How the nuclear lamina (NL) impacts on global chromatin architecture is poorly understood. Here, we show that NL disruption in Drosophila S2 cells leads to chromatin compaction and repositioning from ...the nuclear envelope. This increases the chromatin density in a fraction of topologically-associating domains (TADs) enriched in active chromatin and enhances interactions between active and inactive chromatin. Importantly, upon NL disruption the NL-associated TADs become more acetylated at histone H3 and less compact, while background transcription is derepressed. Two-colour FISH confirms that a TAD becomes less compact following its release from the NL. Finally, polymer simulations show that chromatin binding to the NL can per se compact attached TADs. Collectively, our findings demonstrate a dual function of the NL in shaping the 3D genome. Attachment of TADs to the NL makes them more condensed but decreases the overall chromatin density in the nucleus by stretching interphase chromosomes.
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We present multi-scale simulation of plastic deformation in molybdenum. The temperature-dependent mobility functions of screw and edge dislocations were calculated from molecular ...dynamics simulation with two different interatomic potentials. The simulations of screw dislocation movement under applied shear stress revealed that the process can proceed in two different regimes: through thermally activated motion and athermal motion. Hence, the dislocation velocity depends on the shear stress in a non-trivial way. We took this fact into account during calculation of the mobility functions and their implementation in the dislocation dynamics (DD) model. Such model allows us to simulate plastic deformation with consideration of temperature effect on the dislocation mobility. Here we discuss the changes in DD predictions depending on the input parameters obtained from the atomistic simulation. As the main result, we report the yield stress calculated for a single crystal of molybdenum at various temperatures, strain rates, and dislocation densities. Thoroughly discussed comparison of the simulation results with the available experimental data gives opportunity to estimate the accuracy of the created multi-scale model.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
Nanophotonics based on resonant nanostructures and metasurfaces made of halide perovskites have become a prospective direction for efficient light manipulation at the subwavelength scale in advanced ...photonic designs. One of the main challenges in this field is the lack of large‐scale low‐cost technique for subwavelength perovskite structures fabrication preserving highly efficient luminescence. Here, unique properties of halide perovskites addressed to their extremely low thermal conductivity (lower than that of silica glass) and high defect tolerance to apply projection femtosecond laser lithography for nanofabrication with precise spatial control in all three dimensions preserving the material luminescence efficiency are employed. Namely, with CH3NH3PbI3 perovskite highly ordered nanoholes and nanostripes of width as small as 250 nm, metasurfaces with periods less than 400 nm, and nanowire lasers as thin as 500 nm, corresponding to the state‐of‐the‐art in multistage expensive lithographical methods are created. Remarkable performance of the developed approach allows to demonstrate a number of advanced optical applications, including morphology‐controlled photoluminescence yield, structural coloring, optical‐ information encryption, and lasing.
Halide perovskites possess extremely low thermal conductivity and high defect tolerance. In this work, using these advantages and the method of projection femtosecond laser lithography, nanofabrication with precise spatial control in all three dimensions preserving the material luminescence efficiency is demonstrated. Namely, CH3NH3PbI3 perovskite thin film is nanostructured for morphology‐controlled photoluminescence yield, structural coloring, optical‐ information encryption, and lasing.
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BFBNIB, FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SAZU, SBCE, SBMB, UL, UM, UPUK
Diffusion along dislocations, the so-called pipe diffusion (PD), may significantly contribute to self-diffusion in plastically deformed materials. In this work, we carry out a comprehensive ...investigation of PD mechanisms in several representative body-centered cubic transition metals by means of large-scale atomistic simulations. We find that screw and edge dislocations exhibit distinct intrinsic PD mechanisms associated with dynamical formation and migration of kink pairs and bounded Frenkel pairs, respectively. Different atomic structures of both core types are decisive for the character of the migration events, resulting in a very fast 1D diffusion along the screw dislocations and a slower 3D diffusion along the edge dislocations. The predicted PD coefficients are several orders of magnitude greater than the bulk diffusion coefficients, indicating that the PD contribution needs to be taken into account when interpreting diffusion measurements in deformed bcc metals at temperatures below half of the melting temperature.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
Herein, the molecular dynamics (MD) simulations of pure Ni crystallites are performed to show the influence of the grain boundary (GB) geometry on the values of the activation energy of GB migration. ...The considered systems are bicrystal with Σ5010 tilt plane boundary, spherical grain with initial curvature radius 5 nm, and polycrystalline 30 nm × 30 nm × 30 nm block. The motion of three types of GBs (flat, spherical, and polycrystalline) at constant temperatures and no applied forces is studied. The obtained values of activation energy are 0.45, 0.11, and 0.57 eV for flat, spherical, and polycrystalline types of GBs, respectively. These values are smaller than those that are reported in experimental works, which is a common issue for atomistic simulations of GB migration. Possible sources of such disagreement and ways to overcome it are discussed. The particular part of this work is devoted to the development of the automated analysis of polycrystalline structure. This analysis provides detailed information on grain size distribution and its evolution in time.
Herein, the molecular dynamics simulations of pure Ni crystallites are performed to show the influence of the grain boundary (GB) geometry on the values of the activation energy of GB migration. The algorithm to analyze polycrystalline structure that provides detailed information on grain size distribution and its evolution in time is developed.
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FZAB, GIS, IJS, KILJ, NLZOH, NUK, OILJ, SAZU, SBCE, SBMB, UL, UM, UPUK
Fatty acid desaturases (FADs) play important roles in various metabolic and adaptive pathways in all living organisms. They represent a superfamily of oxygenases that introduce double bonds into the ...acyl chains of fatty acids (FAs). These enzymes are highly specific to the length of the carbon chain, position of double bonds formation, etc. The modes by which FADs “count” the position of the double bond formation may differ. In cyanobacteria, the first double bond is formed between 9th and 10th carbons (position Δ9), counting from the carboxylic end of an FA. Other FADs that produce polyunsaturated FAs may introduce double bonds counting from the carboxyl (Δ) or methyl (ω) terminus, or from a pre-existing double bond towards carboxyl or methyl terminus of an FA chain. Here, we expressed the desD gene for the Δ6-FAD from Synechocystis sp. PCC 6803 in Synechococcus elongatus PCC 7942 (which is capable of synthesizing only monoenoic FAs desaturated mainly at position Δ9) and observed the appearance of unusual monoenoic FAs desaturated at position Δ6, as well as Δ6,9 dienoic FAs. Exogenously added cis-10-heptadecenoic acid (17:1Δ10) was converted into cis-6,10-heptadecadienoic (17:2Δ6,10). These data demonstrate the ability of Δ6-FAD to introduce the first double bond into the unsaturated substrates and suggests that it “counts” from the carboxyl end, irrespective of the absence or presence of a previous double bond in an FA chain.
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IZUM, KILJ, NUK, PILJ, PNG, SAZU, UL, UM, UPUK
Fatty acid desaturases (FADs) represent a class of oxygen-dependent enzymes that dehydrogenate C–C bonds in the fatty acids (FAs) producing unsaturated CC double bonds that markedly change the ...properties of biological membranes. FADs are highly specific towards their acyl substrates, the position and configuration of the introduced double bonds. The double bond positioning of soluble acyl-carrier-protein Δ9-FADs was determined relative to the carboxyl end of a FA. Similar mode was suggested for the acyl-lipid Δ12-FADs (also known as ω6-FADs), however, their exact counting order remain unknown. Here we used monounsaturated odd- (17:1Δ10) and even-chain (18:1Δ11) FAs to show that acyl-lipid Δ12-FADs of, at least, two cyanobacterial species, Gloeobacter violaceus and Synechocystis sp. strain PCC 6803, use neither end of the fatty acid (Δ or ω) as a counting reference point; but count three carbons toward the methyl end from an existing double bond in the monoene precursors irrespective of a FA chain length.
•Two cyanobacterial acyl-lipid Δ12-FADs were expressed in another cyanobacterium to produce dienoic fatty acids.•Δ12-FADs “count” 3C toward the methyl end from an existing double bond in the monoene precursors.•This counting does not depend on the chain length of a fatty acid.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
Fatty acid desaturases (FADs) play important roles in various metabolic and adaptive pathways in all living organisms. They represent a superfamily of oxygenases that introduce double bonds into the ...acyl chains of fatty acids (FAs). These enzymes are highly specific to the length of the carbon chain, position of double bonds formation, etc. The modes by which FADs “count” the position of the double bond formation may differ. In cyanobacteria, the first double bond is formed between 9th and 10th carbons (position Δsup.9 ), counting from the carboxylic end of an FA. Other FADs that produce polyunsaturated FAs may introduce double bonds counting from the carboxyl (Δ) or methyl (ω) terminus, or from a pre-existing double bond towards carboxyl or methyl terminus of an FA chain. Here, we expressed the desD gene for the Δ6-FAD from Synechocystis sp. PCC 6803 in Synechococcus elongatus PCC 7942 (which is capable of synthesizing only monoenoic FAs desaturated mainly at position Δsup.9 ) and observed the appearance of unusual monoenoic FAs desaturated at position Δsup.6 , as well as Δsup.6,9 dienoic FAs. Exogenously added cis-10-heptadecenoic acid (17:1Δsup.10 ) was converted into cis-6,10-heptadecadienoic (17:2Δsup.6,10 ). These data demonstrate the ability of Δ6-FAD to introduce the first double bond into the unsaturated substrates and suggests that it “counts” from the carboxyl end, irrespective of the absence or presence of a previous double bond in an FA chain.
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IZUM, KILJ, NUK, PILJ, PNG, SAZU, UL, UM, UPUK
Fighting against the falsification of valuable items remains a crucial social-threatening challenge stimulating a never-ending search for novel anti-counterfeiting strategies. The demanding security ...labels must simultaneously address multiple requirements (high density of the recorded information, high protection degree,
etc
.) and be realized
via
scalable and inexpensive technologies. Here, the direct reproducible femtosecond-laser patterning of thin glass-supported amorphous (α-)Si films is proposed for optical information encryption and the scalable and highly reproducible fabrication of security labels composed of Raman-active hemispherical Si nanoparticles (NPs). Laser printing conditions allow the precise control of the diameter of the formed NPs ensuring translation of their dipolar Mie resonance position within the entire visible spectral range. Two-temperature molecular dynamics simulations clarify the origin of α-Si NP formation by rupture of the molten Si layer driven by a negative GPa-range pressure near the liquid-solid interface. Arrangement of the laser-printed Mie-resonant NP allows the creation of hidden security labels offering several easy-to-realize information encryption strategies (for example, local laser-induced post-crystallization or mixing Mie-resonant and non-resonant NPs), additional protection modalities, facile Raman mapping readout and dense information recording (up to 60 000 dots per inch) close to the optical diffraction limit. The developed fabrication strategy is simple, inexpensive, and scalable and can be realized based on cheap Earth-abundant materials and commercially-available equipment justifying its practical applicability and attractiveness for anti-counterfeit and security applications.
Direct femtosecond-laser patterning of thin amorphous Si films is proposed for optical information encryption and highly reproducible fabrication of security labels composed of Raman-active hemispherical Si nanoparticles.
We present a new classical interatomic potential designed for simulation of the W-Mo-Nb system. The angular-dependent format of the potential allows for reproduction of many important properties of ...pure metals and complex concentrated alloys with good accuracy. Special attention during the development and validation of the potential was paid to the description of vacancies, screw dislocations and planar defects, as well as thermo-mechanical properties. Here, the applicability of the developed model is demonstrated by studying the temperature dependence of the elastic moduli and average atomic displacement in pure metals and concentrated alloys up to the melting point.
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GEOZS, IJS, IMTLJ, KILJ, KISLJ, NLZOH, NUK, OILJ, PNG, SAZU, SBCE, SBJE, UILJ, UL, UM, UPCLJ, UPUK, ZAGLJ, ZRSKP
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