Light-Induced Quantum Droplet Phases of Lattice Bosons in Multimode Cavities.

Multimode optical cavities can be used to implement interatomic interactions which are highly tunable in strength and range. For bosonic atoms trapped in an optical lattice we show that, for any finite range of the cavity-mediated interaction, quantum self-bound droplets dominate the ground state phase diagram. Their size and in turn density is not externally fixed but rather emerges from the competition between local repulsion and finite-range cavity-mediated attraction. We identify two different regimes of the phase diagram. In the strongly glued regime, the interaction range exceeds the droplet size and the physics resembles the one of the standard Bose-Hubbard model in a (self-consistent) external potential, where in the phase diagram two incompressible droplet phases with different filling are separated by one with a superfluid core. In the opposite weakly glued regime, we find instead direct first order transitions between the two incompressible phases, as well as pronounced metastability. The cavity field leaking out of the mirrors can be measured to distinguish between the various types of droplets.

Disorder-Free Localization in an Interacting 2D Lattice Gauge Theory.

Disorder-free localization has been recently introduced as a mechanism for ergodicity breaking in low-dimensional homogeneous lattice gauge theories caused by local constraints imposed by gauge invariance. We show that also genuinely interacting systems in two spatial dimensions can become nonergodic as a consequence of this mechanism. This result is all the more surprising since the conventional many-body localization is conjectured to be unstable in two dimensions; hence the gauge invariance represents an alternative robust localization mechanism surviving in higher dimensions in the presence of interactions. Specifically, we demonstrate nonergodic behavior in the quantum link model by obtaining a bound on the localization-delocalization transition through a classical correlated percolation problem implying a fragmentation of Hilbert space on the nonergodic side of the transition. We study the quantum dynamics in this system by introducing the method of "variational classical networks," an efficient and perturbatively controlled representation of the wave function in terms of a network of classical spins akin to artificial neural networks. We identify a distinguishing dynamical signature by studying the propagation of line defects, yielding different light cone structures in the localized and ergodic phases, respectively. The methods we introduce in this work can be applied to any lattice gauge theory with finite-dimensional local Hilbert spaces irrespective of spatial dimensionality.

[BIOINFORMATICS COMPARISON OF HUMAN AND PLANT PHOSPHATOMES].

The study presents the results of bioinformatic comparison of protein phosphatases from higher plants and human phosphatom (150 sequences). Based on sequence and profile comparison with known catalytic domains, 204 plant homologues from Physcomitrella patens and Arabidopsis thaliana where selected. Clustering of joint group of plant and mammalian protein phosphatases revealed fundamental differences in plant and human phosphatomes. At the same time, it was shown significant differences in the set of protein phosphatases in P. patens, A. thaliana, and such monocots as Orysa saliva and Zea mays.

[Docking of low-molecular ligands on the plant FtsZ-protein with application of CUDA-accelerated calculations].

This article provides review and analysis of opportunities for application of the CUDA technology for acceleration of computations in structural biology and bioinformatics. On the example of work with the Hex 6.1 program, comparative analysis of increase in the speed and quality of results of hard-docking of a number of low-molecular compounds on the surface of the FtsZ protein from Arabidopsis thaliana was performed. Several potential benzimidazole--plant FtsZ protein binding sites were identified.

[Reconstruction of spatial structure of plant protein phosphatase type-1 and -2A in complex with okadaic acid].

The homology modeling, based on known temple structures of Homo sapiens protein phosphatase type-1 and -2A was implemented. The spatial structures of the human protein phosphatases and their plant homologs from Arabidopsis thaliana was predicted. The quality of models was confirmed by conformational analysis and root mean square deviations. The sites of okadaic acid binding in molecules of plant protein phosphatases (type-1 and -2A) were proved by the data of comparative analysis and molecular dynamics.

[Bioinformatic search for plant homologs of protein kinase BUB1--the keypoint of mitotic spindle assembly].

Fourteen plant homologs of animal, yeast and myxomycetes spindle assembly checkpoint protein kinases were identified bioinformatically. It was shown that the closest plant homologues of the BUB1 protein kinases are unknown proteins XP_002274770.1 (CBI21878.1) from Vitis vinifera, EEC82122.1 from Oryza sativa Indica, EEE67244.1 from O. sativa Japonica, EEF44403.1 from Ricinus communis and CAL57156.1 from Ostreococcus tauri. The reconstruction and analysis of spatial structures of the EEC82122.1, EEE67244.1 and XP_002274770.1 (CBI21878.1), catalytic domains confirmed their conformity to spindle assembly checkpoint protein kinases BUB1.

[MAST2-like protein kinase from grape vine Vitis vinifera: cloning of catalytic domain cDNA].

The aim of our work is the identification of protein kinases phosphorylating microtubule proteins in plant cells. Using bioinformatic approach, we found genes of putative homologues of microtubule-associated mammalian protein kinase MAST2 in higher plant genomes. The gene of closest MAST2 homologue, putative protein, named GMLK (Grape MAST2-Like Kinase, A7NTE9_VITVI), was found in grape Vitis vinifera. We report here the cloning of cDNA of GMLK (A7NTE9) from Pinot Noir grape vine leaves.

[Bioinformatic search for plant homologs of Ste20-like serine/threonine protein kinases].

Eleven plant homologs of animal and yeast Ste20-like protein kinases were identified. It was shown that the nearest plant homologs of the Ste20-like protein kinases are the unknown proteins A9RVK0 from Physcomitrella patens ssp. patens and A7P2E2 from Vitis vinifera. Cladistic analysis showed a protein kinase dstl from Dictyostelium discoideum as the closest protein to the newly found plant homologs. A predicted spatial structure of the A9RVK0 from P. patens ssp. patens catalytic domain is presented.

[Bioinformatic search of plant protein kinases, participating in microtubule protein phosphorylation and cell division regulation].

Bioinformatic search of plant homologues of human protein kinases SLK, PAK6, PAK7, MARK1, MAST2, TTBK1, TTBK2, AURKA, PLK1, PLK2 and PASK participating in microtubular protein phosphorylation and cell division regulation is carried out. The homologues of protein kinases SLK, MAST2 and AURKA were identified. It is found that closest homologue of human AURKA protein kinase is a protein with unknown function A7PY12_VITVI (STALK--Serine-Threonine Aurora-Like Kinase) from grape (Vitis vinifera). Reconstruction and analysis of three-dimensional structure of STALK protein confirmed its relation to the group of AURKA-like protein kinases.

Phase transitions and pattern formation in ensembles of phase-amplitude solitons in quasi-one-dimensional electronic systems.

Most common types of symmetry breaking in quasi-one-dimensional electronic systems possess a combined manifold of states degenerate with respect to both the phase θ and the amplitude A sign of the order parameter Aexp(iθ). These degrees of freedom can be controlled or accessed independently via either the spin polarization or the charge densities. To understand statistical properties and the phase diagram in the course of cooling under the controlled parameters, we present here an analytical treatment supported by Monte Carlo simulations for a generic coarse-grained two-field model of XY-Ising type. The degeneracies give rise to two coexisting types of topologically nontrivial configurations: phase vortices and amplitude kinks, i.e., the solitons. In two- and three-dimensional states with long-range (or Berezinskii--Kosterlitz--Thouless-type) orders, the topological confinement sets in at a temperature T=T_{1} which binds together the kinks and unusual half-integer vortices. At a lower T=T_{2}, the solitons start to aggregate into walls formed as rods of amplitude kinks which are ultimately terminated by half-integer vortices. With lowering T, the walls multiply, passing sequentially across the sample. The presented results indicate a possible physical realization of a peculiar system of half-integer vortices with rods of amplitude kinks connecting their cores. Its experimental realization becomes feasible in view of recent successes in real-space observations and even manipulations of domain walls in correlated electronic systems.

[Molecular mechanisms of the repair of UV-induced DNA damages in plants].

Solar UV-B radiation is an environmental factor which damage and destabilize genomes. UV-B-induced DNA lesions have cytotoxic and genotoxic effects on the cells of pro- and eucaryotes including plants. In addition, such lesions can cause gene mutations in plants. The products of the damages of cellular DNA caused by UV are examined in the present review and plant reparative pathways including photoreactivation, base excision repair and nucleotide excision repair are analyzed. The review deals as well with the mechanisms of plant DNA damage tolerance which allow to reduce the toxic effects of UV-B radiation.

3D structure prediction of histone acetyltransferase proteins of the MYST family and their interactome in Arabidopsis thaliana.

Histone lysine acetylation is a reversible post-translational modification that does not involve changes in DNA sequences. Enzymes play an important role in developmental processes and their deregulation has been linked to the progression of diverse disorders. The HAT enzyme family fulfills an important role in various developmental processes mediated by the state of chromatin, and have been attributed to its deregulation. To understand acetylation mechanisms and their role in cell signaling, transcriptional regulation, and apoptosis, it is crucial to identify and analyze acetylation sites. Bioinformatics methods can be used to generate relatively precise predictions. Here we applied classical bioinformatics methods-sequence alignment, homology modeling, and docking-to compare approved and predicted lysine acetylation processes in different organisms. HAM1 and HAM2 are analogs of KAT8 and KAT7 (MYST1 and MYST2), members of the MYST histone acetyltransferase family, and our results show that HAM1 and HAM2 have much in common with other representatives of MYST families from various organisms. One function of acetyl-CoA binding was predicted with a high level of probability by computational methods. Based on our data, we conclude that, despite huge genetic distances and some structural differences between animal and plant species, a closer look at acetylation mechanism shows that they have much in common.

[Disordered intestinal mechanisms in patients with chronic kidney failure]. / Narushenie kishechnykh mekhanizmov u bol'nykh s khronicheskoi pochechnoi nedostatochnost'iu.

The data on impairment of the intestinal mechanisms in 103 patients with chronic renal failure are presented. This impairment is characterized by inhibition of the absorption capacity of the intestine, an increase of the concentration of urea and creatinine in its contents, and by dysbacteriosis.

[Microecological disorders in the intestines of patients with chronic kidney failure and the arterial hypertension syndrome]. / Mikroékologicheskie narusheniia v kishechnike u bol'nykh s khronicheskoi pochechnoi nedostatochnost'iu i sindromom arterial'noi gipertenzii.

Changes in the microfloral species quality and quantity, blurring of the ecological niche, reduction or disappearance of lacto- and bifidobacteria, emergence of opportunistic and saprogenic flora were found in the intestine of patients with intestinal chronic renal failure. These findings are indicative of microecological abnormalities in the above patients.

[Disorders of the protein-transport function of the intestines in chronic kidney diseases]. / Narusheniia belkovotransportnoi funktsii kishechnikka pri khronicheskikh zabolevaniiakh pochek.

Radioactive albumin studies were performed in patients with chronic renal disorders. The findings evidence an essential decline of intestinal protein-transport function, enhanced catabolism, impairment of protein synthesis and its renal loss which underlie protein deficiency.

[The intestinal mechanisms of the protein metabolic disorder in kidney failure]. / Kishechnye mekhanizmy narusheniia metabolizma belka pri pochechnoi nedostatochnosti.

Data are reported on intestinal mechanisms of protein metabolism in renal failure in patients and experimental animals. These disorders are characterized by inhibition of the intestinal absorption capacities, disturbances of intestinal mechanisms of the amino acid kinetics and they develop along with a reduction of the total excretory renal function.

[Methodological approaches in developing disease prevention in mine workers in northeast Russia]. / Metodicheskie podkhody v razvitii profilaktiki zabolevaemosti sredi rabochikh gornorudnoi promyshlennosti severo-vostoka Rossii.

For many years the Magadan region occupies the leading position as regards the incidence of occupational and some general somatic diseases. Recent social and economic reforms in mining industry led to a decrease in the level of life of workers and their family members and an increase in the incidence of professional and general somatic diseases and mortality of capable people. Improvement of socio-hygienic conditions of miners' life at the expense of enterprises of new forms of property can be hardly expected in the nearest future, which necessitates realization of a complex regional program taking account of economic specificities of the region, aimed at improvement of total resistance to unfavorable climatic conditions of the North.