed with explicitly correlated coupled-cluster theory, CCSD(T)-F12b, with extrapolation to the complete basis set limit (VTZ-F12/VQZ-F12). The new 4D PES was used to compute rovibrational energies, rota- tional constants, and close-coupling quantum scattering calculations at low collision energies. A symmetry-adapted Lanczos algorithm was used to variationally compute the low-lying rovibrational bound states. Rotational constants for states of two isomers were determined from the energy levels and reported in hopes of motivating experiments. The rotationally inelastic state-to-state cross sections of HCS + by collision with para- and ortho-H 2 were computed and compared, and trends and propensities are discussed.
74 ATOMIC AND MOLECULAR PHYSICS↗
Mechanistic manifold in a hemoprotein-catalyzed cyclopropanation reaction with diazoketone
Abstract Hemoproteins have recently emerged as promising biocatalysts for new-to-nature carbene transfer reactions. However, mechanistic understanding of the interplay between productive and unproductive pathways in these processes is limited. Using spectroscopic, structural, and computational methods, we investigate the mechanism of a myoglobin-catalyzed cyclopropanation reaction with diazoketones. These studies shed light on the nature and kinetics of key catalytic steps in this reaction, including the formation of an early heme-bound diazo complex intermediate, the rate-determining nature of carbene formation, and the cyclopropanation mechanism. Our analyses further reveal the existence of a complex mechanistic manifold for this reaction that includes a competing pathway resulting in the formation of an N-bound carbene adduct of the heme cofactor, which was isolated and characterized by X-ray crystallography, UV-Vis, and Mössbauer spectroscopy. This species can regenerate the active biocatalyst, constituting a non-productive, yet non-destructive detour from the main catalytic cycle. These findings offer a valuable framework for both mechanistic analysis and design of hemoprotein-catalyzed carbene transfer reactions.
59 BASIC BIOLOGICAL SCIENCES↗
$CP$ violation from $τ, t$ and $b$ dimension-6 Yukawa couplings — interplay of baryogenesis, EDM and Higgs physics
We explore the implications of the Standard Model effective field theory (SMEFT) with dimension-six terms involving the Higgs boson and third-generation fermion fields on the rate of Higgs boson production and decay into fermions, on the electric dipole moments (EDMs) of the electron, and on the baryon asymmetry of the Universe. We study the consequences of allowing these additional terms for each flavor separately and for combinations of two flavors. We find that a complex $\tau$ Yukawa coupling can account for the observed baryon asymmetry $Y_B^{\rm obs}$ within current LHC and EDM bounds. A complex $b$ ($t$) Yukawa coupling can account for $4\%$ ($2\%$) of $Y_B^{\rm obs}$, whereas a combination of the two can reach $12\%$. Combining $\tau$ with either $t$ or $b$ enlarges the viable parameter space owing to cancellations in the EDM and in either Higgs production times decay or the total Higgs width, respectively. Interestingly, in such a scenario there exists a region in parameter space where the SMEFT contributions to the electron EDM cancel and collider signal strengths are precisely SM-like, while producing sufficient baryon asymmetry. Measuring $CP$ violation in Higgs decays to $\tau$ leptons is the smoking gun for this scenario.
72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
Arsenic stress triggers active exudation of arsenic–phytochelatin complexes from Lupinus albus roots
Abstract Arsenic (As) contamination of soils threatens the health of millions globally through accumulation in crops. While plants detoxify As via phytochelatin (PC) complexation and efflux of arsenite from roots, arsenite efflux mechanisms are not fully understood. Here, white lupin (Lupinus albus) was grown in semi-hydroponics, and exudation of glutathione (GSH) derivatives and PCs in response to As was measured using LC-MS/MS. Inhibiting synthesis of the PC precursor GSH with l-buthionine sulfoximine (BSO) or ABC transporters with vanadate drastically reduced (>22%) GSH derivative and PC2 exudation, but not PC3 exudation. This was accompanied by As hypersensitivity in plants treated with BSO and moderate sensitivity with vanadate treatment. Investigating As–PC complexation revealed two distinct As–PC complexes, As bound to GSH and PC2 (GS–As–PC2) and As bound to PC3 (As–PC3), in exudates of As-treated lupin plants. Vanadate inhibited As–PC exudation, while BSO inhibited both the synthesis and exudation of As–PC complexes. These results demonstrate a role for GSH derivatives and PC exudation in lupin As tolerance and reveal As–PC exudation as a new potential mechanism contributing to active As efflux in plants. Overall, this study uncovers insights into rhizosphere As detoxification with potential to help mitigate pollution and reduce As accumulation in crops.
Plant Sciences↗
A unified understanding of minimum lattice thermal conductivity
Here, we propose a first-principles model of minimum lattice thermal conductivity ($κ^{min}_L$) based on a unified theoretical treatment of thermal transport in crystals and glasses. We apply this model to thousands of inorganic compounds and find a universal behavior of $κ^{min}_L$ in crystals in the high-temperature limit: The isotropically averaged $κ^{min}_L$ is independent of structural complexity and bounded within a range from ~0.1 to ~2.6 W/(m K), in striking contrast to the conventional phonon gas model which predicts no lower bound. We unveil the underlying physics by showing that for a given parent compound, $κ^{min}_L$ is bounded from below by a value that is approximately insensitive to disorder, but the relative importance of different heat transport channels (phonon gas versus diffuson) depends strongly on the degree of disorder. Moreover, we propose that the diffuson-dominated $κ^{min}_L$ in complex and disordered compounds might be effectively approximated by the phonon gas model for an ordered compound by averaging out disorder and applying phonon unfolding. With these insights, we further bridge the knowledge gap between our model and the well-known Cahill–Watson–Pohl (CWP) model, rationalizing the successes and limitations of the CWP model in the absence of heat transfer mediated by diffusons. Finally, we construct graph network and random forest machine learning models to extend our predictions to all compounds within the Inorganic Crystal Structure Database (ICSD), which were validated against thermoelectric materials possessing experimentally measured ultralow κ L . Our work offers a unified understanding of $κ^{min}_L$, which can guide the rational engineering of materials to achieve .
42 ENGINEERING↗
Anatomy of the electroweak phase transition for dark sector induced baryogenesis
We investigate the electroweak phase transition patterns for a recently proposed baryogenesis model with CP violation originated in the dark sector. The model includes a complex scalar singlet-Higgs boson portal, a U(1) l gauge lepton symmetry with a Z ' gauge boson portal and a fermionic dark matter particle. We find a novel thermal history of the scalar sector, featuring a Z 2 breaking singlet vacuum in the early Universe driven by a dark Yukawa coupling, that induces a one-step strongly first order electroweak phase transition. We explore the parameter space that generates the observed matter-antimatter asymmetry and dark matter relic abundance, while being consistent with constraints from electric dipole moment, collider searches, and dark matter direct detection bounds. The complex singlet can be produced via the Higgs portal and decays into Standard Model particles after traveling a certain distance. We explore the reach for long-lived singlet scalars at the 13 TeV Large Hadron Collider with \( \mathcal{L} \) = 139 fb - 1 and show its impact on the parameter space of the model. Setting aside currently unresolved theoretical uncertainties, we estimate the gravitational wave signatures detectable at future observatories.
72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
pH Homeostasis and Sodium Ion Pumping by Multiple Resistance and pH Antiporters in Pyrococcus furiosus
Multiple Resistance and pH (Mrp) antiporters are seven-subunit complexes that couple transport of ions across the membrane in response to a proton motive force (PMF) and have various physiological roles, including sodium ion sensing and pH homeostasis. The hyperthermophilic archaeon Pyrococcus furiosus contains three copies of Mrp encoding genes in its genome. Two are found as integral components of two respiratory complexes, membrane bound hydrogenase (MBH) and the membrane bound sulfane sulfur reductase (MBS) that couple redox activity to sodium translocation, while the third copy is a stand-alone Mrp. Sequence alignments show that this Mrp does not contain an energy-input (PMF) module but contains all other predicted functional Mrp domains. The P. furiosus Mrp deletion strain exhibits no significant changes in optimal pH or sodium ion concentration for growth but is more sensitive to medium acidification during growth. Cell suspension hydrogen gas production assays using the deletion strain show that this Mrp uses sodium as the coupling ion. Mrp likely maintains cytoplasmic pH by exchanging protons inside the cell for extracellular sodium ions. Deletion of the MBH sodium-translocating module demonstrates that hydrogen gas production is uncoupled from ion pumping and provides insights into the evolution of this Mrp-containing respiratory complex.
59 BASIC BIOLOGICAL SCIENCES↗
Synthesis and thermodynamics of uranium-incorporated α-Fe 2 O 3 nanoparticles
Hematite nanoparticles were synthesized with U(VI) in circumneutral water through a coprecipitation and hydrothermal treatment process. XRD, TEM, and EXAFS analyses reveal that uranium may aggregate along grain boundaries and occupy Fe sites within hematite. The described synthesis method produces crystalline, single-phase iron oxide nanoparticles absent of surface-bound uranyl complexes. EXAFS data were comparable to spectra from existing studies whose syntheses were more representative of naturally occurring, extended aging processes. Herein this work provides and validates an accelerated method of synthesizing uranium-immobilized iron oxide nanoparticles for further mechanistic studies. High temperature oxide melt solution calorimetry measurements were performed to calculate the thermodynamic stability of uranium-incorporated iron oxide nanoparticles. Increasing uranium content within hematite resulted in more positive formation enthalpies. Standard formation enthalpies of U x Fe 2–2x O 3 were as high as 76.88 ± 2.83 kJ/mol relative to their binary oxides, or -764.04 ± 3.74 kJ/mol relative to their constituent elements, at x = 0.037. Data on the thermodynamic stability of uranium retention pathways may assist in predicting waste uranyl remobilization, as well as in developing more effective methods to retain uranium captured from aqueous environments.
36 MATERIALS SCIENCE↗