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At least 163 records · Page 9

The encapsulin from Thermotoga maritima is a flavoprotein with a symmetry matched ferritin-like cargo protein

Abstract Bacterial nanocompartments, also known as encapsulins, are an emerging class of protein-based ‘organelles’ found in bacteria and archaea. Encapsulins are virus-like icosahedral particles comprising a ~ 25–50 nm shell surrounding a specific cargo enzyme. Compartmentalization is thought to create a unique chemical environment to facilitate catalysis and isolate toxic intermediates. Many questions regarding nanocompartment structure–function remain unanswered, including how shell symmetry dictates cargo loading and to what extent the shell facilitates enzymatic activity. Here, we explore these questions using the model Thermotoga maritima nanocompartment known to encapsulate a redox-active ferritin-like protein. Biochemical analysis revealed the encapsulin shell to possess a flavin binding site located at the interface between capsomere subunits, suggesting the shell may play a direct and active role in the function of the encapsulated cargo. Furthermore, we used cryo-EM to show that cargo proteins use a form of symmetry-matching to facilitate encapsulation and define stoichiometry. In the case of the Thermotoga maritima encapsulin, the decameric cargo protein with fivefold symmetry preferentially binds to the pentameric-axis of the icosahedral shell. Taken together, these observations suggest the shell is not simply a passive barrier—it also plays a significant role in the structure and function of the cargo enzyme.

59 BASIC BIOLOGICAL SCIENCES↗

A method for correcting aspect solution errors in ROSAT HRI observations of compact sources

X-ray point sources observed with the ROSAT High Resolution Imager (HRI) often appear elongated over scales of approximately 5 sec-10 sec from the image core. This elongation has been attributed to errors in the attitude correction as the satellite is wobbled during the observations, and affects sources with both soft and hard X-ray spectra. In this paper, I report the results of an attempt to rid a high signal-to-noise observation of the soft X-ray point source HZ 43 of its characteristic elongation. I divided the observation into 181 separate images, each containing photons from only a small region on the detector through which the source passed during the satellite's wobble. By measuring the positions of the individual image centroids, I found clear evidence for systematic offsets from a common mean by up to approximately +/- 3 sec in both right ascension and declination as a function of phase in the satellite wobble. Shifting the subimages to a common center and then restacking them into a single image measurably improved the symmetry of the point-spread function. HRI observations are wobbled primarily to smooth out variations in the pixel-to-pixel sensitivity of the detector and also to extend the lifetime of the microchannel plates in the detector since these decay at a given location as a function of the number of photons detected. However, the elongations introduced by the aspect errors inhibit the identification of possible extended X-ray emission associated with sources such as pulsars and active galactic nuclei. In light of these results, I suggest that until the aspect errors are understood, observations of compact sources, where this effect may be important, should not be wobbled.

Morse, Jon A.↗

Postbuckling of laminated anisotropic panels

A two-part study of the buckling and postbuckling of laminated anisotropic plates with bending-extensional coupling is presented. The first part involves the development and application of a modified Rayleigh-Ritz analysis technique. Modifications made to the classical technique can be grouped into three areas. First, known symmetries of anisotropic panels are exploited in the selection of approximation functions. Second, a reduced basis technique based on these same symmetries is applied in the linear range. Finally, geometric boundary conditions are enforced via an exterior penalty function approach, rather than relying on choice of approximation functions to satisfy these boundary conditions. Numerical results are presented for both the linear and nonlinear range, with additional studies made to determine the effect of variation in penalty parameter and number of basis vectors. In the second part, six panels possessing anisotropy and bending-extensional coupling are tested. Detailed comparisons are made between experiment and finite element results in order to gain insight into the postbuckling and failure characteristics of such panels. The panels are constructed using two different lamination sequences, and panels with three different aspect ratios were constructed for each lamination sequence.

Jeffrey, Glenda L.↗

The cosmological bootstrap: inflationary correlators from symmetries and singularities

Scattering amplitudes at weak coupling are highly constrained by Lorentz invariance, locality and unitarity, and depend on model details only through coupling constants and the particle content of the theory. For example, four-particle amplitudes are analytic for contact interactions and have simple poles with appropriately positive residues for tree-level exchange. In this paper, we develop an understanding of inflationary correlators which parallels that of flat-space scattering amplitudes. Specifically, we study slow-roll inflation with weak couplings to extra massive particles, for which all correlation functions are controlled by an approximate conformal symmetry on the boundary of the spacetime. After systematically classifying all possible contact terms in de Sitter space, we derive an analytic expression for the four-point function of conformally coupled scalars mediated by the tree-level exchange of massive scalars. Conformal symmetry implies that the correlator satisfies a pair of differential equations with respect to spatial momenta, encoding bulk time evolution in purely boundary terms. The absence of unphysical singularities (and the correct normalization of physical ones) completely fixes this correlator. Moreover, a “spin-raising” operator relates it to the correlators associated with the exchange of particles with spin, while “weight-shifting” operators map it to the four-point function of massless scalars. We explain how these de Sitter four-point functions can be perturbed to obtain inflationary three-point functions. Using our formalism, we reproduce many classic results in the literature, such as the three-point function of slow-roll inflation, and provide a complete classification of all inflationary three- and four-point functions arising from weakly broken conformal symmetry. Remarkably, the inflationary bispectrum associated with the exchange of particles with arbitrary spin is completely characterized by the soft limit of the simplest scalar-exchange four-point function of conformally coupled scalars and a series of contact terms. Finally, we demonstrate that the inflationary correlators contain flat-space scattering amplitudes via a suitable analytic continuation of the external momenta, which can also be directly connected with the signals for particle production seen in the squeezed limit.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Efficient computation of N -point correlation functions in D dimensions

We present efficient algorithms for computing the N-point correlation functions (NPCFs) of random fields in arbitrary D-dimensional homogeneous and isotropic spaces. Such statistics appear throughout the physical sciences and provide a natural tool to describe stochastic processes. Typically, algorithms for computing the NPCF components have $\mathscr O$(n N ) complexity (for a dataset containing n particles); their application is thus computationally infeasible unless N is small. By projecting the statistic onto a suitably defined angular basis, we show that the estimators can be written in a separable form, with complexity $\mathscr O$(n 2 ) or $\mathscr O$(n g log n g ) if evaluated using a Fast Fourier Transform on a grid of size n g . Our decomposition is built upon the D-dimensional hyperspherical harmonics; these form a complete basis on the (D – 1) sphere and are intrinsically related to angular momentum operators. Concatenation of (N – 1) such harmonics gives states of definite combined angular momentum, forming a natural separable basis for the NPCF. As N and D grow, the number of basis components quickly becomes large, providing a practical limitation to this (and all other) approaches: However, the dimensionality is greatly reduced in the presence of symmetries; for example, isotropic correlation functions require only states of zero combined angular momentum. We provide a Julia package implementing our estimators and show how they can be applied to a variety of scenarios within cosmology and fluid dynamics. The efficiency of such estimators will allow higher-order correlators to become a standard tool in the analysis of random fields.

97 MATHEMATICS AND COMPUTING↗

Some aspects of the five-dimensional Lovelock black hole spacetime: Strong homotopy retract, perihelion precession and quasistationary levels

Highlights: • Some topological aspects are explored. • The perihelion precession is calculated. • The general Heun functions are applied to obtain analytical solutions. • The quasibound states and the radial wave eigenfunctions are obtained. In this work we explore some mathematical physics aspects of the spherically symmetric Lovelock black hole in high dimensions. Intended for this aim, we thoroughly consider the metric corresponding to the five-dimensional Lovelock black hole spacetime. We construct the strong retractions by the geodesic equations on the background under consideration. As a result, from the topological point of view, we construct the theory of strong homotopy retract, which will allow us, in principle, to better understand some of its suitable applications on astrophysics and cosmology, in particular, in the analysis of the spacetime singularities. We find the solutions of the equation of motion for both radial and angular coordinates, and then we describe the outer (“exterior”) and lower (“interior”) apparent horizons. Indeed, the outer apparent horizon is the last surface from which the light waves could still escape from the black hole. Thus, it is meaningful to analyze some physical phenomena related to quantum particles propagating outside the exterior apparent horizon, in particular, we discuss the quasistationary levels of scalar fields and their radial wave functions, which are given in terms of the general Heun functions. We also calculate the perihelion precession in this background.

71 CLASSICAL AND QUANTUM MECHANICS, GENERAL PHYSIC↗

Gauge constrained algorithm of variational discrete action theory at N = 3 for the multiorbital Hubbard model

The recently developed variational discrete action theory (VDAT) provides a systematic variational approach to the ground state of the quantum many-body problem, where the quality of the solution is controlled by an integer N, and increasing N monotonically approaches the exact solution. VDAT can be exactly evaluated in the d = ∞ multiorbital Hubbard model using the self-consistent canonical discrete action theory (SCDA), which requires a self-consistency condition for the integer time Green's functions. Previous work demonstrates that N = 3 accurately captures multiorbital Mott/Hund physics at a cost similar to the Gutzwiller approximation. Here we employ a gauge constraint to automatically satisfy the self-consistency condition of the SCDA at N = 3, yielding an even more efficient algorithm with enhanced numerical stability. We derive closed form expressions of the gauge constrained algorithm for the multiorbital Hubbard model with general density-density interactions, allowing VDAT at N = 3 to be straightforwardly applied to the seven-orbital Hubbard model. We present results and a performance analysis using N = 2 and N = 3 for the SU⁡(2⁢N orb ) Hubbard model in d = ∞ with N orb = 2–8, and compare to numerically exact dynamical mean-field theory solutions where available. Finally, the developments in this work will greatly facilitate the application of VDAT at N = 3 to strongly correlated electron materials.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Crystallization of polarons through charge and spin ordering transitions in 1T-TaS 2

The interaction of electrons with the lattice in metals can lead to reduction of their kinetic energy to the point where they may form heavy, dressed quasiparticles—polarons. Unfortunately, polaronic lattice distortions are difficult to distinguish from more conventional charge- and spin-ordering phenomena at low temperatures. Here we present a study of local symmetry breaking of the lattice structure on the picosecond timescale in the prototype layered dichalcogenide Mott insulator 1T-TaS 2 using X-ray pair-distribution function measurements. We clearly identify symmetry-breaking polaronic lattice distortions at temperatures well above the ordered phases, and record the evolution of broken symmetry states from 915 K to 15 K. The data imply that charge ordering is driven by polaron crystallization into a Wigner crystal-like state, rather than Fermi surface nesting or conventional electron-phonon coupling. At intermediate temperatures the local lattice distortions are found to be consistent with a quantum spin liquid state.

36 MATERIALS SCIENCE↗

The connection between nonzero density and spontaneous symmetry breaking for interacting scalars

We consider U(1)-symmetric scalar quantum field theories at zero temperature. At nonzero charge densities, the ground state of these systems is usually assumed to be a superfluid phase, in which the global symmetry is spontaneously broken along with Lorentz boosts and time translations. We show that, in d > 2 spacetime dimensions, this expectation is always realized at one loop for arbitrary non-derivative interactions, confirming that the physically distinct phenomena of nonzero charge density and spontaneous symmetry breaking occur simultaneously in these systems. We quantify this result by deriving universal scaling relations for the symmetry breaking scale as a function of the charge density, at low and high density. Moreover, we show that the critical value of μ above which a nonzero density develops coincides with the pole mass in the unbroken, Poincaré invariant vacuum of the theory. The same conclusions hold non-perturbatively for an O(N) theory with quartic interactions in d = 3 and 4, at leading order in the 1/N expansion. We derive these results by computing analytically the zero-temperature, finite-μ one-loop effective potential, paying special attention to subtle points related to the iε terms. We check our results against the one-loop low-energy effective action for the superfluid phonons in λΦ 4 theory in d = 4 previously derived by Joyce and ourselves, which we further generalize to arbitrary potential interactions and arbitrary dimensions. As a byproduct, we find analytically the one-loop scaling dimension of the lightest charge-n operator for the λΦ 6 conformal superfluid in d = 3, at leading order in 1/n, reproducing a numerical result of Badel et al. For a λΦ 4 superfluid in d = 4, we also reproduce the Lee-Huang-Yang relation and compute relativistic corrections to it. Finally, we discuss possible extensions of our results beyond perturbation theory.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Iterated projected position algorithm for constructing exponentially localized generalized Wannier functions for periodic and nonperiodic insulators in two dimensions and higher

Localized bases play an important role in understanding electronic structure. In periodic insulators, a natural choice of localized basis is given by the Wannier functions which depend on a choice of unitary transform known as a gauge transformation. Over the past few decades, there have been many works that have focused on optimizing the choice of the gauge so that the corresponding Wannier functions are maximally localized or reflect some symmetry of the underlying system. In this work, we consider fully nonperiodic materials where the usual Wannier functions are not well defined and gauge optimization is impractical. To tackle the problem of calculating exponentially localized generalized Wannier functions in both periodic and nonperiodic systems, we discuss the ‘iterated projected position (IPP)” algorithm. Here, the IPP algorithm is based on matrix diagonalization and therefore unlike optimization-based approaches, it does not require initialization and cannot get stuck at a local minimum. Furthermore, the IPP algorithm is guaranteed by a rigorous analysis to produce exponentially localized functions under certain mild assumptions. We numerically demonstrate that the IPP algorithm can be used to calculate exponentially localized bases for the Haldane model, the Kane-Mele model (in both Z 2 invariant even and Z 2 invariant odd phases), and the p x + ip y model on a quasicrystal lattice.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗

Large Magnetoresistance in Scandium Nitride Magnetic Tunnel Junctions Using First Principles

Abstract The state‐of‐the‐art magnetic tunnel junction, a cornerstone of spintronic devices and circuits, uses a magnesium oxide tunnel barrier that provides a uniquely large tunnel magnetoresistance at room temperature. However, the wide bandgap and band alignment of magnesium oxide‐iron systems increases the resistance‐area product and creates variability and breakdown challenges. Here, the authors study using first principles narrower‐bandgap scandium nitride (ScN) transport properties in magnetoresistive junctions in comparison to magnesium oxide. The results show a high magnetoresistance in Fe/ScN/Fe via Δ 1 and symmetry filtering with low wave function decay rates, suggesting scandium nitride could be a new barrier material for spintronic devices.

Karki, Suyogya↗

In Silico Screening of CO 2 –Dipeptide Interactions for Bioinspired Carbon Capture

Carbon capture, sequestration and utilization offers a viable solution for reducing the total amount of atmospheric CO 2 concentrations. On an industrial scale, amine-based solvents are extensively employed for CO 2 capture through chemisorption. Nevertheless, this method is marked by the high cost associated with solvent regeneration, high vapor pressure, and the corrosive and toxic attributes of by-products, such as nitrosamines. An alternative approach is the biomimicry of sustainable materials that have strong affinity and selectivity for CO 2 . Bioinspired approaches, such as those based on naturally occurring amino acids, have been proposed for direct air capture methodologies. In this study, we present a database consisting of 960 dipeptide molecular structures, composed of the 20 naturally occurring amino acids. Furthermore, those structures were analyzed with a novel computational workflow presented in this work that considers certain interaction sites that determine CO 2 affinity. Density functional theory (DFT) and symmetry-adapted perturbation theory (SAPT) computations were performed for the calculation of CO 2 interaction energies, which allowed to limit our search space to 400 unique dipeptide structures. Using this computational workflow, we provide statistical insights into dipeptides and their affinity for CO 2 binding, as well as design principles that can further enhance CO 2 capture through cooperative binding.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Joint thrust and TMD resummation in electron-positron and electron-proton collisions

In this work, we present the framework for obtaining precise predictions for the transverse momentum of hadrons with respect to the thrust axis in e + e - collisions. This will enable a precise extraction of transverse momentum dependent (TMD) fragmentation functions from a recent measurement by the Belle Collaboration. Our analysis takes into account, for the first time, the nontrivial interplay between the hadron transverse momentum and the cut on the thrust event shape. To this end, we identify three different kinematic regions, derive the corresponding factorization theorems within Soft Collinear Effective Theory, and present all ingredients needed for the joint resummation of the transverse momentum and thrust spectrum at NNLL accuracy. One kinematic region can give rise to non-global logarithms (NGLs), and we describe how to include the leading NGLs. We also discuss alternative measurements in e + e - collisions that can be used to access the TMD fragmentation function. Finally, by using crossing symmetry, we obtain a new way to constrain TMD parton distributions, by measuring the displacement of the thrust axis in ep collisions.

72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗

Modeling magnetic fields with helical solutions to Laplace’s equation

The series solution to Laplace's equation in a helical coordinate system is derived and refined using symmetry and chirality arguments. These functions and their more commonplace counterparts are used to model solenoidal magnetic fields via linear, multidimensional curve-fitting. A judicious choice of functional forms, a small number of free parameters and sparse input data can lead to highly accurate, fine-grained modeling of solenoidal magnetic fields, including helical features arising from the winding of the solenoid, with overall field accuracy at better than one part per million.

46 INSTRUMENTATION RELATED TO NUCLEAR SCIENCE AND ↗

Optimizing lane reversals in transportation networks to reduce traffic congestion: A global optimization approach

This paper studies how to reduce the overall travel time of commuters in a transportation network by reversing the direction of some lanes in the network using a macroscopic network-wide perspective. Similar to the Network Design Problem, the lane reversal problem has been shown to be NP-hard given the dependence of the users’ route selection on the lane direction decision. Herein, we propose and compare three efficient methods to solve the routing and lane reversal problem jointly. First, we introduce an alternating method that decouples the routing and lane assignment problems. Second, we propose a Frank–Wolfe method that jointly takes gradient steps to adjust both the lane assignment and routing decisions. Third, we propose a convex approximation method that uses a threshold-based approach to convexify the joint routing and lane reversal objective. The convex approximation method is advantageous since it finds a global optimum solution for the approximated problem and it enables the possibility to include linear constraints. Using this method, we extend the main formulation to be able to limit a maximum number of reversed lanes, as well as to incorporate multiple origin–destination (OD) patterns. We test the proposed methods in a case study using the transportation network of Eastern Massachusetts where our results indicate an overall reduction in travel times of 4.7% by selecting the best 15 reversals. Moreover, using a small test network, we investigate the performance of the lane reversal strategies as a function of the OD demand symmetry. As expected, we observe that when the OD demand is very asymmetric (e.g., for a single OD pair, evacuations, large events), the reduction in travel times is larger than the symmetric case, reaching travel time reductions of 60%.

32 ENERGY CONSERVATION, CONSUMPTION, AND UTILIZATI↗

Iron(III)–Oxo Cluster Chemistry with Dimethylarsinate Ligands: Structures, Magnetic Properties, and Computational Studies

A program has been initiated to develop Fe III /oxo cluster chemistry with the ‘pseudo-carboxylate’ ligand dimethylarsinate (Me 2 AsO 2 - ) for comparison with the well investigated Fe III /oxo/carboxylate cluster area. The synthesis and characterization of three polynuclear Fe III complexes are reported, [Fe 12 O 4 (O 2 C t Bu) 8 (O 2 AsMe 2 ) 17 (H 2 O) 3 ]Cl 3 (1), Na 2 [Fe 12 Na 2 O 4 (O 2 AsMe 2 ) 20 (NO 3 ) 6 (Me 2 AsO 2 H) 2 (H 2 O) 4 ](NO 3 ) 6 (2) and [Fe 3 (O 2 AsMe 2 ) 6 (Me 2 AsO 2 H) 2 (hqn) 2 ](NO 3 ) (3), where hqn is 8-hydroxyquinoline. The Fe 12 core of 1 is a type never previously encountered in Fe III carboxylate chemistry, consisting of two Fe 6 units each of which comprises two {Fe 3 (μ 3 -O 2- )} units bridged by three Me 2 AsO 2 - groups and linked into an Fe 12 loop structure by two anti-anti η 1 :η 1 :μ Me 2 AsO 2 - groups, a bridging mode extremely rare with carboxylates. 2 also consists of two Fe 6 units, differing in their ligation from those in 1, and this time linked together into a linear structure by a central {Na 2 (NO 3 ) 2 } bridging unit. 3 is a linear Fe 3 complex with no monoatomic bridges between Fe III ions, a very rare situation in Fe III chemistry with any ligands, and unprecedented in Fe carboxylate chemistry. The distinct differences observed in arsinate vs carboxylate ligation modes are rationalized largely based on the greater basicity of the former vs the latter. Variable-temperature dc and ac magnetic susceptibility data reveal all Fe 2 pairwise interactions to be antiferromagnetic. For 1 and 2, the different J ij couplings were estimated by use of a magnetostructural correlation for high nuclearity Fe III -oxo clusters and by density functional theory calculations using broken symmetry methods, allowing identification of their relative spin vector alignments and thus rationalization of their S = 0 ground states. The J ij values were then used as input values to give excellent fits of the experimental χM T vs T data. For 3, the fits of the experimental χM T vs T data to the Van Vleck equation or with PHI gave a very weak J 12 = -0.8(1) cm -1 (H = –2JŠ i ·Š j convention) between adjacent Fe III ions, and an S = 5/2 ground state. Furthermore, these initial Fe III arsinate complexes also provide structural parameters that help validate literature assignments of arsinate binding modes to iron oxide/hydroxide minerals as part of environmental concerns of using arsenic-containing herbicides in agriculture.

37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗

Unconventional spectral signature of $T_c$ in a pure d -wave superconductor

We report in conventional superconductors, the phase transition into a zero-resistance and perfectly diamagnetic state is accompanied by a jump in the specific heat and the opening of a spectral gap. In the high-transition-temperature (high-T c ) cuprates, although the transport, magnetic and thermodynamic signatures of T c have been known since the 1980s, the spectroscopic singularity associated with the transition remains unknown. Here we resolve this long-standing puzzle with a high-precision angle-resolved photoemission spectroscopy (ARPES) study on overdoped (Bi,Pb) 2 Sr 2 CaCu 2 O 8+δ (Bi2212). We first probe the momentum-resolved electronic specific heat via spectroscopy and reproduce the specific heat peak at T c , completing the missing link for a holistic description of superconductivity. Then, by studying the full momentum, energy and temperature evolution of the spectra, we reveal that this thermodynamic anomaly arises from the singular growth of in-gap spectral intensity across T c . Furthermore, we observe that the temperature evolution of in-gap intensity is highly anisotropic in the momentum space, and the gap itself obeys both the d-wave functional form and particle–hole symmetry. These findings support the scenario that the superconducting transition is driven by phase fluctuations. They also serve as an anchor point for understanding the Fermi arc and pseudogap phenomena in underdoped cuprates.

75 CONDENSED MATTER PHYSICS, SUPERCONDUCTIVITY AND↗