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Abstract Summary pKa values of ionizable residues and isoelectric points of proteins provide valuable local and global insights about their structure and function. These properties can be estimated with reasonably good accuracy using Poisson–Boltzmann and Monte Carlo calculations at a considerable computational cost (from some minutes to several hours). pKPDB is a database of over 12 M theoretical pKa values calculated over 120k protein structures deposited in the Protein Data Bank. By providing precomputed pKa and pI values, users can retrieve results instantaneously for their protein(s) of interest while also saving countless hours and resources that would be spent on repeated calculations. Furthermore, there is an ever-growing imbalance between experimental pKa and pI values and the number of resolved structures. This database will complement the experimental and computational data already available and can also provide crucial information regarding buried residues that are under-represented in experimental measurements. Availability and implementation Gzipped csv files containing p Ka and isoelectric point values can be downloaded from https://pypka.org/pKPDB. To query a single PDB code please use the PypKa free server at https://pypka.org. The pKPDB source code can be found at https://github.com/mms-fcul/pKPDB. Supplementary information Supplementary data are available at Bioinformatics online.
ABSTRACT We explore two widely used empirical models for the galaxy–halo connection, subhalo abundance matching (SHAM) and the halo occupation distribution (HOD), and compare them with the hydrodynamical simulation IllustrisTNG (TNG) for multiple statistics quantifying the galaxy distribution at $n_{\rm gal}\approx 1.3\times 10^{-3}\, ({\rm Mpc}\,h^{-1})^{-3}$. We observe that in their most straightforward implementations, both models fail to reproduce the two-point clustering measured in TNG. We find that SHAM models that use the relaxation velocity, Vrelax, and the peak velocity, Vpeak, perform best, and match the clustering reasonably well, although neither captures adequately the one-halo clustering. Splitting the total sample into sub-populations, we discover that SHAM overpredicts the clustering of high-mass, blue, star-forming, and late-forming galaxies and underpredicts that of low-mass, red, quiescent, and early-forming galaxies. We also study various baryonic effects, finding that subhaloes in the dark-matter-only simulation have consistently higher values of their SHAM-proxy properties than their full-physics counterparts. We then consider a 2D implementation of the HOD model augmented with a secondary parameter (environment, velocity anisotropy, σ2Rhalf-mass, and total potential) tuned so as to match the two-point clustering of the IllustrisTNG galaxies on large scales. We analyse these galaxy populations adopting alternative statistical tools such as galaxy–galaxy lensing, void–galaxy cross-correlations, and cumulants of the density field, finding that the hydrodynamical galaxy distribution disfavours σ2Rhalf-mass and the total potential as secondary parameters, while the environment and velocity anisotropy samples are consistent with full physics across all statistical probes examined. Our results demonstrate the power of examining multiple statistics for determining the secondary parameters that are vital for understanding the galaxy–halo connection.
Abstract Protein activity, abundance, and stability can be regulated by post-translational modification including ubiquitination. Ubiquitination is conserved among eukaryotes and plays a central role in modulating cellular function; yet, we lack comprehensive catalogs of proteins that are modified by ubiquitin in plants. In this study, we describe an antibody-based approach to enrich ubiquitinated peptides coupled with isobaric labeling to enable quantification of up to 18-multiplexed samples. This approach identified 17,940 ubiquitinated lysine sites arising from 6,453 proteins from Arabidopsis (Arabidopsis thaliana) primary roots, seedlings, and rosette leaves. Gene ontology analysis indicated that ubiquitinated proteins are associated with numerous biological processes including hormone signaling, plant defense, protein homeostasis, and metabolism. We determined ubiquitinated lysine residues that directly regulate the stability of three transcription factors, CRYPTOCHROME-INTERACTING BASIC-HELIX-LOOP-HELIX 1 (CIB1), CIB1 LIKE PROTEIN 2 (CIL2), and SENSITIVE TO PROTON RHIZOTOXICITY1 (STOP1) using in vivo degradation assays. Furthermore, codon mutation of CIB1 to create a K166R conversion to prevent ubiquitination, via CRISPR/Cas9-derived adenosine base editing, led to an early flowering phenotype and increased expression of FLOWERING LOCUS T (FT). These comprehensive site-level ubiquitinome profiles provide a wealth of data for future functional studies related to modulation of biological processes mediated by this post-translational modification in plants.
Phenomenological calculations of the properties of dense matter, such as relativistic mean-field theories, represent a pathway to predicting the microscopic and macroscopic properties of neutron stars. However, such theories do not generically have well-controlled uncertainties and may break down within neutron stars. To faithfully represent the uncertainty in this breakdown scale, we develop a hybrid representation of the dense-matter equation of state, which assumes the form of a relativistic mean-field theory at low densities, while remaining agnostic to any nuclear theory at high densities. To achieve this, we use a nonparametric equation of state model to incorporate the correlations of the underlying relativistic mean-field theory equation of state at low pressures and transition to more flexible correlations above some chosen pressure scale. We perform astrophysical inference under various choices of the transition pressure between the theory-informed and theory-agnostic models. Here, we further study whether the chosen relativistic mean-field theory breaks down above some particular pressure and find no such evidence. Using simulated data for future astrophysical observations at about two-to-three times the precision of current constraints, we show that our method can identify the breakdown pressure associated with a potential strong phase transition.
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This article solves two major tasks that frequently arise in the theory of electron collisions with a target molecular cation. First, it extends the energy-dependent frame transformation (EDFT) treatment, which is needed to map fixed-nuclei electron-molecule scattering matrices into an energy-dependent laboratory-frame scattering matrix with vibrational channel indices. The EDFT mapping can now be carried out even when the target molecule possesses multiple low-energy potential curves, significantly transcending previous applications. Second, it implements a method to extract the rest of the full laboratory-frame scattering matrix, i.e., the columns and rows describing input and/or output dissociation channels. The treatment is benchmarked in this article against the essentially exact solution of a refined two-dimensional model of the singlet gerade Σ symmetry of H 2 . Our tests demonstrate that the theory accurately maps fixed-nuclei scattering information, of the type provided by existing electron-molecule computer codes, into a laboratory-frame scattering matrix that includes both ionization and dissociation. Furthermore, this treatment can provide a general framework applicable to a broad class of electron collision processes involving diatomic target ions, suitable for an accurate description of challenging processes such as dissociative recombination.
Photonic addressing of superconducting circuits has been proposed to overcome wiring complexity and heat-load challenges. However, such superconducting-photonic links suffer from an efficiency-noise trade-off that limits scalability. This trade-off arises because increasing power conversion efficiency entails reducing optical power, which makes the converted signal susceptible to shot noise. We analyze this trade-off and find that the laser-driven qubit gate infidelity scales inversely with the number of photons used. While methods such as nonlinear detection or squeezed light could mitigate this effect, we consider generating higher-frequency electrical signals, such as millimeter waves (100 GHz), using laser light. At these higher frequencies, circuits have higher operating temperatures and cooling power budgets and alleviate constraints posed by the trade-off. Therefore, we demonstrate an optically driven cryogenic millimeter-wave source with a maximum power efficiency of 8 ×10 −5 that can generate a maximum of 0.7 μW of 80 GHz power, with a 1200-thermal-photon equivalent of added noise at 4K. Using this source, we perform frequency-domain spectroscopy of superconducting NbTiN resonators at 80–90 GHz. Our results show a promising approach to lessen the efficiency-noise constraints on superconducting-photonic links, while leveraging the benefits of photonic signal delivery. Further optimization of power efficiency and noise at high frequencies could make scalable photonic control of superconducting qubits viable at temperatures exceeding 1K.
We establish, in the spirit of the Lieb-Schultz-Mattis theorem, lower bounds on the spectral degeneracy of quantum systems with higher (gaugelike) symmetries with rather generic physical boundary conditions in an arbitrary number of spatial dimensions. Contrary to applying twists or equivalent adiabatic operations, we exploit the effects of modified boundary conditions. We find that when a general choice of boundary geometry is immaterial in determining spectral degeneracies while approaching the thermodynamic limit, systems that exhibit rigid noncommuting gaugelike symmetries, such as the orbital compass model, must have an exponential (in the size of the boundary) degeneracy of each of their spectral levels.
The Hauser-Feshbach fission fragment decay model, HF 3 D, which calculates the statistical decay of fission fragments, has been expanded to include multichance fission, up to neutron incident energies of 20 MeV. The deterministic decay takes as input prescission quantities—fission probabilities and the average energy causing fission—and postscission quantities—yields in mass, charge, total kinetic energy, spin, and parity. From these fission fragment initial conditions, the full decay is followed through both prompt and delayed particle emissions, allowing for the calculation of prompt neutron and γ properties, such as multiplicity and energy distributions, both independent and cumulative fission yields, and delayed neutron observables. Here, we describe the implementation of multichance fission in the HF 3 D model, and show an example of prompt and delayed quantities beyond first-chance fission, using the example of neutron-induced fission on 235 U. This expansion represents significant progress in consistently modeling the emission of prompt and delayed particles from fissile systems.
Theoretical ab initio studies of resonances in the unbound 7 He nucleus are presented. We perform no-core shell-model calculations with NN interactions Daejeon16 and JISP16 and utilize the SS-HORSE method to calculate the S matrix for two-body channels n + 6 He and n + 6 He* with 6He respectively in the ground and excited 2 + states as well as for the four-body democratic decay channel 4 He + n + n + n. The resonant energies and widths are obtained by numerical location of the S-matrix poles. Here, we describe all experimentally known 7 He resonances and suggest an interpretation of an observed wide resonance of unknown spin-parity.
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We present a new version of the hadron interaction event generator SIBYLL. While the core ideas of the model have been preserved, the new version handles the production of baryon pairs and leading particles in a new way. In addition, production of charmed hadrons is included. Updates to the model are informed by high-precision measurements of the total and inelastic cross sections with the forward detectors at the LHC that constrain the extrapolation to ultrahigh energy. Minimum-bias measurements of particle spectra and multiplicities support the tuning of fragmentation parameters. This paper demonstrates the impact of these changes on air-shower observables such as X max and N μ , drawing comparisons with other contemporary cosmic-ray interaction models.
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The phase-space approach (PSA), which was originally introduced in Lacroix [] to describe neutrino flavor oscillations for interacting neutrinos emitted from stellar objects is extended to describe arbitrary numbers of neutrino beams. The PSA is based on mapping the quantum fluctuations into a statistical treatment by sampling initial conditions followed by independent mean-field evolution. A new method is proposed to perform this sampling that allows treating an arbitrary number of neutrinos in each neutrino beams. We validate the technique successfully and confirm its predictive power on several examples where a reference exact calculation is possible. We show that it can describe many-body effects, such as entanglement and dissipation induced by the interaction between neutrinos. Due to the complexity of the problem, exact solutions can only be calculated for rather limited cases, with a limited number of beams and/or neutrinos in each beam. The PSA approach considerably reduces the numerical cost and provides an efficient technique to accurately simulate arbitrary numbers of beams. Examples of PSA results are given here, including up to 200 beams with time-independent or time-dependent Hamiltonians. We anticipate that this approach will be useful to bridge exact microscopic techniques with more traditional transport theories used in neutrino oscillations. It will also provide important reference calculations for future quantum computer applications where other techniques are not applicable to classical computers. Published by the American Physical Society 2024
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