Solution Structure Research Articles

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.

Origami of multi-layered spaced sheets

Two-dimensional (2D) origami tessellations such as the Miura-ori are often generalized to build three-dimensional (3D) architected materials with sandwich or cellular structures. However, such 3D blocks are densely packed with continuity of the internal material, while for many engineering structures with multi-physical functionality, it is necessary to have thin sheets that are separately spaced and sparsely connected. This work presents a framework for the design and analysis of multi-layered spaced origami, which provides an origami solution for 3D structures where multiple flat sheets are intentionally spaced apart. We connect Miura-ori sheets with sparsely installed thin-sheet parallelogram-like linkages. To explore how this connectivity approach affects the behavior of the origami system, we model the rigid-folding kinematics using analytic trigonometry and rigid-body transformations, and we characterize the elastic-folding mechanics by generalizing a reduced order bar and hinge model for these 3D assemblies. The orientation of the linkages in the multi-layered spaced origami determines which of three folding paths the system will follow including a flat foldable type, a self-locking type, and a double-branch type. When the origami is flat foldable, a maximized packing ratio and a uniform in-plane shear stiffness can be achieved by strategically choosing the link orientation. We show possible applications by demonstrating how the multi-layered spaced origami can be used to build deployable acoustic cloaks and heat shields.

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.

Geometric Structure of an Aqueous Solution of Paramagnetic Nanoparticles in the Presence of a Magnetic Field

Geometric Structure of an Aqueous Solution of Paramagnetic Nanoparticles in the Presence of a Magnetic Field

GENETIC SYNTHESIS OF HYBRID ELECTRO-MECHANICAL SYSTEMS FOR MOTOR-SPINDLE UNITS WITH ADAPTIVE SPATIAL STRUCTURE

The results of fundamental research carried out at the Department of Electromechanics of KPI named after Igor Sikorsky, it was established that the structural organization and evolution of arbitrary classes of technical systems that function on the principles of electromechanical energy conversion is determined by the principles and laws of genetically organized systems. Motor-spindles (M-Ш) also belong to the category of such systems. The energy and genetic core of technical systems with electromechanical energy converters is the active zone of the energy converter, which is a physical and information carrier of genetic information and the corresponding genetic code. The trend of creating multi-coordinate motor-spindle units with a spatially adaptive structure, designed to function as part of metalworking centers and machines with digital control systems, is analyzed. In genetically organized systems, the processes of structuring objects of any level of complexity are implemented on the basis of the elemental information base of genetic programs using genetic synthesis operators. From the point of view of the theory of genetic structure formation, spatial adaptation is the result of chromosomal transformations using the principles of hybridization, mutation, replication, and isomerism. The problem of synthesizing a hybrid multifunctional EM structure for motor-spindle units with a spatially adaptive modular structure was formulated and solved. A generalized genetic model of chromosomal synthesis of hybrid electromechanical modules of motor-spindle units according to a given function has been developed. The structural formulas of hybrid electromagnetic chromosomes, which determine the population structure of original technical solutions, have been determined. Based on the simulation results, the structures of spatially adaptive motor-spindle units with two-, three-, and four-coordinate movement of the working body were synthesized. Based on the results of the research, a genetic catalog was created, which serves as a system basis for the development of original technical solutions for motor-spindle units.

Formation of Amyloid-Like Conformational States of β-Structured Membrane Proteins on the Example of OMPF Porin from the Yersinia pseudotuberculosis Outer Membrane.

The work presents results of the invitro and insilico study of formation of amyloid-like structures under harsh denaturing conditions by non-specific OmpF porin of Yersinia pseudotuberculosis (YpOmpF), a membrane protein with β-barrel conformation. It has been shown that in order to obtain amyloid-like porin aggregates, preliminary destabilization of its structure in a buffer solution with acidic pH at elevated temperature followed by long-term incubation at room temperature is necessary. After heating at 95°C in a solution with pH4.5, significant conformational rearrangements are observed in the porin molecule at the level of tertiary and secondary structure of the protein, which are accompanied by the increase in the content of total β-structure and sharp decrease in the value of characteristic viscosity of the protein solution. Subsequent long-term exposure of the resulting unstable intermediate YpOmpF at room temperature leads to formation of porin aggregates of various shapes and sizes that bind thioflavin T, a specific fluorescent dye for the detection of amyloid-like protein structures. Compared to the initial protein, early intermediates of the amyloidogenic porin pathway, oligomers, have been shown to have increased toxicity to the Neuro-2aCCL-131™ mouse neuroblastoma cells. The results of computer modeling and analysis of the changes in intrinsic fluorescence during protein aggregation suggest that during formation of amyloid-like aggregates, changes in the structure of YpOmpF affect not only the areas with an internally disordered structure corresponding to the external loops of the porin, but also main framework ofthe molecule, which has a rigid spatial structure inherent to β-barrel.

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.

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.

Polysaccharide Hydro-Gel from Arid Plant Seed

There is a limited information on the structure and gelation process in mucilagepolysaccharides because of the complex conformation and non-homogeneity of the constituent polysaccharides that typically show large molecular weights in excess of 1 MDa. Only a few works have been done in this area of characterizing mucilage structure and rheological behaviour for different gel solutions. Exploring this area would surely open the new horizons for drug delivery, soil conditioning and pharmaceutical industry. In this study, we aimed to extract polysaccharides found in P.ovata Seed (Isabgol) via mucilage extraction controlling molecular weight of polymers in hot water extraction stage and tried to formulate gel formation dissolving different conc. of extracted freeze-dried material along with the characterization of gel network through Rheological studies and Dynamic Light Scattering (DLS) studies in different solvents. The study confirmed the relationship between molecular associations, chain relaxation time and entanglement behaviour of P. ovata hot water extracted (HW) solutions using polydispersity index and shear rheology. Moreover, two power law regions obtained for different concentration solution are of great importance because of their wide applications in the industrial prospective.

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.