STUDY OF POTASSIUM INTERCALATION IN TO THE GRAPHENE/MoS STRUCTURE

Используя современные расчеты из первых принципов, в данной работе мы систематически изучали интеркаляцию атомов калия в гибридную двухслойную структуру графене/ MoS. В ходе исследования были определенны концентрации атомов калия при которых энергия формирования является отрицательной. Так в частности при концентрации атомов калия, по отношению к атомам молибдена, не более x = 0,43 формирование слоя атомов калия между слоями графен/ MoS является энергетически выгодным. Начиная с концентрации атомов калия x > 0,75 наблюдается увеличение расстояние между слоями графен и MoS, что в дальнейшем приводит к разрушению структуры. Расчет зарядов показал, что атом калия при небольших концентрациях отдает примерно 0,8 - 0,85 электрона, 0,35 из которых перетекает на атомы углерода, а 0,4 - 0,5 перетекает на дисульфид молибдена. Расчёт разность электронных плотностей показал, что связь между слоями графена, дисульфид молибдена и калия имеет ковалентный характер. Using modern ab-initio calculations, in this work, we systematically studied the intercalation of potassium atoms into a hybrid two-layer graphene/MoS structure. In the course of the study, concentrations of potassium atoms were determined at which the formation energy is negative. So, in particular, when the concentration of potassium atoms (in relation to molybdenum atoms) is not more than x = 0,43, formation of a layer of potassium atoms between the graphene/ MoS layers is energetically favorable. Beginning with the concentration of potassium atoms x > 0,75 , an increase in the distance between the graphene and MoS layers is observed, which further leads to destruction of the structure. Calculation of charges showed that a potassium atom at low concentrations gives up about 0,8 - 0,85 electrons, 0,35 of which flow on carbon atoms, and 0,4 - 0,5 to molybdenum disulfide. Calculation of the difference in electron densities showed that the bond between the layers of graphene, molybdenum and potassium disulfide has a covalent nature.

Towards Comparable Carbon Credits: Harmonization of LCA Models of Cellulosic Biofuels

Decarbonization programs are being proposed worldwide to reduce greenhouse gas (GHG) emissions from transportation fuels, using Life Cycle Assessment (LCA) models or tools. Although such models are broadly accepted, varying results are often observed. This study describes similarities and differences of key decarbonization programs and their GHG calculators and compares established LCA models for assessing 2G ethanol from lignocellulosic feedstock. The selected LCA models were GHGenius, GREET, JRC’s model, and VSB, which originated calculators for British Columbia’s Low Carbon Fuel Standard, California’s Low Carbon Fuel Standard, Renewable Energy Directive, and RenovaBio, respectively. We performed a harmonization of the selected models by inserting data of one model into other ones to illustrate the possibility of obtaining similar results after a few harmonization steps and to determine which parameters have higher contribution to closing the gap between default results. Differences among 2G ethanol from wheat straw were limited to 0.1 gCO2eq. MJ−1, and discrepancies in emissions decreased by 95% and 78% for corn stover and forest residues, respectively. Better understanding of structure, calculation procedures, parameters, and methodological assumptions among the LCA models is a first step towards an improved harmonization that will allow a globally accepted and exchangeable carbon credit system to be created.

An automated iterative approach for protein structure refinement using pseudocontact shifts

NMR structure calculation using NOE-derived distance restraints requires a considerable number of assignments of both backbone and sidechains resonances, often difficult or impossible to get for large or complex proteins. Pseudocontact shifts (PCSs) also play a well-established role in NMR protein structure calculation, usually to augment existing structural, mostly NOE-derived, information. Existing refinement protocols using PCSs usually either require a sizeable number of sidechain assignments or are complemented by other experimental restraints. Here, we present an automated iterative procedure to perform backbone protein structure refinements requiring only a limited amount of backbone amide PCSs. Already known structural features from a starting homology model, in this case modules of repeat proteins, are framed into a scaffold that is subsequently refined by experimental PCSs. The method produces reliable indicators that can be monitored to judge about the performance. We applied it to a system in which sidechain assignments are hardly possible, designed Armadillo repeat proteins (dArmRPs), and we calculated the solution NMR structure of YM4A, a dArmRP containing four sequence-identical internal modules, obtaining high convergence to a single structure. We suggest that this approach is particularly useful when approximate folds are known from other techniques, such as X-ray crystallography, while avoiding inherent artefacts due to, for instance, crystal packing.

POKY: a software suite for multidimensional NMR and 3D structure calculation of biomolecules

Summary The need for an efficient and cost-effective method is compelling in biomolecular NMR. To tackle this problem, we have developed the Poky suite, the revolutionized platform with boundless possibilities for advancing research and technology development in signal detection, resonance assignment, structure calculation, and relaxation studies with the help of many automation and user interface tools. This software is extensible and scalable by scripting and batching as well as providing modern graphical user interfaces and a diverse range of modules right out of the box. Availability Poky is freely available to non-commercial users at https://poky.clas.ucdenver.edu. Supplementary information Supplementary data are available at Bioinformatics online.

Patterns in Protein Flexibility: A Comparison of NMR “Ensembles”, MD Trajectories, and Crystallographic B-Factors

Proteins are molecular machines requiring flexibility to function. Crystallographic B-factors and Molecular Dynamics (MD) simulations both provide insights into protein flexibility on an atomic scale. Nuclear Magnetic Resonance (NMR) lacks a universally accepted analog of the B-factor. However, a lack of convergence in atomic coordinates in an NMR-based structure calculation also suggests atomic mobility. This paper describes a pattern in the coordinate uncertainties of backbone heavy atoms in NMR-derived structural “ensembles” first noted in the development of FindCore2 (previously called Expanded FindCore: DA Snyder, J Grullon, YJ Huang, R Tejero, GT Montelione, Proteins: Structure, Function, and Bioinformatics 82 (S2), 219–230) and demonstrates that this pattern exists in coordinate variances across MD trajectories but not in crystallographic B-factors. This either suggests that MD trajectories and NMR “ensembles” capture motional behavior of peptide bond units not captured by B-factors or indicates a deficiency common to force fields used in both NMR and MD calculations.