Spatially proximate amino acids in a protein tend to coevolve. A protein's three-dimensional (3D) structure hence leaves an echo of correlations in the evolutionary record. Reverse engineering 3D structures from such correlations is an open problem in structural biology, pursued with increasing vigor as more and more protein sequences continue to fill the data banks. Within this task lies a statistical inference problem, rooted in the following: correlation between two sites in a protein sequence can arise from firsthand interaction but can also be network-propagated via intermediate sites; observed correlation is not enough to guarantee proximity. To separate direct from indirect interactions is an instance of the general problem of inverse statistical mechanics, where the task is to learn model parameters (fields, couplings) from observables (magnetizations, correlations, samples) in large systems. In the context of protein sequences, the approach has been referred to as direct-coupling analysis. Here we show that the pseudolikelihood method, applied to 21-state Potts models describing the statistical properties of families of evolutionarily related proteins, significantly outperforms existing approaches to the direct-coupling analysis, the latter being based on standard mean-field techniques. This improved performance also relies on a modified score for the coupling strength. The results are verified using known crystal structures of specific sequence instances of various protein families. Code implementing the new method can be found at http://plmdca.csc.kth.se/.
The identification of coherent structures from experimental or numerical data is an essential task when conducting research in fluid dynamics. This typically involves the construction of an empirical mode base that appropriately captures the dominant flow structures. The most prominent candidates are the energy-ranked proper orthogonal decomposition (POD) and the frequency-ranked Fourier decomposition and dynamic mode decomposition (DMD). However, these methods are not suitable when the relevant coherent structures occur at low energies or at multiple frequencies, which is often the case. To overcome the deficit of these ‘rigid’ approaches, we propose a new method termed spectral proper orthogonal decomposition (SPOD). It is based on classical POD and it can be applied to spatially and temporally resolved data. The new method involves an additional temporal constraint that enables a clear separation of phenomena that occur at multiple frequencies and energies. SPOD allows for a continuous shifting from the energetically optimal POD to the spectrally pure Fourier decomposition by changing a single parameter. In this article, SPOD is motivated from phenomenological considerations of the POD autocorrelation matrix and justified from dynamical systems theory. The new method is further applied to three sets of PIV measurements of flows from very different engineering problems. We consider the flow of a swirl-stabilized combustor, the wake of an airfoil with a Gurney flap and the flow field of the sweeping jet behind a fluidic oscillator. For these examples, the commonly used methods fail to assign the relevant coherent structures to single modes. The SPOD, however, achieves a proper separation of spatially and temporally coherent structures, which are either hidden in stochastic turbulent fluctuations or spread over a wide frequency range. The SPOD requires only one additional parameter, which can be estimated from the basic time scales of the flow. In spite of all these benefits, the algorithmic complexity and computational cost of the SPOD are only marginally greater than those of the snapshot POD.
Direct numerical simulations (DNS) are conducted to investigate the effects of spanwise domain size on stably stratified turbulent shear layers. The focus is on the formation and spatial organization of elongated large-scale structures (ELSS), which emerge following the transition from Kelvin–Helmholtz instability and characterized by streamwise extents far exceeding the shear layer’s thickness. Simulations are conducted for a temporally developing shear layer under stable density stratification. The spanwise extent is varied, while the streamwise and vertical domain sizes are fixed. Flow visualizations, one-point statistics, energy spectra, and two-point correlation functions are used to assess the influence of spanwise confinement on the transition process and late-time turbulence characteristics. The results show that when the spanwise domain size is very small, the transition process is altered and ELSS fail to develop properly. For intermediate domain sizes, the streamwise elongation of ELSS is captured, but their meandering and spatial repetition are suppressed. Statistical analysis reveals that while the meandering of ELSS contributes to large-scale structure, the presence of multiple alternating ELSS in the spanwise direction is more critical to the overall flow statistics. These findings emphasize the importance of spanwise configurations of ELSS in the dynamics and energetics of stably stratified shear layers.
Mechanical engineering and machinery, Mechanics of engineering. Applied mechanics
Reducing the ratio of box girders' span to their height reduces bending moments and makes them deep members that are controlled by shear behavior. The presence of horizontal curvature generates torsional moments and different deflection between the outer and inner web as a result of twisting. Two experimental specimens with the same dimensions were cast and tested, one straight and the other horizontally curved. The two specimens were numerically modeled using the ABAQUS software for the purpose of verifying the numerical model to study more parameters. The finite element analysis showed a good agreement with the experimental values with a difference of (98-99) %, (94-97)% and 103% of the experiment for ultimate loading, deflection and twisting angle, respectively. It also showed stress paths that match the experimental and theoretical results that explain the behavior of deep beams, such as the Strut and Tie method (STM). The effect of compressive strength, whole width, and the width of the bearing and supporting plates was studied. Results showed that increasing the concrete's compressive strength by about 40-120%, increased the load capacity and decreased its deflection by approximately 6-14% and 3-15%, respectively. The deep box section torsional resistance increased when its width was increased by approximately 17–50%, although this had no significantly affect on the load capacity level. A reduction of 17-33% in the width of the loading and supporting bearing plates caused a 6-16% drop in load capacity besides a notable decrease in stiffness.
Engineering machinery, tools, and implements, Mechanics of engineering. Applied mechanics
Nathaniel Morgan, Caleb Yenusah, Adrian Diaz
et al.
Efficiently simulating solid mechanics is vital across various engineering applications. As constitutive models grow more complex and simulations scale up in size, harnessing the capabilities of modern computer architectures has become essential for achieving timely results. This paper presents advancements in running parallel simulations of solid mechanics on multi-core CPUs and GPUs using a single-code implementation. This portability is made possible by the C++ <b>mat</b>rix and <b>ar</b>ray (MATAR) library, which interfaces with the C++ Kokkos library, enabling the selection of fine-grained parallelism backends (e.g., CUDA, HIP, OpenMP, pthreads, etc.) at compile time. MATAR simplifies the transition from Fortran to C++ and Kokkos, making it easier to modernize legacy solid mechanics codes. We applied this approach to modernize a suite of constitutive models and to demonstrate substantial performance improvements across different computer architectures. This paper includes comparative performance studies using multi-core CPUs along with AMD and NVIDIA GPUs. Results are presented using a hypoelastic–plastic model, a crystal plasticity model, and the viscoplastic self-consistent generalized material model (VPSC-GMM). The results underscore the potential of using the MATAR library and modern computer architectures to accelerate solid mechanics simulations.
BackgroundSpeech analysis has been expected to help as a screening tool for early detection of Alzheimer’s disease (AD) and mild-cognitively impairment (MCI). Acoustic features and linguistic features are usually used in speech analysis. However, no studies have yet determined which type of features provides better screening effectiveness, especially in the large aging population of China.ObjectiveFirstly, to compare the screening effectiveness of acoustic features, linguistic features, and their combination using the same dataset. Secondly, to develop Chinese automated diagnosis model using self-collected natural discourse data obtained from native Chinese speakers.MethodsA total of 92 participants from communities in Shanghai, completed MoCA-B and a picture description task based on the Cookie Theft under the guidance of trained operators, and were divided into three groups including AD, MCI, and heathy control (HC) based on their MoCA-B score. Acoustic features (Pitches, Jitter, Shimmer, MFCCs, Formants) and linguistic features (part-of-speech, type-token ratio, information words, information units) are extracted. The machine algorithms used in this study included logistic regression, random forest (RF), support vector machines (SVM), Gaussian Naive Bayesian (GNB), and k-Nearest neighbor (kNN). The validation accuracies of the same ML model using acoustic features, linguistic features, and their combination were compared.ResultsThe accuracy with linguistic features is generally higher than acoustic features in training. The highest accuracy to differentiate HC and AD is 80.77% achieved by SVM, based on all the features extracted from the speech data, while the highest accuracy to differentiate HC and AD or MCI is 80.43% achieved by RF, based only on linguistic features.ConclusionOur results suggest the utility and validity of linguistic features in the automated diagnosis of cognitive impairment, and validated the applicability of automated diagnosis for Chinese language data.
Modelling, simulation, and applications of Fractional Calculus have recently become increasingly popular subjects, with impressive growth concerning applications. The founding and limited ideas on fractional derivatives have achieved an incredibly valuable status. The variety of applications in mathematics, physics, engineering, economics, biology, and medicine, have opened new, challenging fields of research. For instance, in soil mechanics, a suitable definition of the fractional operator has shed some light on viscoelasticity, explaining memory effects on materials. Needless to say, these applications require the development of practical mathematical tools in order to extract quantitative information from models, newly reformulated in terms of fractional differential equations. Even confining ourselves to the field of ordinary differential equations, the well-known Bagley-Torvik model showed that fractional derivatives may actually arise naturally within certain physical models, and are not merely fanciful mathematical generalizations. This Special Issue focuses on the most recent advances in fractional calculus, applied to dynamic problems, linear and nonlinear fractional ordinary and partial differential equations, integral fractional differential equations, and stochastic integral problems arising in all fields of science, engineering, and other applied fields. In this issue, we have collected several significant papers devoted to applications of fractional methods with a focus on dynamical aspects. The applications range from theoretical mathematical-numerical aspects [1,2] to bio-medical subjects [3–7]. Applications to complex materials are investigated in [8], aiming at proposing a generalized definition of fractional operators. Special diffusion models are studied in [9–11].
Alexandra Șoica, Gheorghe-Bogdan Urdea, Vlad Alexandru Florea
This paper presents the analysis by the finite element method of the tensions and deformations produced in the mechanized support beams. The finite element method allows the analysis of physical phenomena that can be described with the help of mathematical models made up of systems of differential equations with initial and boundary conditions. From the results obtained in this paper, it was observed that the asymmetries with the greatest influence are those with respect to the vertical-longitudinal plane of the mechanized support
Libor Ižvolt, Peter Dobeš, Michaela Holešová
et al.
The paper investigates whether foam glass could reduce the structural thickness of the protection layer in the construction of the railway track (saving of natural materials – crushed aggregate) and, at the same time, also provide sufficient thermal protection of the frost-susceptible subgrade surface. It also discusses whether the incorporation of foam glass would have a relevant effect on the increase of the deformation resistance of the railway track structure at the level of the sub-ballast upper surface. Following these assumptions, the paper presents the results of experimental measurements of the deformation resistance of the modified structural composition of the sub-ballast layers (with an embedded foam glass layer) and their comparison with the results determined on a structure with a standard composition of the sub-ballast layers (crushed aggregate sub-ballast layer/protective layer). Also, numerical and mathematical analysis of the influence of the built-in thermal insulation foam glass layer on the reduction of the structural thickness of the protective crushed aggregate layer in terms of the effect of climatic factors is conducted in the paper. The mathematical model, developed by the research, provides the possibility of continuous monitoring of the change in the railway track structure freezing depending on climatic characteristics.
We investigate the load transmission along an elastic rod of finite cross-section in contact with a rigid cylinder, as system often referred to as the generalized capstan problem . In the presence of friction, the idealized classic capstan equation predicts that the tension along a perfectly thin and flexible filament increases exponentially along the contact region. In practical applications, however, the validity of the idealized capstan equation is compromised due to the interplay between finite rod thickness, bending stiffness, and the forces applied at the rod extremities. Here, we combine precision model experiments, finite element simulations, and theoretical modeling to investigate the contact mechanics and the force transmission along an elastic rod in frictional contact with a rigid cylinder. We study two cases when the rod is either static or sliding. First, we focus on the static case, in the absence of friction, by considering equal loads at both extremities of the rod. We show that as the loading force is increased, the nature of contact transitions from a localized region to an extended band at the surface of the cylinder. The latter is characterized by double-peaked contact force distribution. In the sliding case, friction is activated by inducing a relative motion between the rod and the cylinder. We applied a fixed loading force at one rod extremity while pulling the other extremity at a constant velocity. The driving force is monitored during sliding. For increasing loading forces, we find that the force ratio is non-monotonic and displays a local minimum, in contradiction with the constant ideal capstan prediction. This minimum force ratio coincides with the transition from a single contact point to an extended contact region. A theoretical analysis based on Euler’s elastica serves to rationalize the results from the physical and numerical experiments. In addition to predicting the nature of the contact region (single point versus extended line), our model provides quantitative predictions for the wrapping angle and the driving-to-loading force ratio. Finally, we leverage our mechanics-based framework to predictively understand the force ratio at the ends of two commercially available engineering belts (spring-steel and polyurethane) in sliding contact with a steel cylinder.
The ultrasonic joining of phosphor bronze sheets is analyzed using a 3-D finite element model for the study and prediction of the thermal profiles at the weld interface. The heat fluxes are calculated and assigned as boundary conditions during the thermal simulation. The forecast of temperature is done under various welding conditions. The maximum temperature obtained by transient simulation at the weld interface is 366.74℃. The continuous reduction in the temperature is observed towards the extremes of the weld metal. The sonotrode and the anvil achieve a lower temperature in comparison to the weld interface. The effect of clamping force and bonding ratio on the interface temperature is observed as positive. The model is validated with an error of 1.576% between the observed and predicted temperature results and a correlation co-efficient 0.96 is established between the simulated temperature results and the weld strength. Sufficiently strong joints were obtained at the optimum welding conditions with 74% joint efficiency. It is evident that the interface temperature has a strong linear relationship with joint strength and is a major deciding factor for achieving strong joints.
Mechanical engineering and machinery, Mechanics of engineering. Applied mechanics
In 1913 A. D. Bilimovich observed that rheonomic constraints which are linear and homogeneous in generalized velocities are ideal. As a typical example, he considered rheonomic nonholonomic deformation of the Euler equations whose scleronomic version is equivalent to the nonholonomic Suslov system. For the Bilimovich system, equations of motion are reduced to quadrature, which is discussed in rheonomic and scleronomic cases.