Statistical-mechanical lattice models for protein-DNA binding in chromatin

Statistical-mechanical lattice models for protein-DNA binding are well established as a method to describe complex ligand binding equilibriums measured in vitro with purified DNA and protein components. Recently, a new field of applications has opened up for this approach since it has become possible to experimentally quantify genome-wide protein occupancies in relation to the DNA sequence. In particular, the organization of the eukaryotic genome by histone proteins into a nucleoprotein complex termed chromatin has been recognized as a key parameter that controls the access of transcription factors to the DNA sequence. New approaches have to be developed to derive statistical mechanical lattice descriptions of chromatin-associated protein-DNA interactions. Here, we present the theoretical framework for lattice models of histone-DNA interactions in chromatin and investigate the (competitive) DNA binding of other chromosomal proteins and transcription factors. The results have a number of applications for quantitative models for the regulation of gene expression.Comment: 19 pages, 7 figures, accepted author manuscript, to appear in J. Phys.: Cond. Mat

Specific features of the luminescence and conductivity of zinc selenide on exposure to X-ray and optical excitation

The set of experimental data on the X-ray-excited luminescence and X-ray induced conductivity of ZnSe are compared to the data on the photoluminescence and photoconductivity. It is experimentally established that the current-voltage characteristics and the kinetics of phosphorescence and current relaxation depend on the type of excitation. It is found that the external electric field influences the intensity and shape of bands in the luminescence spectra. It is shown that the character of excitation defines the kinetics of recombination, charge carrier trapping, and conductivity in wide-gap semiconductors.Comment: 7 pages, 7 figures, published in Fizika i Tekhnika Poluprovodnikov, 2010, Vol. 44, No. 5, pp. 594-59

ПРОЦЕССЫ ДЕСОРБЦИИ КИСЛОРОДА В ВЫСОКОПЛОТНОМ ЛАНТАН СТРОНЦИЕВОМ МАНГАНИТЕ La0.6Sr0.4MnO3-d

Characteristic properties of the formation of physical - chemical properties of a manganite with the composition La0.6Sr0.4MnO3-d were considered. It was determined that two titration current minima depending on the heating rate and the partial pressure of oxygen (pO2) exist at different temperatures, heating rates and partial pressures of oxygen. It is supposed that extreme values of the titration current are caused by breaking of bands of anions existing in two different forms with the tetravalent manganese, as well as by the excessive superstoichiometric oxygen which partially compensate the presence of Mn4+ cations, and by oxygen recovering the electroneutrality of the system appearing due to a decrease of the charge value due to the introduction of Sr2+. It was established that the activation energy of oxygen diffusion is decreasing and reached the minimal value 241 kJ/mole at pO2=5 Pa, with a subsequent increase up to ~273 kJ/mole at pO2= 150 Pa and d=0,004, with the increase of oxygen defects concentration in the La0.6Sr0.4MnO3-d anion sublattice. Concentration dependence of the activation energy of oxygen diffusion is motivated by a formation of the stressed layer, placed near the surface of grains which are depleted with oxygen and at the same time they are a buffer for the oxygen diffusion.Расcмотрены особенности формирования физико-химических свойств манганита состава La0.6Sr0.4MnO3-d. В процессе выделения кислорода из La0.6Sr0.4MnO3-d при различных температурах, скоростях нагрева и парциальных давлениях кислорода существует два минимума тока титрования, зависящих от скорости нагрева и парциального давления кислорода. Экстремумы тока титрования, по-видимому, обусловлены разрывами связей между анионами, находящимися в двух различных формах, и четырехвалентным марганцем. Первая форма - это сверхстехиометрический кислород, частично компенсирующий присутствие катионов Mn4+. Вторая форма - кислород, восстанавливающий электронейтральность при введении Sr2+. При изменении концентрации кислородных дефектов в анионной подрешетке La0.6Sr0.4MnO3-d изменяется и энергия активации диффузии кислорода в интервале 0,0024≤d≤0,0031. Минимальное значение энергии активации при pO2=5 Па составляет 241 кДж/моль. При pO2=150 Па и d=0,004 она возрастает до ~ 273 кДж/моль. Концентрационная зависимость энергии активации диффузии кислорода обосновывается образованием напряженного слоя, расположенного вблизи поверхности зерен, обедненных кислородом и одновременно являющимся буфером для его диффузии

ОПТИМИЗАЦИЯ УСЛОВИЙ СИНТЕЗА КОМПОЗИТОВ ЦИРКОНАТА-ТИТАНАТА СВИНЦА БАРИЯ, СОДЕРЖАЩИХ АТОМЫ МЕТАЛЛОВ, И ИХ ДИЭЛЕКТРИЧЕСКИЕ СВОЙСТВА

Composition materials on the base of Pb0,75Ba0,15Zr0,53Ti0,47O3 (PBZT) with micro-inclusions of Cu and Ni are prepared by a complex ceramic technology. This technology includes metallization procedures by means of the chemical deposition method from standard solutions of nickel and copper. At determination of correlation of the structure of PBZT composites and their dielectric properties it was shown that dielectric losses increase with decreasing temperature. This is caused by the domination of the real part of the complex dielectric permittivity.C помощью комплексной керамической технологии, включающей процедуры металлизации методом химического осаждения из стандартных растворов никеля и меди, подготовлены композиционные материалы на основе соединения Pb0,75Ba0,15Zr0,53Ti0,47O3 (ЦТБС) с микро-включениями Cu и Ni. При установлении корреляций между структурой композитов ЦТБС и их диэлектрическими характеристиками показано, что при низких частотах диэлектрические потери возрастают с увеличением температуры, что обусловлено доминированием действительной части комплексной диэлектрической проницаемости

Nucleosomes in gene regulation: theoretical approaches

This work reviews current theoretical approaches of biophysics and bioinformatics for the description of nucleosome arrangements in chromatin and transcription factor binding to nucleosomal organized DNA. The role of nucleosomes in gene regulation is discussed from molecular-mechanistic and biological point of view. In addition to classical problems of this field, actual questions of epigenetic regulation are discussed. The authors selected for discussion what seem to be the most interesting concepts and hypotheses. Mathematical approaches are described in a simplified language to attract attention to the most important directions of this field