scholarly journals The physical origin of rate promoting vibrations in enzymes revealed by structural rigidity

2020 ◽  
Vol 10 (1) ◽  
Author(s):  
Yann Chalopin
Keyword(s):  
Active Sites ◽  
Stability Function ◽  
Structural Rigidity ◽  
Catalytic Sites ◽  
Enzyme Topology ◽  
The Stability ◽  
Localized Vibrations ◽  
Experimental Strategies ◽  
Selection Of ◽  
Catalytic Power

Abstract Enzymes are the most efficient catalysts known to date. However, decades of research have failed to fully explain the catalytic power of enzymes, and most of the current attempts to uncloak the details of atomic motions at active sites remain incomplete. Here, a straightforward manner for understanding the interplay between the complex or irregular enzyme topology and dynamical effects at catalytic sites is introduced, by revealing how fast localized vibrations form spontaneously in the stiffest parts of the scaffold. While shedding light on a physical mechanism that allowed the selection of the picosecond (ps) timescale to increase the catalytic proficiency, this approach exposes the functional importance of localized motions as a by-product of the stability-function tradeoff in enzyme evolution. From this framework of analysis—directly accessible from available diffraction data—experimental strategies for engineering the catalytic rate in enzymatic proteins are proposed.

scholarly journals Spatio-temporal selection of reference genes in the two congeneric species of Glycyrrhiza

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Yuping Li ◽  
Xiaoju Liang ◽  
Xuguo Zhou ◽  
Yu An ◽  
Ming Li ◽  
...  
Keyword(s):  
Gene Expression ◽  
Developmental Stage ◽  
Reference Genes ◽  
Developmental Stages ◽  
Individual Factors ◽  
Congeneric Species ◽  
Spatio Temporal ◽  
The Stability ◽  
Different Tissues ◽  
Selection Of

AbstractGlycyrrhiza, a genus of perennial medicinal herbs, has been traditionally used to treat human diseases, including respiratory disorders. Functional analysis of genes involved in the synthesis, accumulation, and degradation of bioactive compounds in these medicinal plants requires accurate measurement of their expression profiles. Reverse transcription quantitative real-time PCR (RT-qPCR) is a primary tool, which requires stably expressed reference genes to serve as the internal references to normalize the target gene expression. In this study, the stability of 14 candidate reference genes from the two congeneric species G. uralensis and G. inflata, including ACT, CAC, CYP, DNAJ, DREB, EF1, RAN, TIF1, TUB, UBC2, ABCC2, COPS3, CS, R3HDM2, were evaluated across different tissues and throughout various developmental stages. More importantly, we investigated the impact of interactions between tissue and developmental stage on the performance of candidate reference genes. Four algorithms, including geNorm, NormFinder, BestKeeper, and Delta Ct, were used to analyze the expression stability and RefFinder, a comprehensive software, provided the final recommendation. Based on previous research and our preliminary data, we hypothesized that internal references for spatio-temporal gene expression are different from the reference genes suited for individual factors. In G. uralensis, the top three most stable reference genes across different tissues were R3HDM2, CAC and TUB, while CAC, CYP and ABCC2 were most suited for different developmental stages. CAC is the only candidate recommended for both biotic factors, which is reflected in the stability ranking for the spatio (tissue)-temporal (developmental stage) interactions (CAC, R3HDM2 and DNAJ). Similarly, in G. inflata, COPS3, R3HDM2 and DREB were selected for tissues, while RAN, COPS3 and CS were recommended for developmental stages. For the tissue-developmental stage interactions, COPS3, DREB and ABCC2 were the most suited reference genes. In both species, only one of the top three candidates was shared between the individual factors and their interactions, specifically, CAC in G. uralensis and COPS3 in G. inflata, which supports our overarching hypothesis. In summary, spatio-temporal selection of reference genes not only lays the foundation for functional genomics research in Glycyrrhiza, but also facilitates these traditional medicinal herbs to reach/maximize their pharmaceutical potential.

scholarly journals Insights on forming N,O-coordinated Cu single-atom catalysts for electrochemical reduction CO2 to methane

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Yanming Cai ◽  
Jiaju Fu ◽  
Yang Zhou ◽  
Yu-Chung Chang ◽  
Qianhao Min ◽  
...  
Keyword(s):  
Energy Barrier ◽  
Active Sites ◽  
Theoretical Calculations ◽  
High Energy ◽  
Single Atom ◽  
Faradaic Efficiency ◽  
High Energy Barrier ◽  
Catalytic Sites ◽  
Electron Reduction ◽  
First Time

AbstractSingle-atom catalysts (SACs) are promising candidates to catalyze electrochemical CO2 reduction (ECR) due to maximized atomic utilization. However, products are usually limited to CO instead of hydrocarbons or oxygenates due to unfavorable high energy barrier for further electron transfer on synthesized single atom catalytic sites. Here we report a novel partial-carbonization strategy to modify the electronic structures of center atoms on SACs for lowering the overall endothermic energy of key intermediates. A carbon-dots-based SAC margined with unique CuN2O2 sites was synthesized for the first time. The introduction of oxygen ligands brings remarkably high Faradaic efficiency (78%) and selectivity (99% of ECR products) for electrochemical converting CO2 to CH4 with current density of 40 mA·cm-2 in aqueous electrolytes, surpassing most reported SACs which stop at two-electron reduction. Theoretical calculations further revealed that the high selectivity and activity on CuN2O2 active sites are due to the proper elevated CH4 and H2 energy barrier and fine-tuned electronic structure of Cu active sites.

scholarly journals Study on the adsorption selection of CH$$_4$$ on CuO (110) versus (111) surfaces: a density functional theory study

2021 ◽  
Vol 3 (4) ◽  
Author(s):  
Long Lin ◽  
Linwei Yao ◽  
Shaofei Li ◽  
Zhengguang Shi ◽  
Kun Xie ◽  
...  
Keyword(s):  
Density Functional Theory ◽  
Adsorption Capacity ◽  
Active Sites ◽  
Density Functional ◽  
Oxygen Vacancies ◽  
Density Functional Theory Calculations ◽  
Density Functional Theory Study ◽  
Functional Theory ◽  
Strong Adsorption ◽  
Selection Of

AbstractFinding the active sites of suitable metal oxides is a key prerequisite for detecting CH$$_4$$ 4 . The purpose of the paper is to investigate the adsorption of CH$$_4$$ 4 on intrinsic and oxygen-vacancies CuO (111) and (110) surfaces using density functional theory calculations. The results show that CH$$_4$$ 4 has a strong adsorption energy of −0.370 to 0.391 eV at all site on the CuO (110) surface. The adsorption capacity of CH$$_4$$ 4 on CuO (111) surface is weak, ranging from −0.156 to −0.325 eV. In the surface containing oxygen vacancies, the adsorption capacity of CuO surface to CH$$_4$$ 4 is significantly stronger than that of intrinsic CuO surface. The results indicate that CuO (110) has strong adsorption and charge transfer capacity for CH$$_4$$ 4 , which may provide experimental guidance.

MASTER STABILITY FUNCTIONS FOR SYNCHRONIZED COUPLED SYSTEMS

1999 ◽  
Vol 09 (12) ◽  
pp. 2315-2320 ◽  
Author(s):  
LOUIS M. PECORA ◽  
THOMAS L. CARROLL
Keyword(s):  
Simple Form ◽  
Coupled Systems ◽  
Stability Function ◽  
Coupled Oscillator ◽  
Synchronous State ◽  
Master Stability Function ◽  
Stability Functions ◽  
The Stability

We show that many coupled oscillator array configurations considered in the literature can be put into a simple form so that determining the stability of the synchronous state can be done by a master stability function which solves, once and for all, the problem of synchronous stability for many couplings of that oscillator.

Stabilization of networked switched affine systems with event-triggered strategy

2021 ◽  
pp. 014233122110213
Author(s):  
Dandan Li ◽  
Zhiqiang Zuo ◽  
Yijing Wang
Keyword(s):  
Affine Systems ◽  
Switching Law ◽  
Event Time ◽  
Sliding Motion ◽  
State Dependent ◽  
Event Triggering ◽  
Stability Issue ◽  
The Stability ◽  
Event Based ◽  
Selection Of

Using an event-based switching law, we address the stability issue for continuous-time switched affine systems in the network environment. The state-dependent switching law in terms of the region function is firstly developed. We combine the region function with the event-triggering mechanism to construct the switching law. This can provide more candidates for the selection of the next activated subsystem at each switching instant. As a result, it is possible for us to activate the appropriate subsystem to avoid the sliding motion. The Zeno behavior for the switched affine system can be naturally ruled out by guaranteeing a positive minimum inter-event time between two consecutive executions of the event-triggering threshold. Finally, two numerical examples are given to demonstrate the effectiveness of the proposed method.

scholarly journals Superior FexN electrocatalyst derived from 1,1′-diacetylferrocene for oxygen reduction reaction in alkaline and acidic media

2020 ◽  
Vol 9 (1) ◽  
pp. 843-852
Author(s):  
Hunan Jiang ◽  
Jinyang Li ◽  
Mengni Liang ◽  
Hanpeng Deng ◽  
Zuowan Zhou
Keyword(s):  
Oxygen Reduction Reaction ◽  
Oxygen Reduction ◽  
Current Density ◽  
Active Sites ◽  
Reduction Reaction ◽  
Alkaline Media ◽  
Acidic Media ◽  
Onset Potential ◽  
Acidic And Alkaline Media ◽  
The Stability

AbstractAlthough Fe–N/C catalysts have received increasing attention in recent years for oxygen reduction reaction (ORR), it is still challenging to precisely control the active sites during the preparation. Herein, we report FexN@RGO catalysts with the size of 2–6 nm derived from the pyrolysis of graphene oxide and 1,1′-diacetylferrocene as C and Fe precursors under the NH3/Ar atmosphere as N source. The 1,1′-diacetylferrocene transforms to Fe3O4 at 600°C and transforms to Fe3N and Fe2N at 700°C and 800°C, respectively. The as-prepared FexN@RGO catalysts exhibited superior electrocatalytic activities in acidic and alkaline media compared with the commercial 10% Pt/C, in terms of electrochemical surface area, onset potential, half-wave potential, number of electrons transferred, kinetic current density, and exchange current density. In addition, the stability of FGN-8 also outperformed commercial 10% Pt/C after 10000 cycles, which demonstrates the as-prepared FexN@RGO as durable and active ORR catalysts in acidic media.

Tuning electronic states of catalytic sites enhances SCR activity of hexagonal WO3by Mo framework substitution

2017 ◽  
Vol 7 (12) ◽  
pp. 2467-2473 ◽  
Author(s):  
Yaxin Chen ◽  
Zichenxi Dong ◽  
Zhiwei Huang ◽  
Meijuan Zhou ◽  
Jiayi Gao ◽  
...  
Keyword(s):  
Active Sites ◽  
Electronic States ◽  
Catalytic Sites ◽  
Catalytically Active

The electronic states of the catalytically active sites of HWO were tuned by Mo framework substitution.

The Weight of Fear of Violence in Household Budgets

2021 ◽  
pp. 073401682110383
Author(s):  
Bruno Truzzi ◽  
Marcelo Justus ◽  
Henrique C. Kawamura ◽  
Thomas V. Conti
Keyword(s):  
Instrumental Variables ◽  
Regularization Method ◽  
Household Level ◽  
Household Spending ◽  
Goods And Services ◽  
Level Ii ◽  
The Stability ◽  
The Relationship ◽  
Selection Of

This article investigates the relationship between the perception of violence and the spending on security goods and services in households. Individual microdata from a random national survey on family budget carried out in Brazil in 2008-2009 were used for modeling the household spending using two instrumental variables. The stability of results was checked by applying the Lasso-Gaussian regularization method in the selection of the statistically significant variables. Positive relationships were found between household spending on security goods and services and (i) the fear of insecurity at the household level, (ii) the neighbors’ spending on security, and (iii) the registered criminality, but no evidence was found on the relationship between the role of police on household spending on security goods and services.

Adhesion of Partially and Fully Collapsed Nanotubes

2018 ◽  
Vol 86 (1) ◽  
Author(s):  
Ming Li ◽  
Hao Li ◽  
Fengwei Li ◽  
Zhan Kang
Keyword(s):  
Finite Deformation ◽  
Adhesion Energy ◽  
Van Der Waals Interactions ◽  
Critical Conditions ◽  
Nano Composites ◽  
Deformation Model ◽  
Analysis And Design ◽  
Structural Rigidity ◽  
Multiwall Nanotubes ◽  
The Stability

The competition between the structural rigidity and the van der Waals interactions may lead to collapsing of aligned nanotubes, and the resulting changes of both configurations and properties promise the applications of nanotubes in nano-composites and nano-electronics. In this paper, a finite-deformation model is applied to study the adhesion of parallel multiwall nanotubes with both partial and full collapsing, in which the noncontact adhesion energy is analytically determined. The analytical solutions of both configurations and energies of collapsed nanotubes are consistent with the molecular dynamics (MD) results, demonstrating the effectiveness of the finite-deformation model. To study the critical conditions of generating the partially and fully collapsed multiwall nanotubes, our analytical model gives the predictions for both the geometry- and energy-related critical diameters, which are helpful for the stability analysis and design of nanotube-based nano-devices.

scholarly journals SURVEYING IN THE STUDIES OF THE STABILITY OF EARTHY CONSTRUCTIONS, FOCUS ON SELECTED HISTORICAL MOUNDS IN KRAKOW (POLAND)

2016 ◽  
Vol 22 (2) ◽  
pp. 324-341
Author(s):  
Rafał Gawałkiewicz ◽  
Anna Szafarczyk
Keyword(s):  
Landslide Monitoring ◽  
Measurement Technology ◽  
Degree Of Deformation ◽  
Soil Creep ◽  
Measurement Series ◽  
Efficient Protection ◽  
The Stability ◽  
The Impact ◽  
Measurement Base ◽  
Selection Of

Mounds, as anthropogenic constructions of a very delicate structure, are subdued to constant changes, which, due to the impact of external factors (prolonged precipitation, tremors) are subdued to deformations in the form of mass movements. These phenomena usually have the character of mild soil creep in time and sometimes, as a result of rapid loss of stability, they are seriously damaged by landslide. This phenomenon causes temporary exclusion of the object from use. In the framework of the protection of these objects, the maintenance was carried out within the preventive measures referring to the construction and surveying monitoring of the geometry changes in time, as a result of phenomena taking place in the ground medium under the influence of environmental factors causing strains. The process of the deformation of mounds is similar to the characteristic, according to the Terzagie's theory. The application of surveying technologies of high precision allows the monitoring of changes in their geometry in time. The properly defined study area and the proper selection of measurement technology in the aspect of the accuracy of the prediction of changes, can efficiently help in defining the scale of deformations in the decisive process referring to the way of efficient protection of barrows. The article presents the results of point monitoring carried out with surveying technologies within 11 measurement series carried out on the selected measurement base of the Wanda Mound. The use of measurement technologies of integrated and specialist software, allows complex assessment of the degree of deformation and the trends of these changes in time, as well as identifying anomaly zones in the framework of the landslide monitoring.

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