Theoretical Study Research Articles

Three-metal ion mechanism of cross-linked and uncross-linked DNA polymerase β: A theoretical study.

In our recent publication, we have proposed a revised base excision repair pathway in which DNA polymerase β (Polβ) catalyzes Schiff base formation prior to the gap-filling DNA synthesis followed by β-elimination. In addition, the polymerase activity of Polβ employs the "three-metal ion mechanism" instead of the long-standing "two-metal ion mechanism" to catalyze phosphodiester bond formation based on the fact derived from time-resolved x-ray crystallography that a third Mg2+ was captured in the polymerase active site after the chemical reaction was initiated. In this study, we develop the models of the uncross-linked and cross-linked Polβ complexes and investigate the "three-metal ion mechanism" vs the "two-metal ion mechanism" by using the quantum mechanics/molecular mechanics molecular dynamics simulations. Our results suggest that the presence of the third Mg2+ ion stabilizes the reaction-state structures, strengthens correct nucleotide binding, and accelerates phosphodiester bond formation. The improved understanding of Polβ's catalytic mechanism provides valuable insights into DNA replication and damage repair.

Probing the eccentricity in protostellar discs: Modelling kinematics and morphologies

Protostellar discs are mostly modelled as circular structures of gas and dust orbiting a protostar. However, a number of physical mechanisms, for example, the presence of a (sub)stellar companion or initial axial asymmetry, can cause the gas and dust orbital motion to become eccentric. Theoretical studies have revealed that, when present, disc eccentricity is expected to occur with predictable profiles that can be long-lasting and potentially observable in protostellar systems. We construct an analytical model predicting the typical features of the kinematics and morphology of eccentric protostellar discs, with the final goal of characterising the observational appearance of eccentricity in discs. We validate the model using a numerical simulation of a circumbinary disc (where the binary makes the disc eccentric). We finally post-process the simulation with Monte Carlo radiative transfer to study how eccentric features would appear through the 'eyes' of ALMA. Besides the motion of the material on eccentric Keplerian orbits in the disc orbital plane, the most characteristic eccentric feature emerging from the analytical model is strong vertical motion with a typical anti-symmetric pattern (with respect to the disc line of pericentres). A circumbinary disc with a $ 40$ au eccentric cavity cav =0.2$), carved by an $a_ bin =15$ au binary, placed at a distance $d=130$ pc, is expected to host in its upper emission surface vertical oscillations up to $v_ z ms $ close to the cavity edge, that is to say, well within ALMA spectral and spatial resolution capabilities. A residual spiral pattern in the vertical velocity $ z ms $ of the simulation cannot be captured by the theoretical model, we speculate it to be possibly linked to the presence of a companion in the system.

Factors Affecting the Land Investment Decisions in the Old Members of the European Union: A Systematic Literature Review

In response to concerns over land concentration and access within the European Union, this study seeks to elucidate the factors influencing farmers’ decisions to invest in land and the consequent growth of farm size. Employing a systematic literature review utilizing the PRISMA method, we delve into theoretical and empirical studies to bridge the gap between agricultural management practices and land market dynamics. Our analysis reveals a complex interplay of endogenous and exogenous factors, including technological advancements, farm characteristics, demographic factors, macroeconomic conditions, and policy environment, significantly impacting investment behaviours and farm growth trajectories. The research highlights the underexplored impact of external factors like policy and land regulation, which are scarcely addressed in empirical studies despite their substantial influence on farm-size evolution and investment decisions. Furthermore, the study emphasizes the need for future research to incorporate a more comprehensive framework that integrates internal farm dynamics with broader economic and policy contexts, thereby facilitating a deeper understanding of the agricultural sector’s resilience and sustainability. The findings underscore the critical role of adopting innovative methodologies and approaches to fully understand the dynamics of farm growth and land investments, aiming to support policymakers, stakeholders, and researchers in fostering sustainable agricultural practices.

Theoretical study of PdNi and PdCu clusters embedded on graphene modified by monovacancy and nitrogen doping.

The stability and reactivity of Pd4Ni4 and Pd4Cu4 clusters embedded on graphene modified by monovacancy and nitrogen doping were investigated using auxiliary density functional theory (ADFT) calculations. The most stable structure of the Pd4Ni4 cluster is found in high spin multiplicity, whereas the lowest stable energy structure of the Pd4Cu4 cluster is a close shell system. The interaction energies between the bimetallic clusters and the defective graphene systems are significantly higher than those reported in the literature for the Pd-based clusters deposited on pristine graphene. It is observed that the composites studied present a HOMO-LUMO gap less than 1 eV, which suggests that they may present a good chemical reactivity. Therefore, from the results obtained in this work it can be inferred that the single vacancy graphene and pyridinic N-doped graphene are potentially good support materials for Pd-based clusters.

COMPUTER SIMULATION OF THE STRUCTURE OF SOME AZO-DERIVATIVES OF β-DIKETONES BY THE METHODS OF QUANTUM CHEMISTRY

The electronic and spatial structures of newly synthesized derivatives of β-diketones were studied based on the results of quantum chemical calculations. The properties of β-diketones with substituted phenyldiazonium chloride, namely 8 tautomers aryl derivatives of β-diketones-(E)-3-(2-(1-(dimethylamino)-1,3-dioxobutan-2-ylidene)hydrazinyl)-2-hydroxy-5-nitrobenzene sulfonic acid (H3L1) have been studied using the PM3 semi-empirical quantum chemistry method and the density functional theory (DFT) method with the B3LYP hybrid functional and 6-31+G(d,p) basis set. Energy and electronic characteristics of 8 tautomers are investigated. The effect of intramolecular hydrogen bonding on the structure of the investigated compounds has been studied. The formation of hydrogen bonds was confirmed by Natural Bond Orbital (NBO) analysis. Theoretical studies using the PM3 and DFT methods confirm the practical conclusions about the superiority of the hydrazone form in real samples.

Synthesis, Photophysical Properties, Theoretical Studies, and Living Cancer Cell Imaging Applications of New 7-(Diethylamino)quinolone Chalcones

Synthesis, Photophysical Properties, Theoretical Studies, and Living Cancer Cell Imaging Applications of New 7-(Diethylamino)quinolone Chalcones

A 2.5V In-Plane Flexi-Pseudocapacitor with Unprecedented Energy and Cycling Efficiency for All-Weather Applications.

As electronic devices for aviation, space, and satellite applications become more sophisticated, built-in energy storage devices also require a wider temperature spectrum. Herein, an all-climate operational, energy and power-dense, flexible, in-plane symmetric pseudocapacitor is demonstrated with utmost operational safety and long cycle life. The device is constructed with interdigital-patterned laser-scribed carbon-supported electrodeposited V5O12·6H2O as a binder-free electrode and a novel high-voltage anti-freezing water-in-salt-hybrid electrolyte. The anti-freezing electrolyte can operate over a wide temperature range of -40-60°C while offering a stable potential window of ≈2.5V. The device undergoes rigorous testing under diverse environmental conditions, including rapid and regular temperature and mechanical transition over multiple cycles. Additionally, detailed theoretical simulation studies are performed to understand the interfacial interactions with the active material as well as the local behavior of the anti-freeze electrolyte at different temperatures. As a result, the all-weather pseudocapacitor at 1Ag-1 shows a high areal capacitance of 234.7mFcm-2 at room temperature and maintains a high capacitance of 129.8mFcm-2 even at -40°C. Besides, the cell operates very reliably for over 80950 cycles with a capacitance of 25.7mFcm-2 at 10Ag-1 and exhibits excellent flexibility and bendability under different stress conditions.

A Study on The Problematization of Logistics in Agricultural Production in The State of Tocantins

Objective: the research aims to describe the logistical service system, observing the problematization of agricultural production in the state of Tocantins, considering that this sector is one of the most promising in terms of socioeconomic and regional development in the country.
  
 Theoretical benchmark: with the growing advancement of agricultural production and the exploration of new frontiers, Brazil stands out as one of the main exporters of agricultural products today. Given the significant development of agriculture, it is observed that the logistical factor, mainly costs and infrastructure, is among the elements with the greatest impact on the efficiency of the entire agricultural production chain in the state of Tocantins.
  
 Method: the methodology adopted will be the deductive method, based on theoretical logistics studies, applicable legislation, and support materials for logistics learning systems, in addition to economic representation in the state of Tocantins. The resources used include bibliographic and documentary material and other instruments or research techniques in accordance with the adopted methodology, aiming to provide support for research on the proposed theme.
  
 Results and conclusion: given the content of this study, it is highlighted that the chain of agricultural processes encompasses a complex network of activities in the production chain, and cannot be conceived solely as a relationship between producer and consumer, given its breadth of action. In this context, it should be noted that logistics services end up representing one of the obstacles to the development of agriculture in the State of Tocantins, mainly due to its geographic location.
  
 Implications of the research: the approach adopted in this research offers unprecedented scientific contributions to the field of logistics, providing theoretical bases for interventions and public policies that can impact this economic activity in a Brazilian state with strong economic and social growth trends, whose production has repercussions at national and international levels.
  
 Originality/value: the social transformations of recent decades, related to the process of globalization of the economy and technology, have directly influenced the social and economic life of countries, affecting production and service chains and interfering in labor relations. Therefore, the increase in regions dedicated to agribusiness activities is a general trend among emerging countries, requiring a deeper understanding of the territorial approach to regional development, especially in economic activities hampered by bottlenecks in the logistics system, both national and international. Thus, new reflections and planning are necessary and imperative elements in Brazilian states like Tocantins.

THEORETICAL STUDY FOR COMPARISON OF pKa OF A NUMBER OF SCHIFF BASES BY EMPLOYING PARAMETERS DERIVED FROM DFT AND MP2 METHOD

The ionization constants of seven compounds derived from Schiff bases have been studied theoretically. In this study, the factors affecting the ionization constant pKa of Schiff bases were found, which are van der Waals forces, energy levels, hardness, chemical potential and spherical electrophile index by conducting a theoretical study of these compounds using two methods of quantum mechanics for the purpose comparison, which is the Ab-initio basic calculation methods. Two methods were chosen, which are the density function theory (DFT) method and the MP2 Mueller-Pleist perturbation theory method using Chem program. Office 2008 the extent to which these two methods correspond to the known chemical bases was determined by discussing the theoretical variables that were calculated using the two methods referred to above and finding the relationship between the calculated physical variables with each other and determining their nature. After conducting the multiple statistical analysis process, it was found that the best variables that affect the ionization constant in the DFT method are (Bond C1-C7, Bend, VDW) and the rest of the variables were theoretically excluded because the coefficients of those variables are very few or equal to zero and accordingly these variables were adopted to obtain A relationship with better results, as it is noted that the values of the correlation coefficient in this DFT method are (0.994). As for the MP2 method, the best variables that affect the ionization constant are (Ƞ, KE, Tors) and the rest of the variables were theoretically excluded because the coefficients of these variables are very few or equal Therefore, these variables were adopted to obtain a relationship with better results, as it is noted that the values of the correlation coefficient in this MP2 method are (0.989). By comparing the theoretical values with the practical values, it was found that the results of the DFT method were closer to the process than the results of the MP2 method.

Vinyl-Group-Anchored Covalent Organic Framework for Promoting the Photocatalytic Generation of Hydrogen Peroxide.

The artificial photosynthesis of H2O2 from water and oxygen using semiconductor photocatalysts is attracting increasing levels of attention owing to its green, environmentally friendly, and energy-saving characteristics. Although covalent organic frameworks (COFs) are promising materials for promoting photocatalytic H2O2 production owing to their structural and functional diversity, they typically suffer from low charge-generation and -transfer efficiencies as well as rapid charge recombination, which restricts their use as catalysts for photocatalytic H2O2 production. Herein, we report a strategy for anchoring vinyl moieties to a COF skeleton to facilitate charge separation and migration, thereby promoting photocatalytic H2O2 generation. This vinyl-group-bearing COF photocatalyst exhibits a H2O2-production rate of 84.5 μmol h-1 (per 10 mg), which is ten-times higher than that of the analog devoid of vinyl functionality and superior to most reported COF photocatalysts. Both experimental and theoretical studies provide deep insight into the origin of the improved photocatalytic performance. These findings are expected to facilitate the rational design and modification of organic semiconductors for use in photocatalytic applications.

Pacemaker Effects on Online Social Rhythms on a Social Network

Abstract The dynamics of coupled oscillators in a network are a significant topic in complex systems science. People with daily social rhythms interact through social networks in everyday life. This can be considered as a coupled oscillator in social networks, which is also true in online society (online social rhythms). Controlling online social rhythms can contribute to healthy daily rhythms and mental health. We consider controlling online social rhythms by introducing periodic forcing (pacemakers). However, theoretical studies predict that pacemaker effects do not spread widely across mutually connected networks such as social networks. We aimed to investigate the characteristics of the online social rhythms with pacemakers on an empirical online social network. Therefore, we conducted an intervention experiment on the online social rhythms of hundreds of players (participants who were pacemakers) using an avatar communication application ($N=416$). We found that the intervention had little effect on neighbors' online social rhythms. This may be because mutual entrainment stabilizes the neighbors' and their friends' rhythms. That is, their online social rhythms were stable despite the disturbances. However, the intervention affected on neighbors' rhythms when a participant and their neighbor shared many friends. This suggests that interventions to densely connected player groups may make their and their friends' rhythms better. We discuss the utilization of these properties to improve healthy online social rhythms.

Vinyl‐Group‐Anchored Covalent Organic Framework for Promoting the Photocatalytic Generation of Hydrogen Peroxide

AbstractThe artificial photosynthesis of H2O2 from water and oxygen using semiconductor photocatalysts is attracting increasing levels of attention owing to its green, environmentally friendly, and energy‐saving characteristics. Although covalent organic frameworks (COFs) are promising materials for promoting photocatalytic H2O2 production owing to their structural and functional diversity, they typically suffer from low charge‐generation and ‐transfer efficiencies as well as rapid charge recombination, which restricts their use as catalysts for photocatalytic H2O2 production. Herein, we report a strategy for anchoring vinyl moieties to a COF skeleton to facilitate charge separation and migration, thereby promoting photocatalytic H2O2 generation. This vinyl‐group‐bearing COF photocatalyst exhibits a H2O2‐production rate of 84.5 μmol h−1 (per 10 mg), which is ten‐times higher than that of the analog devoid of vinyl functionality and superior to most reported COF photocatalysts. Both experimental and theoretical studies provide deep insight into the origin of the improved photocatalytic performance. These findings are expected to facilitate the rational design and modification of organic semiconductors for use in photocatalytic applications.

Mechanistic regulation of planarian shape during growth and degrowth.

Adult planarians can grow when fed and degrow (shrink) when starved while maintaining their whole-body shape. It is unknown how the morphogens patterning the planarian axes are coordinated during feeding and starvation or how they modulate the necessary differential tissue growth or degrowth. Here we investigate the dynamics of planarian shape together with a theoretical study of the mechanisms regulating whole-body proportions and shape. We found that the planarian body proportions scale isometrically following similar linear rates during growth and degrowth, but that fed worms are significantly wider than starved worms. By combining a descriptive model of planarian shape and size with a mechanistic model of anterior-posterior and medio-lateral signaling calibrated with a novel parameter optimization methodology, we theoretically demonstrate that the feedback loop between these positional information signals and the shape they control can regulate the planarian whole-body shape during growth. Furthermore, the computational model produced the correct shape and size dynamics during degrowth due to a predicted increase in apoptosis rate and pole signal during starvation. These results offer mechanistic insights into the dynamic regulation of whole-body morphologies.

Large optoelectronic chromatic dispersion in PN-type silicon photodiodes and photovoltaic cells.

Optoelectronic chromatic dispersion (OED) is a significant source of effective chromatic dispersion in photodiodes. We present an experimental and theoretical study of OED in PN-type Si photodiodes and photovoltaic cells and report on a very large effective chromatic dispersion in these devices. As measured with the modulation phase-shift technique at a frequency of 4 kHz for these slow devices, the OED spectral sensitivity for a commercial Si photodiode is approx. 0.02 deg/nm in the 720-850 nm wavelength band and increases to 0.25 deg/nm at λ = 1µm. For a Si photovoltaic cell, the OED is approx. 0.09 deg/nm in this spectral region. These values translate into an effective chromatic dispersion parameter of approx. 1012ps/(n m ×k m) for these sub-millimeter device lengths, which is over eight orders of magnitude larger than high-dispersion materials such as chalcogenide glass. The enormous dispersion in these sub-millimeter sized silicon-based devices can be utilized for on-chip optoelectronic sensors such as wavelength monitoring and spectroscopy. The substantial OED of photovoltaic cells can be utilized for the characterization and optimization and new applications for optical sensing with these self-powered devices.

Theoretical study on Stark effect of Rydberg atom in super low frequency electric field measurement

AbstractSuper low frequency electric field measurements are crucial in analysing electromagnetic compatibility, assessing equipment status, and other related fields. Rydberg atom‐based super low frequency electric field measurements are performed by observing the Stark shift in the spectrum of the Rydberg state. In a specific range of field strength (E < Eavoid, where Eavoid is the threshold to avoid crossing electric fields), the Rydberg atomic spectrum experiences a quadratic frequency shift in relation to the field strength, with the coefficient being determined by the atomic polarisability α. The authors establish a dynamic equation for the interaction between the external electric field and the atomic system, and present the Stark structure diagram of the Caesium Rydberg atom. The mathematical formulae for α and Eavoid in different Rydberg states are also obtained: α = A × (n*)6 + B × (n*)7 and Eavoid = C/(n*)5 + D/(n*)7, where A(B) = 2.2503 × 10−9(7.49,948 × 10−11) and C(D) = 1.68,868 × 108(2.45,991 × 109). The error of α and Eavoid compared with the experimental values does not exceed 8% and is even lower in the low Rydberg states. Accurately calculating the values of α and Eavoid is crucial in incorporating the Rydberg atom quantum coherence effect into super low frequency electric field measurements in new power systems.

Sulfur-Tuned Main-Group Sb-N-C Catalysts for Selective 2-Electron and 4-Electron Oxygen Reduction.

The selective oxygen reduction reaction (ORR) is important for various energy conversion processes such as the fuel cells and metal-air batteries for the 4e- pathway and hydrogen peroxide (H2O2) electrosynthesis for the 2e- pathway. However, it remains a challenge to tune the ORR selectivity of a catalyst in a controllable manner. Herein, we report an efficient strategy for introducing sulfur dopants to regulate the ORR selectivity of main-group Sb-N-C single-atom catalysts. Significantly, Sb-N-C with the highest sulfur content follows a 2e- pathway with a high H2O2 selectivity (96.8%) and a remarkable mass activity (96.1 A g-1 at 0.65V), while the sister catalyst with the lowest sulfur content directs a 4e- pathway with a half-wave potential (E1/2 = 0.89V) that is more positive than commercial Pt/C. In addition, practical applications for these two 2e-/4e- ORR catalysts are demonstrated by bulk H2O2 electrosynthesis for the degradation of organic pollutants and a high-power zinc-air battery, respectively. Combined experimental and theoretical studies reveals that the excellent selectivity for the sulfurized Sb-N-Cs is attributed to the optimal adsorption-desorption of the ORR intermediates realized through the electronic structure modulation by the sulfur dopants. This article is protected by copyright. All rights reserved.

Accessing the O Vacancy with Anionic Redox Chemistry Toward Superior Electrochemical Performance in O3 type Na‐Ion Oxide Cathode

AbstractAnionic redox chemistry is now viewed as the effective paradigm of improving the capacity of layered oxide materials in Sodium‐ion battery. In this study, O3‐type layered oxide NaLi0.18Co0.23Ru0.59O2 (NLCR) with O redox ability is successfully synthesized via a facile solid‐state synthesis method. By manipulating the calcinate atmosphere with air and argon (sort by NLCR‐Air NLCR‐Ar respectively), a large amount of O vacancy is introduced in the NLCR‐Air cathode. NLCR‐Air with sufficient O vacancy exhibited superior rate performance which showed 87.7% capacity retention after 1000 cycles at 20 C. Both NLCR‐Air and NLCR‐Ar showed activation of O redox properties which is supported by the soft X‐ray absorption spectroscopy (sXAS). Nevertheless, the in‐situ X‐ray diffraction and sXAS studies disclosed the O vacancy can promote the reversible phase transition and effectively suppress the irreversible O redox upon cycling. These are further supported by theoretical study which suggested a fast kinetic of Na diffusion and less electron agglomeration around the O atom for NLCR‐Air with O vacancy.The research proposed a modification strategy with extraordinary reversible O redox property within O3‐type layered cathode and offered a novel insight into understanding the anionic redox mechanism thus provide guidance of material design advanced energy storage systems.

Convergence Study of 2D Transport Method for Multigroup k-Eigenvalue Problems with High-Order Scattering Source Using Fourier Analysis

The convergence behavior of a two-dimensional (2D) transport method has been derived by Fourier analysis for single-group problems with isotropic sources. However, in real calculation, to pursue precision, a high-order scattering source is a common option, and its influence on convergence performance is worth investigating. No theoretical convergence study of a 2D transport method for multigroup problems with high-order scattering sources was previously performed, but it is important work that would complement existing studies. This study presents a Fourier analysis for solving multigroup problems with high-order scattering. First, the influences of the number of inner iterations for the multigroup isotropic scattering problem are analyzed. It is found that with an increase of the number of inner iterations, the spectral radius decreases and finally reaches an asymptotic value. When the scattering ratio is increased, more inner iterations are required to reach the asymptotic value. Then, the influences of high-order scattering are analyzed. The Fourier analysis results show that for high-order scattering source problems, the influence of the number of inner iterations is different from the isotropic scattering case. The influences of first-order scattering and second-order scattering are not the same. With an increase of first-order scattering, the spectral radius first decreases in the small optical thickness region and then increases in the large optical thickness region, which may lead to the divergence of iterations. If second-order scattering is not too large, an increase of second-order scattering decreases the spectral radius for all optical thickness regions. First-order scattering and second-order scattering that are too large may result in an unpredictable slope of the spectral radius for optical thicknesses between 10−1 and 1.

Stereoselective Synthesis and Catalytical Application of Perillaldehyde-Based 3-Amino-1,2-diol Regioisomers

A library of regioisomeric monoterpene-based aminodiols was synthesised and applied as chiral catalysts in the addition of diethylzinc to benzaldehyde. The synthesis of the first type of aminodiols was achieved starting from (−)-8,9-dihydroperillaldehyde via reductive amination, followed by Boc protection and dihydroxylation with the OsO4/NMO system. Separation of formed stereoisomers resulted in a library of aminodiol diastereoisomers. The library of regioisomeric analogues was obtained starting from (−)-8,9-dihydroperillic alcohol, which was transformed into a mixture of allylic trichloroacetamides via Overman rearrangement. Changing the protecting group to a Boc function, the protected enamines were subjected to dihydroxylation with the OsO4/NMO system, leading to a 71:16:13 mixture of diastereoisomers, which were separated, affording the three isomers in isolated form. The obtained primary aminodiols were transformed into secondary derivatives. The regioselectivity of the ring closure of the N-benzyl-substituted aminodiols with formaldehyde was also investigated, resulting in 1,3-oxazines in an exclusive manner. To explain the stability difference between diastereoisomeric 1,3-oxazines, a series of comparative theoretical modelling studies was carried out. The obtained potential catalysts were applied in the reaction of aromatic aldehydes and diethylzinc with moderate to good enantioselectivities (up to 94% ee), whereas the opposite chiral selectivity was observed between secondary aminodiols and their ring-closed 1,3-oxazine analogues.

Joint Diagnostic Approach to Pressure and Tracer Responses from Reservoirs: An Experimental and Theoretical Study to Estimate the Accuracy of Reservoir Models

This study presents a novel perspective for improving the understanding of permeable structures at geothermal prospects by jointly diagnosing the responses of conventional pressure transient and tracer testing. The pressure and tracer responses individually yield apparent porosity–thickness products. The difference between them implies the existence of unknown dead-end features involved in a reservoir model. Laboratory experiments and numerical simulations validate this concept. Potential application to hypothetical exploration demonstrates that the logarithmic ratio of the porosity–thickness products, determined based on pressure and tracer responses, indicates the accuracy of the reservoir model to be successively updated with the progress of the exploration. The reservoir model successfully reproduced the synthetic observations regardless of the accuracy of permeable structure if different porosity–thickness products were allowed to be assumed to individually reproduce pressure and tracer responses. These porosity–thickness products coincided only if the reservoir model correctly captured the permeable structure. This novel perspective will provide strategic guides for successful exploration and development at the prospects of geothermal and, potentially, general geofluid resources.