Base pair opening and bubble transport in a DNA double helix induced by a protein molecule in a viscous medium

We study the nonlinear dynamics of a protein-DNA molecular system by treating DNA as a set of two coupled linear chains and protein in the form of a single linear chain sliding along the DNA at the physiological temperature in a viscous medium. The nonlinear dynamics of the above molecular system in general is governed by a perturbed nonlinear Schr\"{o}dinger equation. In the non-viscous limit, the equation reduces to the completely integrable nonlinear Schr\"{o}dinger (NLS) equation which admits N-soliton solutions. The soliton excitations of the DNA bases make localized base pair opening and travel along the DNA chain in the form of a bubble. This may represent the bubble generated during the transcription process when an RNA-polymerase binds to a promoter site in the DNA double helical chain. The perturbed NLS equation is solved using a perturbation theory by treating the viscous effect due to surrounding as a weak perturbation and the results show that the viscosity of the solvent in the surrounding damps out the amplitude of the soliton.Comment: 4. Submitted to Phys. Rev.

Correlation of optical conductivity and ARPES spectra of strong-coupling large polarons and its display in cuprates

Common approach is used to calculate band due to strong-coupling large polaron (SCLP) photodissociation in ARPES and in optical conductivity (OC) spectra. It is based on using the coherent-states representation for the phonon field in SCLP. The calculated positions of both band maximums are universal functions of one parameter - the SCLP binding energy Ep: ARPES band maximum lies at binding energy about 3.2Ep; the OC band maximum is at the photon energy about 4.2Ep. The half-widths of the bands are mainly determined by Ep and slightly depend on Frohlich electron-phonon coupling constant: for its value 6-8 the ARPES band half-width is 1.7-1.3Ep and the OC band half-width is 2.8-2.2Ep. Using these results one can predict approximate position of ARPES band maximum and half-width from the maximum of mid-IR OC band and vice versa. Comparison of the results with experiments leads to a conclusion that underdoped cuprates contain SCLPs with Ep=0.1-0.2 eV that is in good conformity with the medium parameters in cuprates. The values of the polaron binding energy determined from experimental ARPES and OC spectra of the same material are in good conformity too: the difference between them is within 10 percent.Comment: 17 pages, 6 figure

Aspicilia stalagmitica (Megasporaceae) - A new lichen species with isidia-like thalline outgrowths

Aspicilia stalagmitica Paukov et Davydov from the Altai Mts, a species with isidia-like outgrowths on areoles, is described as new to science. From other species of the genus Aspicilia stalagmitica differs by the following set of characters: short narrow marginal lobes, conidiomata in the isidia-like outgrowths, appressed to almost substipitate apothecia, long picnoconidia, and stictic acid as a main secondary metabolite. A phylogenetic analysis of Aspicilia stalagmitica (ITS) showing its relationships within Aspicilia is presented. © 2020 Altai State University. All rights reserved.Russian Foundation for Basic Research, RFBR: 18-04-00414Ministry of Education and Science of the Russian Federation, MinobrnaukaUppsala UniversitetEvgeny Davydov thanks Dr Wen-Li Chen for organizing the expedition to China. Alexander Paukov would like to thank RFBR (project 18-04-00414) and the Ministry of Education and Science of the Russian Federation (agreement no. 02.A03.21.0006) for financial support. We are grateful to Anders Nordin (Museum of Evolution, Uppsala University) whose comments have greatly improved the manuscript

Yang-Mills condensates in cosmology

We discuss homogeneous and isotropic cosmological models driven by SU(2) gauge fields in the framework of Einstein gravity. There exists a Yang-Mills field configuration, parametrized by a single scalar function, which consists of parallel electric and magnetic fields and has the stress tensor mimicking an homogeneous and isotropic fluid. The unique SU(2) gauge theory with spontaneous symmetry breaking sharing the same property is the Yang-Mills coupled to the complex doublet Higgs, this exists only in the case of the closed universe. This model contains an intrinsic mechanism for inflation due to the Higgs potential. Our second goal is to show that a successful inflation can be achieved also within the pure Yang-Mills theory adding an appropriate theta-term.Comment: Submitted to Proceedings of "Quantum field theory under the influence of external conditions", Benasque, Spain, September 18-24, 2011 2011, Sep 18 -- Sep 2

A Note on Stress-Energy Tensor and Variational Principle for Null Strings

A straightforward application of the variational principle to null strings meets difficulties since string's world-sheets are degenerate. It is known that the variational principle in this case can be formulted with the help of two-vector density on the string world-sheet which plays a role of Lagrange multipliers. It is shown that recently suggested stress-energy tensor of null strings can be derived by variation over the background metric of the action used to describe tensionless limit in the string theory. One of the Lagrange multipliers is related to the energy of the null string.Comment: 4 page

Benchmarking calculations of excitonic couplings between bacteriochlorophylls

Excitonic couplings between (bacterio)chlorophyll molecules are necessary for simulating energy transport in photosynthetic complexes. Many techniques for calculating the couplings are in use, from the simple (but inaccurate) point-dipole approximation to fully quantum-chemical methods. We compared several approximations to determine their range of applicability, noting that the propagation of experimental uncertainties poses a fundamental limit on the achievable accuracy. In particular, the uncertainty in crystallographic coordinates yields an uncertainty of about 20% in the calculated couplings. Because quantum-chemical corrections are smaller than 20% in most biologically relevant cases, their considerable computational cost is rarely justified. We therefore recommend the electrostatic TrEsp method across the entire range of molecular separations and orientations because its cost is minimal and it generally agrees with quantum-chemical calculations to better than the geometric uncertainty. We also caution against computationally optimizing a crystal structure before calculating couplings, as it can lead to large, uncontrollable errors. Understanding the unavoidable uncertainties can guard against striving for unrealistic precision; at the same time, detailed benchmarks can allow important qualitative questions--which do not depend on the precise values of the simulation parameters--to be addressed with greater confidence about the conclusions