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PROFILE program solves diverse and inverse airfoil-flow problems. It combines conformational mapping method for design of airfoils with prescribed velocity-distribution characteristics, panel method for potential-flow analysis, and boundary-layer method. PROFILE is written in FORTRAN IV for implementation on CDC 6000-series computer.
We apply the theory of harmonic analysis on the fundamental domain of SL(2, Z) to partition functions of two-dimensional conformal field theories. We decompose the partition function of c free bosons on a Narain lattice into eigenfunctions of the Laplacian of worldsheet moduli space H/SL(2, Z), and of target space moduli space O(c, c; Z)\O(c, c; R)/O(c)×O(c). This decomposition manifests certain properties of Narain theories and ensemble averages thereof. We extend the application of spectral theory to partition functions of general two-dimensional conformal field theories, and explore its meaning in connection to AdS 3 gravity. An implication of harmonic analysis is that the local operator spectrum is fully determined by a certain subset of degeneracies.
Small instantons can play an important role in Yang-Mills theories whose gauge couplings are sizeable at small distances. An interesting class of theories where this could occur is in weakly-gauged holographic models (dual to Yang-Mills theories interacting with strongly-coupled CFTs), since gauge couplings are indeed enhanced towards the UV boundary of the 5D AdS space. However, contrary to expectations, we show that small instantons in these non-asymptotically-free models are highly suppressed and ineffective. This is due to the conservation of topological charge that forbids instantons to be localized near the UV boundary. Despite this fact we find non-trivial UV localized instanton-anti-instanton solutions of the Yang-Mills equations where the topological charges annihilate in the AdS bulk. These analytic solutions arise from a 5D conformal transformation of the uplifted 4D instanton. Our analysis therefore reveals unexpected nonperturbative configurations of Yang-Mills theories when they interact with strongly-coupled CFTs.
The fundamental interest in actinide chemistry, particularly for the development of thorium-based materials, is experiencing a renaissance owing to the recent and rapidly growing attention to fuel cycle reactors, radiological daughters for nuclear medicine, and efficient nuclear stockpile development. Herein, we uncover fundamental principles of thorium chemistry on the example of Th-based extended structures such as metal–organic frameworks in comparison with the discrete systems and zirconium extended analogs, demonstrating remarkable over two-and-half-year chemical stability of Th-based frameworks as a function of metal node connectivity, amount of defects, and conformational linker rigidity through comprehensive spectroscopic and crystallographic analysis as well as theoretical modeling. Despite exceptional chemical stability, we report the first example of studies focusing on the reactivity of the most chemically stable Th-based frameworks in comparison with the discrete Th-based systems such as metal–organic complexes and a cage, contrasting multicycle recyclability and selectivity (>97%) of the extended structures in comparison with the molecular compounds. Altogether, the presented work not only establishes the conceptual foundation for evaluating the capabilities of Th-based materials but also represents a milestone for their multifaceted future and foreshadows their potential to shape the next era of actinide chemistry.
Cytochromes P450 (CYPs) form one of the largest enzyme superfamilies, with similar structural folds yet biological functions varying from synthesis of physiologically essential compounds to metabolism of myriad xenobiotics. Sterol 14α-demethylases (CYP51s) represent a very special P450 family, regarded as a possible evolutionary progenitor for all currently existing P450s. In metazoans CYP51 is critical for the biosynthesis of sterols including cholesterol. Here we determined the crystal structures of ligand-free CYP51s from the abyssal fish Coryphaenoides armatus and human-. Comparative sequence–structure–function analysis revealed specific structural elements that imply elevated conformational flexibility, uncovering a molecular basis for faster catalytic rates, lower substrate selectivity, and intrinsic resistance to inhibition. In addition, the C. armatus structure displayed a large-scale repositioning of structural segments that, in vivo, are immersed in the endoplasmic reticulum membrane and border the substrate entrance (the FG arm, >20 Å, and the β4 hairpin, >15 Å). The structural distinction of C. armatus CYP51, which is the first structurally characterized deep sea P450, suggests stronger involvement of the membrane environment in regulation of the enzyme function. We interpret this as a co-adaptation of the membrane protein structure with membrane lipid composition during evolutionary incursion to life in the deep sea.
A centrifugal impeller based on an existing backswept design was defined. In addition, a vaned diffuser was designed to match this impeller and also to be compatible with an existing 6:1 compressor test rig. The mechanical integrity of this design was verified by analysis. Hardware was procured and inspected to insure conformity with design tolerances. An overspeed test was successfully conducted on one of the impellers fabricated under this program.
Bottlebrush polymers are a unique class of macromolecular architectures with a plethora of potential industrial and pharmaceutical applications that critically depend on the bottlebrush shape and dimensions. Here, a systematic series of 12 cylindrical and 12 cone-shaped (tapered) bottlebrush polymers with poly(tert-butyl acrylate) (PtBA) or polystyrene (PS) side chains were synthesized using the sequential addition of macromonomers ring-opening metathesis polymerization (SAM-ROMP) grafting-through method. Small-angle neutron scattering (SANS) studies on dilute solutions of the two types of bottlebrush polymers provided noninvasive characterization of their structural dimensions and chain conformations. Simulated SANS traces, generated using coarse-grained molecular dynamics simulations, reproduced the distinctive features observed in the experimental SANS signals and provided necessary validation for data modeling. The combined analysis of experimental and simulated SANS signals yielded key structural and conformational parameters, including the bottlebrush radius, length, and Kuhn length as well as the excluded volume parameter and the correlation length of the polymer side chains. Importantly, the obtained structural parameters followed well-defined scaling laws as a function of the backbone and side chain degrees of polymerization, as predicted by mean field theories. In conclusion, these findings provide clear experimental and computational evidence of the interdependence of structural and conformational properties in an important class of polymer architectures.
The Ku70/80 heterodimer is the first repair protein in the initial binding of double-strand break (DSB) ends following DNA damage, and is a component of nonhomologous end joining repair, the primary pathway for DSB repair in mammalian cells. In this study we constructed a full-length human Ku70 structure based on its crystal structure, and performed 20 ns conventional molecular dynamic (CMD) simulations on this protein and several other complexes with short DNA duplexes of different sequences. The trajectories of these simulations indicated that, without the topological support of Ku80, the residues in the bridge and C-terminal arm of Ku70 are more flexible than other experimentally identified domains. We studied the two missing loops in the crystal structure and predicted that they are also very flexible. Simulations revealed that they make an important contribution to the Ku70 interaction with DNA. Dislocation of the previously studied SAP domain was observed in several systems, implying its role in DNA binding. Targeted molecular dynamic (TMD) simulation was also performed for one system with a far-away 14bp DNA duplex. The TMD trajectory and energetic analysis disclosed detailed interactions of the DNA-binding residues during the DNA dislocation, and revealed a possible conformational transition for a DSB end when encountering Ku70 in solution. Compared to experimentally based analysis, this study identified more detailed interactions between DNA and Ku70. Free energy analysis indicated Ku70 alone is able to bind DNA with relatively high affinity, with consistent contributions from various domains of Ku70 in different systems. The functional implications of these domains in the processes of Ku heterodimerization and DNA damage recognition and repair can be characterized in detail based upon this analysis.
Herein, we present a novel method to incorporate structural results from surface-sensitive scattering, such as X-ray or neutron reflectometry, into molecular dynamics simulations. While reflectometry techniques generally provide a means to determine the molecular-scale structures of organized interfacial films, they were recently shown to offer the capability to characterize the structures of protein-membrane complexes supported by a solid substrate. One-dimensional information inherent in the experimental results is used in the form of component volume occupancy (CVO) profiles, which describe the distribution of molecular components within an interfacial architecture, to construct real-space constraints in the form of a biasing potential for the simulation that vanishes when the simulated and experimental profiles agree. This approach improves the correspondence between simulation and experiment, as shown in the re-evaluation of an neutron-reflection-derived structure which was approximated by an independent molecular dynamics simulation in earlier work, and it also leads to faster equilibration of ensemble structures. We further show that time averaging the CVO profile that develops in the simulation while biasing with this approach permits fluctuations about the average that are necessary for conformational exploration of the system. This method is particularly valuable for studies of proteins at interfaces that contain disordered regions since the conformation of such regions is difficult to judge from the analysis of one-dimensional experimental profiles and may take prohibitively long to equilibrate in simulations.
Temperature analysis during a pause in injection operations, known as warmback analysis, has been used in the petroleum industry for evaluating the injection conformance and estimating the location of the flooded front in applications, such as waterflooding oil reservoirs. Here in this work, methods are introduced to extend the application of temperature warmback analysis to estimate the zonal CO 2 injection rate and zonal CO 2 plume extent during geologic CO 2 storage in a saline aquifer. First, novel analytical solutions are developed to model transient temperature in the aquifer during the injection and subsequent shut-in periods considering two-phase flow (gaseous CO 2 and aqueous brine) conditions in the aquifer. The solution involves a discretization of the aquifer into regions; the energy and mass conservation equations for the regions are solved simultaneously considering appropriate boundary conditions at the interfaces. Two solutions techniques are presented: multi-region and three-region solutions. Inverse models are developed accordingly to evaluate the injection profile and estimate the extent of the plume front in the reservoir during the injection period. The multi-region solution results in an inversion approach that requires regression analysis. However, the three-region formulation results in a simple graphical technique for inverse modeling. The analytical solutions are validated against a thermally coupled reservoir simulation tool using different synthetic cases for CO 2 injection in deep saline aquifers. The results of the developed solutions provide a good match with numerical results during forward and inverse modeling.
We present a global analysis program for the generalized parton distributions (GPDs) based on conformal moment expansion. We apply the strategy of universal moment parameterization to fit both the collinear parton distribution functions (PDFs) from phenomenology and generalized form factors from lattice calculations, and show that the parameterization is flexible enough to accommodate these constraints. In addition, we can also fit direct lattice calculations of GPDs from large-momentum effective theory. In this work we focus on the analysis of t-dependent PDFs which correspond to GPDs in the ξ → 0 limit. The strategy also applies to the ξ ≠ 0 region with extra parameters, and therefore can be fitted to experimental observables in the future. With a demonstrative example of fitted GPDs, we exhibit the quark transverse angular momentum densities of the proton as well as the impact parameter space distributions of quarks in both unpolarized and transversely polarized protons.
The paper presents data on the accumulated V-band orbital phase curves of polarization in Cygnus X-1 which disagree with the analysis of Simmons, Aspin, and Brown (1980). No curves which conform to the canonical model were observed, and a noncanonical structure is indicated by F tests on third, fourth, and fifth harmonics, which have a probability of 0.85 as a group. The fifth harmonic has a probability of 0.99; in contrast, the fundamental harmonic has a probability of only 0.6, which is below the detection threshold. Therefore, major conclusions of Simmons et al based on a nonsymmetrical canonical model assuming that fundamental harmonics are present, but harmonics with n greater than 2 are absent, are unacceptable. Analysis of the author's data by Simmons et al is criticized on the grounds that he did not take into account the cumulative aspects of the data and did not recognize the need to average out the random noise generated by Cygnus X-1 over many orbital cycles.
The constant fragment (Fc) of the immunoglobulin G1 (IgG1) subtype is increasingly recognized as a crucial scaffold in the development of advanced therapeutics due to its enhanced specificity, efficacy, and extended half‐life. A prime example is VEGF‐Trap (Aflibercept), a recombinant fusion protein that merges the Fc region of the IgG1 subtype with the binding domains of vascular endothelial growth factor receptors (VEGFR)‐1 and VEGFR‐2. The Fc region's role in N‐glycosylation is particularly important, as it significantly influences protein stability. Herein, the first near‐physiological temperature structures of the N‐glycan‐bound Fc fragment of IgG1 subtype from a biosimilar VEGF‐Trap are presented, determined using the SPring‐8 Angstrom Compact free electron LAser (SACLA) and the Turkish Light Source (Turkish DeLight). Comparative analysis with cryogenic structures, including existing data, reveals alternate conformations within the glycan‐binding pocket. Furthermore, molecular dynamics simulations indicate the presence of a high degree of structural plasticity, explaining how the protein adapts its structure through conformational changes. The observed structural fluctuations/conformational changes demonstrate the effect of N‐glycans on protein stability. These findings offer new insights into the molecular basis of Fc‐mediated functions and provide valuable information for the design of next‐generation therapeutics.
Abstract The Nucleocapsid protein (N) of SARS-CoV-2 plays a critical role in the viral lifecycle by regulating RNA replication and by packaging the viral genome. N and RNA phase separate to form condensates that may be important for these functions. Both functions occur at membrane surfaces, but how N toggles between these two membrane-associated functional states is unclear. Here, we reveal that phosphorylation switches how N condensates interact with membranes, in part by modulating condensate material properties. Our studies also show that phosphorylation alters N’s interaction with viral membrane proteins. We gain mechanistic insight through structural analysis and molecular simulations, which suggest phosphorylation induces a conformational change in N that softens condensate material properties. Together, our findings identify membrane association as a key feature of N condensates and provide mechanistic insights into the regulatory role of phosphorylation. Understanding this mechanism suggests potential therapeutic targets for COVID infection.
The molecule r(GCG)d(TATACGC) is self-complementary and forms two DNA-RNA hybrid segments surrounding a central region of double helical DNA; its molecular structure has been solved by X-ray analysis. All three parts of the molecule adopt a conformation which is close to that seen in the 11-fold RNA double helix. The conformation of the ribonucleotides is partly determined by water molecules bridging between the ribose O2' hydroxyl group and cytosine O2. The hybrid-DNA duplex junction contains no structural discontinuities. However, the central DNA TATA sequence has some structural irregularities.
The viscous airfoil design analysis code XFOIL was extended to allow optimization using conformal mapping coefficients as design variables. The optimization technique used was the Steepest Descent method applied to a Penalty Function. The gradients of the aerodynamic variables with respect to the design variables were cheaply calculated as by-products of XFOIL's integral boundary layer Newton solver. The speed of the optimization process further increased by updating the Newton system boundary layer variables after each optimization step using the available gradient information. Two examples are presented.
The coupling between the desired CPW mode and the unwanted coupled slotline mode is presented for finite ground coplanar waveguides with unequal ground plane widths. Measurements, quasi-static conformal mapping, and Finite-Difference Time-Domain analysis are performed to determine the dependence of the slotline mode excitation on the physical dimensions of the FGC line and on the frequency range of operation. It is shown that the ratio of the slotline mode to the CPW mode can be as high as 18 dB. The use of airbridges is shown to reduce the slotline mode by 15 dB, but that the slotline mode fully reestablishes itself after 2000 microns. Furthermore, these results are independent of frequency.
The goal was to develop suitable methods and software for the analysis of antennas on cylindrical coated and uncoated platforms. Specifically, the finite element boundary integral and finite element ABC methods were employed successfully and associated software were developed for the analysis and design of wraparound and discrete cavity-backed arrays situated on cylindrical platforms. This work led to the successful implementation of analysis software for such antennas. Developments which played a role in this respect are the efficient implementation of the 3D Green's function for a metallic cylinder, the incorporation of the fast Fourier transform in computing the matrix-vector products executed in the solver of the finite element-boundary integral system, and the development of a new absorbing boundary condition for terminating the finite element mesh on cylindrical surfaces.