Physicochemical properties of blue fluorescent protein determined via molecular dynamics simulation

Blue fluorescent protein (BFP) is a mutant of green fluorescent protein (GFP), where the chromophore has been modified to shift the emitted fluorescence into the blue spectral region. In this study, MD calculations were performed with the GROMACS simulation package and AMBER force field to investigate the dependence of BFPs physicochemical properties on temperature and applied pressure. The MD approach enabled us to calculate the compressibility of protein itself, separately from the nontrivial contribution of the hydration shell, which is difficult to achieve experimentally. The computed compressibility of BFP (3.94 ×10 −5 MPa −1 ) is in agreement with experimental values of globular proteins. The center-of-mass diffusion coefficient of BFP and its dependence on temperature and pressure, which plays an important role in its application as a probe for intracellular liquid viscosity measurement, was calculated and found to be in good agreement with photobleaching recovery experimental data. We have shown that decreased temperature as well as applied pressure increases the water viscosity, but the concomitant decrease of the BFP diffusion coefficient behaves differently from Stokes-Einstein formula. It is shown that the number of hydrogen bonds around the protein grows with pressure, which explains the aforementioned deviation. Pressure also reduces root mean square (RMS) fluctuations, especially those of the most flexible residues situated in the loops. The analysis of the RMS fluctuations of the backbone C Α atoms also reveals that the most rigid part of BFP is the center of the Β-barrel, in accord with temperature B factors obtained from the Protein Data Bank. © 2008 Wiley Periodicals, Inc. Biopolymers 89: 1136–1143, 2008. This article was originally published online as an accepted preprint. The “Published Online” date corresponds to the preprint version. You can request a copy of the preprint by emailing the Biopolymers editorial office at [email protected] Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/61210/1/21065_ftp.pd

Water Splitting on Multifaceted SrTiO3 Nanocrystals: Computational Study

The financial support of M-ERA.NET2 Sun2Chem project is greatly acknowledged by E.K. Authors thank Dr. Marjeta Ma?ek Kr?manc and prof. Chi-Sheng Wu, for the fruitful discussions. The financial support of FLAG-ERA JTC project To2Dox is acknowledged by Y.A.M. This paper is based upon the work from COST Action 18234, supported by COST (European Cooperation in Science and Technology). The support is greatly acknowledged by Y.A.M. and V.K. The grant No. 1.1.1.2/VIAA/l/16/147 (1.1.1.2/16/I/001) under the activity of Post-doctoral research aid is greatly acknowledged by M.S. and D.B. The Institute of Solid State Physics, University of Latvia (Latvia) as the Centre of Excellence has received funding from the European Union?s Horizon 2020 Framework Programme H2020-WIDESPREAD-01-2016-2017-Teaming Phase2 under grant agreement No. 739508, project CAMART2 . The computer resources were provided by the Stuttgart Supercomputing Center (project DEFTD 12939) and Latvian Super Cluster (LASC).Recent experimental findings suggest that strontium titanate SrTiO3 (STO) photocatalytic activity for water splitting could be improved by creating multifaceted nanoparticles. To understand the underlying mechanisms and energetics, the model for faceted nanoparticles was created. The multifaceted nanoparticles’ surface is considered by us as a combination of flat and “stepped” facets. Ab initio calculations of the adsorption of water and oxygen evolution reaction (OER) intermediates were performed. Our findings suggest that the “slope” part of the step showed a natural similarity to the flat surface, whereas the “ridge” part exhibited significantly different adsorption configurations. On the “slope” region, both molecular and dissociative adsorption modes were possible, whereas on the “ridge”, only dissociative adsorption was observed. Water adsorption energies on the “ridge” (−1.50 eV) were significantly higher than on the “slope” (−0.76 eV molecular; −0.83 eV dissociative) or flat surface (−0.79 eV molecular; −1.09 eV dissociative). © 2021 by the authors. Licensee MDPI, Basel, Switzerland. Published under the CC BY 4.0 license.M-ERA.NET2 Sun2Chem; FLAG-ERA JTC project To2Dox; COST Action 18234; Post-doctoral research grant No. 1.1.1.2/VIAA/l/16/147 (1.1.1.2/16/I/001); Institute of Solid State Physics, University of Latvia as the Center of Excellence has received funding from the European Union’s Horizon 2020 Framework Programme H2020-WIDESPREAD-01-2016-2017-TeamingPhase2 under grant agreement No. 739508, project CAMART2

Electronic Band Transitions in γ-Ge3N4

This work has been carried out within the framework of the EUROfusion Consortium and has received funding from the Euratom research and training programme 2014-2018 and 2019-2020 under grant agreement No 633053. The views and opinions expressed herein do not necessarily reflect those of the European Commission. Support from Estonian Research Council grant PUT PRG 619 is gratefully acknowledged. The multi-anvil experiments at LMV were supported by the French Government Laboratory of Excellence initiative no ANR-10-LABX-0006, the Région Auvergne and the European Regional Development Fund (ClerVolc Contribution Number 478).Electronic band structure in germanium nitride having spinel structure, γ-Ge3N4, was examined using two spectroscopic techniques, cathodoluminescence and synchrotron-based photoluminescence. The sample purity was confirmed by x-ray diffraction and Raman analyses. The spectroscopic measurements provided first experimental evidence of a large free exciton binding energy De≈0.30 eV and direct interband transitions in this material. The band gap energy Eg = 3.65 ± 0.05 eV measured with a higher precision was in agreement with that previously obtained via XES/XANES method. The screened hybrid functional Heyd–Scuseria–Ernzerhof (HSE06) calculations of the electronic structure supported the experimental results. Based on the experimental data and theoretical calculations, the limiting efficiency of the excitation conversion to light was estimated and compared with that of w-GaN, which is the basic material of commercial light emitting diodes. The high conversion efficiency, very high hardness and rigidity combined with a thermal stability in air up to ~ 700 °C reveal the potential of γ-Ge3N4 for robust and efficient photonic emitters. © 2021, The Korean Institute of Metals and Materials. Published under the CC BY license.Euratom research and training programme 2014-2018 633053; Eesti Teadusagentuur ANR-10-LABX-0006, PUT PRG 619; ERDF; Institute of Solid State Physics, University of Latvia as the Center of Excellence has received funding from the European Union’s Horizon 2020 Framework Programme H2020-WIDESPREAD-01-2016-2017-TeamingPhase2 under grant agreement No. 739508, project CAMART2

First Principles Calculations of Hydrogen Evolution Reaction and Proton Migration on Stepped Surfaces of SrTiO3

The financial support of FLAG-ERA JTC project To2Dox is acknowledged by Y.M., G.Z., and E.K. This paper is based upon the work from COST Action 18234, supported by COST (European Cooperation in Science and Technology). The support is greatly acknowledged by Y.M., V.K., and K.S.E. The grant No. 1.1.1.2/VIAA/l/16/147 (1.1.1.2/16/I/001) under the activity of Post-doctoral research aid is greatly acknowledged by M.S. and D.B. K.S.E. acknowledges funding by the Ministry of Culture and Science of the Federal State of North Rhine-Westphalia (NRW Return Grant). K.S.E. is associated with the CRC/TRR247: “Heterogeneous Oxidation Catalysis in the Liquid Phase” (Project number 388390466-TRR 247), the RESOLV Cluster of Excellence, funded by the Deutsche Forschungsgemeinschaft under Germany’s Excellence Strategy – EXC 2033 – 390677874 – RESOLV, and the Center for Nanointegration (CENIDE). Authors thank Dr. Marjeta Maˇcek Kržmanc and Prof. Chi-Sheng Wu, for the fruitful discussions. The Institute of Solid State Physics, University of Latvia (Latvia) as the Centre of Excellence has received funding from the European Union’s Horizon 2020 Frame-work Programme H2020-WIDESPREAD-01-2016-2017-Teaming Phase2 under grant agreement No. 739508, project CAMART2. The computer resources were provided by the Stuttgart Supercomputing Center (project DEFTD 12939) and Latvian Super Cluster (LASC). Open access funding enabled and organized by Projekt DEAL.Recent research suggests that photocatalytic activity toward water splitting of strontium titanate SrTiO3 (STO) is enhanced by creating multifaceted nanoparticles. To better understand the source of this activity, a previously designed model is used for two types of surfaces of this nanoparticle, flat and double-stepped. Density functional theory calculations of water adsorption on these surfaces are performed to gain insight into water adsorption and proton migration processes, as well as thermodynamics of hydrogen evolution reaction within the framework of computational hydrogen electrode. It is concluded that ridges of single- and double-stepped surfaces are nearly identical in terms of adsorption configurations and energetics. Also, it is demonstrated that protons have migration barriers lower than 0.7 eV and that surface morphology impacts catalytic activity toward hydrogen evolution reaction, with flat surface demonstrating higher catalytic activity. --//-- This is an open access article Sokolov, M., Mastrikov, Y. A., Zvejnieks, G., Bocharov, D., Krasnenko, V., Exner, K. S., Kotomin, E. A., First Principles Calculations of Hydrogen Evolution Reaction and Proton Migration on Stepped Surfaces of SrTiO3. Adv. Theory Simul. 2023, 6, 2200619. https://doi.org/10.1002/adts.202200619 published under the CC BY-NC-ND licence.FLAG-ERA JTC project To2Dox; COST Action 18234, supported by COST (European Cooperation in Science and Technology); The grant No. 1.1.1.2/VIAA/l/16/147 (1.1.1.2/16/I/001) under the activity of Post-doctoral research aid; the Ministry of Culture and Science of the Federal State of North Rhine-Westphalia (NRW Return Grant); CRC/TRR247: “Heterogeneous Oxidation Catalysis in the Liquid Phase” (Project number 388390466-TRR 247), the RESOLV Cluster of Excellence, funded by the Deutsche Forschungsgemeinschaft under Germany’s Excellence Strategy – EXC 2033 – 390677874 – RESOLV, and the Center for Nanointegration (CENIDE); The Institute of Solid State Physics, University of Latvia (Latvia) as the Centre of Excellence has received funding from the European Union’s Horizon 2020 Frame-work Programme H2020-WIDESPREAD-01-2016-2017-Teaming Phase2 under grant agreement No. 739508, project CAMART2

Modeling of the Lattice Dynamics in Strontium Titanate Films of Various Thicknesses: Raman Scattering Studies

This paper is partly based upon COST (European Cooperation in Science and Technology) Action 18234 (E.A.K., M.S., and V.K.) and financially supported by FLAG-ERA JTC project To2Dox (Y.A.M). The Institute of Solid State Physics, University of Latvia (Latvia), as the Centre of Excellence has received funding from the European Union’s Horizon 2020 Frame-work Programme H2020-WIDESPREAD-01-2016-2017-Teaming Phase2 under grant agreement No. 739508, project CAMART2. The computer resources were provided by the High-Performance Computing Centre Stuttgart (HLRS project DEFTD 12939). In addition, the research of V.K. and A.P. was partly supported by the RADON project (GA 872494) within the H2020-MSCA-RISE-2019 call.While the bulk strontium titanate (STO) crystal characteristics are relatively well known, ultrathin perovskites’ nanostructure, chemical composition, and crystallinity are quite complex and challenging to understand in detail. In our study, the DFT methods were used for modelling the Raman spectra of the STO bulk (space group I4/mcm) and 5–21-layer thin films (layer group p4/mbm) in tetragonal phase with different thicknesses ranging from ~0.8 to 3.9 nm. Our calculations revealed features in the Raman spectra of the films that were absent in the bulk spectra. Out of the seven Raman-active modes associated with bulk STO, the frequencies of five modes (2Eg, A1g, B2g, and B1g) decreased as the film thickness increased, while the low-frequency B2g and higher-frequency Eg modes frequencies increased. The modes in the films exhibited vibrations with different amplitudes in the central or surface parts of the films compared to the bulk, resulting in frequency shifts. Some peaks related to bulk vibrations were too weak (compared to the new modes related to films) to distinguish in the Raman spectra. However, as the film thickness increased, the Raman modes approached the frequencies of the bulk, and their intensities became higher, making them more noticeable in the Raman spectrum. Our results could help to explain inconsistencies in the experimental data for thin STO films, providing insights into the behavior of Raman modes and their relationship with film thickness. © 2023 by the authors. --//-- Krasnenko V., Platonenko A., Liivand A., Rusevich L.L., Mastrikov Y.A., Zvejnieks G., Sokolov M., Kotomin E.A.; Modeling of the Lattice Dynamics in Strontium Titanate Films of Various Thicknesses: Raman Scattering Studies; (2023) Materials, 16 (18), art. no. 6207; DOI: 10.3390/ma16186207; https://www.scopus.com/inward/record.uri?eid=2-s2.0-85172725318&doi=10.3390%2fma16186207&partnerID=40&md5=32f343f9cb8da145c6647566cb534c32. Published under the CC BY 4.0 license.COST Action 18234 and FLAG-ERA JTC project To2Dox. The Institute of Solid State Physics, University of Latvia (Latvia), as the Centre of Excellence has received funding from the European Union’s Horizon 2020 Frame-work Programme H2020-WIDESPREAD-01-2016-2017-Teaming Phase2 under grant agreement No. 739508, project CAMART2. HLRS project DEFTD 12939. RADON project (GA 872494) within the H2020-MSCA-RISE-2019 call

Defects induced by He+ irradiation in γ-Si3N4

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