Distribution Of Binding Energy Research Articles

Deep learning model for predicting the spatial distribution of binding energy from atomic configurations

Understanding plasma-material interaction is crucial for achieving steady-state operation of magnetic confinement fusion devices. Kinetic Monte Carlo (kMC) simulation is a powerful tool for investigating the motion of atoms in the plasma facing materials under the influence of this interaction. To predict trapping sites and migration energies necessary for kMC simulations, we developed a deep learning model based on pix2pix for predicting the spatial distribution of binding energy. Results show that the model can reproduce spatial distributions similar to the true values. However, larger errors occur in regions with steep value gradients.

Compatibility mechanism of Qishen Yiqi Dripping Pills for treatment of myocardial ischemia based on UPLC-Q-Exactive Orbitrap-MS and network pharmacology

Clinical efficacy and mechanism of Qishen Yiqi Dripping Pills(QSYQ) have been well researched, but the compatibility mechanism underlying its therapeutic effect still requires further analysis. This study aims to explore the compatibility mechanism of QSYQ in treating myocardial ischemia. UPLC-Q-Exactive Orbitrap-MS technique was used to obtain the absorbed blood components of QSYQ. Target proteins of the absorbed components were collected and screened using TCMSP, TCMIP, and SwissTargetPrediction databases. Disease proteins related to myocardial ischemia were obtained through GeneCards, OMIM, and DisGeNET databases. Core targets and core components were obtained using online plotting software Venny 2.1.0, STRING, and Cytoscape 3.9.1 software. David database was used for GO functional annotation and KEGG pathway enrichment of core targets, obtaining the main pathways of QSYQ in treating myocardial ischemia and drawing visualized network diagrams. The compatibility mechanism was analyzed based on "component-target", "drug-pathway", and "PI3K-AKT" characteristic pathways, and molecular docking was used for validation. This study obtained 42 absorbed blood components of QSYQ, 556 component targets, 1 980 disease targets, 69 core targets, and 15 core components. QSYQ can exert therapeutic effects on myocardial ischemia by regulating proteins such as MAPK1, RELA, SRC, JUN, and STAT3, acting on signaling pathways such as HIF-1, PI3K-AKT, Toll-like, MAPK, VEGF, etc. The interaction network diagrams of "component-target" and "drug-pathway" preliminarily elucidated the synergy among the four drugs in this prescription at the level of targets and pathways. The PI3K-AKT characteristic pathway indicated that the sovereign drug Huangqi(Astragali Radix) and minister drug Danshen(Salviae Miltiorrhizae Radix et Rhizoma) could regulate most targets in this pathway, while the assistant drug Sanqi(Notoginseng Radix et Rhizoma) cooperated with Huangqi and Danshen on IL6 and AKT proteins, and the envoy drug Jiangxiang(Dalbergiae Odoriferae Lignum) acted on AKT and RXRA proteins, with all drugs acting synergistically on proteins such as AKT, RXRA, NFKB to regulate cell survival and promote angiogenesis. Molecular docking indicated that hydrogen bonding and hydrophobic interactions might be the main forms of action, also validating the distribution of binding energy of the PI3K-AKT signaling pathway. This study analyzed the compatibility connotation of QSYQ from multiple dimensions including drugs, components, targets, and pathways, providing reference basis for the study of the mechanism of action and compatibility rules of QSYQ.

Mechanics of woven roving/ mat laminate failure in a quasi-static tensile test

Based on tensile tests of non-standard specimens with large dimensions, an attempt was made to explain the mechanics of failure of woven roving/mat laminates with different numbers of layers. The need to use non-standard specimens in tests resulted from the impossibility of interpreting the processes taking place in tensile specimens in specimens with standard dimensions, the results of which are published in the scientific literature. In the tensile tests, four loading phases were observed, in which in the last two the structure of matrix was failed by micro- and macro-cracks, and finally by delamination through the laminates. To describe the fracture mechanics of the discussed laminates, the principle of energy equivalence was used in the transformation of elastic strain energy into binding energy. Although the processes of laminate destruction occur in the matrix, depending on the number of layers, it was found that two different processes of destruction of the internal structure with three variants of elastic strain energy distribution lead to the final delamination of the laminates. The use of energy to describe the failure of laminates in the third phase of specimen loading leads to the definition of such concepts as the dominance of failure stresses and the dominance of failure strains in the process of cracking the laminate structure. Experimental studies indicate a gradient distribution of binding energy towards the center of unloaded specimens, assumed on the basis of a literature review.

Removal and recovering of anionic and cationic dyes using Neem Leaf ash prepared at 250, 500 and 750 °C: Analyzed by adsorption isotherm and physicochemical parameters

Need of sustainable environment to develop the green adsorbent with high efficiency, cheapest for the removal of organic pollutant from waste water. Therefore, herein, we report, the adsorption of cationic and anionic dyes on the surface of ash of dry leaves of Neem (Azadirachta indica) prepared at 250, 500 and 750 °C, a benign attempt towards waste water treatment. The UV/Visible and physicochemical analysis revealed the interaction of organic pollutants with ash of dry leaves in terms of variation in the data. In X-ray diffraction, the lower intensity counts of adsorbent after adsorption than before has inferred the dye adsorption. Cationic dyes have shown impressive adsorption up to 81.25, 71.88 and 62.50% by ash prepared at 250, 500 and 750 °C respectively as CationicMB > CationicCV > AnionicCR > AnionicMO where crystal violet has shown 91.98% adsorption. In support of this, the interaction spontaneity was analysed as Methylene BlueΔG0 > Crystal VioletΔG0 > Congo RedΔG0 > Methyl OrangeΔG0 inferring stronger adsorption with cationic dyes. The adsorption isotherms for solid (ash)-liquid (dye solution) equilibrium inferred the maximum uniform distribution of binding energy, favourability of interaction, interaction capacity and intensity associated with cationic dyes. +ve interaction sites with N atoms having greater capacity to donate lone pair as compared to S and O associated with –ve dyes. The increase in conductance, surface tension and viscosity after interaction as compared to initial dye solution, confirms the adsorption phenomenon explained with Ameta Physicochemical Adsorption Analysis model. The quantitative analysis shows that crystal violet and methylene blue have been adsorbed more than 700 mg per gram of ash. The recovered dyes have been analysed through FTIR and UV/ Visible spectroscopy. The reusability of ANL was found consistently about 81% for MB even after fifth cycle.

Fe2+/Fe3+ based MOIFs + dye interaction study: Thermodynamic and kinetic analysis estimated through spectrophotometrically

Herein, the interaction study of organic dyes with newly reported metal organic ionic frameworks (MOIF) based on [Fe(CN)6]3-/[Fe(CN)6]4-/[Fe(CN)5NO]2- and cetylpyridinium cation, investigated through spectrophotometric method. Measurements were carried out at 303.15, 308.15 and 313.15 K where interaction found to be decreased with increase in temperatures. The 60–90% maximum interaction was noted for [Fe(CN)5NO]2- based MOIF with all chosen dyes at 303.15 K inferring the high interaction ability associated with dissymmetry of this MOIF due to presence of different ligands. The oxidation state and hydrophilicophobic domains of MOIFs have been found accountable for the stronger interaction where Fe2+ with high hydrophobicity was found more interacting as compared to Fe3+ with less hydrophobicity. The activation parameters ΔG0, ΔH0 have been found greater for MOIFs and methylene blue dye systems due to stronger interaction of their hydrophobic domains. The ΔS0 noted greater for [Fe(CN)5NO]2- based MOIF showing the impact of availability of interacting sites and distortion in symmetry. The isotherm analysis has inferred about the maximum uniform distribution of binding energy, favorability of interaction, interaction capacity and intensity, was associated with methylene blue and MOIFs systems. The positive slope (2.303/K) of a plot of log(Ao/At) vs t (time) inferred the first order kinetic of MOIF and chosen dyes.

Unraveling the possible inhibitors for Chorismate synthase to combat tuberculosis using in silico approach

Tuberculosis antibiotic resistance is a huge concern to the global population. The goal of this study was to find new and effective compounds to treat multidrug-resistant tuberculosis by targeting Chorismate synthase (CS), a crucial enzyme for Mycobacterium tuberculosis survival (MbT). The potential of a library of compounds as selective anti - tuberculosis drugs was investigated. Docking was first conducted using MoE to determine the effectiveness of the compounds. Molecular docking studies followed by MD simulation studies (total of 500 ns) in combination with free energy calculations grade the ligands in terms of their binding affinities. In the ligand bound state of the CS, MD simulations revealed a change from stretched to bended motional shift in loop L19. The RMSF analysis also revealed this flexibility, which was confirmed by visual inspection of L19 at various time intervals during the experiment. It appears that ZF1(-25.43Kcal/mol) and ZF2 (-22.04Kcal/mol) form hbonds and have a high binding energy in the active region of protein. Residues wise distribution of binding energy reveals that Arg144, Trp4, Thr6, and L19 amino acid residues are engaged in binding of CS with inhibitors. In summary, the findings suggest that compounds ZF1 and ZF2 may be more effective and selective anti-TB agents than currently available drugs. Also the role of L19, mediated by αH9 and αH5 in the retention of ligand inside the active pocket, through the formation of lid was also revealed. This knowledge will aid in the discovery of drugs that are potent CS inhibitors. More experimental research and a better understanding of the structure-activity relationship could aid in the development of possible candidates with better CS inhibition. Communicated by Ramaswamy H. Sarma

Impurity states in InGaAsP/InP core–shell quantum dot under external electric field

In the framework of effective mass envelope function approximation, the impurity states are calculated in InGaAsP/InP core–shell quantum dots by plane wave expansion method, and the effect of electric field is considered. The impurity binding energies in 1s and 2p ± states, and the impurity transition energy between 1s state and 2p ± state are calculated and analyzed in detail with the change of shell thickness, core radius, impurity position, and electric field strength. The results show that the impurity states in the core are stable when the shell thickness is more than 0.4a * . The binding energies and transition energies decrease with the increase of core radius. The applied electric field destroys the symmetrical distribution of binding energy and transition energy about the core center. The increase or decrease of the binding energy and transition energy depend upon the position of impurity and the direction of electric field.

Role of β-lactamase residues in a common interface for binding the structurally unrelated inhibitory proteins BLIP and BLIP-II.

The β-lactamase inhibitory proteins (BLIPs) are a model system for examining molecular recognition in protein-protein interactions. BLIP and BLIP-II are structurally unrelated proteins that bind and inhibit TEM-1 β-lactamase. Both BLIPs share a common binding interface on TEM-1 and make contacts with many of the same TEM-1 surface residues. BLIP-II, however, binds TEM-1 over 150-fold tighter than BLIP despite the fact that it has fewer contact residues and a smaller binding interface. The role of eleven TEM-1 amino acid residues that contact both BLIP and BLIP-II was examined by alanine mutagenesis and determination of the association (k on) and dissociation (k off) rate constants for binding each partner. The substitutions had little impact on association rates and resulted in a wide range of dissociation rates as previously observed for substitutions on the BLIP side of the interface. The substitutions also had less effect on binding affinity for BLIP than BLIP-II. This is consistent with the high affinity and small binding interface of the TEM-1-BLIP-II complex, which predicts per residue contributions should be higher for TEM-1 binding to BLIP-II versus BLIP. Two TEM-1 residues (E104 and M129) were found to be hotspots for binding BLIP while five (L102, Y105, P107, K111, and M129) are hotspots for binding BLIP-II with only M129 as a common hotspot for both. Thus, although the same TEM-1 surface binds to both BLIP and BLIP-II, the distribution of binding energy on the surface is different for the two target proteins, that is, different binding strategies are employed.

Microwave-assisted preparation of pumpkin seed hull activated carbon and its application for the adsorptive removal of 2,4-dichlorophenoxyacetic acid

This study explores the feasibility of pumpkin seed hull as a potential raw precursor for preparation of mesoporous activated carbon by microwave induced KOH activation. The pumpkin seed hull activated carbon (PSHAC) was characterized by pore structural analysis, zero-point-of-charge, Fourier transform infra-red spectroscopy and scanning electron microscopy. The adsorptive performance of PSHAC was quantified using pesticide, 2,4-dichlorophenoxyacetic acid (2,4-D) as model adsorbate. The effects of contact time, initial concentration, and solution pH on the adsorption process were evaluated. Results indicated high percent of removal, with the adsorptive removal of 98.28%, 97.57%, 96.03%, 93.40%, 78.11% and 65.07% at the initial concentration 50, 100, 150, 200, 300 and 400mg/L, respectively. Kinetic studies showed that the adsorption process was well described by the pseudo-second-order kinetic model. The adsorption isotherm was analyzed using the nonlinear Langmuir, Freundlich and Temkin isotherm models. The best fit was obtained with the Temkin isotherm model, predicting a uniform distribution of binding energy over the heterogeneous surface binding sites. The maximum monolayer adsorption capacity of 2,4-D for PSHAC was identified to be 260.79mg/g.

Protein Modularity, Cooperative Binding, and Hybrid Regulatory States Underlie Transcriptional Network Diversification

We examine how different transcriptional network structures can evolve from an ancestral network. By characterizing how the ancestral mode of gene regulation for genes specific to a-type cells in yeast species evolved from an activating paradigm to a repressing one, we show that regulatory protein modularity, conversion of one cis-regulatory sequence to another, distribution of binding energy among protein-protein and protein-DNA interactions, and exploitation of ancestral network features all contribute to the evolution of a novel regulatory mode. The formation of this derived mode of regulation did not disrupt the ancestral mode and thereby created a hybrid regulatory state where both means of transcription regulation (ancestral and derived) contribute to the conserved expression pattern of the network. Finally, we show how this hybrid regulatory state has resolved in different ways in different lineages to generate the diversity of regulatory network structures observed in modern species.

Evaluation of adsorption characteristics of an anionic azo dye Brilliant Yellow onto hen feathers in aqueous solutions

PURPOSE AND AIM: Removal of an anionic azo dye Brilliant Yellow has been carried out from its aqueous solutions by using hen feathers as potential adsorbent. Hen feathers procured from local poultry were cut, washed, and activated. Detailed chemical and physical analysis of hen feathers and its characterization through scanning electron microscopy, X-ray diffraction, and infrared measurements have been made. Procured dye has been adsorbed over under batch measurements and adsorption process is monitored using UV spectrophotometer. Optimum parameters for the adsorption of Brilliant Yellow over hen feathers have been determined by studying the effect of pH, temperature, concentration of dye, and amount of adsorbent. On the basis of Langmuir adsorption, isotherms feasibility of the ongoing adsorption has been ascertained and thermodynamic parameters have been calculated. Attempts have also been made to verify Freundlich, Tempkin, and Dubinin–Radushkevich adsorption isotherm models. It is found that during adsorption, uniform distribution of binding energy takes place due to interaction of the dye molecules and the ongoing adsorption process is chemisorptions. The kinetic measurements indicate dominance of pseudo-second-order process during the adsorption. The mathematical treatment on the kinetic data reveals the rate-determining step to be governed through particle diffusion at 8 × 10−5 M and involvement of film diffusion mechanism at higher concentration at temperatures at all the temperatures. The developed process is highly efficient and it can be firmly concluded that hen feather exhibits excellent adsorption capacity towards hazardous azo dye Brilliant Yellow.

Electric field and stepped barrier effects on hydrogenic impurity states in semiconducting stepped quantum wells

Based on the effective-mass approximation, the electric field and stepped barrier effects on hydrogenic impurity states in semiconducting stepped quantum wells (QWs) are investigated theoretically. Numerical results show that electron and impurity states are highly dependent on the electric field and stepped barrier in the stepped QWs. The applied symmetric electric fields induce asymmetric distribution of the donor binding energy in the stepped QWs. When the electric field is applied opposite to the growth direction of stepped barrier layer, it has a remarkable influence on the donor binding energy of impurities located at any position in the stepped QWs with any stepped barrier height. However, when the electric field is applied along the growth direction of the stepped barrier layer, the donor binding energy of impurities located at any impurity position is insensitive to variation of the stepped barrier height in the stepped QWs.

EFFECT OF APPLIED ELECTRIC FIELD ON ACCEPTOR STATES IN ZINC-BLENDE InGaN/GaN QUANTUM DOT

Based on the effective-mass approximation, the acceptor binding energy in a cylindrical zinc-blende (ZB) InGaN / GaN single quantum dot (QD) is investigated variationally in the presence of the applied electric field. Numerical results show that the acceptor binding energy is highly dependent on the applied electric field, impurity positions and QD size. The applied electric field also induces an asymmetric distribution of the acceptor binding energy with respect to the center of the QD. Moreover, in the presence of the applied electric field, the acceptor binding energy is insensitive to dot height when the impurity is located at the left boundary of the ZB In 0.1 Ga 0.9 N / GaN QD with large dot height (H≥6 nm). In particular, the acceptor binding energy of the impurity located at the left boundary of the ZB In 0.1 Ga 0.9 N / GaN QD is identical for different dot height when the applied electric field F≥350 KV/cm. This result can be of interest for the technological purpose, as it could involve a source of control some impurity-related properties in these systems under the applied electric field.

HYDROGENIC IMPURITY STATES IN WURTZITE ZnO/MgZnO QUANTUM DOT

Based on the effective-mass approximation, considering the built-in electric field effect due to the spontaneous and piezoelectric polarizations, the ground-state donor binding energy of a hygrogenic impurity in a cylindrical wurzite (WZ) ZnO / MgZnO strained quantum dot (QD) is investigated variationally. Numerical results show that the ground-state donor binding energy is highly dependent on the Mg composition, the impurity positions and the QD size. The built-in electric field also induces an asymmetric distribution of the ground-state donor binding energy with respect to the center of the QD. In particular, it is found that the ground-state donor binding energy is insensible to the dot height when the impurity is located at the right boundary of the WZ ZnO / MgZnO strained QD if the dot height is large.

Hydrogenic impurity states in wurtzite symmetric ZnO/MgZnO coupled quantum dots

Within the framework of effective-mass approximation, the ground-state donor binding energy of a hydrogenic impurity in cylindrical wurtzite (WZ) symmetric ZnO/MgZnO strained coupled quantum dots (QDs) is calculated by means of a variational method, considering the strong built-in electric field induced by the spontaneous and piezoelectric polarizations. Numerical results show that the strong built-in electric field induces an asymmetric distribution of the donor binding energy with respect to the center of the coupled QDs. When the impurity is located at the center of the dot which is opposite to the growth direction, the donor binding energy has a maximum value with increasing dot height; and it is also insensitive to the middle barrier width if the middle barrier width is large. Moreover, numerical results also indicate that the donor binding energy of impurity located at the right boundary of the dot which is opposite to the growth direction is insensitive to the Mg composition if the Mg composition is large.

Electric field effect on the donor impurity states in zinc-blende symmetric InGaN/GaN coupled quantum dots

Based on the effective-mass approximation, the donor binding energy in a cylindrical zinc-blende (ZB) symmetric InGaN/GaN coupled quantum dots (QDs) is investigated variationally in the presence of an applied electric field. Numerical results show that the ground-state donor binding energy is highly dependent on the impurity positions, coupled QDs structure parameters and applied electric field. The applied electric field induces an asymmetric distribution of the donor binding energy with respect to the center of the coupled QDs. When the impurity is located at the center of the right dot, the donor binding energy has a maximum value with increasing the dot height. Moreover, the donor binding energy is the largest and insensitive to the large applied electric field ( F ⩾ 400 kV / cm ) when the impurity is located at the center of the right dot in ZB symmetric In 0.1Ga 0.9N/GaN coupled QDs. In addition, if the impurity is located inside the right dot, the donor binding energy is insensitive to large middle barrier width ( L mb ⩾ 2.5 nm ) of ZB symmetric In 0.1Ga 0.9N/GaN coupled QDs.

External electric field effect on the hydrogenic donor impurity in zinc-blende GaN/AlGaN cylindrical quantum dot

The binding energy of a hydrogenic donor impurity in a zinc-blende GaN/AlGaN cylindrical quantum dot (QD) is calculated in the framework of effective-mass envelope-function theory using the plane wave basis. It is shown that the donor binding energy is highly dependent on the impurity position and QD size. The external electric field induces an asymmetrical distribution of the donor binding energy with respect to the center of the QD. The maximum of the donor binding energy is shifted from the center of the QD. The degenerating energy levels for symmetrical positions with respect to the center of QD are also split. The splitting increases with the increase in QD height while the splitting increases up to a maximum and then decreases with the increase in QD radius. In the presence of the external electric field, the donor binding energy is insensitive to dot height when the impurity is located at the left side of the QD with large dot height. In addition, Stark shift dependence on hydrogenic impurity position is calculated.

Hydrogenic impurity states in wurtzite GaN/AlGaN coupled quantum dots

The ground-state binding energy of a hydrogenic donor impurity in wurtzite (WZ) GaN/AlGaN coupled quantum dots (QDs) is calculated by means of a variational method, considering the strong built-in electric fields caused by the piezoelectricity and spontaneous polarizations. The strong built-in electric fields induce an asymmetrical distribution of the ground-state binding energy with respect to the center of the coupled QDs. If the impurity is located at the low dot, the ground-state binding energy is insensitive to the interdot barrier width of WZ GaN/AlGaN coupled QDs.

Built-in electric field effect on the hydrogenic donor impurity in wurtzite InGaN quantum dot

The donor binding energy of the hydrogenic impurity is calculated as functions of the impurity position and structural parameters of wurtzite (WZ) InGaN/GaN quantum dot (QD). Numerical results show that the strong built-in electric field induces an asymmetrical distribution of the donor binding energy with respect to the center of the QD. When the impurity is located at the right boundary of the WZ InGaN/GaN QD, the donor binding energy is insensitive to the dot height, and it is largest when In composition x = 0.3 for different WZ InGaN/GaN QD. Realistic cases, including the impurity in the QD and the surrounding barriers.

Hydrogenic donor states in wurtzite InGaN/GaN coupled quantum dots

The binding energies of the hydrogenic impurity in wurtzite InGaN coupled quantum dots (QDs) are calculated by means of a variational method, considering the strong built-in electric field induced by the spontaneous and piezoelectric polarizations. Numerical results show that the strong built-in electric field induces an asymmetrical distribution of the donor binding energy with respect to the center of the coupled QDs. When the impurity is located in the center of the left dot, the donor binding energy is largest and insensitive to the barrier height of the wurtzite InGaN coupled QDs.