Two 6D origins of 4D SCFTs: Class S and 6D (1, 0) on a torus
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72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
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Higgs branch, Coulomb branch, and Hall-Littlewood index
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72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
Auxiliary Space Preconditioning of Finite Element Equations Using a Nonconforming Interior Penalty Reformulation and Static Condensation
We modify the well-known interior penalty finite element discretization method so that it allows for element-by-element assembly. This is possible due to the introduction of additional unknowns associated with the interfaces between neighboring elements. The resulting bilinear form, and a Schur complement (reduced) version of it, are utilized in a number of auxiliary space preconditioners for the original conforming finite element discretization problem. Furthermore, these preconditioners are analyzed on the fine scale, and their performance is illustrated on model second order scalar elliptic problems discretized with high order elements.
97 MATHEMATICS AND COMPUTING↗
Deep Direct-Use Feasibility Study Development of 3-D Structural Surface Model for the Tuscarora Sandstone, Morgantown, WV
This dataset contains grid files for subsurface maps created in GES interpretation software and exported as Zmap formated grid files. Depth values in SSTVD (subsea true vertical depth). The methods used for analysis and a detailed discussion of the results are presented in a paper by McCleery et al., (2018).
15 GEOTHERMAL ENERGY↗
Development of Coarse-Grained Models for Poly(4-vinylphenol) and Poly(2-vinylpyridine): Polymer Chemistries with Hydrogen Bonding
In this paper, we identify the modifications needed in a recently developed generic coarse-grained (CG) model that captured directional interactions in polymers to specifically represent two exemplary hydrogen bonding polymer chemistries—poly(4-vinylphenol) and poly(2-vinylpyridine). We use atomistically observed monomer-level structures (e.g., bond, angle and torsion distribution) and chain structures (e.g., end-to-end distance distribution and persistence length) of poly(4-vinylphenol) and poly(2-vinylpyridine) in an explicitly represented good solvent (tetrahydrofuran) to identify the appropriate modifications in the generic CG model in implicit solvent. For both chemistries, the modified CG model is developed based on atomistic simulations of a single 24-mer chain. This modified CG model is then used to simulate longer (36-mer) and shorter (18-mer and 12-mer) chain lengths and compared against the corresponding atomistic simulation results. We find that with one to two simple modifications (e.g., incorporating intra-chain attraction, torsional constraint) to the generic CG model, we are able to reproduce atomistically observed bond, angle and torsion distributions, persistence length, and end-to-end distance distribution for chain lengths ranging from 12 to 36 monomers. We also show that this modified CG model, meant to reproduce atomistic structure, does not reproduce atomistically observed chain relaxation and hydrogen bond dynamics, as expected. Simulations with the modified CG model have significantly faster chain relaxation than atomistic simulations and slower decorrelation of formed hydrogen bonds than in atomistic simulations, with no apparent dependence on chain length.
36 MATERIALS SCIENCE↗
Bimetallic Copper/Ruthenium/Osmium Complexes: Observation of Conformational Differences Between the Solution Phase and Solid State by Atomic Pair Distribution Function Analysis
High-energy X-ray scattering and pair distribution function analysis (HEXS/PDF) is a powerful method to reveal the structure of materials lacking long-range order, but is underutilized for molecular complexes in solution. Here we demonstrate the application of HEXS/PDF with 0.26 Å resolution to uncover the solution structure of five bimetallic Cu I /Ru II /Os II complexes. HEXS/PDF of each complex in acetonitrile solution confirms the pairwise distances in the local coordination sphere of each metal center as well as the metal...metal distances separated by over 12 Å. The metal…metal distance detected in solution is compared with that from the crystal structure and molecular models to confirm that distortions to the metal bridging ligand are unique to the solid state. This work presents the first example of observing sub-Ångström conformational differences by direct comparison of solution phase and solid-state structures and shows the potential for HEXS/PDF in the determination of solution structure of single molecules.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Modeling diffusion and depletion in high-aspect-ratio atomic layer deposition processes: Process parameters and manufacturing impacts
Atomic layer deposition (ALD) is a powerful technique for modifying the surface chemistry and properties of substrates with complex and nonplanar topologies. However, achieving uniform and conformal deposition on ultrahigh-aspect-ratio substrates remains challenging, typically requiring large quantities of precursors and long exposure times. Furthermore, process optimization is often performed empirically and involves substantial trial and error. In this work, we perform a combined experimental and computational study of ALD Al 2 O 3 infiltration into silica aerogel monoliths (aspect ratio >10 5 ). A reaction-diffusion model is used to explore the effects of key processing parameters, namely, exposure time per dose, precursor source temperature, number of aerogels in the reactor, and reactor volume. The model is based on quasi-static mode ALD, where the dosed precursor is held in the chamber for a fixed period of time before purging. We analyze the trade-offs between process throughput and precursor utilization for each of these parameters. Furthermore, we investigate the co-optimization and interactions between multiple process parameters, demonstrating the potential for further improvements. Furthermore, this physics-based model can be used to identify a set of process parameters for high-aspect-ratio ALD that meet specific manufacturing objective functions, including throughput, cost, and sustainability.
Aerogel↗
Resurgence, conformal blocks, and the sum over geometries in quantum gravity
In two dimensional conformal field theories the limit of large central charge plays the role of a semi-classical limit. Certain universal observables, such as conformal blocks involving the exchange of the identity operator, can be expanded around this classical limit in powers of the central charge c. This expansion is an asymptotic series, so — via the same resurgence analysis familiar from quantum mechanics — necessitates the existence of non-perturbative effects. In the case of identity conformal blocks, these new effects have a simple interpretation: the CFT must possess new primary operators with dimension of order the central charge. This constrains the data of CFTs with large central charge in a way that is similar to (but distinct from) the conformal bootstrap. We study this phenomenon in three ways: numerically, analytically using Zamolodchikov’s recursion relations, and by considering non-unitary minimal models with large (negative) central charge. In the holographic dual to a CFT2, the expansion in powers of c is the perturbative loop expansion in powers of ћ. So our results imply that the graviton loop expansion is an asymptotic series, whose cure requires the inclusion of new saddle points in the gravitational path integral. In certain cases these saddle points have a simple interpretation: they are conical excesses, particle-like states with negative mass which are not in the physical spectrum but nevertheless appear as non-manifold saddle points that control the asymptotic behaviour of the loop expansion. This phenomenon also has an interpretation in SL(2, R) Chern-Simons theory, where the non-perturbative effects are associated with the non-Teichmüller component of the moduli space of flat connections.
72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
Insight into molecular basis and dynamics of full-length CRaf kinase in cellular signaling mechanisms
Raf kinases play key roles in signal transduction in cells for regulating proliferation, differentiation, and survival. Despite decades of research into functions and dynamics of Raf kinases with respect to other cytosolic proteins, understanding Raf kinases is limited by the lack of their full-length structures at the atomic resolution. Here, we present the first model of the full-length CRaf kinase obtained from artificial intelligence/machine learning algorithms with a converging ensemble of structures simulated by large-scale temperature replica exchange simulations. Our model is validated by comparing simulated structures with the latest cryo-EM structure detailing close contacts among three key domains and regions of the CRaf. Our simulations identify potentially new epitopes of intramolecule interactions within the CRaf and reveal a dynamical nature of CRaf kinases, in which the three domains can move back and forth relative to each other for regulatory dynamics. The dynamic conformations are then used in a docking algorithm to shed insight into the paradoxical effect caused by vemurafenib in comparison with a paradox breaker PLX7904. In this study, we propose a model of Raf-heterodimer/KRas-dimer as a signalosome based on the dynamics of the full-length CRaf.
59 BASIC BIOLOGICAL SCIENCES↗
Simulation studies of polypeptoids using replica exchange with dynamical scaling and dihedral biasing
Polypeptoids differ from polypeptides in that the amide bond can more frequently adopt both cis and trans conformations. The transition between the two conformations requires overcoming a large energy barrier, making it difficult for conventional molecular simulations to adequately visit the cis and trans structures. A replica-exchange method is presented that allows for easy rotations of the amide bond and also an efficient linking to a high temperature replica. The method allows for just three replicas (one at the temperature and Hamiltonian of interest, a second high temperature replica with a biased dihedral potential, and a third connecting them) to overcome the amide bond sampling problem and also enhance sampling for other coordinates. Here our results indicate that for short peptoid oligomers, the conformations can range from all cis to all trans with an average cis/trans ratio that depends on side chain and potential model.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Scattering equations in AdS: scalar correlators in arbitrary dimensions
We introduce a bosonic ambitwistor string theory in AdS space. Even though the theory is anomalous at the quantum level, one can nevertheless use it in the classical limit to derive a novel formula for correlation functions of boundary CFT operators in arbitrary space-time dimensions. The resulting construction can be treated as a natural extension of the CHY formalism for the flat-space S-matrix, as it similarly expresses tree-level amplitudes in AdS as integrals over the moduli space of Riemann spheres with punctures. These integrals localize on an operator-valued version of scattering equations, which we derive directly from the ambitwistor string action on a coset manifold. As a testing ground for this formalism we focus on the simplest case of ambitwistor string coupled to two cur- rent algebras, which gives bi-adjoint scalar correlators in AdS. In order to evaluate them directly, we make use of a series of contour deformations on the moduli space of punctured Riemann spheres and check that the result agrees with tree level Witten diagram computations to all multiplicity. We also initiate the study of eigenfunctions of scattering equations in AdS, which interpolate between conformal partial waves in different OPE channels, and point out a connection to an elliptic deformation of the Calogero-Sutherland model.
72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
Spontaneous breaking of U(1) symmetry in coupled complex SYK models
As shown in [1], two copies of the large N Majorana SYK model can produce spontaneous breaking of a Z 2 symmetry when they are coupled by appropriate quartic terms. In this paper we similarly study two copies of the complex SYK model coupled by a quartic term preserving the U(1) x U(1) symmetry. We also present a tensor counterpart of this coupled model. When the coefficient α of the quartic term lies in a certain range, the coupled large N theory is nearly conformal. We calculate the scaling dimensions of fermion bilinear operators as functions of α. We show that the operator c$^†_{1i}$c 2i , which is charged under the axial U(1) symmetry, acquires a complex dimension outside of the line of fixed points. We derive the large N Dyson-Schwinger equations and show that, outside the fixed line, this U(1) symmetry is spontaneously broken at low temperatures because this operator acquires an expectation value. We support these findings by exact diagonalizations extrapolated to large N.
1/N expansion↗
Multiscale Modeling of Vinyl-Addition Polynorbornenes: The Effect of Stereochemistry
Vinyl-addition polynorbornenes are candidates for designing high-performance polymers due to unique characteristics, which include a high glass transition temperature associated with a rigid backbone. Recent studies have established that the processability and properties of these polymers can be fine-tuned by using targeted substitutions. However, synthesis with different catalysts results in materials with distinct properties, potentially due to the presence of various stereoisomers that are difficult to quantify experimentally. Herein, we develop all-atom models of polynorbornene oligomers based on classical force fields and density functional theory. To establish the relationship between chemical architecture, chain conformations, and melt structure, we perform detailed molecular dynamics simulations with the fine-tuned atomistic force field and propose simpler coarse-grained descriptions to address the high molecular weight limit. All-atom simulations of oligomers suggest high glass transition temperatures in the range of 550–600 K. In the melt state (800 K), meso chains form highly rigid extended coils (C∞≈11) with amorphous structural characteristics similar to the X-ray diffraction data observed in the literature. In contrast, simulations with racemo chains predict highly helical tubular chain conformations that could promote assembly into crystalline structures.
Polymer Science↗
Light dilaton in rare meson decays and extraction of its CP property
Abstract The dilatonϕis a pseudo-Nambu-Goldstone boson associated with the spontaneous breaking of scale invariance in a nearly conformal theory, and couples to the trace of the stress-energy tensor. We analyze experimental constraints on a light dilaton with mass in the MeV–GeV range from rare meson decays. New model-independent inclusive bounds for theb→sϕtransition largely exclude the parameter space of a light dilaton that could explain the muong− 2 anomaly. Despite similarities between a dilaton and a Higgs-portal scalar, the dilaton-photon coupling is enhanced compared to the Higgs-portal scalar due to contributions from loops of the conformal sector. Consequently, the shortened lifetime of the dilaton relaxes bounds fromK→π+ invisible searches at the NA62 experiment and constraints from the Big Bang Nucleosynthesis. We utilize this fact to search for the dilaton signature at a lepton collider such as the ongoing Belle II experiment. Further, we demonstrate how to extract the CP property of the dilaton using the variation of the differential cross-section ofe + e − →e + e − ϕwith the azimuthal angle between the outgoing leptons.
Physics↗
Prehydrodynamic evolution and its signatures in final-state heavy-ion observables
We investigate the effects of prehydrodynamic evolution on final-state observables in heavy-ion collisions using state-of-the art event simulations coupled to different prehydrodynamic scenarios, which include the recently developed effective kinetic transport theory evolution model KøMPøST. Differential flow observables are found to be mostly insensitive to the details of prehydrodynamic evolution. The main effect we observe is in the p T spectra, particularly the mean transverse momentum. However, at least part of this effect is a consequence of the underlying conformal invariance assumption currently present in such approaches, which is known to be violated in the temperature regime probed in heavy-ion collisions. This assumption of early time conformal invariance leads to an artificially large out-of-equilibrium bulk pressure when switching from (conformal) prehydrodynamic evolution to hydrodynamics (using the nonconformal QCD equation of state), which in turn increases the transverse momentum. Our study indicates that a consistent treatment of prehydrodynamic evolution in heavy-ion collisions requires the use of nonconformal models of early time dynamics.
73 NUCLEAR PHYSICS AND RADIATION PHYSICS↗
Vapor-phase grafting of a model aminosilane compound to Al 2 O 3 , ZnO, and TiO 2 surfaces prepared by atomic layer deposition
Atomic layer deposition (ALD) is a highly versatile surface functionalization technique that can conformally coat both planar and porous substrates. Here we use ALD metal oxide layers to establish a well-defined starting surface for vapor-phase surface organic modification. Vapor-phase (3-aminopropyl)triethoxysilane (APTES) surface silanization of ALD Al 2 O 3 , ZnO and TiO 2 surfaces were studied at 100 °C, 150 °C and 200 °C. In situ quartz crystal microbalance (QCM) and Fourier-transform infrared (FTIR) spectroscopy measurements, and ex situ atomic force microscopy (AFM) and X-ray photoelectron spectroscopy (XPS) measurements showed uniform monolayer silane formation through self-limiting APTES reaction. We observed a higher surface density of grafted APTES species following silanization at 100 °C compared to 200 °C, and we attribute this to the temperature-dependent reactivity of the surface hydroxyls and changes in the mode of APTES reaction. The FTIR and XPS measurements revealed that APTES reacts with Al 2 O 3 and ZnO exclusively through metal siloxy bond formation. However, APTES reacts with TiO 2 through both siloxy bond formation and ammonium salt formation via the amine group.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Zinc binding alters the conformational dynamics and drives the transport cycle of the cation diffusion facilitator YiiP
YiiP is a secondary transporter that couples Zn 2+ transport to the proton motive force. Structural studies of YiiP from prokaryotes and Znt8 from humans have revealed three different Zn 2+ sites and a conserved homodimeric architecture. These structures define the inward-facing and outward-facing states that characterize the archetypal alternating access mechanism of transport. To study the effects of Zn 2+ binding on the conformational transition, we use cryo-EM together with molecular dynamics simulation to compare structures of YiiP from Shewanella oneidensis in the presence and absence of Zn 2+ . To enable single-particle cryo-EM, we used a phage-display library to develop a Fab antibody fragment with high affinity for YiiP, thus producing a YiiP/Fab complex. To perform MD simulations, we developed a nonbonded dummy model for Zn 2+ and validated its performance with known Zn 2+ -binding proteins. Using these tools, we find that, in the presence of Zn 2+ , YiiP adopts an inward-facing conformation consistent with that previously seen in tubular crystals. After removal of Zn 2+ with high-affinity chelators, YiiP exhibits enhanced flexibility and adopts a novel conformation that appears to be intermediate between inward-facing and outward-facing states. This conformation involves closure of a hydrophobic gate that has been postulated to control access to the primary transport site. Comparison of several independent cryo-EM maps suggests that the transition from the inward-facing state is controlled by occupancy of a secondary Zn 2+ site at the cytoplasmic membrane interface. This work enhances our understanding of individual Zn 2+ binding sites and their role in the conformational dynamics that govern the transport cycle.
59 BASIC BIOLOGICAL SCIENCES↗