Pathways to folding, nucleation events and native geometry

We perform extensive Monte Carlo simulations of a lattice model and the Go potential to investigate the existence of folding pathways at the level of contact cluster formation for two native structures with markedly different geometries. Our analysis of folding pathways revealed a common underlying folding mechanism, based on nucleation phenomena, for both protein models. However, folding to the more complex geometry (i.e. that with more non-local contacts) is driven by a folding nucleus whose geometric traits more closely resemble those of the native fold. For this geometry folding is clearly a more cooperative process.Comment: Accepted in J. Chem. Phy

Stochastic theory of non-equilibrium wetting

We study a Langevin equation describing non-equilibrium depinning and wetting transitions. Attention is focused on short-ranged attractive substrate-interface potentials. We confirm the existence of first order depinning transitions, in the temperature-chemical potential diagram, and a tricritical point beyond which the transition becomes a non-equilibrium complete wetting transition. The coexistence of pinned and depinned interfaces occurs over a finite area, in line with other non-equilibrium systems that exhibit first order transitions. In addition, we find two types of phase coexistence, one of which is characterized by spatio-temporal intermittency (STI). A finite size analysis of the depinning time is used to characterize the different coexisting regimes. Finally, a stationary distribution of characteristic triangles or facets was shown to be responsible for the structure of the STI phase.Comment: To appear in Europhys. Lett. // 3 figure

Newspaper covers as display windows in a pandemic season: analysis of three Portuguese daily newspapers

Neste artigo, que é uma síntese de um estudo realizado no MediaLab CIES-Iscte , parte-se da ideia de pandemia enquanto evento mediático e da mediatização como aspeto estruturante da narrativa jornalística, para propor três modelos de montras jornalísticas – de saldos, de produto e de diversidade em que se considera as características e critérios de noticiabilidade adotados por cada um dos veículos analisados. A análise englobou três dimensões: a distribuição do conteúdo no espaço físico e hierárquico do jornal (manchete, centro e periferia); as marcas, que podem ser palavras destacadas nos títulos e chamadas; e os recursos imagéticos utilizados. A pesquisa teve em conta 90 capas dos jornais Correio da Manhã, Jornal de Notícias e Público publicadas durante os primeiros 30 dias de cobertura da pandemia em Portugal, divididos em três ciclos: o primeiro, entre a divulgação dos primeiros casos identificados de COVID-19 em Portugal (3 de março de 2020) e a declaração do estado de alerta em Portugal (12 de março); o segundo, desde o encerramento das escolas (13 de março) à véspera da notícia do decreto presidencial que autoriza ao governo decretar estado de emergência (18 de março); o terceiro, da repercussão do decreto presidencial (19 de março) até à véspera da aprovação do decreto de emergência na Assembleia da República (1 de abril). O estudo conclui que as narrativas nas capas dos jornais são diferentes entre si e afetadas pelos modelos de montras, os quais refletem a dicotomia entre os interesses jornalísticos e os interesses comerciais, questionando se o público-modelo que norteia a construção das diferentes montras é apenas um, entre vários possíveis, “retrato-robô”, para fazer «vender» jornais, ou um claro identificador sociocultural dos públicos da imprensa escrita portuguesa?info:eu-repo/semantics/publishedVersio

Interfacial motion in flexo- and order-electric switching between nematic filled states

We consider a nematic liquid crystal, in coexistence with its isotropic phase, in contact with a substrate patterned with rectangular grooves. In such a system, the nematic phase may fill the grooves without the occurrence of complete wetting. There may exist multiple (meta)stable filled states, each characterised by the type of distortion (bend or splay) in each corner of the groove and by the shape of the nematic-isotropic interface, and additionally the plateaux that separate the grooves may be either dry or wet with a thin layer of nematic. Using numerical simulations, we analyse the dynamical response of the system to an externally- applied electric field, with the aim of identifying switching transitions between these filled states. We find that order-electric coupling between the fluid and the field provides a means of switching between states where the plateaux between grooves are dry and states where they are wet by a nematic layer, without affecting the configuration of the nematic within the groove. We find that flexoelectric coupling may change the nematic texture in the groove, provided that the flexoelectric coupling differentiates between the types of distortion at the corners of the substrate. We identify intermediate stages of the transitions, and the role played by the motion of the nematic-isotropic interface. We determine quantitatively the field magnitudes and orientations required to effect each type of transition.Comment: 14 pages, 12 fig

[68Ga]Ga-DOTANOC Uptake at Pancreatic Head/Uncinate Process: Is It a Persistent Diagnostic Pitfall Over Time?

Simple Summary The purpose of the present study is to describe the frequency of non-malignant [68Ga]Ga-DOTANOC uncinate process (UP) uptake and to evaluate its variations over time. Among the first 6 months of enrolment of a monocentric prospective observational electronic archive, analyses of a large number of PET/CT scans (n = 268) of NEN pts (n = 172) demonstrated that: UP uptake is a frequent finding (observed in almost half of the cases, slightly higher than previously reported), mostly presenting with a diffuse pattern and, interestingly, characterized by variations over time in almost one third of the cases. The consciousness of this diagnostic pitfall is of utmost importance for accurate [68Ga]Ga-DOTANOC PET/CT reporting, since the pancreas represents one of the most frequent sites of NEN. Purpose: [68Ga]Ga-DOTA-peptide uptake in the pancreatic head/uncinate process (UP) is a frequent PET/CT finding. Although mostly physiologic, it can represent a pitfall in PET/CT reading, especially when focal. An increased frequency of UP uptake has been reported in patients (pts) affected by diabetes mellitus (DM). The aim of the study is to describe the frequency of [68Ga]Ga-DOTANOC UP uptake to evaluate its variations over time and its possible correlation with DM. Methods: In September 2017, a monocentric prospective observational electronic archive was initiated at our center to collect clinical and imaging data of pts undergoing [68Ga]Ga-DOTANOC PET/CT. Among the pts enrolled in the first 6 months (Sept 2017 to Feb 2018), those presenting [68Ga]Ga-DOTANOC PET/CT uptake at UP level were included. Pts with UP lesions already documented on CT/MRI or those that underwent surgical excision of UP before PET/CT were excluded from the analysis. [68Ga]Ga-DOTANOC UP uptake was classified as diffuse or focal and compared with the pattern observed in previous PET/CT scans performed at our center. An increased frequency of UP uptake was also correlated with the presence of DM. Results: In the first 6 months, 253 pts were enrolled in the archive and 172 out of them were included in the analysis. UP increased uptake was frequently observed (77/172, 44.8%) and was mostly diffuse (62/77). In 75/172 pts (43.6%), previous [68Ga]Ga-DOTANOC PET/CT scans were available (overall 268 scans; number of previous PET per pt range: 1-20) and were retrospectively reviewed. Despite the fact that, in most pts, the uptake pattern was stable over time (54/75 pts, 72%), it changed in approximately one third of cases (21/75, 28%). Among DM pts (29/172), only 10/29 (34.4%) presented increased UP uptake. Conclusions: UP [68Ga]Ga-DOTANOC uptake is a frequent non-malignant finding (slightly higher than previously reported), mostly presenting with a diffuse pattern. However, contrary to previous reports, our data show that the pattern of uptake may vary over time in approximately one third of the cases and it is not more frequently observed in pts with DM

Nonequilibrium wetting transitions with short range forces

We analyze within mean-field theory as well as numerically a KPZ equation that describes nonequilibrium wetting. Both complete and critical wettitng transitions were found and characterized in detail. For one-dimensional substrates the critical wetting temperature is depressed by fluctuations. In addition, we have investigated a region in the space of parameters (temperature and chemical potential) where the wet and nonwet phases coexist. Finite-size scaling analysis of the interfacial detaching times indicates that the finite coexistence region survives in the thermodynamic limit. Within this region we have observed (stable or very long-lived) structures related to spatio-temporal intermittency in other systems. In the interfacial representation these structures exhibit perfect triangular (pyramidal) patterns in one (two dimensions), that are characterized by their slope and size distribution.Comment: 11 pages, 5 figures. To appear in Physical Review

Orientational transitions in a nematic confined by competing surfaces

The effect of confinement on the orientational structure of a nematic liquid crystal model has been investigated by using a version of density-functional theory (DFT). We have focused on the case of a nematic confined by opposing flat surfaces, in slab geometry (slit pore), which favor planar molecular alignment (parallel to the surface) and homeotropic alignment (perpendicular to the surface), respectively. The spatial dependence of the tilt angle of the director with respect to the surface normal has been studied, as well as the tensorial order parameter describing the molecular order around the director. For a pore of given width, we find that, for weak surface fields, the alignment of the nematic director is perpendicular to the surface in a region next to the surface favoring homeotropic alignment, and parallel along the rest of the pore, with a interface separating these regions (S phase). For strong surface fields, the director is distorted uniformly, the tilt angle exhibiting a linear dependence with the distance normal to the surface (L phase). Our calculations reveal the existence of a first-order transition between the two director configurations, which is driven by changes in the surface field strength, and also by changes in the pore width. In the latter case the transition occurs, for a given surface field, between the S phase for narrow pores and the L phase for wider pores. A link between the L-S transition and the anchoring transition observed for the semi-infinite case is proposed. We also provide calculations with a phenomenological approach that yields the same main result that DFT in the scale length where this is valid.Comment: submitted to PR

Equilibrium self-assembly of colloids with distinct interaction sites: Thermodynamics, percolation, and cluster distribution functions

We calculate the equilibrium thermodynamic properties, percolation threshold, and cluster distribution functions for a model of associating colloids, which consists of hard spherical particles having on their surfaces three short-ranged attractive sites (sticky spots) of two different types, A and B. The thermodynamic properties are calculated using Wertheim's perturbation theory of associating fluids. This also allows us to find the onset of self-assembly, which can be quantified by the maxima of the specific heat at constant volume. The percolation threshold is derived, under the no-loop assumption, for the correlated bond model: In all cases it is two percolated phases that become identical at a critical point, when one exists. Finally, the cluster size distributions are calculated by mapping the model onto an effective model, characterized by a-state-dependent-functionality (f) over bar and unique bonding probability (p) over bar. The mapping is based on the asymptotic limit of the cluster distributions functions of the generic model and the effective parameters are defined through the requirement that the equilibrium cluster distributions of the true and effective models have the same number-averaged and weight-averaged sizes at all densities and temperatures. We also study the model numerically in the case where BB interactions are missing. In this limit, AB bonds either provide branching between A-chains (Y-junctions) if epsilon(AB)/epsilon(AA) is small, or drive the formation of a hyperbranched polymer if epsilon(AB)/epsilon(AA) is large. We find that the theoretical predictions describe quite accurately the numerical data, especially in the region where Y-junctions are present. There is fairly good agreement between theoretical and numerical results both for the thermodynamic (number of bonds and phase coexistence) and the connectivity properties of the model (cluster size distributions and percolation locus)

Geometrically-controlled twist transitions in nematic cells

We study geometrically-controlled twist transitions of a nematic confined between a sinusoidal grating and a flat substrate. In these cells the transition to the twisted state is driven by surface effects. We have identified the mechanisms responsible for the transition analytically and used exact numerical calculations to study the range of surface parameters where the twist instability occurs. Close to these values the cell operates under minimal external fields or temperature variations