Resonant raman scattering in complexes of nc-Si/SiO₂ quantum dots and oligonucleotides

We report on the functionalization of nanocrystalline nc-Si/SiO2 semiconductor quantum dots (QDs) by short d(20G, 20T) oligonucleotides. The obtained complexes have been studied by Raman spectroscopy techniques with high spectral and spatial resolution. A new phenomenon of multiband resonant light scattering on single oligonucleotide molecules has been discovered, and peculiarities of this effect related to the nonradiative transfer of photoexcitation from nc-Si/SiO2 quantum dots to d(20G, 20T) oligonucleotide molecules have been revealed

Conformal mapping methods for interfacial dynamics

The article provides a pedagogical review aimed at graduate students in materials science, physics, and applied mathematics, focusing on recent developments in the subject. Following a brief summary of concepts from complex analysis, the article begins with an overview of continuous conformal-map dynamics. This includes problems of interfacial motion driven by harmonic fields (such as viscous fingering and void electromigration), bi-harmonic fields (such as viscous sintering and elastic pore evolution), and non-harmonic, conformally invariant fields (such as growth by advection-diffusion and electro-deposition). The second part of the article is devoted to iterated conformal maps for analogous problems in stochastic interfacial dynamics (such as diffusion-limited aggregation, dielectric breakdown, brittle fracture, and advection-diffusion-limited aggregation). The third part notes that all of these models can be extended to curved surfaces by an auxilliary conformal mapping from the complex plane, such as stereographic projection to a sphere. The article concludes with an outlook for further research.Comment: 37 pages, 12 (mostly color) figure

A Generalized Allosteric Mechanism for cis-Regulated Cyclic Nucleotide Binding Domains

Cyclic nucleotides (cAMP and cGMP) regulate multiple intracellular processes and are thus of a great general interest for molecular and structural biologists. To study the allosteric mechanism of different cyclic nucleotide binding (CNB) domains, we compared cAMP-bound and cAMP-free structures (PKA, Epac, and two ionic channels) using a new bioinformatics method: local spatial pattern alignment. Our analysis highlights four major conserved structural motifs: 1) the phosphate binding cassette (PBC), which binds the cAMP ribose-phosphate, 2) the “hinge,” a flexible helix, which contacts the PBC, 3) the β2,3 loop, which provides precise positioning of an invariant arginine from the PBC, and 4) a conserved structural element consisting of an N-terminal helix, an eight residue loop and the A-helix (N3A-motif). The PBC and the hinge were included in the previously reported allosteric model, whereas the definition of the β2,3 loop and the N3A-motif as conserved elements is novel. The N3A-motif is found in all cis-regulated CNB domains, and we present a model for an allosteric mechanism in these domains. Catabolite gene activator protein (CAP) represents a trans-regulated CNB domain family: it does not contain the N3A-motif, and its long range allosteric interactions are substantially different from the cis-regulated CNB domains

Water adsorption and polar properties of self-assembled diphenylalanine nanotubes

Experimental part of this work was performed within the scope of the project CICECO-Aveiro Institute of Materials, FCT Ref. UID/CTM/50011/2019, financed by national funds through the FCT/MCTES. Theoretical part of the work was supported by Russian Science Foundation (Grant No. 18-72-00052). S.K., P.Z. and A.K. are grateful to FCT project PTDC/CTM-CTM/31679/2017. P.Z. is grateful to FCT project PTDC/QEQ-QAN/6373/2014. S.K and A.K are grateful to joint Portugal-Turkey project (TUBITAK/0006/2014)

The regulatory subunit of PKA-I remains partially structured and undergoes β-aggregation upon thermal denaturation

Background: The regulatory subunit (R) of cAMP-dependent protein kinase (PKA) is a modular flexible protein that responds with large conformational changes to the binding of the effector cAMP. Considering its highly dynamic nature, the protein is rather stable. We studied the thermal denaturation of full-length RIα and a truncated RIα(92-381) that contains the tandem cyclic nucleotide binding (CNB) domains A and B. Methodology/Principal Findings: As revealed by circular dichroism (CD) and differential scanning calorimetry, both RIα proteins contain significant residual structure in the heat-denatured state. As evidenced by CD, the predominantly α-helical spectrum at 25°C with double negative peaks at 209 and 222 nm changes to a spectrum with a single negative peak at 212-216 nm, characteristic of β-structure. A similar α→β transition occurs at higher temperature in the presence of cAMP. Thioflavin T fluorescence and atomic force microscopy studies support the notion that the structural transition is associated with cross-β-intermolecular aggregation and formation of non-fibrillar oligomers. Conclusions/Significance: Thermal denaturation of RIα leads to partial loss of native packing with exposure of aggregation-prone motifs, such as the B' helices in the phosphate-binding cassettes of both CNB domains. The topology of the β-sandwiches in these domains favors inter-molecular β-aggregation, which is suppressed in the ligand-bound states of RIα under physiological conditions. Moreover, our results reveal that the CNB domains persist as structural cores through heat-denaturation. © 2011 Dao et al

Magnetoelectric ordering of BiFeO3 from the perspective of crystal chemistry

In this paper we examine the role of crystal chemistry factors in creating conditions for formation of magnetoelectric ordering in BiFeO3. It is generally accepted that the main reason of the ferroelectric distortion in BiFeO3 is concerned with a stereochemical activity of the Bi lone pair. However, the lone pair is stereochemically active in the paraelectric orthorhombic beta-phase as well. We demonstrate that a crucial role in emerging of phase transitions of the metal-insulator, paraelectric-ferroelectric and magnetic disorder-order types belongs to the change of the degree of the lone pair stereochemical activity - its consecutive increase with the temperature decrease. Using the structural data, we calculated the sign and strength of magnetic couplings in BiFeO3 in the range from 945 C down to 25 C and found the couplings, which undergo the antiferromagnetic-ferromagnetic transition with the temperature decrease and give rise to the antiferromagnetic ordering and its delay in regard to temperature, as compared to the ferroelectric ordering. We discuss the reasons of emerging of the spatially modulated spin structure and its suppression by doping with La3+.Comment: 18 pages, 5 figures, 3 table

Mutations in the Catalytic Loop HRD Motif Alter the Activity and Function of Drosophila Src64

The catalytic loop HRD motif is found in most protein kinases and these amino acids are predicted to perform functions in catalysis, transition to, and stabilization of the active conformation of the kinase domain. We have identified mutations in a Drosophila src gene, src64, that alter the three HRD amino acids. We have analyzed the mutants for both biochemical activity and biological function during development. Mutation of the aspartate to asparagine eliminates biological function in cytoskeletal processes and severely reduces fertility, supporting the amino acid's critical role in enzymatic activity. The arginine to cysteine mutation has little to no effect on kinase activity or cytoskeletal reorganization, suggesting that the HRD arginine may not be critical for coordinating phosphotyrosine in the active conformation. The histidine to leucine mutant retains some kinase activity and biological function, suggesting that this amino acid may have a biochemical function in the active kinase that is independent of its side chain hydrogen bonding interactions in the active site. We also describe the phenotypic effects of other mutations in the SH2 and tyrosine kinase domains of src64, and we compare them to the phenotypic effects of the src64 null allele

Thomson scattering diagnostics at the Globus M2 tokamak

The paper is devoted to the Thomson scattering (TS) diagnostics recently developed for the Globus-M2 spherical tokamak and prototyping the ITER divertor TS diagnostics. The distinctive features of the system are the use of spectrometers, acquisition system and lasers that meet the base requirements for ITER TS diagnostics. The paper describes the diagnostic system that allows precise measurements of TS signals, as well as the results of the first measurements of electron temperature and density in both central region of the plasma column and scrape-off layer. The system provides measurements of electron temperature $T_{e}$ in the range of 5 eV to 5 keV and density $n_{e}$ in the range of $5{\cdot}10^{17}{\div}3.25{\cdot}10^{20} m^{-3}$. The use of two ITER-grade probing lasers of different wavelengths (Nd:YAG 1064.5 nm and Nd:YLF 1047.3 nm) allows reliable measurement of $T_{e}$ in multi-colour mode, i.e., assuming that spectral calibration is unknown

Mobile π−\pi-kinks and half-integer zero-field-like steps in highly discrete alternating 0−π0-\pi Josephson junction arrays

The dynamics of a one-dimensional, highly discrete, linear array of alternating $0-$ and $\pi-$ Josephson junctions is studied numerically, under constant bias current at zero magnetic field. The calculated current - voltage characteristics exhibit half-integer and integer zero-field-like steps for even and odd total number of junctions, respectively. Inspection of the instantaneous phases reveals that, in the former case, single $\pi-$kink excitations (discrete semi-fluxons) are supported, whose propagation in the array gives rise to the $1/2-$step, while in the latter case, a pair of $\pi-$kink -- $\pi-$antikink appears, whose propagation gives rise to the $1-$step. When additional $2\pi-$kinks are inserted in the array, they are subjected to fractionalization, transforming themselves into two closely spaced $\pi-$kinks. As they propagate in the array along with the single $\pi-$kink or the $\pi-$kink - $\pi-$antikink pair, they give rise to higher half-integer or integer zero-field-like steps, respectively.Comment: 7 pages, 8 figures, submitted to Supercond. Sci. Techno