High-Dimensional Bayesian Optimisation with Large-Scale Constraints -- An Application to Aeroelastic Tailoring

Design optimisation potentially leads to lightweight aircraft structures with lower environmental impact. Due to the high number of design variables and constraints, these problems are ordinarily solved using gradient-based optimisation methods, leading to a local solution in the design space while the global space is neglected. Bayesian Optimisation is a promising path towards sample-efficient, global optimisation based on probabilistic surrogate models. While Bayesian optimisation methods have demonstrated their strength for problems with a low number of design variables, the scalability to high-dimensional problems while incorporating large-scale constraints is still lacking. Especially in aeroelastic tailoring where directional stiffness properties are embodied into the structural design of aircraft, to control aeroelastic deformations and to increase the aerodynamic and structural performance, the safe operation of the system needs to be ensured by involving constraints resulting from different analysis disciplines. Hence, a global design space search becomes even more challenging. The present study attempts to tackle the problem by using high-dimensional Bayesian Optimisation in combination with a dimensionality reduction approach to solve the optimisation problem occurring in aeroelastic tailoring, presenting a novel approach for high-dimensional problems with large-scale constraints. Experiments on well-known benchmark cases with black-box constraints show that the proposed approach can incorporate large-scale constraints.Comment: Conference paper submitted to AIAA Scitech 2024 Foru

A Diversity of Conserved and Novel Ovarian MicroRNAs in the Speckled Wood (Pararge aegeria)

microRNAs (miRNAs) are important regulators of animal development and other processes, and impart robustness to living systems through post-transcriptional regulation of specific mRNA transcripts. It is postulated that newly emergent miRNAs are generally expressed at low levels and with spatiotemporally restricted expression domains, thus minimising effects of spurious targeting on animal transcriptomes. Here we present ovarian miRNA transcriptome data for two geographically distinct populations of the Speckled Wood butterfly (Pararge aegeria). A total of 74 miRNAs were identified, including 11 newly discovered and evolutionarily-young miRNAs, bringing the total of miRNA genes known from P. aegeria up to 150. We find a positive correlation between miRNA age and expression level. A common set of 55 miRNAs are expressed in both populations. From this set, we identify seven that are consistently either ovary-specific or highly upregulated in ovaries relative to other tissues. This ‘ovary set’ includes miRNAs with known contributions to ovarian function in other insect species with similar ovaries and mode of oogenesis, including miR-989 and miR-2763, plus new candidates for ovarian function. We also note that conserved miRNAs are overrepresented in the ovary relative to the whole body

Activated Ion Electron Capture Dissociation (AI ECD) of proteins: synchronization of infrared and electron irradiation with ion magnetron motion.

Here, we show that to perform activated ion electron capture dissociation (AI-ECD) in a Fourier transform ion cyclotron resonance (FT-ICR) mass spectrometer equipped with a CO(2) laser, it is necessary to synchronize both infrared irradiation and electron capture dissociation with ion magnetron motion. This requirement is essential for instruments in which the infrared laser is angled off-axis, such as the Thermo Finnigan LTQ FT. Generally, the electron irradiation time required for proteins is much shorter (ms) than that required for peptides (tens of ms), and the modulation of ECD, AI ECD, and infrared multiphoton dissociation (IRMPD) with ion magnetron motion is more pronounced. We have optimized AI ECD for ubiquitin, cytochrome c, and myoglobin; however the results can be extended to other proteins. We demonstrate that pre-ECD and post-ECD activation are physically different and display different kinetics. We also demonstrate how, by use of appropriate AI ECD time sequences and normalization, the kinetics of protein gas-phase refolding can be deconvoluted from the diffusion of the ion cloud and measured on the time scale longer than the period of ion magnetron motion

The Role of the D13 (1520) Resonance in eta Electroproduction

We investigate the electroproduction of eta mesons below a center of momentum energy of 1.6 GeV, with particular emphasis on the roles of the N*(1535) and N*(1520) resonances. Using the effective Lagrangian approach, we show that the transverse helicity amplitude of the N*(1535) can be extracted with good accuracy from the new eta electroproduction data, under reasonable assumptions for the strength of the longitudinal helicity amplitude. In addition, although the differential cross section is found to to have a small sensitivity to the N*(1520) resonance, it is shown that a recently completed double polarization experiment is very sensitive to this resonance.Comment: 7 pages, Revtex, 3 figure

Topoisomer Differentiation of Molecular Knots by FTICR MS: Lessons from Class II Lasso Peptides

Lasso peptides constitute a class of bioactive peptides sharing a knotted structure where the C-terminal tail of the peptide is threaded through and trapped within an N-terminalmacrolactamring. The structural characterization of lasso structures and differentiation from their unthreaded topoisomers is not trivial and generally requires the use of complementary biochemical and spectroscopic methods. Here we investigated two antimicrobial peptides belonging to the class II lasso peptide family and their corresponding unthreaded topoisomers: microcin J25 (MccJ25), which is known to yield two-peptide product ions specific of the lasso structure under collisioninduced dissociation (CID), and capistruin, for which CID does not permit to unambiguously assign the lasso structure. The two pairs of topoisomers were analyzed by electrospray ionization Fourier transform ion cyclotron resonance mass spectrometry (ESI-FTICR MS) upon CID, infrared multiple photon dissociation (IRMPD), and electron capture dissociation (ECD). CID and ECDspectra clearly permitted to differentiate MccJ25 from its non-lasso topoisomer MccJ25-Icm, while for capistruin, only ECD was informative and showed different extent of hydrogen migration (formation of c\bullet/z from c/z\bullet) for the threaded and unthreaded topoisomers. The ECD spectra of the triply-charged MccJ25 and MccJ25-lcm showed a series of radical b-type product ions {\eth}b0In{\TH}. We proposed that these ions are specific of cyclic-branched peptides and result from a dual c/z\bullet and y/b dissociation, in the ring and in the tail, respectively. This work shows the potentiality of ECD for structural characterization of peptide topoisomers, as well as the effect of conformation on hydrogen migration subsequent to electron capture

Quasifree Pion Electroproduction from Nuclei in the Δ\Delta Region

We present calculations of the reaction $A(e,e^\prime \pi N)B$ in the distorted wave impulse approximation. The reaction allows for the study of the production process in the nuclear medium without being obscured by the details of nuclear transition densities. First, a pion electroproduction operator suitable for nuclear calculations is obtained by extending the Blomqvist-Laget photoproduction operator to the virtual photon case. The operator is gauge invariant, unitary, reference frame independent, and describes the existing data reasonably well. Then it is applied in nuclei to predict nuclear cross sections under a variety of kinematic arrangements. Issues such as the effects of gauge-fixing, the interference of the $\Delta$ resonance with the background, sensitivities to the quadrupole component of the $\Delta$ excitation and to the electromagnetic form factors, the role of final-state interactions, are studied in detail. Methods on how to experimentally separate the various pieces in the coincidence cross section are suggested. Finally, the model is compared to a recent SLAC experiment.Comment: 27 pages in REVTEX, plus 22 PS figures embedded using psfig.sty (included), uuencode

The relativistic impulse approximation for the exclusive electrodisintegration of the deuteron

The electrodisintegration of the deuteron in the frame of the Bethe-Salpeter approach with a separable kernel of the nucleon-nucleon interaction is considered. This conception keeps the covariance of a description of the process. A comparison of relativistic and nonrelativistic calculations is presented. The factorization of the cross section of the reaction in the impulse approximation is obtained by analytical calculations. It is shown that the photon-neutron interaction plays an important role.Comment: 31 pages, 14 figures, 1 tabl

Electron Capture Dissociation Mass Spectrometry of Tyrosine Nitrated Peptides

In vivo protein nitration is associated with many disease conditions that involve oxidative stress and inflammatory response. The modification involves addition of a nitro group at the position ortho to the phenol group of tyrosine to give 3-nitrotyrosine. To understand the mechanisms and consequences of protein nitration, it is necessary to develop methods for identification of nitrotyrosine-containing proteins and localization of the sites of modification.Here, we have investigated the electron capture dissociation (ECD) and collision-induced association (CID) behavior of 3-nitrotyrosine-containing peptides. The presence of nitration did not affect the CID behavior of the peptides. For the doubly-charged peptides, addition of nitration severely inhibited the production of ECD sequence fragments. However, ECD of the triply-charged nitrated peptides resulted in some singly-charged sequence fragments. ECD of the nitrated peptides is characterized by multiple losses of small neutral species including hydroxyl radicals, water and ammonia. The origin of the neutral losses has been investigated by use of activated ion (AI) ECD. Loss of ammonia appears to be the result of non-covalent interactions between the nitro group and protonated lysine side-chains

Electromagnetic Meson Production in the Nucleon Resonance Region

Recent experimental and theoretical advances in investigating electromagnetic meson production reactions in the nucleon resonance region are reviewed.Comment: 75 pages, 42 figure

Covariant description of inelastic electron--deuteron scattering:predictions of the relativistic impulse approximation

Using the covariant spectator theory and the transversity formalism, the unpolarized, coincidence cross section for deuteron electrodisintegration, $d(e,e'p)n$, is studied. The relativistic kinematics are reviewed, and simple theoretical formulae for the relativistic impulse approximation (RIA) are derived and discussed. Numerical predictions for the scattering in the high $Q^2$ region obtained from the RIA and five other approximations are presented and compared. We conclude that measurements of the unpolarized coincidence cross section and the asymmetry $A_\phi$, to an accuracy that will distinguish between different theoretical models, is feasible over most of the wide kinematic range accessible at Jefferson Lab.Comment: 54 pages and 24 figure