Solution Structure Research Articles

Every Problem, Every Step, All in Focus: Learning to Solve Vision-Language Problems With Integrated Attention.

Integrating information from vision and language modalities has sparked interesting applications in the fields of computer vision and natural language processing. Existing methods, though promising in tasks like image captioning and visual question answering, face challenges in understanding real-life issues and offering step-by-step solutions. In particular, they typically limit their scope to solutions with a sequential structure, thus ignoring complex inter-step dependencies. To bridge this gap, we propose a graph-based approach to vision-language problem solving. It leverages a novel integrated attention mechanism that jointly considers the importance of features within each step as well as across multiple steps. Together with a graph neural network method, this attention mechanism can be progressively learned to predict sequential and non-sequential solution graphs depending on the characterization of the problem-solving process. To tightly couple attention with the problem-solving procedure, we further design new learning objectives with attention metrics that quantify this integrated attention, which better aligns visual and language information within steps, and more accurately captures information flow between steps. Experimental results on VisualHow, a comprehensive dataset of varying solution structures, show significant improvements in predicting steps and dependencies, demonstrating the effectiveness of our approach in tackling various vision-language problems.

Skirt piles in foundation: a structural rehabilitation solution for fixed offshore platforms

An analysis and structural design of strength and ductility level earthquake is presented in this paper. Numerical results show that structural failure under seismic loads is sensitive to the degree of deterioration of structural steel. The structural elements do not present any excess stress, that is, all stress ratios are less than unity. The maximum stress ratio is 0.942, in the superstructure of element 1586-1571, which corresponds to a main deck beam elevation (+) 15,850 m.

Platinum-Iridium Alloy Nanoparticle Coatings Produced by Electrophoretic Deposition Reduce Impedance in 3D Neural Electrodes.

Platinum-based neural electrodes frequently alloyed with Ir or W are routinely used for the treatment of neurological conditions. However, their performance is hampered by impaired electrical contact between electrode and tissue that compromises long-term implant stability. Though there are multiple coating techniques available to address this issue, electrode, and base material often exhibit a compositional mismatch, which impairs mechanical stability and may lead to toxicological side effects. In this work we coated Pt wire electrodes with ligand-free electrostatically stabilized colloidal Pt90Ir10, Pt90W10, and Pt50W50 alloy nanoparticles (NPs) matching electrode compositions using electrophoretic deposition (EPD) with direct-current (DC) and pulsed-DC fields in aqueous medium. The generated alloy NPs exhibit a solid solution structure as evidenced by HR-TEM-EDX and XRD, though additional WOx phases were identified in the Pt50W50 samples. Consequently, coating efficiency was also impaired in the presence of high W mass fractions in the alloy NPs. Characterization of the NP coatings by cyclic voltammetry and impedance spectroscopy yielded a significant reduction of the impedance in the Pt90Ir10 sample in comparison to the Pt control. The electrochemical surface area (ECSA) of the PtW alloy coatings, on the other hand, was significantly reduced.

DPPM-Bridged Binuclear Pt(II) Pincer Complexes: Chemistry, Structure, and Photophysics in Solution Revisited.

A series of luminescent binuclear ([dppm{Pt(NNC)}2]2+) and mononuclear ([PPh3Pt(NNC)]+) complexes containing pincer ligands were synthesized and characterized. Photophysical characteristics of both types of complexes were studied in dichloromethane solution. In the solid phase, the binuclear compounds adopt a syn configuration where the {Pt(NNC)} fragments are held together due to intramolecular Pt-Pt bonding and π-stacking of the pincer ligand aromatic systems. Analysis of the complexes' molecular structure in solution by multinuclear NMR spectroscopy showed that the stacked intramolecular configuration is retained in fluid media, which is in complete agreement with a considerable red shift of the emission wavelength due to formation of the intramolecular Pt-Pt bond, leading to the transformation of an emissive excited state to 3MMLCT. It was also found that triethylamine quenches the emission of both types of complexes; the mechanism of quenching is a combination of dynamic and static channels of excited-state deactivation. In the case of binuclear complexes, deprotonation of the dppm methylene bridge by triethylamine also contributes to the chromophore quenching. To explain the observed chemistry of binuclear complex interactions with Et3N, a chemical equilibrium scheme was suggested, which was confirmed by quantitative monitoring of the 31P signal variations as a function of triethylamine concentration.

Targeting SHP2 Cryptic Allosteric Sites for Effective Cancer Therapy.

SHP2, a pivotal component downstream of both receptor and non-receptor tyrosine kinases, has been underscored in the progression of various human cancers and neurodevelopmental disorders. Allosteric inhibitors have been proposed to regulate its autoinhibition. However, oncogenic mutations, such as E76K, convert SHP2 into its open state, wherein the catalytic cleft becomes fully exposed to its ligands. This study elucidates the dynamic properties of SHP2 structures across different states, with a focus on the effects of oncogenic mutation on two known binding sites of allosteric inhibitors. Through extensive modeling and simulations, we further identified an alternative allosteric binding pocket in solution structures. Additional analysis provides insights into the dynamics and stability of the potential site. In addition, multi-tier screening was deployed to identify potential binders targeting the potential site. Our efforts to identify a new allosteric site contribute to community-wide initiatives developing therapies using multiple allosteric inhibitors to target distinct pockets on SHP2, in the hope of potentially inhibiting or slowing tumor growth associated with SHP2.

Convolutional neural network based methodology for flexible phase prediction of high entropy alloys

ABSTRACT The advent of high entropy alloys has created a design space that is unfeasible to explore solely through experimentation, thus necessitating the use of computational methods, such as artificial neural networks. This study proposes a new architecture utilizing a convolutional layer to extract relevant elemental features from the alloy composition without limiting the model to specific elements by treating the elemental composition of the high entropy alloy in a similar manner to a row of pixels, using relevant elemental properties in lieu of color values. This convolutional model was able to predict the crystal structure of solid solutions in a high entropy alloy composition with an accuracy of 89.3% in a six-way classification and the formation of intermetallics with an accuracy of 91.4% during holdout validation, while being capable of accurately predicting the primary crystal structure of high entropy alloys containing elements the model was not trained on. Significant space still exists for further experimentation and improvement with this methodology, including augmenting the available datasets and implementation of additional convolutional layers. Due to the limited interpretability of the model architecture, care should be taken when inferring trends from the model prior to validation through experimental, or well-established computational methods.

Domain Swapping in Abiotic Foldamers.

Foldamer sequences that adopt tertiary helix-turn-helix folds mediated by helix-helix hydrogen bonding in organic solvents have been previously reported. In an attempt to create genuine abiotic quaternary structures, i.e. assemblies of tertiary structures, new sequences were prepared that possess additional hydrogen bond donors at positions that may promote an association between the tertiary folds. However, a solid state structure and extensive solution state investigations by Nuclear Magnetic Resonance (NMR) and Circular Dichroism (CD) show that, instead of forming a quaternary structure, the tertiary folds assemble into stable domain-swapped dimer motifs. Domain swapping entails a complete reorganization of the arrays of hydrogen bonds and changes in relative helix orientation and handedness that can all be rationalized.

Domain Swapping in Abiotic Foldamers

AbstractFoldamer sequences that adopt tertiary helix‐turn‐helix folds mediated by helix‐helix hydrogen bonding in organic solvents have been previously reported. In an attempt to create genuine abiotic quaternary structures, i.e. assemblies of tertiary structures, new sequences were prepared that possess additional hydrogen bond donors at positions that may promote an association between the tertiary folds. However, a solid state structure and extensive solution state investigations by Nuclear Magnetic Resonance (NMR) and Circular Dichroism (CD) show that, instead of forming a quaternary structure, the tertiary folds assemble into stable domain‐swapped dimer motifs. Domain swapping entails a complete reorganization of the arrays of hydrogen bonds and changes in relative helix orientation and handedness that can all be rationalized.

A hybrid TIM complex mediates protein import into hydrogenosomes of Trichomonas vaginalis

BackgroundHydrogenosomes are a specific type of mitochondria that have adapted for life under anaerobiosis. Limited availability of oxygen has resulted in the loss of the membrane-associated respiratory chain, and consequently in the generation of minimal inner membrane potential (Δψ), and inefficient ATP synthesis via substrate-level phosphorylation. The changes in energy metabolism are directly linked with the organelle biogenesis. In mitochondria, proteins are imported across the outer membrane via the Translocase of the Outer Membrane (TOM complex), while two Translocases of the Inner Membrane, TIM22, and TIM23, facilitate import to the inner membrane and matrix. TIM23-mediated steps are entirely dependent on Δψ and ATP hydrolysis, while TIM22 requires only Δψ. The character of the hydrogenosomal inner membrane translocase and the mechanism of translocation is currently unknown.ResultsWe report unprecedented modification of TIM in hydrogenosomes of the human parasite Trichomonas vaginalis (TvTIM). We show that the import of the presequence-containing protein into the hydrogenosomal matrix is mediated by the hybrid TIM22-TIM23 complex that includes three highly divergent core components, TvTim22, TvTim23, and TvTim17-like proteins. The hybrid character of the TvTIM is underlined by the presence of both TvTim22 and TvTim17/23, association with small Tim chaperones (Tim9-10), which in mitochondria are known to facilitate the transfer of substrates to the TIM22 complex, and the coupling with TIM23-specific ATP-dependent presequence translocase-associated motor (PAM). Interactome reconstruction based on co-immunoprecipitation (coIP) and mass spectrometry revealed that hybrid TvTIM is formed with the compositional variations of paralogs. Single-particle electron microscopy for the 132-kDa purified TvTIM revealed the presence of a single ring of small Tims complex, while mitochondrial TIM22 complex bears twin small Tims hexamer. TvTIM is currently the only TIM visualized outside of Opisthokonta, which raised the question of which form is prevailing across eukaryotes. The tight association of the hybrid TvTIM with ADP/ATP carriers (AAC) suggests that AAC may directly supply ATP for the protein import since ATP synthesis is limited in hydrogenosomes.ConclusionsThe hybrid TvTIM in hydrogenosomes represents an original structural solution that evolved for protein import when Δψ is negligible and remarkable example of evolutionary adaptation to an anaerobic lifestyle.

Multi-Aspect Shaping of the Building’s Heat Balance

In the European Union, buildings account for 42% of the energy consumption and 36% of the direct and indirect energy-related greenhouse gas emissions. Reducing thermal power for heating purposes is crucial to achieve climate neutrality. The main purpose of this article is to identify the places in the building where it is possible to significantly improve energy efficiency through the use of appropriate construction and material solutions. This article contains a multi-aspect approach to the heat balance of a building. Solutions that have a direct impact on building energy consumption were analysed, taking into account architectural, technological, and material aspects. Particular attention was paid to energy-efficient design and material solutions for non-transparent and transparent external walls and thermal storage walls (Trombe walls). An analysis of heat transfer through building elements was carried out, along with the optimisation of energy-efficient solutions for non-transparent and transparent barriers. Two methods for determining the equivalent heat transfer coefficient Ue for solar active partitions are presented. The analysis presented in the work using the original method of the balanced heat transfer coefficient Ue is a testing ground for identifying unfavourable features of the building structure, as well as the most energy-efficient solutions that can be used in establishing standards for the construction and modernisation of buildings. The value of the Ue coefficient illustrates the actual heat transfer through the partition. Having Ue values for various structural solutions of building envelopes, the designer can easily select the most effective ones. The use of the presented methodology will allow for the optimisation of technical solutions for building elements to improve its energy efficiency.

Revealing molecular insights into surface charge and local viscosity in electroosmotic flows

The limitations of the continuum theory in predicting osmotic response at the nanoscale stem from its lack of molecular-level insight into local fluid properties and the interfacial structure of fluid and electrolyte solutions. To overcome this challenge, our study integrates molecular dynamics (MD) simulation with the continuum framework to explore how surface charge and various hydrodynamic properties impact electroosmotic flow (EOF). The failure of continuum theories to account for molecular interactions and geometric boundaries leads to significant disparities between MD simulations and continuum predictions, influenced by local fluid properties and the electric field. Emphasizing the importance of incorporating appropriate local hydrodynamic properties and atomic interface boundary conditions, our findings bridge the gap between MD simulations and continuum EOF predictions. Our computational results and theoretical model, considering surface charge, atomic interface boundaries, and dynamic structure-based hydrodynamic properties, provide crucial insights and guidance for EOF investigations.

Emergence of non-trivial solutions from trivial solutions in reaction–diffusion equations for pattern formation

Reaction–diffusion equations serve as fundamental tools in describing pattern formation in biology. In these models, nonuniform steady states often represent stationary spatial patterns. Notably, these steady states are not unique, and unveiling them mathematically presents challenges. In this paper, we introduce a framework based on bifurcation theory to address pattern formation problems, specifically examining whether nonuniform steady states can bifurcate from trivial ones. Furthermore, we employ linear stability analysis to investigate the stability of the trivial steady-state solutions. We apply the method to two classic reaction–diffusion models: the Schnakenberg model and the Gray–Scott model. For both models, our approach effectively reveals many nonuniform steady states and assesses the stability of the trivial solution. Numerical computations are also presented to validate the solution structures for these models.

A Study of Flavor Mixing and Solution Structures in Dyson-Schwinger Equations for a Two-Flavor System

A Study of Flavor Mixing and Solution Structures in Dyson-Schwinger Equations for a Two-Flavor System

Exact solutions and bifurcations for the (3+1)-dimensional generalized KdV-ZK equation

In this paper, a class of (3+1)-dimensional generalized Korteweg–de Vries-Zakharov-Kuznetsov (KdV-ZK) equation is studied by utilizing the bifurcation theory of the planar dynamical systems and the Fan sub-function method. This model can be used to explain the effects of magnetic fields on weakly nonlinear ion-acoustic waves investigated in plasma fields composed of cold and hot electrons. Under the different parameter conditions, the phase portraits and bifurcations are derived, and new exact solutions including soliton, periodic, kink and breaking wave solutions for the model are constructed. Moreover, some exact solutions, which contain soliton, kink, trigonometric function, hyperbolic function, Jacobi elliptic function solutions, are derived via the improved Fan sub-function method. The types of solutions obtained completely correspond to the types of the orbits acquired above, which verifies the validity of the method. Finally, the physical structures of some exact solutions are analyzed in graphical forms.

Evaluating the deep learning software tools for large-scale enterprises using a novel TODIFFA-MCDM framework

Deep learning (DL) is one of the most promising technological developments emerging in the fourth industrial revolution era for businesses to improve processes, increase efficiency, and reduce errors. Accordingly, hierarchical learning software selection is one of the most critical decision-making problems in integrating neural network applications into business models. However, selecting appropriate reinforcement learning software for integrating deep learning applications into enterprises’ business models takes much work for decision-makers. There are several reasons for this: first, practitioners’ limited knowledge and experience of DL makes it difficult for decision-makers to adapt this technology into their enterprises’ business model and significantly increases complex uncertainties. Secondly, according to the authors’ knowledge, no study in the literature addresses deep structured learning solutions with the help of MCDM approaches. Consequently, making inferences concerning criteria that should be considered in an evaluation process is impossible by considering the studies in the relevant literature. Considering these gaps, this study presents a novel decision-making approach developed by the authors. It involves the combination of two new decision-making approaches, MAXC (MAXimum of Criterion) and TODIFFA (the total differential of alternative), which were developed to solve current decision-making problems. When the most important advantages of this model are considered, it associates objective and subjective approaches and eliminates some critical limitations of these methodologies. Besides, it has an easily followable algorithm without the need for advanced mathematical knowledge for practitioners and provides highly stable and reliable results in solving complex decision-making problems. Another novelty of the study is that the criteria are determined with a long-term negotiation process that is part of comprehensive fieldwork with specialists. When the conclusions obtained using this model are briefly reviewed, the C2 “Data Availability and Quality” criterion is the most influential in selecting deep learning software. The C7 “Time Constraints” criterion follows the most influential factor. Remarkably, prior research has overlooked the correlation between the performance of Deep Learning (DL) platforms and the quality and accessibility of data. The findings of this study underscore the necessity for DL platform developers to devise solutions to enable DL platforms to operate effectively, notwithstanding the availability of clean, high-quality, and adequate data. Finally, the robustness check carried out to test the validity of the proposed model confirms the accuracy and robustness of the results obtained by implementing the suggested model.

Evidence of a Rod-like Structure for Hydroxypropyl Cellulose Samples in Aqueous Solution.

Because hydroxypropyl cellulose (HpC) is a popular polymeric material that forms a liquid crystalline phase in solutions with various kinds of solvents, including water, it is commonly thought that HpC has a typical rod-like structure in solution. In this study, the structures of commercial HpC samples in aqueous solution with average molar substitution numbers (MS) ranging from 3.6 to 3.9 and weight-average molar masses (Mw) ranging from 36 to 740 kg mol-1 were investigated in detail. We first used multiple techniques, including standard static and dynamic light scattering (SLS and DLS), neutron and X-ray scattering experiments, and viscometric measurements, to obtain clear evidence of rod-like structures quantitatively. The dependence of excess scattering intensities for HpC samples under dilute conditions on the magnitude of the scattering vector over a wide range from 8.9 × 10-3 to 3.0 × 10 nm-1 was reasonably described by the form factor of rod particles with length (L) and diameter (d). Although the determined L value was close to the contour length (lc) calculated from the Mw values in the lower Mw range, L became obviously less than lc with increasing Mw. The radius of gyration (Rg) determined via SLS measurements was proportional to L by a factor of approximately 3.5 ∼ √12 over the Mw range examined. These observations revealed that the conformation of HpC molecules changes from an elongated single chain to a certain folded structure, maintaining the shape of the rod-shaped particles. Moreover, the Mw dependencies of the intrinsic viscosities and translational diffusion coefficients of the HpC samples resulting from DLS measurements were reasonably described with a theoretical rod-like particle model, assuming that L and d are identical to those resulting from the scattering behaviors.

Holistic Approach to Niche Formation: A Case on Transition to Nearly Zero-Energy Buildings in Türkiye

The long-term challenges of climate change are becoming increasingly evident. Considering the ever-increasing need for energy in parallel with population growth and the impact of greenhouse gases, the built environment is among the issues that should be addressed as a priority. As international agreements, the EU, and national legislation become institutionalized, the need to decarbonize the built environment increases. For this reason, there is a need for an understanding that enables the transition to a more sustainable society. In line with this understanding, a transition to zero-energy buildings is required. In this article, the evaluation framework is created by combining the Transition Management (TM) approach, which is a framework developed to understand long-term changes in culture, structure, and practices for sustainable development solutions, and the Strategic Niche Management (SNM) approach, which encourages technological and social change to initiate sustainable innovations at the niche level. Applications regarding energy efficiency and niche formation for the built environment in Türkiye (Gaziantep) were discussed. When the applications and theories are evaluated together, it can be seen that the applications carried out in Gaziantep regarding Nearly Zero Energy Buildings may be starter experiments. However, these projects are insufficient to create a niche, and the developments are progressing very slowly.

Control of artificial membrane fusion in physiological ionic solutions beyond the limits of electroformation

Membrane fusion, merging two lipid bilayers, is crucial for fabricating artificial membrane structures. Over the past 40 years, in contrast to precise and controllable membrane fusion in-vivo through specific molecules such as SNAREs, controlling the fusion in-vitro while fabricating artificial membrane structures in physiological ionic solutions without fusion proteins has been a challenge, becoming a significant obstacle to practical applications. We present an approach consisting of an electric field and a few kPa hydraulic pressure as an additional variable to physically control the fusion, enabling tuning of the shape and size of the 3D freestanding lipid bilayers in physiological ionic solutions. Mechanical model analysis reveals that pressure-induced parallel/normal tensions enhance fusion among membranes in the microwell. In-vitro peptide-membrane assay, mimicking vesicular transport via pressure-assisted fusion, and stability of 38 days with in-chip pressure control via pore size-regulated hydrogel highlight the potential for diverse biological applications.

Enhancing the plasticity of HfZrTiCr x alloys by forming single phase solid solutions via reducing Cr content

ABSTRACT The solid solution design strategy bolsters the comprehensive mechanical properties of high/medium entropy alloys (H/MEAs), yet its utilisation within hexagonal close-packed (HCP) H/MEAs remains notably limited. Here, exploring the impact of reduced Cr content (x = 0.3, 0.1, and 0) from the HfZrTiCr0.5 prototype alloy, our study successfully obtained a novel HCP single phase MEA and investigated the relationship between microstructure and mechanical properties. Decreasing Cr content led to the diminishing presence of the Laves phase, culminating in a single HCP phase solid solution at x = 0.1. The Laves phase, arising from negative enthalpy between Cr and other elements and lower atomic radius of Cr, acted as crack initiation sites, resulting in brittle fracture (x = 0.5) alloy and limited plasticity strain of 3.5% (x = 0.3). Conversely, the HfZrTiCr0.1 alloy exhibited impressive combined yield strength (1360 MPa) and plasticity strain (14.5%), attributed to prominent solid solution strengthening and enhanced dislocation movement within the solid solution structure. These findings offer insights into manipulating Cr content to form HCP solid solution structures, potentially broadening solid solution alloy design strategies for superior mechanical properties in HCP H/MEAs.

Three-Dimensional Reconstruction of the Early Christian Temples of the Roman Fortress of Pitiunt

Since 2018, the authors have been working on reconstructing the exterior of the Great Pitiunt Roman fortress in 3D. This article presents the results of the visualization of the exterior and interior of the temple complex. During the study, the dimensions and plans of the site were analyzed, revealing discrepancies in various sources. To clarify the complex’s dimensions, aerial photography using UAV was conducted, and photogrammetric models, orthophoto, and digital surface models were created. The research also uncovered previously unrecorded architectural features. During the reconstruction of the temples, much attention was paid to the structural design of the buildings, connections and load distribution. Engineering calculations have been carried out for the clarification of the structural solutions. The article presents the results of a detailed reconstruction of the exterior, interior and structural features of Temple Nos. 1–4, based on preserved archaeological evidence, excavation results, contemporaneous Early Christian sites, and an analysis of the materials and technologies used at the time. The reconstruction of the mosaic floor of Temple No. 2 allowed a realistic visualization of the interior.