Not gate in a cis-trans photoisomerization model

We numerically study the implementation of a NOT gate by laser pulses in a model molecular system presenting two electronic surfaces coupled by non adiabatic interactions. The two states of the bit are the fundamental states of the cis-trans isomers of the molecule. The gate is classical in the sense that it involves a one-qubit flip so that the encoding of the outputs is based on population analysis which does not take the phases into account. This gate can also be viewed as a double photo-switch process with the property that the same electric field controls the two isomerizations. As an example, we consider one-dimensional cuts in a model of the retinal in rhodopsin already proposed in the literature. The laser pulses are computed by the Multi Target Optimal Control Theory with chirped pulses as trial fields. Very high fidelities are obtained. We also examine the stability of the control when the system is coupled to a bath of oscillators modelled by an Ohmic spectral density. The bath correlation time scale being smaller than the pulse duration the dynamics is carried out in the Markovian approximation.Comment: 29 pages, 7 figure

Selective One-Dimensional \u3csup\u3e13\u3c/sup\u3eC-\u3csup\u3e13\u3c/sup\u3eC Spin-Diffusion Solid-State Nuclear Magnetic Resonance Methods to Probe Spatial Arrangements in Biopolymers including Plant Cell Walls, Peptides, and Spider Silk

© 2020 American Chemical Society. All rights reserved. Two-dimensional (2D) and 3D through-space 13C-13C homonuclear spin-diffusion techniques are powerful solid-state nuclear magnetic resonance (NMR) tools for extracting structural information from 13C-enriched biomolecules, but necessarily long acquisition times restrict their applications. In this work, we explore the broad utility and underutilized power of a chemical shift-selective one-dimensional (1D) version of a 2D 13C-13C spin-diffusion solid-state NMR technique. The method, which is called 1D dipolar-assisted rotational resonance (DARR) difference, is applied to a variety of biomaterials including lignocellulosic plant cell walls, microcrystalline peptide fMLF, and black widow dragline spider silk. 1D 13C-13C spin-diffusion methods described here apply in select cases in which the 1D 13C solid-state NMR spectrum displays chemical shift-resolved moieties. This is analogous to the selective 1D nuclear Overhauser effect spectroscopy (NOESY) experiment utilized in liquid-state NMR as a faster (1D instead of 2D) and often less ambiguous (direct sampling of the time domain data, coupled with increased signal averaging) alternative to 2D NOESY. Selective 1D 13C-13C spin-diffusion methods are more time-efficient than their 2D counterparts such as proton-driven spin diffusion (PDSD) and dipolar-assisted rotational resonance. The additional time gained enables measurements of 13C-13C spin-diffusion buildup curves and extraction of spin-diffusion time constants TSD, yielding detailed structural information. Specifically, selective 1D DARR difference buildup curves applied to 13C-enriched hybrid poplar woody stems confirm strong spatial interaction between lignin and acetylated xylan polymers within poplar plant secondary cell walls, and an interpolymer distance of ∼0.45-0.5 nm was estimated. Additionally, Tyr/Gly long-range correlations were observed on isotopically enriched black widow spider dragline silks

Performance of ab initio and density functional methods for conformational equilibria of CnH2n+2 alkane isomers (n=2-8)

Conformational energies of n-butane, n-pentane, and n-hexane have been calculated at the CCSD(T) level and at or near the basis set limit. Post-CCSD(T) contribution were considered and found to be unimportant. The data thus obtained were used to assess the performance of a variety of density functional methods. Double-hybrid functionals like B2GP-PLYP and B2K-PLYP, especially with a small Grimme-type empirical dispersion correction, are capable of rendering conformational energies of CCSD(T) quality. These were then used as a `secondary standard' for a larger sample of alkanes, including isopentane and the branched hexanes as well as key isomers of heptane and octane. Popular DFT functionals like B3LYP, B3PW91, BLYP, PBE, and PBE0 tend to overestimate conformer energies without dispersion correction, while the M06 family severely underestimates GG interaction energies. Grimme-type dispersion corrections for these overcorrect and lead to qualitatively wrong conformer orderings. All of these functionals also exhibit deficiencies in the conformer geometries, particularly the backbone torsion angles. The PW6B95 and, to a lesser extent, BMK functionals are relatively free of these deficiencies. Performance of these methods is further investigated to derive conformer ensemble corrections to the enthalpy function, $H_{298}-H_0$, and the Gibbs energy function, ${\rm gef}(T)\equiv - [G(T)-H_0]/T$, of these alkanes. While $H_{298}-H_0$ is only moderately sensitive to the level of theory, ${\rm gef}(T)$ exhibits more pronounced sensitivity. Once again, double hybrids acquit themselves very well.Comment: J. Phys. Chem. A, revised [Walter Thiel festschrift

Исследование водородостойкости и коррозионной стойкости сплава Zr-1Nb, легированного титаном методом высокодозовой имплантации низкоэнергетических ионов

Выпускная квалификационная работа направлена на исследование возможности повышения водородостойкости и коррозионной стойкости сплава Zr-1Nb путем формирования модифицированного поверхностного слоя методом высокодозовой низкоэнергетичной ионной имплантации титана.Final qualification work is aimed at studying the possibility of increasing the hydrogen resistance and corrosion resistance of the Zr-1Nb alloy by forming a modified surface layer by the method of high-dose low-energy ion implantation of titanium

Glycosylation Is Vital for Industrial Performance of Hyperactive Cellulases

In the terrestrial biosphere, biomass deconstruction is conducted by microbes employing a variety of complementary strategies, many of which remain to be discovered. Moreover, the biofuels industry seeks more efficient (and less costly) cellulase formulations upon which to launch the nascent sustainable bioenergy economy. The glycan decoration of fungal cellulases has been shown to protect these enzymes from protease action and to enhance binding to cellulose. We show here that thermal tolerant bacterial cellulases are glycosylated as well, although the types and extents of decoration differ from their Eukaryotic counterparts. Our major findings are that glycosylation of CelA is uniform across its three linker peptides and composed of mainly galactose disaccharides (which is unique) and that this glycosylation dramatically impacts the hydrolysis of insoluble substrates, proteolytic and thermal stability, and substrate binding and changes the dynamics of the enzyme. This study suggests that the glycosylation of CelA is crucial for its exceptionally high cellulolytic activity on biomass and provides the robustness needed for this enzyme to function in harsh environments including industrial settings

Target highlights in CASP14 : Analysis of models by structure providers

Abstract The biological and functional significance of selected CASP14 targets are described by the authors of the structures. The authors highlight the most relevant features of the target proteins and discuss how well these features were reproduced in the respective submitted predictions. The overall ability to predict three-dimensional structures of proteins has improved remarkably in CASP14, and many difficult targets were modelled with impressive accuracy. For the first time in the history of CASP, the experimentalists not only highlighted that computational models can accurately reproduce the most critical structural features observed in their targets, but also envisaged that models could serve as a guidance for further studies of biologically-relevant properties of proteins. This article is protected by copyright. All rights reserved.Peer reviewe

Glycosylation Is Vital for Industrial Performance of Hyperactive Cellulases

In the terrestrial biosphere, biomass deconstruction is conducted by microbes employing a variety of complementary strategies, many of which remain to be discovered. Moreover, the biofuels industry seeks more efficient (and less costly) cellulase formulations upon which to launch the nascent sustainable bioenergy economy. The glycan decoration of fungal cellulases has been shown to protect these enzymes from protease action and to enhance binding to cellulose. We show here that thermal tolerant bacterial cellulases are glycosylated as well, although the types and extents of decoration differ from their Eukaryotic counterparts. Our major findings are that glycosylation of CelA is uniform across its three linker peptides and composed of mainly galactose disaccharides (which is unique) and that this glycosylation dramatically impacts the hydrolysis of insoluble substrates, proteolytic and thermal stability, and substrate binding and changes the dynamics of the enzyme. This study suggests that the glycosylation of CelA is crucial for its exceptionally high cellulolytic activity on biomass and provides the robustness needed for this enzyme to function in harsh environments including industrial settings

Benchmark thermochemistry of the C_nH_{2n+2} alkane isomers (n=2--8) and performance of DFT and composite ab initio methods for dispersion-driven isomeric equilibria

The thermochemistry of linear and branched alkanes with up to eight carbons has been reexamined by means of W4, W3.2lite and W1h theories. `Quasi-W4' atomization energies have been obtained via isodesmic and hypohomodesmotic reactions. Our best atomization energies at 0 K (in kcal/mol) are: 1220.04 n-butane, 1497.01 n-pentane, 1774.15 n-hexane, 2051.17 n-heptane, 2328.30 n-octane, 1221.73 isobutane, 1498.27 isopentane, 1501.01 neopentane, 1775.22 isohexane, 1774.61 3-methylpentane, 1775.67 diisopropyl, 1777.27 neohexane, 2052.43 isoheptane, 2054.41 neoheptane, 2330.67 isooctane, and 2330.81 hexamethylethane. Our best estimates for $\Delta H^\circ_{f,298K}$ are: -30.00 n-butane, -34.84 n-pentane, -39.84 n-hexane, -44.74 n-heptane, -49.71 n-octane, -32.01 isobutane, -36.49 isopentane, -39.69 neopentane, -41.42 isohexane, -40.72 3-methylpentane, -42.08 diisopropyl, -43.77 neohexane, -46.43 isoheptane, -48.84 neoheptane, -53.29 isooctane, and -53.68 hexamethylethane. These are in excellent agreement (typically better than 1 kJ/mol) with the experimental heats of formation at 298 K obtained from the CCCBDB and/or NIST Chemistry WebBook databases. However, at 0 K a large discrepancy between theory and experiment (1.1 kcal/mol) is observed for only neopentane. This deviation is mainly due to the erroneous heat content function for neopentane used in calculating the 0 K CCCBDB value. The thermochemistry of these systems, especially of the larger alkanes, is an extremely difficult test for density functional methods. A posteriori corrections for dispersion are essential. Particularly for the atomization energies, the B2GP-PLYP and B2K-PLYP double-hybrids, and the PW6B95 hybrid-meta GGA clearly outperform other DFT functionals.Comment: (J. Phys. Chem. A, in press

Target highlights in CASP13: experimental target structures through the eyes of their authors

The functional and biological significance of selected CASP13 targets are described by the authors of the structures. The structural biologists discuss the most interesting structural features of the target proteins and assess whether these features were correctly reproduced in the predictions submitted to the CASP13 experiment