Coarse-grained modelling of supercoiled RNA

We study the behaviour of double-stranded RNA under twist and tension using oxRNA, a recently developed coarse-grained model of RNA. Introducing explicit salt-dependence into the model allows us to directly compare our results to data from recent single-molecule experiments. The model reproduces extension curves as a function of twist and stretching force, including the buckling transition and the behaviour of plectoneme structures. For negative supercoiling, we predict denaturation bubble formation in plectoneme end-loops, suggesting preferential plectoneme localisation in weak base sequences. OxRNA exhibits a positive twist-stretch coupling constant, in agreement with recent experimental observations.Comment: 8 pages + 5 pages Supplementary Materia

FIRE-PROTECTION WITH ALKALI-ACTIVATED CEMENT BINDER

Fire resistance of unprotected steel structures is very low and steel elements must be protected from fire. One possibility is to create a protective layer of a cement-based material. Most types of cement have a low resistance to high temperatures, reducing mechanical properties. In flammability tests, cement activated with alkaline compounds showed better properties compared to conventional types of cement. This paper represents the determination of the properties of two H-Cement mortars with experlite or fireclay sand. Experiments carried out in a small kiln simulating a 1D load showed differences between elements in terms of heat transfer to the tested elements. The calculation model created to predict the course of the experiments has been validated and the unknown properties of the material have been calculated based on the data collected. The samples were tested in a small fire furnace. Finally, the thermal conductivity pattern was determined depending on the temperature

Two-step nucleation in a binary mixture of patchy particles

Nucleation in systems with a metastable liquid–gas critical point is the prototypical example of a two-step nucleation process in which the appearance of the critical nucleus is preceded by the formation of a liquid-like density fluctuation. So far, the majority of studies on colloidal and protein crystallization have focused on one-component systems, and we are lacking a clear description of two-step nucleation processes in multicomponent systems, where critical fluctuations involve coupled density and concentration inhomogeneities. Here, we examine the nucleation process of a binary mixture of patchy particles designed to nucleate into a diamond lattice. By combining Gibbs-ensemble simulations and direct nucleation simulations over a wide range of thermodynamic conditions, we are able to pin down the role of the liquid–gas metastable phase diagram on the nucleation process. In particular, we show that the strongest enhancement of crystallization occurs at an azeotropic point with the same stoichiometric composition of the crystal

Sequence-dependent thermodynamics of a coarse-grained DNA model

We introduce a sequence-dependent parametrization for a coarse-grained DNA model [T. E. Ouldridge, A. A. Louis, and J. P. K. Doye, J. Chem. Phys. 134, 085101 (2011)] originally designed to reproduce the properties of DNA molecules with average sequences. The new parametrization introduces sequence-dependent stacking and base-pairing interaction strengths chosen to reproduce the melting temperatures of short duplexes. By developing a histogram reweighting technique, we are able to fit our parameters to the melting temperatures of thousands of sequences. To demonstrate the flexibility of the model, we study the effects of sequence on: (a) the heterogeneous stacking transition of single strands, (b) the tendency of a duplex to fray at its melting point, (c) the effects of stacking strength in the loop on the melting temperature of hairpins, (d) the force-extension properties of single strands and (e) the structure of a kissing-loop complex. Where possible we compare our results with experimental data and find a good agreement. A simulation code called oxDNA, implementing our model, is available as free software.Comment: 15 page

Symmetries of the finite Heisenberg group for composite systems

Symmetries of the finite Heisenberg group represent an important tool for the study of deeper structure of finite-dimensional quantum mechanics. As is well known, these symmetries are properly expressed in terms of certain normalizer. This paper extends previous investigations to composite quantum systems consisting of two subsystems - qudits - with arbitrary dimensions n and m. In this paper we present detailed descriptions - in the group of inner automorphisms of GL(nm,C) - of the normalizer of the Abelian subgroup generated by tensor products of generalized Pauli matrices of orders n and m. The symmetry group is then given by the quotient group of the normalizer.Comment: Submitted to J. Phys. A: Math. Theo

Rufous Common Cuckoo chicks are not always female

This is the author accepted manuscript. The final version is available from Springer Verlag via the DOI in this recordThe Common Cuckoo (hereafter Cuckoo) shows two adult plumage morphs—adult male plumage is grey and adult females are either grey or, less frequently, rufous. The situation is less clear in juveniles, as both sexes exhibit variable proportions of grey and rufous colour. We thus describe the patterns related to sex-specific plumage colour variation in a central European Cuckoo population. We genetically determined the sex of 91 Cuckoo chicks and using visual classification of photographs we scored juvenile plumage colouration of individual chicks into five classes based upon the increasing proportion of rufous colour on feathers. To verify these scores, we sampled chick feathers and quantified the proportion of rufous colour of individual feathers by digital image analysis. We found that juvenile females had a higher proportion of rufous colour of feathers than juvenile males. However, the difference was marginally non-significant based on visual inspection alone, and some male chicks even showed intensively rufous plumage like those of juvenile females. In contrast, we captured only grey adult males (n = 37), while five out of 20 adult females were rufous. The rufous colour of Cuckoo feathers considerably differed from the grey colour and the difference seemed to be larger in adults than in juveniles. We show that chicks, unlike adult females, cannot be visually assigned to either of the adult morphs. Therefore, we encourage further investigation of Cuckoo plumage colouration across the species’ range to examine the process of plumage maturation. A detailed genetic analysis is necessary to understand the origin of Cuckoo feather colouration.This study was supported by the Czech Science Foundation (project 17-12262S) and by the Institutional Research Plan (RVO: 68081766)

Group theoretical construction of mutually unbiased bases in Hilbert spaces of prime dimensions

Mutually unbiased bases in Hilbert spaces of finite dimensions are closely related to the quantal notion of complementarity. An alternative proof of existence of a maximal collection of N+1 mutually unbiased bases in Hilbert spaces of prime dimension N is given by exploiting the finite Heisenberg group (also called the Pauli group) and the action of SL(2,Z_N) on finite phase space Z_N x Z_N implemented by unitary operators in the Hilbert space. Crucial for the proof is that, for prime N, Z_N is also a finite field.Comment: 13 pages; accepted in J. Phys. A: Math. Theo

Coarse-grained modelling of DNA-RNA hybrids

We introduce oxNA, a new model for the simulation of DNA-RNA hybrids which is based on two previously developed coarse-grained models\unicode{x2014}oxDNA and oxRNA. The model naturally reproduces the physical properties of hybrid duplexes including their structure, persistence length and force-extension characteristics. By parameterising the DNA-RNA hydrogen bonding interaction we fit the model's thermodynamic properties to experimental data using both average-sequence and sequence-dependent parameters. To demonstrate the model's applicability we provide three examples of its use\unicode{x2014}calculating the free energy profiles of hybrid strand displacement reactions, studying the resolution of a short R-loop and simulating RNA-scaffolded wireframe origami.Comment: 15 pages, 10 figure

Feynman's path integral and mutually unbiased bases

Our previous work on quantum mechanics in Hilbert spaces of finite dimensions N is applied to elucidate the deep meaning of Feynman's path integral pointed out by G. Svetlichny. He speculated that the secret of the Feynman path integral may lie in the property of mutual unbiasedness of temporally proximal bases. We confirm the corresponding property of the short-time propagator by using a specially devised N x N -approximation of quantum mechanics in L^2(R) applied to our finite-dimensional analogue of a free quantum particle.Comment: 12 pages, submitted to Journal of Physics A: Math. Theor., minor correction

Symmetries of finite Heisenberg groups for k-partite systems

Symmetries of finite Heisenberg groups represent an important tool for the study of deeper structure of finite-dimensional quantum mechanics. This short contribution presents extension of previous investigations to composite quantum systems comprised of k subsystems which are described with position and momentum variables in Z_{n_i}, i=1,...,k. Their Hilbert spaces are given by k-fold tensor products of Hilbert spaces of dimensions n_1,...,n_k. Symmetry group of the corresponding finite Heisenberg group is given by the quotient group of a certain normalizer. We provide the description of the symmetry groups for arbitrary multipartite cases. The new class of symmetry groups represents very specific generalization of finite symplectic groups over modular rings.Comment: 6 pages, to appear in Proceedings of QTS7 "Quantum Theory and Symmetries 7", Prague, August 7-13, 201