Dynamics of supercoiled DNA with complex knots: Large-scale rearrangements and persistent multi-strand interlocking

Knots and supercoiling are both introduced in bacterial plasmids by catalytic processes involving DNA strand passages. While the effects on plasmid organization has been extensively studied for knotting and supercoiling taken separately, much less is known about their concurrent action. Here, we use molecular dynamics simulations and oxDNA, an accurate mesoscopic DNA model, to study the kinetic and metric changes introduced by complex (five-crossing) knots and supercoiling in 2 kbp-long DNA rings. We find several unexpected results. First, the conformational ensemble is dominated by two distinct states, differing in branchedness and knot size. Secondly, fluctuations between these states are as fast as the metric relaxation of unknotted rings. In spite of this, certain boundaries of knotted and plectonemically-wound regions can persist over much longer timescales. These pinned regions involve multiple strands that are interlocked by the cooperative action of topological and supercoiling constraints. Their long-lived character may be relevant for the simplifying action of topoisomerases

Directional translocation resistance of Zika xrRNA

xrRNAs from flaviviruses survive in host cells because of their exceptional dichotomic response to the unfolding action of different enzymes. They can be unwound, and hence copied, by replicases, and yet can resist degradation by exonucleases. How the same stretch of xrRNA can encode such diverse responses is an open question. Here, by using atomistic models and translocation simulations, we uncover an elaborate and directional mechanism for how stress propagates when the two xrRNA ends, 5 \u2032 and 3 \u2032, are driven through a pore. Pulling the 3 \u2032 end, as done by replicases, elicits a progressive unfolding; pulling the 5 \u2032 end, as done by exonucleases, triggers a counterintuitive molecular tightening. Thus, in what appears to be a remarkable instance of intra-molecular tensegrity, the very pulling of the 5 \u2032 end is what boosts resistance to translocation and consequently to degradation. The uncovered mechanistic principle might be co-opted to design molecular meta-materials

Dynamic scaling approach to study time series fluctuations

We propose a new approach for properly analyzing stochastic time series by mapping the dynamics of time series fluctuations onto a suitable nonequilibrium surface-growth problem. In this framework, the fluctuation sampling time interval plays the role of time variable, whereas the physical time is treated as the analog of spatial variable. In this way we found that the fluctuations of many real-world time series satisfy the analog of the Family-Viscek dynamic scaling ansatz. This finding permits to use the powerful tools of kinetic roughening theory to classify, model, and forecast the fluctuations of real-world time series.Comment: 25 pages, 7 figures, 1 tabl

Structural Modeling of Straw Bale Loadbearing Wall

In Ecuador, there are qualitative and quantitative housing deficits that must be covered with materials that produce seismic-resistant, energy-efficient buildings that do not require a large amount of energy to be produced. Several studies indicate that the answer lies in straw bale structures. However, for these to be considered by designers, aids are needed to facilitate their structural modeling in specialized computer programs. Through literature reviews, the present research proposes a model that adapts the specific structural considerations of straw bale buildings to the tools available in a design program. Keywords: structure, bales, straw, model, program, design. Resumen En el Ecuador existe un déficit cualitativo y cuantitativo de viviendas que debe ser cubierto con materiales que produzcan edificaciones sismo resistentes, energéticamente eficientes y a la vez que no requieran gran cantidad de energía para ser producidos. Varios estudios señalan que la respuesta está en las estructuras elaboradas con fardos de paja. Sin embargo, para que éstas sean consideradas por los diseñadores son necesarias ayudas para facilitar su modelamiento estructural en programas informáticos especializados. La presente investigación, a través de revisiones bibliográficas, propone un modelo que adapta las consideraciones estructurales específicas de las construcciones con fardos de paja a las herramientas disponibles en un programa de diseño. Palabras Clave: estructura, fardos, paja, modelo, programa, diseñ

In silico ischaemia-induced reentry at the Purkinjeventricle interface

This computational modelling work illustrates the influence of hyperkalaemia and electrical uncoupling induced by defined ischaemia on action potential (AP) propagation and the incidence of reentry at the Purkinjeventricle interface in mammalian hearts. Unidimensional and bidimensional models of the Purkinjeventricle subsystem, including ischaemic conditions (defined as phase 1B) in the ventricle and an ischaemic border zone, were developed by altering several important electrophysiological parameters of the LuoRudy AP model of the ventricular myocyte. Purkinje electrical activity was modelled using the equations of DiFrancesco and Noble. Our study suggests that an extracellular potassium concentration [K](o) 14 mM and a slight decrease in intercellular coupling induced by ischaemia in ventricle can cause conduction block from Purkinje to ventricle. Under these conditions, propagation from ventricle to Purkinje is possible. Thus, unidirectional block (UDB) and reentry can result. When conditions of UDB are met, retrograde propagation with a long delay (320 ms) may re-excite Purkinje cells, and give rise to a reentrant pathway. This induced reentry may be the origin of arrhythmias observed in phase 1B ischaemia. In a defined setting of ischaemia (phase 1B), a small amount of uncoupling between ventricular cells, as well as between Purkinje and ventricular tissue, may induce UDBs and reentry. Hyperkalaemia is also confirmed to be an important factor in the genesis of reentrant rhythms, since it regulates the range of coupling in which UDBs may be induced.This work was supported: (i) by the European Commission preDiCT grant (DG-INFSO-224381), (ii) by the 'VI Plan Nacional de Investigacion Cientifica, Desarrollo e Innovacion Tecnologica' from the Ministerio de Economia y Competitividad of Spain (grant number TIN2012-37546-C03-01) and the European Commission (European Regional Development Funds - ERDF - FEDER), and (iii) by the Programa de Apoyo a la Investigacioon y Desarrollo (PAID-06-11-2002) de la Universidad Politecnica de Valencia, Programa Prometeo (PROMETEO/2012/030) de la Conselleria d'Educacio Formacio I Ocupacio, Generalitat Valenciana, and (iv) Direccion General de Politica Cientifica de la Generalitat Valenciana (GV/2013/119).Esteban Ramírez, J.; Saiz Rodríguez, FJ.; Romero Pérez, L.; Ferrero De Loma-Osorio, JM.; Trénor Gomis, BA. (2014). In silico ischaemia-induced reentry at the Purkinjeventricle interface. EP-Europace. 16(3):444-451. https://doi.org/10.1093/europace/eut386S44445116

Empirical Study Between Compiled, Interpreted, and Dynamic Programming Languages Applying Stable Ordering Algorithms (Case Study: Java, Python, Jython, Jpype and Py4J)

This article allows to investigate benchmark between programming languages, with the objective of identifying the performance between the execution time and the memory use between the Java and Python languages, as well as, in three implementations of dynamic languages that combine the two aforementioned languages: Jython, Jpype, Py4J. According to the results, it is concluded that the language that obtains the best performance is Py4J.   Keywords: programming languages, benchmark, algorithms, compiler

Activity and efficiency trends for the residential sector across countries

The residential sector is a major contributor to climate change, accounting for almost a quarter of global energy consumption and a fifth of CO2 emissions in 2019. Since 2000, residential consumption has grown at a sustained rate of 1%/year, driven by the development of emerging economies, despite stagnation in developed countries. The increasing demand for living space, energy services and comfort levels seems difficult to curb, especially in the developing world on its fair attempt to reduce inequality. To understand these trends, this paper analyses the trajectories of key indicators of activity and efficiency in this sector, for emerging and developed regions, as well as for major consuming nations, mainly China, United States, European Union, Russia, India, Japan and Brazil. Despite data limitations, meaningful cross-country comparisons are presented for fuel mixes, energy services and dwelling types. Heating, ventilation and air conditioning (HVAC) systems account for a third of residential consumption and will grow rapidly as increasing wealth in emerging economies allows for satisfying the thermal comfort demand. Economic development will naturally increase housing size and equipment level and reduce household size, and could close the per capita consumption gap between developing and developed regions. Efficiency improvements could reduce the energy use intensity to around 10 koe/m(2) but will not be enough to curb residential consumption. International cooperation, policy support and funding are essential to accelerate development and efficiency gains in developing countries without compromising environmental targets. In the meantime, politicians should focus on decarbonising the energy mix and promoting energy efficiency, while citizens focus on energy conservation to avoid irreversible environmental damage. (c) 2022 The Authors. Published by Elsevier B.V. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/by-nc-nd/4.0/)

Open Data Portal Prototype for the Conservation of Biodiversity of the ‘Universidad Nacional de Loja’

This article describes the possibilities of research and development that exist in the ‘Universidad Nacional de Loja’ (UNL) in the field of biodiversity through the use and exploitation of information and communication technology (ICT) resources. First, the existing methodologies, processes, and initiatives for the publication of open data was explored. Subsequently, a brief description of the biodiversity conservation centers maintained by the UNL was made, highlighting the IT initiatives that have been carried out. Finally, the results of the proposal include the methodology for the release of open data and the creation of the prototype of the biodiversity open data portal of the UNL.     Keywords: programming, open data, biodiversity, botany, artificial intelligenc