The Surprising Utility of Group Partitioning in Improving Conformal Prediction of Visual Classifiers under Distributional Shifts
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Conformal multi-hop relation detection and classification in knowledge graphs
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Mathematics and Computing↗
Dynamics of Confined Flexible and Unentangled Polymer Melts in Highly Adsorbing Cylindrical Pores
Inspired by the recent neutron spin echo experiments (NSE) designed to address the dynamic phenomena in polymer melts that are induced by interactions with a confining surface, we performedcoarse-grained molecular dynamics simulations to replicate the experimental results in order to provide new molecular insight for the observations. The results show excellent agreement in the values obtained for the normalized coherent single chain dynamic structure factor, S(Q;Dt)/S(Q;0) , between experiments and simulations. The simulations indicate that using different chain molecular weights that are used to achieve scattering contrast results in the uneven distribution of scatterers in the radial direction because lower molecular weight chains prefer to adsorb in the confining surface. In the bulk configuration, both simulations and experiments confirm that the polymer chains follow Rouse dynamics. However, under confinement, the Rouse modes are suppressed. The mean-squared radius of gyration, R2g, and the average relative shape anisotropy k2 of the conformation of the polymer chains indicate a pancake-like conformation near the surface and a bulk-like conformation near the center of the confining cylinder. Direct visualization of the polymers in the simulation confirm the pancake-like conformation of the adsorbed chains and the presence of trains, loops and tails in the region between the adsorbed chains and the chains not in contact with the surface. Despite the presence of these different conformations, the average form factor of the confined chains still follows the Debye function which describes linear ideal chains, which is in agreement with small angle neutron scattering (SANS) experiments. The experimentally inaccessible mean squared displacement of the confined monomers, calculated as a function of radial distance from the pore surface, was obtained in the simulations. The simulation shows a gradual increase of the MSD from the adsorbed, but mobile layer, to that similar to the bulk far away from the surface.
Carrillo, Jan-Michael Y.↗
On-Demand Designing of Cathode Internal Surface Architecture for Dramatic Enhancement of SOFC Performance and Durability
This project is aimed to design and modify the internal surfaces of porous composite cathode from currently commercially viable Solid Oxide Fuel Cells (SOFCs), using additive manufacturing process of Atomic Layer Deposition (ALD). The material systems being investigated are commercial composite electrodes complex three-dimensional topographies. In term of the chemistry of the ALD layer applied on the internal surface of the porous cathode, this project has employed commercially relevant electrolyte, electrocatalyst and noble metal materials set. Such materials are fully compatible with the commercial fuel cells, and this project has developed special nanostructure on the surface of the commercial composite cathodes. The formation of the designed nanoarchitecture on the surface of SOFC cathode has been achieved through precise control of ALD parameters and their effect on overall cell performance and resultant electrochemical reaction mechanism of cathodes has been investigated through full cell electrochemical performance testing and nanostructure characterization by transmission electron microscopy (TEM). Under the support of this award, following has been achieved: (1). For cathode materials in solid oxide fuel cells (SOFCs), such as perovskite mixed conductor La 0.6 Sr 0.4 Co 0.2 Fe 0.8 O 3-x (LSCF), cation surface segregation and consequently losing conductivity and active sites for the oxygen reduction reaction (ORR) are problematic. To mitigate the cation segregation and enhance SOFC durability, further decorating the internal backbone surface using the desired electrocatalysts could be a promoting approach. Commonly, the cation segregation such as Sr is very volatile, so the effective surface decoration is ideally conformal. Nevertheless, the conformal surface coating would inevitably alter the ORR pathways that initially take place on the surface of the backbone. To reveal the impact of the conformal coating on both the catalytic activity and the conductivity of the cathode, the unary electrocatalyst of Pt or CoO x , was applied to the LSCF/SDC composite electrode of inherently functional SOFCs, respectively. Both ALD coating layers evolve strong interaction with the LSCF composite cathode. Upon operations, the Pt coating layer remains conformal on LSCF grain surfaces but turns into discrete particles on SDC grain surfaces. Meanwhile, CoO x conformal coating grows to be the discrete nanograins on both the LSCF and SDC grains. ALD coating of the cathode alone reduces the ohmic resistance up to 28 % for the entire cells. The increased conductivity induced by the ALD coating of Pt or CoO x is ascribed to different mechanisms. For the inherent functional SOFCs, the present study presents a novel and feasible approach to apply a conformal, dense coating layer on the surface of a mixed conductor, simultaneously increasing the conductivity and durability of the SOFC cathode. (2). High resistance of the oxygen electrode still significantly hinders the state-of-the-art Solid Oxide Fuel Cells (SOFCs). In particular, for an oxygen electrode consisting of mixed electronic and ionic conductors, such as perovskite lanthanum strontium cobalt ferrite (LSCF), it deteriorates due to its low chemical stability of the grain surface. Such degradation is often associated with the segregation of cations. To prevent the cation surface segregation and its resultant perovskite phase decomposition, we demonstrate a conformal ultra-thin (7-10 nm) surface heterogeneous coating layer consisting of subjacent discrete Pt nanoparticles capped with a superjacent fully dense conformal CoO x layer. The performance studies indicate the ALD coating reduces the cell series resistance by up to 40 %. The conformal CoO x layer consists of randomly orientated but single-layered nanograins, with high-density intergranular and surface grain boundaries serving as the electrochemical reaction sites and facilitating mass transport. The conformal coating layer appears to have successfully suppressed the Sr outward diffusion and confined the Sr enriched layer to a ~ 2 nm interface perovskite phase between the coating layer and the LSCF grain surface. Moreover, this ultra-thin Sr enriched perovskite layer presumably possesses high oxygen vacancy and high ionic conductivity and further imposes tensile strain to the LSCF grain surfaces. With the combination of a conformal CoO x nanoionics, Sr enriched layer, and its strained interface, the ALD coating induced surface layer is estimated to have a conductivity of ~ 1.27x10 4 S/cm, which is over two orders magnitude of that from LSCF at 750 ºC.
30 DIRECT ENERGY CONVERSION↗
Secondary Structures of Ubiquitin Ions Soft-Landed onto Self-Assembled Monolayer Surfaces
The secondary structures of multiply charged ubiquitin ions soft-landed onto self-assembled monolayer (SAM) surfaces were studied using in situ infrared reflection-absorption spectroscopy (IRRAS). Two charge states of ubiquitin, 5+ and 13+, were mass selected separately from a mixture of different charge states produced by electrospray ionization (ESI). The low 5+ charge state represents a native-like folded state of ubiquitin, while the high 13+ charge state assumes an extended, almost linear conformation. Each of the two charge states was soft-landed onto a CH 3- and COOH-terminated SAM of alkylthiols on gold (HSAM and COOH-SAM). HSAM is a hydrophobic surface known to stabilize helical conformations of soft-landed protonated peptides, whereas COOH-SAM is a hydrophilic surface that preferentially stabilizes β-sheet conformations. IRRAS spectra of the soft-landed ubiquitin ions were acquired as a function of time during and after ion soft-landing. Similar to smaller peptide ions, helical conformations of ubiquitin are found to be more abundant on HSAM, while the relative abundance of β-sheet conformations increases on COOH-SAM. The initial charge state of ubiquitin also has a pronounced effect on its conformation on the surface. Specifically, on both surfaces, a higher relative abundance of helical conformations and lower relative abundance of β-sheet conformations is observed for the 13+ charge state compared to the 5+ charge state. Time-resolved experiments indicate that the α-helical band in the spectrum of the 13+ charge state slowly increases with time on the HSAM surface and decreases in the spectrum of the 13+ charge state on COOH-SAM. These results further support the preference of the hydrophobic HSAM surface toward helical conformations and demonstrate that soft-landed protein ions may undergo slow conformational changes during and after deposition.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Precursory signatures of protein folding/unfolding: From time series correlation analysis to atomistic mechanisms
Folded conformations of proteins in thermodynamically stable states have long lifetimes. Before it folds into a stable conformation, or after unfolding from a stable conformation, the protein will generally stray from one random conformation to another leading thus to rapid fluctuations. Brief structural changes therefore occur before folding and unfolding events. These short-lived movements are easily overlooked in studies of folding/unfolding for they represent momentary excursions of the protein to explore conformations in the neighborhood of the stable conformation. The present study looks for precursory signatures of protein folding/unfolding within these rapid fluctuations through a combination of three techniques: (1) ultrafast shape recognition, (2) time series segmentation, and (3) time series correlation analysis. The first procedure measures the differences between statistical distance distributions of atoms in different conformations by calculating shape similarity indices from molecular dynamics simulation trajectories. The second procedure is used to discover the times at which the protein makes transitions from one conformation to another. Finally, we employ the third technique to exploit spatial fingerprints of the stable conformations; this procedure is to map out the sequences of changes preceding the actual folding and unfolding events, since strongly correlated atoms in different conformations are different due to bond and steric constraints. The aforementioned high-frequency fluctuations are therefore characterized by distinct correlational and structural changes that are associated with rate-limiting precursors that translate into brief segments. Guided by these technical procedures, we choose a model system, a fragment of the protein transthyretin, for identifying in this system not only the precursory signatures of transitions associated with α helix and β hairpin, but also the important role played by weaker correlations in such protein folding dynamics.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
Massive celestial fermions
In an effort to further the study of amplitudes in the celestial CFT (CCFT), we construct conformal primary wavefunctions for massive fermions. Upon explicitly calculating the wavefunctions for Dirac fermions, we deduce the corresponding transformation of momentum space amplitudes to celestial amplitudes. The shadow wavefunctions are shown to have opposite spin and conformal dimension 2 - Δ. The Dirac conformal primary wave- functions are delta function normalizable with respect to the Dirac inner product provided they lie on the principal series with conformal dimension Δ = 1 + iλ for λ ∈ $\mathbb{R}$. It is shown that there are two choices of a complete basis: single spin J=$\frac{1}{2}$ or J=-$\frac{1}{2}$ and λ ∈ $\mathbb{R}$ or multiple spin J=±$\frac{1}{2}$ and λ $\mathbb{R}$ +∪0 . The massless limit of the Dirac conformal primary wavefunctions is shown to agree with previous literature. The momentum generators on the celestial sphere are derived and, along with the Lorentz generators, form a representation of the Poincaré algebra. Finally, we show that the massive spin-1 conformal primary wavefunctions can be constructed from the Dirac conformal primary wavefunctions using the standard Clebsch-Gordan coefficients. We use this procedure to write the massive spin-$\frac{3}{2}$, Rarita-Schwinger, conformal primary wavefunctions. This provides a prescription for constructing all massive fermionic and bosonic conformal primary wavefunctions starting from spin-$\frac{1}{2}$.
79 ASTRONOMY AND ASTROPHYSICS↗
Reparametrization modes, shadow operators, and quantum chaos in higher-dimensional CFTs
We study two novel approaches to efficiently encoding universal constraints imposed by conformal symmetry, and describe applications to quantum chaos in higher dimensional CFTs. The first approach consists of a reformulation of the shadow operator formalism and kinematic space techniques. We observe that the shadow operator associated with the stress tensor (or other conserved currents) can be written as the descendant of a field ε with negative dimension. Computations of stress tensor contributions to conformal blocks can be systematically organized in terms of the “soft mode” ε, turning them into a simple diagrammatic perturbation theory at large central charge.Our second (equivalent) approach concerns a theory of reparametrization modes, generalizing previous studies in the context of the Schwarzian theory and two-dimensional CFTs. Due to the conformal anomaly in even dimensions, gauge modes of the conformal group acquire an action and are shown to exhibit the same dynamics as the soft mode ε that encodes the physics of the stress tensor shadow. We discuss the calculation of the conformal partial waves or the conformal blocks using our effective field theory. The separation of conformal blocks from shadow blocks is related to gauging of certain symmetries in our effective field theory of the soft mode. These connections explain and generalize various relations between conformal blocks, shadow operators, kinematic space, and reparametrization modes. As an application we study thermal physics in higher dimensions and argue that the theory of reparametrization modes captures the physics of quantum chaos in Rindler space. This is also supported by the observation of the pole skipping phenomenon in the conformal energy-energy two-point function on Rindler space.
1/N Expansion↗
Stereochemistry of polypeptoid chain configurations
Abstract Like polypeptides, peptoids, or N ‐substituted glycine oligomers, have intrinsic conformational preferences due to their amide backbones and close spacing of side chain substituents. However, the conformations that peptoids adopt are distinct from polypeptides due to several structural differences: the peptoid backbone is composed of tertiary amide bonds that have trans and cis conformers similar in energy, they lack a backbone hydrogen bond donor, and have an N ‐substituent. To better understand how these differences manifest in actual peptoid structures, we analyzed 46 high quality, experimentally determined peptoid structures reported in the literature to extract their backbone conformational preferences. One hundred thirty‐two monomer dihedral angle pairs were compared to the calculated energy landscape for the peptoid Ramachandran plot, and were found to fall within the expected minima. Interestingly, only two regions of the backbone dihedral angles ϕ and ψ were found to be populated that are mirror images of each other. Furthermore, these two conformers are present in both cis and trans forms. Thus, there are four primary conformers that are sufficient to describe almost all known backbone conformations for peptoid oligomers, despite conformational constraints imposed by a variety of side chains, macrocyclization, or crystal packing forces. Because these conformers are predominant in peptoid structure, and are distinct from those found in protein secondary structures, we propose a simple naming system to aid in the description and classification of peptoid structure.
Spencer, Ryan K.↗
Late-time structure of the Bunch-Davies de Sitter wavefunction
We examine the late time behavior of the Bunch-Davies wavefunction for interacting light fields in a de Sitter background. We use perturbative techniques developed in the framework of AdS/CFT, and analytically continue to compute tree and loop level contributions to the Bunch-Davies wavefunction. We consider self-interacting scalars of general mass, but focus especially on the massless and conformally coupled cases. We show that certain contributions grow logarithmically in conformal time both at tree and loop level. We also consider gauge fields and gravitons. The four-dimensional Fefferman-Graham expansion of classical asymptotically de Sitter solutions is used to show that the wavefunction contains no logarithmic growth in the pure graviton sector at tree level. Finally, assuming a holographic relation between the wavefunction and the partition function of a conformal field theory, we interpret the logarithmic growths in the language of conformal field theory.
72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
Water‐Based Assembly of Polymer–Metal Organic Framework (MOF) Functional Coatings
Metal organic frameworks (MOFs) have gained attention for their porosity, size selectivity, and structural diversity. There is a need for MOF‐based coatings, particularly in applications such as separations, electronics, and energy; yet forming thin, functional, conformal coatings is prohibitive because MOFs exist as a powder. Layer‐by‐layer assembly, a versatile thin film coating approach, offers a unique solution to this problem, but this approach requires MOFs that are water‐dispersible and bear a surface charge. Here, these issues are addressed by examining water‐based dispersions of MIL‐101(Cr) that facilitate the formation of robust polymer–MOF hybrid coatings. Specifically, the substrate to be coated is alternately exposed to an aqueous solution of poly(styrene sulfonate) and nano MIL‐101(Cr) dispersion, yielding linear film growth and coatings with a MOF content as high as 77 wt%. This approach is surface‐agnostic, in which the coating is successfully applied to silicon, glass, flexible plastic, and even cotton fabric, conformally coating individual fibers. By contrast, prior attempts at forming MOF‐coatings are severely limited to a handful of surfaces, require harsh chemical treatment, and are not conformal. The approach presented here unambiguously confirms that MOFs can be conformally coated onto complex and unusual surfaces, opening the door for a wide variety of applications.
De, Souvik↗
Exploring the Mechanism of β-Lactam Ring Protonation in the Class A β-lactamase Acylation Mechanism Using Neutron and X-ray Crystallography
The catalytic mechanism of class A beta-lactamases is often debated due in part to the large number of amino acids that interact with bound beta-lactam substrates. The role and function of the conserved residue Lys 73 in the catalytic mechanism of class A type beta-lactamase enzymes is still not well understood after decades of scientific research. To better elucidate the functions of this vital residue, we used both neutron and high-resolution X-ray diffraction to examine both the structures of the ligand free protein and the acyl-enzyme complex of perdeuterated E166A Toho-1 beta-lactamase with the antibiotic cefotaxime. The E166A mutant lacks a critical glutamate residue that has a key role in the deacylation step of the catalytic mechanism, allowing the acyl-enzyme adduct to be captured for study. In our ligand free structures, Lys 73 is present in a single conformation, however in all of our acyl-enzyme structures, Lys 73 is present in two different conformations, in which one conformer is closer to Ser 70 while the other conformer is positioned closer to Ser 130, which supports the existence of a possible pathway by which proton transfer from Lys 73 to Ser 130 can occur. This and further clarifications of the role of Lys 73 in the acylation mechanism may facilitate the design of inhibitors that capitalize on the enzymes native machinery.
38 RADIATION CHEMISTRY, RADIOCHEMISTRY, AND NUCLEA↗
Quantitative Infrared Absorption Spectra and Vibrational Assignments of Crotonaldehyde and Methyl Vinyl Ketone Using Gas-Phase Mid-Infrared, Far-Infrared, and Liquid Raman Spectra: s-cis vs s-trans Composition Confirmed via Temperature Studies and ab Initio Methods
Methyl vinyl ketone (MVK) and crotonaldehyde are chemical isomers; both are also important species in tropospheric chemistry. We report quantitative vapor-phase infrared spectra of crotonaldehyde and MVK vapors over the 540-6500 cm-1 range. Vibrational assignments of all fundamental modes are made for both molecules based on far- and mid-infrared vapor-phase spectra, liquid Raman spectra, along with density functional theory and ab initio MP2 and high energy-accuracy compound theoretical models (W1BD). Theoretical results indicate that at room temperature the crotonaldehyde equilibrium mixture is approximately 97% s-trans and only 3% s-cis conformer. Nearly all observed bands are thus associated with the s-trans conformer, but a few appear to be uniquely associated the s-cis conformer, notably ν16c at 730.90 cm-1, which displays a substantial intensity increase with temperature (62% upon going from 5 to 50 oC). The intensity of the corresponding mode of the s-trans conformer decreases with temperature. Under the same conditions, the MVK equilibrium mixture is approximately 69% s-trans conformer and 31% s-cis. W1BD calculations indicate that for MVK this is one of those (rare) cases where there are comparable populations of both conformers, ~doubling the number of observed bands and exacerbating the vibrational assignments. We uniquely assign the bands associated with both the MVK s-cis conformer as well as those of the s-trans, thus completing the vibrational analyses of both conformers from the same set of experimental spectra. Integrated band intensities are reported for both molecules along with global warming potential values. Using the quantitative IR data, potential bands for atmospheric monitoring are also discussed.
Lindenmaier, Rodica↗
Reduced dynamic complexity allows structure elucidation of an excited state of KRAS G13D
Localized dynamics of RAS, including regions distal to the nucleotide-binding site, is of high interest for elucidating the mechanisms by which RAS proteins interact with effectors and regulators and for designing inhibitors. Among several oncogenic mutants, methyl relaxation dispersion experiments reveal highly synchronized conformational dynamics in the active (GMPPNP-bound) KRAS G13D , which suggests an exchange between two conformational states in solution. Methyl and 31 P NMR spectra of active KRAS G13D in solution confirm a two-state ensemble interconverting on the millisecond timescale, with a major Pγ atom peak corresponding to the dominant State 1 conformation and a secondary peak indicating an intermediate state different from the known State 2 conformation recognized by RAS effectors. High-resolution crystal structures of active KRAS G13D and KRAS G13D -RAF1 RBD complex provide snapshots of the State 1 and 2 conformations, respectively. We use residual dipolar couplings to solve and cross-validate the structure of the intermediate state of active KRAS G13D , showing a conformation distinct from those of States 1 and 2 outside the known flexible switch regions. The dynamic coupling between the conformational exchange in the effector lobe and the breathing motion in the allosteric lobe is further validated by a secondary mutation in the allosteric lobe, which affects the conformational population equilibrium.
59 BASIC BIOLOGICAL SCIENCES↗
Structural architecture of prothrombin in solution revealed by single molecule spectroscopy
The coagulation factor prothrombin has a complex spatial organization of its modular assembly that comprises the N-terminal Gla domain, kringle-1, kringle-2, and the C-terminal protease domain connected by three intervening linkers. Here we use single molecule Förster resonance energy transfer to access the conformational landscape of prothrombin in solution and uncover structural features of functional significance that extend recent x-ray crystallographic analysis. Prothrombin exists in equilibrium between two alternative conformations, open and closed. The closed conformation predominates (70%) and features an unanticipated intramolecular collapse of Tyr 93 in kringle-1 onto Trp 547 in the protease domain that obliterates access to the active site and protects the zymogen from autoproteolytic conversion to thrombin. The open conformation (30%) is more susceptible to chymotrypsin digestion and autoactivation, and features a shape consistent with recent x-ray crystal structures. Small angle x-ray scattering measurements of prothrombin wild type stabilized 70% in the closed conformation and of the mutant Y93A stabilized 80% in the open conformation directly document two envelopes that differ 50 Å in length. These findings reveal important new details on the conformational plasticity of prothrombin in solution and the drastic structural difference between its alternative conformations. Prothrombin uses the intramolecular collapse of kringle-1 onto the active site in the closed form to prevent autoactivation. As a result, the open-closed equilibrium also defines a new structural framework for the mechanism of activation of prothrombin by prothrombinase.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
The spontaneous replication error and the mismatch discrimination mechanisms of human DNA polymerase β
To provide molecular-level insights into the spontaneous replication error and the mismatch discrimination mechanisms of human DNA polymerase β (polβ), we report four crystal structures of polβ complexed with dG•dTTP and dA•dCTP mismatches in the presence of Mg 2+ or Mn 2+ . The Mg 2+ -bound ground-state structures show that the dA•dCTP-Mg 2+ complex adopts an ‘intermediate’ protein conformation while the dG•dTTP-Mg 2+ complex adopts an open protein conformation. The Mn 2+ -bound ‘pre-chemistry-state’ structures show that the dA•dCTP-Mn2+ complex is structurally very similar to the dA•dCTP-Mg 2+ complex, whereas the dG•dTTP-Mn 2+ complex undergoes a large-scale conformational change to adopt a Watson–Crick-like dG•dTTP base pair and a closed protein conformation. These structural differences, together with our molecular dynamics simulation studies, suggest that polβ increases replication fidelity via a two-stage mismatch discrimination mechanism, where one is in the ground state and the other in the closed conformation state. In the closed conformation state, polβ appears to allow only a Watson–Crick-like conformation for purine•pyrimidine base pairs, thereby discriminating the mismatched base pairs based on their ability to form the Watson–Crick-like conformation. Overall, the present studies provide new insights into the spontaneous replication error and the replication fidelity mechanisms of polβ.
37 INORGANIC, ORGANIC, PHYSICAL, AND ANALYTICAL CH↗
$\mathcal{N}$ = (1, 0) anomaly multiplet relations in six dimensions
We consider conformal and ’t Hooft anomalies in six-dimensional $\mathcal{N}$ = (1, 0) superconformal field theories, focusing on those conformal anomalies that determine the two- and three-point functions of conserved flavor and SU(2) R currents, as well as stress tensors. By analyzing these correlators in superspace, we explain why the number of independent conformal anomalies is reduced in supersymmetric theories. For instance, non- supersymmetric CFTs in six dimensions have three independent conformal c-anomalies, which determine the stress-tensor two- and three-point functions, but in superconformal theories the three c-anomalies are subject to a linear constraint. We also describe anomaly multiplet relations, which express the conformal anomalies of a superconformal theory in terms of its ’t Hooft anomalies. Following earlier work on the conformal a-anomaly, we argue for these relations by considering the supersymmetric dilaton effective action on the tensor branch of such a theory. We illustrate the utility of these anomaly multiplet relations by presenting exact results for conformal anomalies, and hence current and stress-tensor correlators, in several interacting examples.
72 PHYSICS OF ELEMENTARY PARTICLES AND FIELDS↗
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