scholarly journals Enhancing the Inhomogeneonus Photodynamics of Canonical Bacteriophytochrome

2021 ◽  
Author(s):  
Jakub Rydzewski ◽  
Katarzyna Walczewska-Szewc ◽  
Sylwia Czach ◽  
Wiesław Nowak ◽  
Krzysztof Kuczera
Keyword(s):  
Energy Barrier ◽  
Deinococcus Radiodurans ◽  
Metastable States ◽  
Signal Transduction Pathways ◽  
Nanometer Scale ◽  
Thermal Transition ◽  
Enhanced Sampling ◽  
Temperature Dependent ◽  
Dark Reversion ◽  
First Time

The ability of phytochromes to act as photoswitches in plants and microorganisms depends on interactions between a bilin-like chromophore and a protein. The interconversion occurs between the spectrally distinct red (Pr) and far-red (Pfr) conformers. This conformational change is triggered by the photoisomerization of the chromophore D-ring pyrrole. In this study, as a representative example of a phytochrome-bilin system, we take biliverdin IXα (BV) bound to bacteriophytochrome (BphP) from Deinococcus radiodurans. In the absence of light, we use an enhanced sampling molecular dynamics (MD) method to overcome the photoisomerization energy barrier. We find that the calculated free energy (FE) barriers between essential metastable states agree with spectroscopic results. We show that the enhanced dynamics of the BV chromophore in BphP triggers nanometer-scale conformational movements that propagate by two experimentally determined signal transduction pathways. Most importantly, we describe how the metastable states enable a thermal transition known as the dark reversion between Pfr and Pr, through a previously unknown intermediate state of Pfr. Here, for the first time, the heterogeneity of temperature-dependent Pfr states is presented at the atomistic level. This work paves a way toward understanding the complete mechanism of the photoisomerization of a bilin-like chromophore in phytochromes.

scholarly journals Enhancing the Inhomogeneonus Photodynamics of Canonical Bacteriophytochrome

2021 ◽  
Author(s):  
Jakub Rydzewski ◽  
Katarzyna Walczewska-Szewc ◽  
Sylwia Czach ◽  
Marco Caricato ◽  
Sijin Ren ◽  
...  
Keyword(s):  
Energy Barrier ◽  
Deinococcus Radiodurans ◽  
Metastable States ◽  
Signal Transduction Pathways ◽  
Nanometer Scale ◽  
Thermal Transition ◽  
Enhanced Sampling ◽  
Temperature Dependent ◽  
Dark Reversion ◽  
First Time

The ability of phytochromes to act as photoswitches in plants and microorganisms depends on interactions between a bilin-like chromophore and a protein. The interconversion occurs between the spectrally distinct red (Pr) and far-red (Pfr) conformers. This conformational change is triggered by the photoisomerization of the chromophore D-ring pyrrole. In this study, as a representative example of a phytochrome-bilin system, we take biliverdin IXα (BV) bound to bacteriophytochrome (BphP) from Deinococcus radiodurans. In the absence of light, we use an enhanced sampling molecular dynamics (MD) method to overcome the photoisomerization energy barrier. We find that the calculated free energy (FE) barriers between essential metastable states agree with spectroscopic results. We show that the enhanced dynamics of the BV chromophore in BphP triggers nanometer-scale conformational movements that propagate by two experimentally determined signal transduction pathways. Most importantly, we describe how the metastable states enable a thermal transition known as the dark reversion between Pfr and Pr, through a previously unknown intermediate state of Pfr. Here, for the first time, the heterogeneity of temperature-dependent Pfr states is presented at the atomistic level. This work paves a way toward understanding the complete mechanism of the photoisomerization of a bilin-like chromophore in phytochromes.

scholarly journals Free Energy Surfaces and Barriers for Vacancy Diffusion on Al(100), Al(110), Al(111) Reconstructed Surfaces

Nanomaterials ◽  
2021 ◽  
Vol 12 (1) ◽  
pp. 76
Author(s):  
Junais Habeeb Mokkath ◽  
Mufasila Mumthaz Muhammed ◽  
Ali J. Chamkha
Keyword(s):  
Free Energy ◽  
Energy Barrier ◽  
Computational Study ◽  
Metastable States ◽  
Vacancy Diffusion ◽  
Enhanced Sampling ◽  
Free Energy Surface ◽  
Collective Variables ◽  
Surface Vacancy ◽  
Energy Surfaces

Metadynamics is a popular enhanced sampling method based on the recurrent application of a history-dependent adaptive bias potential that is a function of a selected number of appropriately chosen collective variables. In this work, using metadynamics simulations, we performed a computational study for the diffusion of vacancies on three different Al surfaces [reconstructed Al(100), Al(110), and Al(111) surfaces]. We explored the free energy landscape of diffusion and estimated the barriers associated with this process on each surface. It is found that the surfaces are unique regarding vacancy diffusion. More specically, the reconstructed Al(110) surface presents four metastable states on the free energy surface having sizable and connected passage-ways with an energy barrier of height 0.55 eV. On the other hand, the reconstructed Al(100)/Al(111) surfaces exhibit two/three metastable states, respectively, with an energy barrier of height 0.33 eV. The findings in this study can help to understand surface vacancy diffusion in technologically relevant Al surfaces.

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 Temperature-Dependent Photoluminescence of ZnO Thin Films Grown on Off-Axis SiC Substrates by APMOCVD

Materials ◽  
2021 ◽  
Vol 14 (4) ◽  
pp. 1035
Author(s):  
Ivan Shtepliuk ◽  
Volodymyr Khranovskyy ◽  
Arsenii Ievtushenko ◽  
Rositsa Yakimova
Keyword(s):  
Optical Properties ◽  
Structural Quality ◽  
Organic Chemical ◽  
Zno Films ◽  
Vicinal Surfaces ◽  
Temperature Dependent ◽  
Step Flow ◽  
Step Flow Growth ◽  
First Time ◽  
Temperature Dependent Photoluminescence

The growth of high-quality ZnO layers with optical properties congruent to those of bulk ZnO is still a great challenge. Here, for the first time, we systematically study the morphology and optical properties of ZnO layers grown on SiC substrates with off-cut angles ranging from 0° to 8° by using the atmospheric pressure meta–organic chemical vapor deposition (APMOCVD) technique. Morphology analysis revealed that the formation of the ZnO films on vicinal surfaces with small off-axis angles (1.4°–3.5°) follows the mixed growth mode: from one side, ZnO nucleation still occurs on wide (0001) terraces, but from another side, step-flow growth becomes more apparent with the off-cut angle increasing. We show for the first time that the off-cut angle of 8° provides conditions for step-flow growth of ZnO, resulting in highly improved growth morphology, respectively structural quality. Temperature-dependent photoluminescence (PL) measurements showed a strong dependence of the excitonic emission on the off-cut angle. The dependences of peak parameters for bound exciton and free exciton emissions on temperature were analyzed. The present results provide a correlation between the structural and optical properties of ZnO on vicinal surfaces and can be utilized for controllable ZnO heteroepitaxy on SiC toward device-quality ZnO epitaxial layers with potential applications in nano-optoelectronics.

scholarly journals Controlling Condensation of Water Using Hybrid Hydrophobic-Hydrophilic Surfaces

2010 ◽  
Author(s):  
Kripa K. Varanasi ◽  
Tao Deng
Keyword(s):  
Nucleation Rate ◽  
Heterogeneous Nucleation ◽  
Energy Barrier ◽  
Superhydrophobic Surfaces ◽  
Industrial Processes ◽  
Spatial Control ◽  
Hydrophilic Surfaces ◽  
Wide Range ◽  
First Time ◽  
Control Water

Heterogeneous nucleation of water plays an important role in wide range of natural and industrial processes. Though heterogeneous nucleation of water is ubiquitous and everyday experience, spatial control of this important phenomenon is extremely difficult. Here we show, for the first time, that spatial control in the heterogeneous nucleation of water can be achieved by manipulating the local nucleation energy barrier and nucleation rate via the modification of the local intrinsic wettability of a surface by patterning hybrid hydrophobic-hydrophilic regions on a surface. Such ability to control water nucleation could address the condensation-related limitations of superhydrophobic surfaces, and has implications for efficiency enhancements in energy and desalination systems.

scholarly journals Growth without Postannealing of Monoclinic VO2 Thin Film by Atomic Layer Deposition Using VCl4 as Precursor

Coatings ◽  
2018 ◽  
Vol 8 (12) ◽  
pp. 431 ◽  
Author(s):  
Wen-Jen Lee ◽  
Yong-Han Chang
Keyword(s):  
Vanadium Dioxide ◽  
Atomic Layer ◽  
Amorphous Structure ◽  
Temperature Dependent ◽  
Vanadium Compounds ◽  
Multifunctional Material ◽  
Layer Deposition ◽  
Vanadium Tetrachloride ◽  
First Time ◽  
Deposited Films

Vanadium dioxide (VO2) is a multifunctional material with semiconductor-to-metal transition (SMT) property. Organic vanadium compounds are usually employed as ALD precursors to grow VO2 films. However, the as-deposited films are reported to have amorphous structure with no significant SMT property, therefore a postannealing process is necessary for converting the amorphous VO2 to crystalline VO2. In this study, an inorganic vanadium tetrachloride (VCl4) is used as an ALD precursor for the first time to grow VO2 films. The VO2 film is directly crystallized and grown on the substrate without any postannealing process. The VO2 film displays significant SMT behavior, which is verified by temperature-dependent Raman spectrometer and four-point-probing system. The results demonstrate that the VCl4 is suitably employed as a new ALD precursor to grow crystallized VO2 films. It can be reasonably imagined that the VCl4 can also be used to grow various directly crystallized vanadium oxides by controlling the ALD-process parameters.

Strongly coupled thermal and chemical expansion in the perovskite oxide system Sr(Ti,Fe)O3−α

2015 ◽  
Vol 3 (7) ◽  
pp. 3602-3611 ◽  
Author(s):  
Nicola H. Perry ◽  
Jae Jin Kim ◽  
Sean R. Bishop ◽  
Harry L. Tuller
Keyword(s):  
Energy Conversion ◽  
Oxide System ◽  
Perovskite Oxide ◽  
Oxygen Stoichiometry ◽  
Temperature Dependent ◽  
Chemical Expansion ◽  
Strongly Coupled ◽  
Expansion Coefficients ◽  
Energy Conversion Devices ◽  
First Time

To evaluate stability in energy conversion devices, thermal and chemical expansion coefficients (CTE, CCE) of Sr(Ti,Fe)O3−α were measured and deconvoluted for the first time, revealing an oxygen stoichiometry-dependent CTE and temperature-dependent CCE.

The Temperature-Dependent Ideal Shear Strength of Solid Single Crystals

2018 ◽  
Vol 85 (3) ◽  
Author(s):  
Tianbao Cheng ◽  
Daining Fang ◽  
Yazheng Yang
Keyword(s):  
Shear Strength ◽  
Theoretical Model ◽  
Melting Point ◽  
Single Crystals ◽  
Elevated Temperatures ◽  
Absolute Zero ◽  
Temperature Dependent ◽  
Temperature Changes ◽  
First Time ◽  
The Ideal

Knowledge of the ideal shear strength of solid single crystals is of fundamental importance. However, it is very hard to determine this quantity at finite temperatures. In this work, a theoretical model for the temperature-dependent ideal shear strength of solid single crystals is established in the view of energy. To test the drawn model, the ideal shear properties of Al, Cu, and Ni single crystals are calculated and compared with that existing in the literature. The study shows that the ideal shear strength first remains approximately constant and then decreases almost linearly as temperature changes from absolute zero to melting point. As an example of application, the “brittleness parameter” of solids at elevated temperatures is quantitatively characterized for the first time.

Modelling Semi-Solid Behaviour and Brittle Temperature Range

2019 ◽  
Vol 285 ◽  
pp. 361-366 ◽  
Author(s):  
Khalil Traidi ◽  
Véronique Favier ◽  
Philippe Lestriez ◽  
Karl Debray ◽  
Laurent Langlois ◽  
...  
Keyword(s):  
Solid State ◽  
Material Properties ◽  
Solid Phase ◽  
Thermal Conditions ◽  
Tensile Tests ◽  
Internal Variable ◽  
Temperature Dependent ◽  
Brittle Transition ◽  
Semi Solid ◽  
First Time

In this paper, a new elastic viscoplastic micromechanical modelling is proposed to represent the semi-solid behaviour and predict the ductile-brittle transition of the C38LTT near the solidus. It is based on a viscoplastic modelling previously presented in [1]. The originality of the new model comes from three main enhancements: the transition between the solid state and the semi-solid state was included meaning that the material properties were taken temperature-dependent, the elastic properties was taken into account similarly as [2] and the evolution of the internal variable describing the degree of agglomeration of the solid phase was enhanced. The model was implemented in the commercial software FORGE©. Tensile tests representing the experimental thermal conditions and obtained using a GLEEBLE© machine were simulated. The comparison of the predicted and experimental results shows that, for the first time to our knowledge, the three steps of the load-displacement response and ductile-brittle transition were successfully described.

scholarly journals The homogenous alternative to biomineralization: Zn- and Mn-rich materials enable sharp organismal “tools” that reduce force requirements

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
R. M. S. Schofield ◽  
J. Bailey ◽  
J. J. Coon ◽  
A. Devaraj ◽  
R. W. Garrett ◽  
...  
Keyword(s):  
Abrasion Resistance ◽  
Energy Savings ◽  
Impact Resistance ◽  
Atom Probe ◽  
Nanometer Scale ◽  
Time Loss ◽  
Protein Residues ◽  
Mandibular Teeth ◽  
First Time ◽  
Measured Hardness

AbstractWe measured hardness, modulus of elasticity, and, for the first time, loss tangent, energy of fracture, abrasion resistance, and impact resistance of zinc- and manganese-enriched materials from fangs, stings and other “tools” of an ant, spider, scorpion and nereid worm. The mechanical properties of the Zn- and Mn-materials tended to cluster together between plain and biomineralized “tool” materials, with the hardness reaching, and most abrasion resistance values exceeding, those of calcified salmon teeth and crab claws. Atom probe tomography indicated that Zn was distributed homogeneously on a nanometer scale and likely bound as individual atoms to more than ¼ of the protein residues in ant mandibular teeth. This homogeneity appears to enable sharper, more precisely sculpted “tools” than materials with biomineral inclusions do, and also eliminates interfaces with the inclusions that could be susceptible to fracture. Based on contact mechanics and simplified models, we hypothesize that, relative to plain materials, the higher elastic modulus, hardness and abrasion resistance minimize temporary or permanent tool blunting, resulting in a roughly 2/3 reduction in the force, energy, and muscle mass required to initiate puncture of stiff materials, and even greater force reductions when the cumulative effects of abrasion are considered. We suggest that the sharpness-related force reductions lead to significant energy savings, and can also enable organisms, especially smaller ones, to puncture, cut, and grasp objects that would not be accessible with plain or biomineralized “tools”.

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