Canonical System Research Articles

Toward understanding the dimensional crossover of canonical spin-glass thin films

Spin-glass thin films exhibit many features different from the bulk. The freezing temperatures of spin-glass films are suppressed for reduced thickness and follow the Kenning relation. The dynamics are altered near the vacuum interface. These phenomena are closely related to the lower critical dimension of spin glasses, the spin-glass correlation length, and the dimensional crossover from d = 3 to d = 2. In this article, we review the experimental facts and theoretical perspectives for spin-glass thin films. We focus on canonical spin-glass systems with the Ruderman–Kittel–Kasuya–Yosida (RKKY) interaction between magnetic impurities in a nonmagnetic host. Open questions to be addressed are emphasized.

The Cycle 46 Configuration of the HARMONIE-AROME Forecast Model

The aim of this technical note is to describe the Cycle 46 reference configuration of the HARMONIE-AROME convection-permitting numerical weather prediction model. HARMONIE-AROME is one of the canonical system configurations that is developed, maintained, and validated in the ACCORD consortium, a collaboration of 26 countries in Europe and northern Africa on short-range mesoscale numerical weather prediction. This technical note describes updates to the physical parametrizations, both upper-air and surface, configuration choices such as lateral boundary conditions, model levels, horizontal resolution, model time step, and databases associated with the model, such as for physiography and aerosols. Much of the physics developments are related to improving the representation of clouds in the model, including developments in the turbulence, shallow convection, and statistical cloud scheme, as well as changes in radiation and cloud microphysics concerning cloud droplet number concentration and longwave cloud liquid optical properties. Near real-time aerosols and the ICE-T microphysics scheme, which improves the representation of supercooled liquid, and a wind farm parametrization have been added as options. Surface-wise, one of the main advances is the implementation of the lake model FLake. An outlook on upcoming developments is also included.

Classification of solid and liquid structures using a deep neural network unveils origin of dynamical heterogeneities in supercooled liquids

As the temperature decreases, the dynamics of supercooled liquids significantly slow down and become increasingly heterogeneous in space. Many previous studies have found that static structures also become heterogeneous and are spatially correlated with the dynamical heterogeneity. However, there are still debates on whether the dynamical heterogeneity is controlled by the structures, and which structural order parameters should be used to describe the structural heterogeneities (if exist) in amorphous systems. The appropriate order parameter depends on the specific details of the system and needs to be determined for each system. To address this difficulty, here, we use a machine-learning-based method that was trained solely by the static structures. This method combines convolutional neural networks and gradient-weighted class activation mapping, providing interpretable characteristic structures, which can quantify the degrees of liquid-like and solid-like structures in every local part of the system. We apply this method to a canonical glass-forming system and demonstrate that particles in the liquid-like structures are mobile, while those in the solid-like structures are immobile. The present work develops a novel approach to accurately characterize amorphous structures, which will be particularly useful for systems where appropriate structural order parameters have not yet been identified.

A DSMC-CFD coupling method using surrogate modelling for low-speed rarefied gas flows

A new Micro-Macro-Surrogate (MMS) hybrid method is presented that couples the Direct Simulation Monte Carlo (DSMC) method with Computational Fluid Dynamics (CFD) to simulate low-speed rarefied gas flows. The proposed MMS method incorporates surrogate modelling instead of direct coupling of DSMC data with the CFD, addressing the limitations CFD has in accurately modelling rarefied gas flows, the computational cost of DSMC for low-speed and multiscale flows, as well as the pitfalls of noise in conventional direct coupling approaches. The surrogate models, trained on the DSMC data using Bayesian inference, provide noise-free and accurate corrections to the CFD simulation enabling it to capture the non-continuum physics. The MMS hybrid approach is validated by simulating low-speed, steady-state, force-driven rarefied gas flows in a canonical 1D parallel-plate system, where corrections to the boundary conditions and stress tensor are considered and shows excellent agreement with DSMC benchmark results. A comparison with the typical domain decomposition DSMC-CFD hybrid method is also presented, to demonstrate the advantages of noise-avoidance in the proposed approach. The method also inherently captures the uncertainty arising from micro-model fluctuations, allowing for the quantification of noise-related uncertainty in the predictions. The proposed MMS method demonstrates the potential to enable multiscale simulations where CFD is inaccurate and DSMC is prohibitively expensive.

Identification of Hamiltonian systems using neural networks and first integrals approaches

This research introduces a class of non-parametric identifiers based on differential neural networks represented by Hamiltonian dynamics. The structure of the identifier corresponds to the form of a canonical Hamiltonian system that uses the evolution of generalized coordinates and momentums. The learning laws of the identifier come from applying the first integrals approach, which justifies the design of an exact identifier considering the time invariance of the Hamiltonian, with a finite number of activation functions in the identifier structure. The first integrals approach derives several learning laws for the proposed class of identifiers. The learning laws design uses the estimated derivative of the generalized momentum assessed via a super-twisting differentiator with multiple inputs and outputs. All proposed laws require the solution of differential continuous-time Riccati equations and nonlinear differential equations for the learning laws, which depend on the identification error and state constraints. The developed identifier was evaluated compared to an identifier that did not consider the Hamiltonian constraint using first integrals. This comparison included a numerical evaluation of the identifier considering its application to a classical Hamiltonian system associated with the Kepler dynamics representing satellite orbital evolution. This evaluation confirmed that the identification results were improved with the proposed learning laws regarding the class of Hamiltonian structures, and the quality indicators based on the mean square error were several times lower.

Refined Prior Guided Category-Level 6D Pose Estimation and Its Application on Robotic Grasping

Estimating the 6D pose and size of objects is crucial in the task of visual grasping for robotic arms. Most current algorithms still require the 3D CAD model of the target object to match with the detected points, and they are unable to predict the object’s size, which significantly limits the generalizability of these methods. In this paper, we introduce category priors and extract high-dimensional abstract features from both the observed point cloud and the prior to predict the deformation matrix of the reconstructed point cloud and the dense correspondence between the reconstructed and observed point clouds. Furthermore, we propose a staged geometric correction and dense correspondence refinement mechanism to enhance the accuracy of regression. In addition, a novel lightweight attention module is introduced to further integrate the extracted features and identify potential correlations between the observed point cloud and the category prior. Ultimately, the object’s translation, rotation, and size are obtained by mapping the reconstructed point cloud to a normalized canonical coordinate system. Through extensive experiments, we demonstrate that our algorithm outperforms existing methods in terms of performance and accuracy on commonly used benchmarks for this type of problem. Additionally, we implement the algorithm in robotic arm-grasping simulations, further validating its effectiveness.

The activity of the quorum sensing regulator HapR is modulated by the bacterial extracellular vesicle (BEV)-associated protein ObfA of Vibrio cholerae.

Vibrio cholerae, a facultative human pathogen and causative agent of the severe diarrheal disease cholera, transits between the human intestinal tract and aquatic reservoirs. Like other bacterial species, V. cholerae continuously releases bacterial extracellular vesicles (BEVs) from its surface, which have been recently characterised for their role during in vivo colonisation. However, between epidemic outbreaks, V. cholerae persists in the biofilm mode for extended periods in aquatic reservoirs, which enhances environmental fitness and host transition. In this study, we investigated the effect of V. cholerae BEVs on biofilm formation, a critical feature for ex vivo survival. In contrast to BEVs from planktonic cultures, our results show that physiological concentrations of BEVs from dynamic biofilm cultures facilitate V. cholerae biofilm formation, which could be linked to a proteinaceous factor. Comparative proteomic analyses of planktonic- and biofilm-derived BEVs identified a previously uncharacterised outer membrane protein as an abundant component of dynamic biofilm-derived BEVs, which was found to be responsible for the BEV-dependent enhancement of biofilm production. Consequently, this protein was named outer membrane-associated biofilm facilitating protein A (ObfA). Comprehensive molecular studies unravelled ObfA as a negative modulator of HapR activity. HapR is a key transcriptional regulator of the V. cholerae quorum sensing (QS) cascade acting as a potent repressor of biofilm formation and virulence. Consistently, obfA mutants not only exhibited reduced biofilm production but also reduced colonisation fitness. Surprisingly, our results demonstrate that ObfA does not affect HapR through the canonical QS system but via the Csr-cascade altering the expression of the small regulatory RNAs CsrC and CsrD. In summary, this study elucidates a novel intraspecies BEV-based communication in V. cholerae that influences biofilm formation and colonisation fitness via a new regulatory pathway involving HapR, Csr-cascade and the BEV-associated protein ObfA.

Investigating the Existence of a Pseudo-Initial State in Proton Transfer during the Volmer Reaction in a Grand Canonical Environment

Protons play a significant role in electrochemical reactions. In a simulated Volmer reaction, we can imagine the initial state as a situation where protons are in a bulk state with an empty metal slab. To study the reaction barrier, we need to move the protons from the reservoir to the surface of the electrode. We term the state where the proton has reached the near-surface layer the pseudo-initial state. This prompts the question of how protons from the bulk migrate to the near-surface and whether this pseudo-initial state truly exists. If protons don't become localized at the near-surface layer but follow a concerted mechanism, the existence of the pseudo-initial state becomes uncertain. In our research, we examined the pathways of protons in the grand canonical system using the solvated jellium method and determined the localization of protons in the near-surface layer, thus confirming the existence of pseudo-initial states.

Hamiltonian formalism for bistable-multilayered plates under non-mechanical stimuli

Bistable multilayered plates have attracted significant attention as morphing and adaptive structures, renowned for their unprecedented exceptional performance. However, accurately predicting both their shape and internal stresses poses formidable challenges due to their geometrically nonlinear nature. For the first time, this paper introduces a Hamiltonian formalism aimed at achieving high-resolution analysis of nonlinear multilayered plates subjected to non-mechanical stimuli, including hygro-thermo-electro-magneto-elastic responses. A canonical system is strategically developed to compute membrane behaviors, yielding symplectic dual differential equations for in-plane field variables. This method elegantly decouples out-of-plane variables from the full-state vector, leading to an exact analytical solution in the membrane problem. To predict the bending behaviors, the first variation of the Hamiltonian energy density function, expressed as a power series of the transverse deflection, ensures flexural equilibrium. The power series effectively captures all admissible out-of-plane deformations, enabling a smooth transition between linear and nonlinear plate responses, including pitchfork bifurcation and limit points. The validity and accuracy of the proposed method are rigorously assessed through convergence tests and satisfaction of boundary conditions across various equilibria, ranging from monostability to bistability. It is cross-verified with high-fidelity finite-element methods (FEM), showing excellent agreements in both deformations and stress resultants. This research presents a physics-based methodology that unveils a parametric interplay between in-plane and out-of-plane field variables, serving as an efficient approach for analyzing adaptive and morphing structures.

Unpacking Alternative Features of the Bacterial Chemotaxis System.

The bacterial chemotaxis system is one of the best-understood cellular pathways and serves as the model for signal transduction systems. Most chemotaxis research has been conducted with transmembrane chemotaxis systems from Escherichia coli and has established paradigms of the system that were thought to be universal. However, emerging research has revealed that many bacteria possess alternative features of their chemotaxis system, demonstrating that these systems are likely more complex than previously assumed. Here, we compare the canonical chemotaxis system of E. coli with systems that diverge in supramolecular architecture, sensory mechanisms, and protein composition. The alternative features have likely evolved to accommodate chemical specificities of natural niches and cell morphologies. Collectively, these studies demonstrate that bacterial chemotaxis systems are a rapidly expanding field that offers many new opportunities to explore this exceedingly diverse system.

What is the hard spectral state in X-ray binaries? Insights from GRRMHD accretion flows simulations and polarization of their X-ray emission

X-ray binaries are known to exhibit different spectral states which are often associated with different black hole accretion modes. The exact geometry and properties of these accretion modes is still uncertain. Recent IXPE measurements of linear polarization of X-ray emission in canonical X-ray binary system Cygnus X-1 allow us to test models for the hard spectral state of accretion in a unique way. We show that general relativistic radiative magnetohydrodynamic (GRRMHD) simulations of accreting stellar black hole in a hard X-ray state may be consistent with the new observational information. In the presented framework, where first-principle models have limited number of free parameters, the polarimetric X-ray observations put constraints on the viewing angle of the inner hot accretion flow.

Interpretation of the Schur–Cohn Test in Terms of Canonical Systems

Interpretation of the Schur–Cohn Test in Terms of Canonical Systems

Predefined-time stabilization of Lorenz system with applications for stabilizing and synchronizing chaotic finance systems

This article investigates the predefined-time stabilization (PtS) of the canonical Lorenz system at first, and then applies the derived results into the chaotic finance systems (CFSs) so as to realize the stabilization and synchronization, respectively. Compared with the traditional finite-/fixed-time stability analysis, the upper-bound of convergence time (UbCT) in this investigation can be set beforehand in need, which is an explicit constant regardless of initial values, system dimension, and controlling parameters. Moreover, the designed control schemes are non-chattering, which do not contain the conventional discontinuous signum and absolute value functions anymore. Via adopting the second Lyapunov method, the sufficient conditions are obtained successively for guaranteeing the realization of PtS for Lorenz system, CFS, as well as the predefined-time synchronization between two CFSs. The numerical experiments are finally arranged to manifest the correctness and effectiveness of the theoretical fruits, in which some comparison and perturbation analysis are made.

Norm and a Singular Administrative Act

Due to the terminological confusion and dispute in contemporary doctrine regarding the nature of singular administrative acts (Canons 35-95), the paper examines the interdependence between the canonical norm and this category of acts. The research goal is set in a broader context, as the issue of canonical norms and the normative system of the canonical legal order are examined synthetically. The author expresses the view that in relation to individual administrative acts it is inappropriate to use the term “norm”, but he considers it appropriate to use the category of “acts” in the sense of legal acts. This position is based on the following arguments: first, during the codification work, consultors did not use the category of “norm” but the category “singular administrative act”; secondly, the first chapter of the Code’s fourth title is “Common Norms” (Normae communes); in the name of the fourth title, “Singular Administrative Acts”, we find the term “acts”; thirdly, in the canonical system some acts (dispensations, privileges) are issued against or in addition to the law, being exceptions to general norm.

МЕТОДИКА РАСЧЕТА КОМБИНИРОВАННОЙ КОНСТРУКЦИИ ПОКРЫТИЯ ШПРЕНГЕЛЬНОГО ТИПА

Hybrid building structures have advantages in terms of efficiency of using high-strength materials and reducing deformations under load. To expand the scope of their practical application, it is necessary to improve techniques for structural analysis and design methods. The object of the present research is a hybrid structure of the strutted-type. The top chord of the structure is formed by rectilinear beams arranged in radial direction and pivotally connected in the ridge joint. The bottom chord consists of high-strength cable elements and hinge struts. For the static analysis of the structure, its flat model is adopted. The static indeterminacy is solved by means of the method of redundant reactions. The applicability of the method is justified by restriction of structural deformations implied by the serviceability limit state. Analytical expressions are proposed to determine the forces and bending moments in the main structural elements. The resulting expressions are unified to perform the structural analysis under pre-stress and external loads by means of supplementary parameters introduced. An improved technique for finding the matrix of coefficients and the vector of free terms of the canonical system of the method of redundant reactions is proposed. The technique allows automating the calculation. A method for taking into account flexible cable elements is developed. The method includes step-by-step eliminating of compressed cables from the design scheme. The results of the work contribute to the development of hybrid strutted-type structures and can be used for developing optimal design solutions, as well as to identify patterns of stress-strain state of the hybrid structures by means of the numerical simulation.

Exploiting the Unique Biology of Caenorhabditis elegans to Launch Neurodegeneration Studies in Space.

The 21st century is likely to be the first century in which large-scale short- and long-term space missions become common. Accordingly, an ever-increasing body of research is focusing on understanding the effects of current and future space expeditions on human physiology in health and disease. Yet the complex experimental environment, the small number of participants, and the high cost of space missions are among the primary factors that hinder a better understanding of the impact of space missions on human physiology. The goal of our research was to develop a cost-effective, compact, and easy-to-manipulate system to address questions related to human health and disease in space. This initiative was part of the Ramon SpaceLab program, an annual research-based learning program designed to cultivate high school students' involvement in space exploration by facilitating experiments aboard the International Space Station (ISS). In the present study, we used the nematode Caenorhabditis elegans (C. elegans), a well-suited model organism, to investigate the effect of space missions on neurodegeneration-related processes. Our study specifically focused on the level of aggregation of Huntington's disease-causing polyglutamine stretch-containing (PolyQ) proteins in C. elegans muscles, the canonical system for studying neurodegeneration in this organism. We compared animals expressing PolyQ proteins grown onboard the ISS with their genetically identical siblings grown on Earth and observed a significant difference in the number of aggregates between the two populations. Currently, it is challenging to determine whether this effect stems from developmental or morphological differences between the cultures or is a result of life in space. Nevertheless, our results serve as a proof of concept and open a new avenue for utilizing C. elegans to address various open questions in space studies, including the effects of space conditions on the onset and development of neurodegenerative diseases.

Diaminopurine in Nonenzymatic RNA Template Copying.

In the RNA World before the emergence of an RNA polymerase, nonenzymatic template copying would have been essential for the transmission of genetic information. However, the products of chemical copying with the canonical nucleotides (A, U, C, and G) are heavily biased toward the incorporation of G and C, which form a more stable base pair than A and U. We therefore asked whether replacing adenine (A) with diaminopurine (D) might lead to more efficient and less biased nonenzymatic template copying by making a stronger version of the A:U pair. As expected, primer extension substrates containing D bound to U in the template more tightly than substrates containing A. However, primer extension with D exhibited elevated reaction rates on a C template, leading to concerns about fidelity. Our crystallographic studies revealed the nature of the D:C mismatch by showing that D can form a wobble-type base pair with C. We then asked whether competition with G would decrease the mismatched primer extension. We performed nonenzymatic primer extension with all four activated nucleotides on randomized RNA templates containing all four letters and used deep sequencing to analyze the products. We found that the DUCG genetic system exhibited a more even product distribution and a lower mismatch frequency than the canonical AUCG system. Furthermore, primer extension is greatly reduced following all mismatches, including the D:C mismatch. Our study suggests that D deserves further attention for its possible role in the RNA World and as a potentially useful component of artificial nonenzymatic RNA replication systems.

Role of Rabenosyn-5 and Rab5b in host cell cytosol uptake reveals conservation of endosomal transport in malaria parasites.

Vesicular trafficking, including secretion and endocytosis, plays fundamental roles in the unique biology of Plasmodium falciparum blood-stage parasites. Endocytosis of host cell cytosol (HCC) provides nutrients and room for parasite growth and is critical for the action of antimalarial drugs and parasite drug resistance. Previous work showed that PfVPS45 functions in endosomal transport of HCC to the parasite's food vacuole, raising the possibility that malaria parasites possess a canonical endolysosomal system. However, the seeming absence of VPS45-typical functional interactors such as rabenosyn 5 (Rbsn5) and the repurposing of Rab5 isoforms and other endolysosomal proteins for secretion in apicomplexans question this idea. Here, we identified a parasite Rbsn5-like protein and show that it functions with VPS45 in the endosomal transport of HCC. We also show that PfRab5b but not PfRab5a is involved in the same process. Inactivation of PfRbsn5L resulted in PI3P and PfRab5b decorated HCC-filled vesicles, typical for endosomal compartments. Overall, this indicates that despite the low sequence conservation of PfRbsn5L and the unusual N-terminal modification of PfRab5b, principles of endosomal transport in malaria parasite are similar to that of model organisms. Using a conditional double protein inactivation system, we further provide evidence that the PfKelch13 compartment, an unusual apicomplexa-specific endocytosis structure at the parasite plasma membrane, is connected upstream of the Rbsn5L/VPS45/Rab5b-dependent endosomal route. Altogether, this work indicates that HCC uptake consists of a highly parasite-specific part that feeds endocytosed material into an endosomal system containing more canonical elements, leading to the delivery of HCC to the food vacuole.

In-silico green toxicology approach toward discovering safer ligands for development of safe-by-design metal–organic frameworks

A vast variety of chemical compounds have been fabricated and commercialized, they not only result in industrial exposure during manufacturing and usage, but also have environmental impacts throughout their whole life cycle. Consequently, attempts to assess the risk of chemicals in terms of toxicology have never ceased. In-silico toxicology, also known as predictive toxicology, has advanced significantly over the last decade as a result of the drawbacks of experimental investigations. In this study, ProTox-III was applied to predict the toxicity of the ligands used for metal–organic framework (MOF) design and synthesis. Initially, 35 ligands, that have been frequently utilized for MOF synthesis and fabrication, were selected. Subsequently, canonical simplified molecular-input line-entry system (SMILES) of ligands were extracted from the PUBCHEM database and inserted into the ProTox-III online server. Ultimately, webserver outputs including LD50 and the probability of toxicological endpoints (cytotoxicity, carcinogenicity, mutagenicity, immunotoxicity, and ecotoxicity) were obtained and organized. According to retrieved LD50 data, the safest ligand was 5-hydroxyisophthalic. In contrast, the most hazardous ligand was 5-chlorobenzimidazole, with an LD50 of 8 mg/kg. Among evaluated endpoints, ecotoxicity was the most active and was detected in several imidazolate ligands. This data can open new horizons in design and development of green MOFs.

Elucidating chirality transfer in liquid crystals of viruses.

Chirality is ubiquitous in nature across all length scales, with major implications spanning fields from biology, chemistry and physics to materials science. How chirality propagates from nanoscale building blocks to meso- and macroscopic helical structures remains an open issue. Here, working with a canonical system of filamentous viruses, we demonstrate that their self-assembly into chiral liquid crystal phases quantitatively results from the interplay between two main mechanisms of chirality transfer: electrostatic interactions from the helical charge patterns on the virus surface, and fluctuation-based helical deformations leading to viral backbone helicity. Our experimental and theoretical approach provides a comprehensive framework for deciphering how chirality is hierarchically and quantitatively propagated across spatial scales. Our work highlights the ways in which supramolecular helicity may arise from subtle chiral contributions of opposite handedness that act either cooperatively or competitively, thus accounting for the multiplicity of chiral behaviours observed for nearly identical molecular systems.