Structural Properties Research Articles

Exploring the unfolding pathways of protein families using Elastic Network Model

We explore how a protein’s native structure determines its unfolding process. We examine how the local structural features, like shear, and the global structural properties, like the number of soft modes, change during unfolding. Simulations are performed using a Gaussian Network Model (GNM) with bond breaking for both thermal and force-induced unfolding scenarios. We find that unfolding starts in areas of high shear in the native structure and progressively spreads to the low shear regions. Interestingly, analysis of single domain protein families (Chymotrypsin inhibitor and Barnase) reveal that proteins with distinct unfolding pathways exhibit divergent behavior of the number of soft modes during unfolding. This suggests that the number of soft modes might be a valuable tool for understanding thermal unfolding pathways. Additionally, we found a strong link between a protein’s overall structural similarity (TM-score) and its unfolding pathways, highlighting the importance of the native structure in determining how a protein unfolds.

Transition-Metal-Related Quantum Emitters in Wurtzite AlN and GaN.

Transition-metal centers exhibit a paramagnetic ground state in wide-bandgap semiconductors and are promising for nanophotonics and quantum information processing. Specifically, there is a growing interest in discovering prominent paramagnetic spin defects that can be manipulated using optical methods. Here, we investigate the electronic structure and magneto-optical properties of Cr and Mn substitutional centers in wurtzite AlN and GaN. We use state-of-the-art hybrid density functional theory calculations to determine level structure, stability, optical signatures, and magnetic properties of these centers. The excitation energies are calculated using the constrained occupation approach and rigorously verified with the complete active space configuration interaction approach. Our simulations of the photoluminescence spectra indicate that in AlN and in GaN are responsible for the observed narrow quantum emission near 1.2 eV. We compute the zero-field splitting (ZFS) parameters and outline an optical spin polarization protocol for and . Our results demonstrate that these centers are promising candidates for spin qubits.

Enhancing Spectrometer Performance with Unsupervised Machine Learning.

Solid-state NMR spectroscopy (SSNMR) is a powerful technique to probe structural and dynamic properties of biomolecules at an atomic level. Modern SSNMR methods employ multidimensional pulse sequences requiring data collection over a period of days to weeks. Variations in signal intensity or frequency due to environmental fluctuation introduce artifacts into the spectra. Therefore, it is critical to actively monitor instrumentation subject to fluctuations. Here, we demonstrate a method rooted in the unsupervised machine learning algorithm principal component analysis (PCA) to evaluate the impact of environmental parameters that affect sensitivity, resolution and peak positions (chemical shifts) in multidimensional SSNMR protein spectra. PCA loading spectra illustrate the unique features associated with each drifting parameter, while the PCA scores quantify the magnitude of parameter drift. This is demonstrated both for double (HC) and triple resonance (HCN) experiments. Furthermore, we apply this methodology to identify magnetic field B0 drift, and leverage PCA to "denoise" multidimensional SSNMR spectra of the membrane protein, EmrE, using several spectra collected over several days. Finally, we utilize PCA to identify changes in B1 (CP and decoupling) and B0 fields in a manner that we envision could be automated in the future. Overall, these approaches enable improved objectivity in monitoring NMR spectrometers, and are also applicable to other forms of spectroscopy.

Antibacterial and antifungal activities of Platycladus orientalis leaf extract-mediated Fe2O3 and Ce-doped Fe2O3 nanoparticles

Green synthesis of nanomaterials harnesses naturally occurring materials, including plant extracts, to offer environmentally friendly alternatives to conventional biomedicine, agriculture, and other field applications. This study explores the green route to Fe2O3 and cerium-doped Fe2O3 (Ce-doped Fe2O3) nanoparticles synthesized for the first time using the leaf extract of Platycladus orientalis. The synthesized nanoparticles were characterized for their structural, morphological, chemical, and optical properties. The hematite phase of Fe2O3 nanoparticles with spherical morphology was obtained. The introduction of Ce as a dopant into Fe2O3 increased the lattice strain of Ce-doped Fe2O3 nanoparticles (0.51%) compared to pristine Fe2O3 (0.46%) even though the size of both nanomaterials was similar. Compared to pristine Fe2O3 nanoparticles, Ce-doped Fe2O3 nanoparticles also demonstrated enhanced antimicrobial and antifungal activities against Escherichia coli, Enterococcus faecalis, Listeria monocytogenes, Penicillium chrysogenum, Aspergillus niger, and Mucor mucedo. The green-synthesized Ce-doped Fe2O3 nanoparticles possess potential for application in biomedical and environmental fields based on their relevance to human health and food safety, diversity in microbial characteristics, and potential for resistance to conventional treatments.

Structural, electronic, magnetic and optical properties of GdCuX2 (X = S, Se and Te) compounds

Structural, electronic, magnetic and optical properties of GdCuX2 (X = S, Se and Te) compounds

Studies on Nitrogen Rich Benzoxazines Containing Schiff Base for Optical, Aggregation Induced Emission and Anti-Microbial Applications

ABSTRACT Dihydroxy derivative of vanillin-based diaminotriazole core monomer (DTV) has been synthesized using sustainable vanillin (V) and 3,5-diamino-1,2,4-triazole (DT) under appropriate experimental conditions and characterized with a view to develop Schiff base core nitrogen-rich benzoxazines capable of exhibiting excellent optical and anti-microbial properties. The monomer DTV has been subsequently converted into benzoxazines separately using six structurally varied amino compounds, viz. aniline (a), 1-(−2-aminoethyl)piperazine (aep), furfurylamine (ffa), 4-H-1,2,4-triazoal-4-amine (ta), 3-aminopyrazol (apy) and 1-(3-aminopropyl)imidazole (api) with paraformaldehyde through Mannich condensation. The corresponding Schiff base based benzoxazines, viz. DTV-a, DTV-aep, DTV-ffa, DTV-ta, DTV-apy and DTV-api were synthesized and characterized for their molecular structure, thermal stability, optical, hydrophobic and anti-microbial properties using different analytical techniques and methods. Data obtained from different analyses for DTV based benzoxazines can be used for wide range of industrial and engineering applications.

Distributionally Robust Portfolio Optimization under Marginal and Copula Ambiguity

AbstractWe investigate a new family of distributionally robust optimization problem under marginal and copula ambiguity with applications to portfolio optimization problems. The proposed model considers the ambiguity set of portfolio returns in which the marginal distributions and their copula are close—in terms of the Wasserstein distance—to their nominal counterparts. We develop a cutting-surface method to solve the proposed problem, in which the distribution separation subproblem is nonconvex and includes bilinear terms. We propose three approaches to solve the bilinear formulation, namely (1) linear relaxation via McCormick inequalities, (2) exact mixed-integer linear program reformulation via disjunctive inequalities, and (3) inner approximation method via a novel iterative procedure that exploits the structural properties of the bilinear optimization problem. We further carry out a comprehensive set of computational experiments with distributionally robust portfolios featuring Conditional Value-at-Risk (CVaR) measures. These tests aim to compare the accuracy of the proposed algorithms, analyze the impact of the radius of the Wasserstein ambiguity ball on the portfolio, and assess portfolio performance. We use a rolling-horizon approach to conduct the out-of-sample tests, which show the superior performance of the portfolios under marginal and copula ambiguity over the equally weighted and ambiguity-free Mean-CVaR benchmark portfolios.

Two Organic-Inorganic Hybrid Manganese Bromides with Highly Efficient Emission toward White LEDs.

Organic-inorganic metal halides have attracted great attention due to their tunable structural and spectroscopic properties. Here, two organic-inorganic hybrid manganese bromides, (TEMA)2MnBr4 (TEMA = triethylmethylammonium) and (TEBA)2MnBr4 (TEBA = benzyltriethylammonium), are synthesized using the evaporation crystallization method. Following a heat-induced phase transition at 363 K, the structure and optical properties of (TEMA)2MnBr4 change but return to their initial state upon cooling to room temperature, as confirmed by X-ray diffraction, photoluminescence (PL), and Raman spectra. Meanwhile, (TEBA)2MnBr4, with a larger Mn-Mn distance, exhibits a higher photoluminescence quantum yield of 98.1% and greater thermal quenching temperature. However, due to the poorer thermal stability of the organic cation, the crystal melts at 400 K, leading to fluorescence quenching. White LEDs based on (TEMA)2MnBr4 and (TEBA)2MnBr4 are successfully fabricated with color rendering indices of 97.4 and 97.2, respectively. The investigation provides deep insights into the structural and optical properties of (TEMA)2MnBr4 and (TEBA)2MnBr4, advancing research for LED display design by tuning organic cations.

Scaling Relationships of the Structural and Rheological Behavior of Tadpole Polymer Chains in Dilute Solution Systems Using Brownian Dynamics Simulations

Tadpole polymers, also known as lasso polymers, feature molecular structures that combine a single ring with a single linear side branch, leading to distinct conformational, dynamical, and rheological characteristics compared to their corresponding counterparts, particularly pure linear and pure ring polymers. To elucidate the mechanisms underlying these distinctive behaviors, comprehensive mesoscopic Brownian dynamics (BD) simulations of dilute solution systems of tadpole polymers were conducted using a bead–rod chain model under both equilibrium and flow conditions. Three types of tadpole polymer chains were prepared by varying the ring-to-linear ratio within the tadpole chain and comparing them with the corresponding linear and ring chains. Depending on this ratio, tadpole polymer chains exhibit entirely different structural properties and rotational dynamics, both in equilibrium and under shear flow. As the linear proportion within the tadpole chain increased, the structural, dynamic, and rheological properties of the tadpole polymer chains became more similar to those of pure linear polymers. Conversely, with an increasing ring proportion, these properties began to resemble those of pure ring polymers. Based on these observed tendencies, a simple general scaling expression is proposed for tadpole polymer properties that integrates scaling expressions for both pure linear and pure ring polymers. Our results indicate that the conformational, dynamic, and rheological properties of tadpole polymers, as predicted by these simple scaling expressions, are in good agreement with the simulated values, a result we consider statistically significant.

Effect of Magnetic Field on the Structure and Sorption Properties of Films Based on Hydroxyethyl Cellulose and Carbon Nanotubes

Effect of Magnetic Field on the Structure and Sorption Properties of Films Based on Hydroxyethyl Cellulose and Carbon Nanotubes

Exploration of the structure, electronic and optical properties of AB 2(PO3)5 polyphosphates: a first-principle approach

The density functional theory method was applied using the gradient PBE, incorporating the hybrid PBE0 functional along with dispersion corrections D3(BJ). These objectives were accomplished through the utilization of the CRYSTAL package, employing a localized atomic orbital basis. Calculations encompassing crystal properties, including electronic, structural, and linear/nonlinear opto-electronic characteristics, were conducted for monoclinic AB 2(PO3)5. Specifically, the polyphosphates investigated in this study are RbPb2(PO3)5, CsPb2(PO3)5, KBa2(PO3)5, and RbBa2(PO3)5. It was demonstrated that in monoclinic phosphates, phosphorus and oxygen atoms form infinite chains [PO4]∞ based on the· ⋯ O1-P-O1 ⋯ ·structure. Alkali metal and lead (barium) atoms are surrounded by oxygen atoms O2, forming polyhedra. Infrared absorption spectra calculations confirmed the presence of chain backbone structural units. Additionally, band structure and partial density of electronic states were determined. The nature of valence and unoccupied states was also investigated. In lead-doped compounds, lead atoms contribute to the formation of upper-valence and lower-unoccupied states. Conversely, in barium-doped compounds, the upper valence states are primarily formed by O2 p-states, while the lower unoccupied states are formed by phosphorus. Also, the coefficients of second harmonic generation and birefringence were calculated, assessing the potential use of phosphates as nonlinear optical materials.

Low-cost fabrication methods of ZnO nanorods and their physical and photoelectrochemical properties for optoelectronic applications

Zinc Oxide (ZnO) nanorods have great potential in several applications including gas sensors, light-emitting diodes, and solar cells because of their unique properties. Here, three low cost and ecofriendly techniques were used to produce ZnO nanorods on FTO substrates: hydrothermal, chemical bath deposition (CBD), and electrochemical deposition (ECD). This study explores the impact of such methods on the optical, structural, electrical, morphological, and photoelectrochemical properties of nanorods using various measurements. XRD analysis confirmed the hexagonal wurtzite structure of ZnO nanorods in all three methods, with hydrothermal showing a preferred orientation (002) and CBD and ECD samples showing multiple growth directions, with average particle sizes of 31 nm, 34 nm, and 33 nm, respectively. Raman spectra revealed hexagonal Wurtzite structure of ZnO, with hydrothermal method exhibiting higher E2 (high) peak at 438 cm−1 than CBD and ECD methods. SEM results revealed hexagonal ZnO nanorods became more regular and thicker for the hydrothermal method, while CBD and ECD led to less uniform with voids. UV-vis spectra showed absorption lines between 390 nm and 360 nm. Optical bandgap energies were calculated as 3.32 eV, 3.22 eV, and 3.23 eV for hydrothermal, CBD, and ECD samples, respectively. PL spectra revealed UV emission band with a small intensity peak around 389 nm and visible emission peaks at 580 nm. Temperature dependent PL measurements for ZnO nanorods indicated that the intensities ratio between bound exciton and free exciton decreases with temperature increases for the three methods. Photocurrent measurements revealed ZnO nanorod films as n-type semiconductors, with photocurrent values of 2.25 µA, 0.28 µA, and 0.3 µA for hydrothermal, CBD, and ECD samples, and photosensitivity values of 8.01, 2.79, and 3.56 respectively. Our results suggest that the hydrothermal method is the most effective approach for fabricating high-quality ZnO nanorods for optoelectronic applications.

Dark current in FTO/CZTS interface: a comprehensive comparison of practical Vs theoretical approach using SCAPS-1D

This study investigates the deposition of Cu2ZnSnS4 (CZTS) thin films on fluorine-doped tin oxide (FTO) and soda-lime glass (SLG) substrates using radio frequency (RF) sputtering at varying temperatures. A comprehensive characterization employing multiple analytical techniques was conducted. X-ray diffraction (XRD) analyses confirmed the amorphous nature of CZTS films being deposited up to 200 °C, while higher temperatures promoted increased crystallinity, with the presence of (112) and (220) planes observed at 300 °C and 400 °C. Rietveld refinement using Profex software revealed an increase in crystallite size with deposition temperature for films grown at 300 °C and 400 °C. Optical characterization through UV–vis spectroscopy unveiled a decrease in band gap energy with increasing deposition temperature, while the Urbach energy, associated with defects and imperfections, exhibited an inverse relationship with band gap and temperature. Experimental current–voltage (I-V) measurements using a Keithley source meter showed variations in the ideality factor with deposition temperature. SCAPS-1D simulations were performed to model the FTO/CZTS interface, incorporating experimental parameters. The simulated I-V behavior demonstrated a transition from recombination to diffusion-dominated current above 1.3 V forward bias. Simulations yielded higher ideality factors due to increased contributions from recombination and diffusion currents. Overall, this study provides insights into the growth, structural, optical, and electrical properties of CZTS thin films deposited by RF sputtering, enabling a comprehensive understanding of the FTO/CZTS heterojunction characteristics and their dependence on deposition temperature.

Calculation of structural, electronic, optical, dynamic and thermoelectric properties of monolayer made of carbon and nitrogen

Calculation of structural, electronic, optical, dynamic and thermoelectric properties of monolayer made of carbon and nitrogen

Development of Pericarp-Based Coatings from Corn Nixtamalization Residue for Stone Fruits: Applications for Peach and Tejocote

This study investigated corn pericarp, a by-product of the nixtamalization process, in developing sustainable films for fruit coatings. These films were evaluated for their optical, structural, barrier, and mechanical properties. The results showed that the pericarp films were transparent, had heterogeneous surfaces, and exhibited favorable mechanical and barrier properties, suggesting their potential as fruit coatings. The pericarp films significantly extended shelf life when applied to peaches and tejocotes postharvest. The films slowed the maturation process, as evidenced by minimal changes in peel and mesocarp color for up to five days for tejocotes and even longer for peaches. Additionally, coated fruits showed slower rates of weight loss, firmness reduction, and decreases in titratable acidity, total soluble solids, and total sugar content compared to control samples. These findings demonstrate the potential of corn pericarp films as effective coatings for extending the shelf life of stone fruits.

Electronic, Optical and Thermoelectric Properties of Two-Dimensional Molybdenum Carbon Mo2C-MXenes

We investigate the structural, electronic, optical, and thermoelectric properties of three compositions of Mo2C-MXenes (Mo2CF2, Mo2C(OH)2, and Mo2CO2) from monolayer to multilayer by first principles calculation within Density Functional Theory (DFT) and Boltzmann transport theory. Firstly, the atomic structures of Mo2C-MXenes are optimized, and their respective structures are created with comparative research. Secondly, their electronic band structures and optical properties are studied in detail. The estimation of the bandgap energy of Mo2C-MXenes with its functionalization reveal that most Mo2CF2 and Mo2C(OH)2 layers are semiconductors, while Mo2CO2 behaves as a metal. The electrical and optical properties can be altered by controlling the on-surface functional groups and the number of layers. Computation of the thermoelectric (TE) properties of Mo2C-MXenes reveals that, upon heating to 600 K, Mo2CF2 and Mo2C(OH)2 exhibit a high Seebeck coefficient and a relatively high electrical conductivity. The Seebeck coefficient reaches ~400 µV K−1 at room temperature for all layers of Mo2CF2 MXenes. Our results prove that Mo2CF2 is considered a promising material for thermoelectric devices, while Mo2CO2 does not possess better thermoelectric performance. Mo2C-MXenes from monolayer to multilayer have outstanding properties, such as flexible bandgap energy and high thermal stability, making them promising candidates for many applications, including energy storage and electrode applications.

Advanced Anti-icing and Deicing Strategies for Overhead Power Transmission Lines Based on Giant Magnetocaloric Effect of La0.7Ca0.254Sr0.046MnO3.

Perovskite manganates (AMnO3) exhibit diverse structural, thermal, electrical, and magnetic properties. Their strong magnetocaloric effect (MCE) near the Curie temperature (TC) makes them ideal for magnetic-thermal anti-icing and deicing in power transmission lines. Below TC, ferromagnetic AMnO3 produces heat through multiple mechanisms, with the changing magnetic field induced by the strong AC current, causing heat through magnetic hysteresis and eddy currents, alongside the direct MCE. Above TC, no heating is generated, as MCE is unfavorable, thus preventing additional energy loss at elevated temperatures. In this work, La0.7Ca0.254Sr0.046MnO3 with TC close to 0 °C were synthesized by solid-state reaction. It is found that particle size >10 μm is beneficial for a large MCE, based on the results of particle size dependence of MCE. The resulting maximum magnetic entropy change at 277 K is 7.69 J·kg-1·K-1, and an adiabatic temperature change of 3.87 K at 277 K is achieved under 5 T. The prototype cable is fabricated using a well-established wire drawing process. A climate-simulation chamber is employed for the anti-icing and deicing experiments. The prototype cables demonstrated a strong capability for deicing and anti-icing. This simple and cost-effective prototype cable shows significant potential for mitigating the icing problem of overhead high-voltage power transmission lines.

A Prediction of All-Inorganic Lead-Free Halide Perovskites for Photovoltaic Application: Rb3Mo2Br9 and Rb3Mo2Cl9.

Lead-based organic-inorganic hybrid perovskites show promise as photovoltaic materials due to their high energy conversion efficiencies. However, concerns regarding lead toxicity and the poor environmental and operational stability of the organic cationic group have limited their widespread application. To address these challenges, the design of all-inorganic lead-free halide perovskites offers potential solutions for photovoltaic applications. Here, two layered perovskite derivatives, Rb3Mo2Cl9 and Rb3Mo2Br9, are explored, and their electronic, structural, and photovoltaic properties are analyzed using advanced theoretical calculations. Rb3Mo2Br9 exhibits a suitable direct bandgap of 1.60eV, making it a promising candidate for use as a light absorber in low-cost, high-efficiency solar cells. On the other hand, Rb3Mo2Cl9 demonstrates a wide direct bandgap exceeding 1.70eV, positioning it as a viable option for use as a top cell in tandem photovoltaic systems alongside silicon. Both materials display ideal optical properties in the visible light region and hold promise as excellent inorganic lead-free perovskite alternatives.

Density functional quantum screening of the structural, electronic, phonon, and thermophysical properties of Cu-based chalcogenides for interface thermal performance and energy applications

Density functional quantum screening of the structural, electronic, phonon, and thermophysical properties of Cu-based chalcogenides for interface thermal performance and energy applications

Ultrasound-assisted extraction of sumac fruit oil and analysis of its fatty acid composition.

The use of ultrasound for enhancing the extraction of sumac fruit oil was investigated to maximize the utilization of available sumac fruit resources. The optimal extraction parameters were determined using single-factor trials and Box-Behnken design optimization and were found to be a liquid-to-material ratio of 13:1mL/g, an ultrasound temperature of 47°C, and an ultrasound duration of 32min. These yielded a 20.59% extraction rate of the oil. The ultrasonic-assisted approach markedly increased the extraction rate and significantly reduced the extraction time when compared to classical Soxhlet extraction. The resulting sumac fruit oil had a brown-yellow color with peroxide, acid, and iodine concentrations of 2.43mg/g, 0.44g/100g, and 135g/100g, respectively, and relative density (d20 20), and refractive index (20°C) values of 0.911, and 1.469, respectively. The primary fatty acids in the oil were stearic, linoleic, palmitic, linolenic, and oleic acids. With a 74.14% unsaturated fatty acid content, it has a high nutritional value as well as significant development and usage potential. PRACTICAL APPLICATION: This study demonstrates a highly efficient method for extracting vegetable oils and fats. It has the advantages of simple operation, low extraction temperature, short extraction time, high extraction rate, no damage to the material structure, excellent phusicai and chemical properties of the extracted vegetable oil, low cost, and the potential application in the food industry is crucial.