Unifying thermodynamic and kinetic descriptions of single-molecule processes: RNA unfolding under tension

We use mesoscopic non-equilibrium thermodynamics theory to describe RNA unfolding under tension. The theory introduces reaction coordinates, characterizing a continuum of states for each bond in the molecule. The unfolding considered is so slow that one can assume local equilibrium in the space of the reaction coordinates. In the quasi-stationary limit of high sequential barriers, our theory yields the master equation of a recently proposed sequential-step model. Non-linear switching kinetics is found between open and closed states. Our theory unifies the thermodynamic and kinetic descriptions and offers a systematic procedure to characterize the dynamics of the unfolding processComment: 13 pages, 3 figure

Introducing the Portuguese sustainability assessment tool for urban areas: SBTool PT – Urban Planning

ISBN 978-99957-0-935-8Given the accelerated urbanization process throughout the twentieth century, many of todayâ s cities reflect a fast and disordered growth, which influences directly the demand for natural resources. For an indispensable change in the current urban infrastructure management models, it is necessary to quantify the sustainability level of actual practices and proposals. In this context, based on widespread methods, SBTool_PT Urban Planning represents an adaptation of the SBTool international method to the Portuguese context. This tool assesses the sustainability level of the practices promoted in urban projects with no size restrictions and is applicable to new urban development and/or urban renovation. The process is conducted by a rigorous analysis of requisites specifically developed to stimulate improvements on energy consumption, management of potable water, solid waste, urban soil and territory and air quality. Aiming at a full introduction of the tool, this article contextualizes its development and characterizes its assessment methodology. Additional application to a case study shows how the assessment of a proposed project is performed. It is intended to demonstrate in which way sustainability assessment methodologies allow the promotion of innovation and urban sustainability through the environmental preservation and the improvement of the quality of life in urban areas

The Organisational Climate of Sustainability: A Survey

This study describes three dimensions of the climate of sustainability and the development of a survey for assessing these dimensions. The authors report the results of two studies conducted to measure the climate of sustainability dimensions of sensitivity to sustainability (six items), motivation for sustainability (six items), and responsibility for sustainability (five items). Results support that the climate of sustainability is a reliable instrument and demonstrate the convergent and discriminant validity of each survey dimension. Furthermore, results show the criterion-related validity of the climate of sustainability with respect to innovation strategy and employee attitudes including satisfaction and turnover intentions. Implications and suggestions for the use of this survey in future research are discussed

Why is the change of the Johari-Goldstein β-relaxation time by densification in ultrastable glass minor?

Ultrastable glasses (USG) formed by vapor deposition are considerably denser. The onset temperature of devitrification, Ton, is significantly higher than Ton or Tg of ordinary glass (OG) formed by cooling, which implies an increase of the structural α-relaxation time by many orders of magnitude in USG compared to that in OG at the same temperature. However, for a special type of secondary relaxation having properties strongly connected to those of the α-relaxation, called the Johari-Goldstein β-relaxation, its relaxation time in USG is about an order of magnitude slower than that in OG and it has nearly the same activation energy, Eβ. The much smaller change in τβ and practically no change in Eβ by densification in USG are in stark contrast to the behavior of the α-relaxation. This cannot be explained by asserting that the Johari-Goldstein (JG) β-relaxation is insensitive to densification in USG, since the JG β-relaxation strength is significantly reduced in USG to such a level that it would require several thousands of years of aging for an OG to reach the same state, and therefore the JG β-relaxation does respond to densification in USG like the α-relaxation. Here, we provide an explanation based on two general properties established from the studies of glasses and liquids at elevated pressures and applied to USG. The increase in density of the glasses formed under high pressure can be even larger than that in USG. One property is the approximate invariance of the ratio τα(Ton)/τβ(Ton) to density change at constant τα(Ton), and the other is the same ργ/T-dependence of τβ in USG and OG where ρ is the density and γ is a material constant. These two properties are derived using the Coupling Model, giving a theoretical explanation of the phenomena. The explanation is also relevant for a full understanding of the experimental result that approximately the same surface diffusion coefficient is found in USG and OG with and without physical aging, and ultrathin films of a molecular glass-former

Why is surface diffusion the same in ultrastable, ordinary, aged, and ultrathin molecular glasses?

Recently Fakhraai and coworkers measured surface diffusion in ultrastable glass produced by vapor deposition, ordinary glass with and without physical aging, and ultrathin films of the same molecular glassformer, N,N0-bis(3-methylphenyl)-N,N0-diphenylbenzidine (TPD). Diffusion on the surfaces of all these glasses is greatly enhanced compared with the bulk diffusion similar to that previously found by others, but remarkably the surface diffusion coefficients DS measured are practically the same. The observed independence of DS from changes of structural a-relaxation due to densification or finite-size effect has an impact on the current understanding of the physical origin of enhanced surface diffusion. We have demonstrated before and also here that the primitive relaxation time t0 of the coupling model, or its analogue tb, the Johari–Goldstein b-relaxation, can explain quantitatively the enhancement found in ordinary glasses. In this paper, we assemble together considerable experimental evidence to show that the changes in tb and t0 of ultrastable glasses, aged ordinary glasses, and ultrathin-films are all insignificant when compared with ordinary glasses. Thus, in the context of the explanation of the enhanced surface diffusion given by the coupling model, these collective experimental facts on tb and t0 further explain approximately the same DS in the different glasses of TPD as found by Fakhraai and coworkers

Probing protein sequences as sources for encrypted antimicrobial peptides

Starting from the premise that a wealth of potentially biologically active peptides may lurk within proteins, we describe here a methodology to identify putative antimicrobial peptides encrypted in protein sequences. Candidate peptides were identified using a new screening procedure based on physicochemical criteria to reveal matching peptides within protein databases. Fifteen such peptides, along with a range of natural antimicrobial peptides, were examined using DSC and CD to characterize their interaction with phospholipid membranes. Principal component analysis of DSC data shows that the investigated peptides group according to their effects on the main phase transition of phospholipid vesicles, and that these effects correlate both to antimicrobial activity and to the changes in peptide secondary structure. Consequently, we have been able to identify novel antimicrobial peptides from larger proteins not hitherto associated with such activity, mimicking endogenous and/or exogenous microorganism enzymatic processing of parent proteins to smaller bioactive molecules. A biotechnological application for this methodology is explored. Soybean (Glycine max) plants, transformed to include a putative antimicrobial protein fragment encoded in its own genome were tested for tolerance against Phakopsora pachyrhizi, the causative agent of the Asian soybean rust. This procedure may represent an inventive alternative to the transgenic technology, since the genetic material to be used belongs to the host organism and not to exogenous sources

Use of Chemical Modification To Elucidate RNA Folding Pathways

As discussed in this overview, chemical modification is sensitive to the accessibility of a nucleotide to the solvent, and many nucleotides become less accessible as an RNA folds into its structured form. Chemical modification reagents are therefore suitable for following RNA folding, and can be used to study the kinetics of structure formation on time scales ranging from minutes to hours.Peer Reviewedhttps://deepblue.lib.umich.edu/bitstream/2027.42/143596/1/cpnc1109.pd

Analysis of portuguese residential buildings’ needs and proposed solutions

The Portuguese housing sector experienced a significant growth throughout the 20th century, particularly in the last quarter, after the democratic revolution in 1974. In fact, the number of buildings built between 1970 and 1990 is more than one third of the buildings actually existing in Portugal. Therefore most of them were built before the publication of the first regulation concerning the energy efficiency in buildings. Regarding this scenario, it would be expected that rehabilitation activities would represent most of the current construction activities. However, given some remaining barriers from old social policies, this situation is not observed; actually building retrofitting is the least significant sector, accentuating the degradation level of major part of the Portuguese housing stock. Several studies show that the main problems are found in the buildings envelope elements, such as roofs and façades. Based on this context, the aim of this paper is to introduce some examples of building retrofitting systems that, adapted to the Portuguese main needs and requirements may represent sustainable solutions to overcome the identified needs of Portuguese buildings' envelope

Distribution of dwell times of a ribosome: effects of infidelity, kinetic proofreading and ribosome crowding

Ribosome is a molecular machine that polymerizes a protein where the sequence of the amino acid residues, the monomers of the protein, is dictated by the sequence of codons (triplets of nucleotides) on a messenger RNA (mRNA) that serves as the template. The ribosome is a molecular motor that utilizes the template mRNA strand also as the track. Thus, in each step the ribosome moves forward by one codon and, simultaneously, elongates the protein by one amino acid. We present a theoretical model that captures most of the main steps in the mechano-chemical cycle of a ribosome. The stochastic movement of the ribosome consists of an alternating sequence of pause and translocation; the sum of the durations of a pause and the following translocation is the time of dwell of the ribosome at the corresponding codon. We derive the analytical expression for the distribution of the dwell times of a ribosome in our model. Whereever experimental data are available, our theoretical predictions are consistent with those results. We suggest appropriate experiments to test the new predictions of our model, particularly, the effects of the quality control mechanism of the ribosome and that of their crowding on the mRNA track.Comment: This is an author-created, un-copyedited version of an article accepted for publication in Physical Biology. IOP Publishing Ltd is not responsible for any errors or omissions in this version of the manuscript or any version derived from it. The definitive publisher authenticated version is available online at DOI:10.1088/1478-3975/8/2/02600

Summary Data from the Sixth AIAA Computational Fluid Dynamics Drag Prediction Workshop: Code Verification

Results from the Sixth AIAA CFD Drag Prediction Workshop (DPW-VI), Case 1 Code Verification are presented. This test case is for the turbulent flow over a 2D NACA 0012 airfoil using Reynolds-Averaged Navier-Stokes (RANS) turbulence models. A numerical benchmark solution is available for the standard Spalart-Allmaras (SA) turbulence model that can be used for code verification purposes, i.e., to verify that the numerical algorithms employed are consistent and that there are no programming mistakes in the software. For the Case 1 code verification study, there were 31 data submissions from 16 teams: 23 with the SA model (using various versions), 4 with the k-omega SST model (two variants), and one each with k-kl, k-epsilon, an explicit algebraic Reynolds stress model, and the lattice Boltzmann method (LBM) with very large eddy simulation (VLES). Various grid types were employed including structured, unstructured, Cartesian, and adapted grids. The benchmark numerical solution was deemed to be the correct solution for the 21 submissions with the standard SA model, the SA-noft2 variant (without the ft2 term), and the SA-neg variant (designed to avoid nonphysical transient states in discrete settings). While many of these 21 submissions did demonstrate first-order convergence on the finer meshes, others showed either nonconvergent solutions in terms of the aerodynamic forces and moments or converged to the wrong answer. Results for this case highlight the continuing need for rigorous code verification to be conducted as a prerequisite for design, model validation, and analysis studies