A nonlinear dynamic model of DNA with a sequence-dependent stacking term

No simple model exists that accurately describes the melting behavior and breathing dynamics of double-stranded DNA as a function of nucleotide sequence. This is especially true for homogenous and periodic DNA sequences, which exhibit large deviations in melting temperature from predictions made by additive thermodynamic contributions. Currently, no method exists for analysis of the DNA breathing dynamics of repeats and of highly G/C- or A/T-rich regions, even though such sequences are widespread in vertebrate genomes. Here, we extend the nonlinear Peyrard–Bishop–Dauxois (PBD) model of DNA to include a sequence-dependent stacking term, resulting in a model that can accurately describe the melting behavior of homogenous and periodic sequences. We collect melting data for several DNA oligos, and apply Monte Carlo simulations to establish force constants for the 10 dinucleotide steps (CG, CA, GC, AT, AG, AA, AC, TA, GG, TC). The experiments and numerical simulations confirm that the GG/CC dinucleotide stacking is remarkably unstable, compared with the stacking in GC/CG and CG/GC dinucleotide steps. The extended PBD model will facilitate thermodynamic and dynamic simulations of important genomic regions such as CpG islands and disease-related repeats

Differential Base Stacking Interactions Induced by Trimethylene Interstrand DNA Cross-Links in the 5′-CpG-3′ and 5′-GpC-3′ Sequence Contexts

Synthetically derived trimethylene interstrand DNA cross-links have been used as surrogates for the native cross-links that arise from the 1,N 2-deoxyguanosine adducts derived from R,β-unsaturated aldehydes. The native enal-mediated cross-linking occurs in the 5′-CpG-3 ′ sequence context but not in the 5′-GpC-3 ′ sequence context. The ability of the native enal-derived 1,N 2-dG adducts to induce interstrand DNA cross-links in the 5′-CpG-3 ′ sequence as opposed to the 5′-GpC-3 ′ sequence is attributed to the destabilization of the DNA duplex in the latter sequence context. Here, we report higher accuracy solution structures of the synthetically derived trimethylene cross-links, which are refined from NMR data with the AMBER force field. When the synthetic trimethylene cross-links are placed into either the 5′-CpG-3′ or the 5′-GpC-3 ′ sequence contexts, the DNA duplex maintains B-DNA geometry with structural perturbations confined to the cross-linked base pairs. Watson-Crick hydrogen bonding is conserved throughout the duplexes. Although different from canonical B-DNA stacking, the cross-linked and the neighbor base pairs stack in the 5′-CpG-3 ′ sequence. In contrast, the stacking at the cross-linked base pairs in the 5′-GpC-3 ′ sequence is greatly perturbed. The π-stacking interactions between the crosslinked and the neighbor base pairs are reduced. This is consistent with remarkable chemical shift perturbations of the C 5 H5 and H6 nucleobase protons that shifted downfield by 0.4-0.5 ppm. In contrast

Magnetic properties of Fe-Bi films

In the paper the results of experimental studies of film structures in the Fe-Bi system are presented. By the method of electron magnetic resonance, it is shown that for bilayer structures the magnetic state depends on the order of deposition of the magnetic and non-magnetic layers. In the three-layer structures, the effect of exchange bias was found, the magnitude of that depends on the thickness of the bismuth layer. © Published under licence by IOP Publishing Ltd

Fds Modeling of the Fire-preventing Eaves Effectiveness to Prevent the Fire Spreading on Facade of High-rise Buildings

Purpose. Applying FDS modelling to detect the influence of structural parameters of facade fire eaves, the effectiveness of fire prevention by vertical building structures in high-rise buildings.Methods. To calculate the temperature in the high-rise building model used Pyrosim computer system that serves as the user's shell application Fire Dynamics Simulator (FDS). This FDS system uses numerical algorithms to solve the complete Navier-Stokes differential equation system to determine temperature and other hazardous factors during a fire.Results. The results of FDS modelling during substantiation of constructive parameters of fire eaves, which protrude beyond the facade and located on the border of fire compartments along the contour of high-rise buildings with a nominal height of more than 73.5 m, are presented. Premises and substantiated the criteria for the destruction of external light openings (windows) as an integral factor in the spread of fire on the external vertical building structures of high-rise ПОЖЕЖНА БЕЗПЕКА40 Вісник ЛДУБЖД, №23, 2021buildings. A study of the effectiveness of the structural parameters of cornices and their impact on the effectiveness of fire prevention by vertical building structures under the same initial conditions of fire development. Constructed comparative dependences of distribution of temperatures of heating of a facade of the house. Also defined the duration of achievement of their critical values.Scientific novelty. The analysis of the data obtained as a result of FDS modelling under the same initial conditions and conclusions on the effectiveness of design parameters of fire facade cornices on the border of fire compartments and ways to further improve their design to prevent the spread of fire in high-rise buildings. These studies are aimed at their use by design institutions during the development of design parameters of fire eaves, which protrude beyond the facade and are located on the border of fire compartments along the contour of high-rise buildings, as well as to improve the regulatory framework for fire safety

ПРОЕКТУВАННЯ СКЛАДІВ ДОРОЖНИХ БЕТОНІВ

Пропонується методика проектування складу дорожніх бетонів. Розглянуті основні особливості, шляхи досягнення і регулювання властивостей дорожніх бетонів, які направлені на підвищення їх довговічності й ефективност