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Detection of Lipid-Bound Bacteriorhodopsin Trimer Complex Directly from Purple Membrane by Native Mass Spectrometry
Not provided.
Bounding Computation and Complexity for Reactive Transport on Supercomputers: A Perspective from Nuclear Waste Repository Performance Assessment.
Abstract not provided.
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.
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.
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.
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.
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.
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.
Cross-linking staphylococcal enterotoxin A bound to major histocompatibility complex class I is required for TNF-alpha secretion
The mechanism of how superantigens function to activate cells has been linked to their ability to bind and cross-link the major histocompatibility complex class II (MHCII) molecule. Cells that lack the MHCII molecule also respond to superantigens, however, with much less efficiency. Therefore, the purpose of this study was to confirm that staphylococcal enterotoxin A (SEA) could bind the MHCI molecule and to test the hypothesis that cross-linking SEA bound to MHCII-deficient macrophages would induce a more robust cytokine response than without cross-linking. We used a capture enzyme-linked immunosorbent assay and an immunprecipitation assay to directly demonstrate that MHCI molecules bind SEA. Directly cross-linking MHCI using monoclonal antibodies or cross-linking bound SEA with an anti-SEA antibody or biotinylated SEA with avidin increased TNF-alpha and IL-6 secretion by MHCII(-/-) macrophages. The induction of a vigorous macrophage cytokine response by SEA/anti-SEA cross-linking of MHCI offers a mechanism to explain how MHCI could play an important role in superantigen-mediated pathogenesis. Copyright 1999 Academic Press.
Self-deactivation of water vapor - Role of the dimer
A phenomenological multiple-relaxation theory of the deactivation rate constant for the nu-2 (1 - 0) bending mode of water vapor is presented which incorporates the role not only of the excited monomer but also of the bound molecular complex, in particular the dimer. The deactivation takes place by means of three parallel processes: (1) collisional deexcitation of the excited monomer, (2) a two-step reaction involving association and spontaneous redissociation of an H2O collision complex, and (3) spontaneous dissociation of the stably bound H2O dimer. Oxygen, but not nitrogen or argon, serves as an effective chaperon for the formation of the activated complex. This observation explains the impurity dependence of the self-deactivation rate constant of water vapor. Analysis of an ultrasonic absorption peak based on the third process yields values for the standard entropy and enthalpy of dissociation of the stably bound H2O dimer.
A lower bound on the minimum Euclidean distance of trellis-coded modulation schemes
A lower bound on the minimum free Euclidean distance of trellis-coded modulation (TCM) is derived that guarantees the existence of good TCM codes of any complexity. The bound is used to compare trellis codes combined with phase-shift keying, pulse amplitude modulation, and quadrature amplitude-shift keying modulation. This random coding bound is the first lower bound on the free distance of trellis codes, is tighter than any upper bound for large constraint lengths, and predicts the asymptotic performance of TCM when the complexity of the code becomes large. The bound can be used with any code rate and any modulation scheme and shows that the free distance increases linearly with the constraint length for large values of the constraint length.
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.
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.
Three measures of decoder complexity
Error correcting decoders, investigating lower bounds on three complexity measures to meet error probability requirement
Monitoring Airspace Complexity and Determining Contributing Factors
The national airspace has evolved over many years to accommodate increased traffic demand while simultaneously maintaining air travel as one of the safest forms of transportation. One of the reasons for this success is the ability of the air traffic control system and the operators to adapt and accommodate to situations that routinely disrupt normal operations. These situations may include: adverse weather, delays, early arrivals, equipment outages, and other factors that are outside the operators’ ability to control. These factors can lead to states where automation is unable to properly handle these issues, and therefore air traffic controllers and pilots have to intervene — ultimately increasing communication between operators resulting in higher workload. As controller workload increases to handle sub-optimal operating conditions, complexity increases. This is because, under these conditions humans are required to make tactical decisions in response to external factors. This results in a departure from the original strategic plan where operations would be more efficiently managed. Human operators manage airspace complexity under rigid regulations but in a constantly changing environment. The airspace is divided into sectors and the number of aircraft assigned to each controller is limited for safe handling. Some prior studies devised airspace complexity metrics in commercial aviation and related these metrics to controller workload. The upper bounds on the system load are pre-determined. Such bounds on complexity make for a safe system, but the system cannot scale and adapt to autonomous, dense, and heterogeneous traffic — including the many types of Unmanned Aerial Vehicles (UAVs) envisioned to be added to the operations. We hypothesize that, as traffic density and heterogeneity grow, and other key metrics change, there will be phase transitions at which the way traffic should be managed changes significantly. We offer a method for in-time detection of contributing factors that lead to phase transitions, characterized by increased complexity. To the best of our knowledge, there is no tool similar to ours that identifies such contributing factors or precursor patterns.
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.
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.