Four-states phase diagram of proteins

A four states phase diagram for protein folding as a function of temperature and solvent quality is derived from an improved 2-d lattice model taking into account the temperature dependence of the hydrophobic effect. The phase diagram exhibits native, globule and two coil-type regions. In agreement with experiment, the model reproduces the phase transitions indicative of both warm and cold denaturations. Finally, it predicts transitions between the two coil states and a critical point.Comment: 7 pages, 5 figures. Accepted for publication in Europhysics Letter

Hamiltonian model for multidimensional epistasis

We propose and solve a Hamiltonian model for multidimensional epistastatic interactions between beneficial mutations. The model is able to give rise either to a phase transition between two equilibrium states, without any coexistence, or exhibits a state where hybrid species can coexist, with gradual passage from one wild type to another. The transition takes place as a function of the "tolerance" of the environment, which we define as the amount of noise in the system.Comment: 3 pages, 2 figures (in seperate files) spelling corrected and a reference adde

Segmentation of DNA sequences into twostate regions and melting fork regions

The accurate prediction and characterization of DNA melting domains by computational tools could facilitate a broad range of biological applications. However, no algorithm for melting domain prediction has been available until now. The main challenges include the difficulty of mathematically mapping a qualitative description of DNA melting domains to quantitative statistical mechanics models, as well as the absence of 'gold standards' and a need for generality. In this paper, we introduce a new approach to identify the twostate regions and melting fork regions along a given DNA sequence. Compared with an ad hoc segmentation used in one of our previous studies, the new algorithm is based on boundary probability profiles, rather than standard melting maps. We demonstrate that a more detailed characterization of the DNA melting domain map can be obtained using our new method, and this approach is independent of the choice of DNA melting model. We expect this work to drive our understanding of DNA melting domains one step further.Comment: 17 pages, 8 figures; new introduction, added refs, minor change

INDCOR white paper on the Design of Complexity IDNs

This white paper was written by the members of the Work Group focusing on design practices of the COST Action 18230 - Interactive Narrative Design for Complexity Representation (INDCOR, WG1). It presents an overview of Interactive Digital Narratives (IDNs) design for complexity representations through IDN workflows and methodologies, IDN authoring tools and applications. It provides definitions of the central elements of the IDN alongside its best practices, designs and methods. Finally, it describes complexity as a feature of IDN, with related examples. In summary, this white paper serves as an orienting map for the field of IDN design, understanding where we are in the contemporary panorama while charting the grounds of their promising futures

Gene Regulation in the Pi Calculus: Simulating Cooperativity at the Lambda Switch

Part of the Lecture Notes in Computer Science book series (LNCS, volume 4230).Also part of the Lecture Notes in Bioinformatics book sub series (volume 4230).International audienceWe propose to model the dynamics of gene regulatory networks as concurrent processes in the stochastic pi calculus. As a first case study, we show how to express the control of transcription initiation at the lambda switch, a prototypical example where cooperative enhancement is crucial. This requires concurrent programming techniques that are new to systems biology, and necessitates stochastic parameters that we derive from the literature. We test all components of our model by exhaustive stochastic simulations. A comparison with previous results reported in the literature, experimental and simulation based, confirms the appropriateness of our modeling approach

Determination of the size distribution of non-spherical nanoparticles by electric birefringence-based methods

The in situ determination of the size distribution of dispersed non-spherical nanoparticles is an essential characterization tool for the investigation and use of colloidal suspensions. In this work, we test a size characterization method based on the measurement of the transient behaviour of the birefringence induced in the dispersions by pulsed electric fields. The specific shape of such relaxations depends on the distribution of the rotational diffusion coefficient of the suspended particles. We analyse the measured transient birefringence with three approaches: the stretched-exponential, Watson-Jennings, and multiexponential methods. These are applied to six different types of rod-like and planar particles: PTFE rods, goethite needles, single- and double-walled carbon nanotubes, sodium montmorillonite particles and gibbsite platelets. The results are compared to electron microscopy and dynamic light scattering measurements. The methods here considered provide good or excellent results in all cases, proving that the analysis of the transient birefringence is a powerful tool to obtain complete size distributions of non-spherical particles in suspension.Financial support of this investigation by Junta de Andalucía, Spain (grant No. PE2012-FQM0694) and University of Granada (Program “Proyectos de investigación precompetitivos”) is gratefully acknowledged

The impact of life events on later life: A latent class analysis of the English longitudinal study of ageing

Objectives: Inequalities in life events can lead to inequalities in older age. This research aimed to explore associations between life events reported by older people and quality of life (QoL) and functional ability. Study Design: A latent class analysis (LCA) of the English Longitudinal Study of Ageing wave 3. Methods: Participants were grouped according to eight life events: parental closeness, educational opportunities in childhood, financial hardship, loss of an unborn child, bereavement due to war, involvement in conflict, violence, and experiencing a natural disaster. Linear and logistic regression were used to explore associations between these groups and the main outcomes of functional ability and QoL. Results: 7,555 participants were allocated to four LCA groups: “Few life events” (n=6,250), “Emotionally cold mother” (n=724), “Violence in combat” (n=274) and “Many life events” (n=307). Reduced QoL was reported in the “many life events” (coefficient -5.33, 95%CI -6.61 to -4.05), “emotionally cold mother” (-1.89, -2.62 to 1.15) and “violence in combat” (-1.95, -3.08 to -0.82) groups, compared to the “few life events” group. The “many life events” group also reported more difficulty with activities of daily living. Conclusions: Policies aimed at reducing inequalities in older age should consider events across the life course

Trajectories of Early Adolescent Loneliness: Implications for Physical Health and Sleep

The current study examines the relationship between prolonged loneliness, physical health, and sleep among young adolescents (10–13 years; N = 1214; 53% girls). Loneliness was measured at 10, 12 and 13 years of age along with parent-reported health and sleep outcomes. Using growth mixture modelling, 6 distinct trajectories were identified: ‘low increasing to high loneliness’ (n = 23, 2%), ‘high reducing loneliness’ (n = 28, 3%), ‘medium stable loneliness’ (n = 60, 5%), ‘medium reducing loneliness’ (n = 185, 15%), ‘low increasing to medium loneliness’ (n = 165, 14%), and ‘low stable loneliness’ (n = 743, 61%). Further analyses found non-significant differences between the loneliness trajectories and parent-report health and sleep outcomes including visits to health professionals, perceived general health, and sleep quality. The current study offers an important contribution to the literature on loneliness and health. Results show that the relationship may not be evident in early adolescence when parent reports of children’s health are used. The current study highlights the importance of informant choice when reporting health. The implications of the findings for future empirical work are discussed

Religious Diversity and Conceptual Schemes: Critically Appraising Internalist Pluralism

Is a philosophical theory needed to ‘underwrite’ attitudes of toleration and respect in a multicultural and religiously diverse world? Many philosophers of religion have thought so, including Victoria Harrison. This article interrogates Harrison’s theory of internalist pluralism, which, though offering a welcome alternative to other theories, such as John Hick’s ‘pluralistic hypothesis’, nevertheless faces problems. Questioning the coherence of the theory’s account of how the existence of objects of worship can avoid being fully conceptual-scheme dependent, and raising doubts about its pretensions to promote interreligious harmony, I also critically discuss the common philosophical tendency to work with under-described and insufficiently analysed examples. What philosophy ought to be able to offer in relation to religious diversity, I propose, is attentiveness to nuances and particularities, thereby aiding religious understanding without the need for a general theory