Children, violence, and social exclusion: Negotiation of everyday insecurity in a Colombian barrio

Discourses on in/security are often concerned with structures and meta-narratives of the state and other institutions; however, such attention misses the complexities of the everyday consequences of insecurity. In Colombia’s protracted conflict, children are disproportionately affected yet rarely consulted, rendering it difficult to account for their experiences in meaningful ways. This article draws on fieldwork conducted with conflict-affected children in an informal barrio community on the periphery of Colombia’s capital, Bogotá, to explore how children articulate experiences of insecurity. It examines how stereotypes of violence and delinquency reinforce insecurity; how multiple violences impact young people’s lives; and how children themselves conceive of responses to these negative experiences. These discussions are underpinned by a feminist commitment of attention to the margins and engage with those for whom insecurity is a daily phenomenon. The effects of deeply embedded insecurity, violence, and fear for young people in Colombia require a more nuanced theoretical engagement with notions of insecurity, as well as the complexities of connections and dissonances within everyday life.

Generalized binomial Tau-leap method for biochemical kinetics incorporating both delay and intrinsic noise

The delay stochastic simulation algorithm (DSSA) by Barrio et al. [Plos Comput. Biol.2, 117–E (2006)] was developed to simulate delayed processes in cell biology in the presence of intrinsic noise, that is, when there are small-to-moderate numbers of certain key molecules present in a chemical reaction system. These delayed processes can faithfully represent complex interactions and mechanisms that imply a number of spatiotemporal processes often not explicitly modeled such as transcription and translation, basic in the modeling of cell signaling pathways. However, for systems with widely varying reaction rate constants or large numbers of molecules, the simulation time steps of both the stochastic simulation algorithm (SSA) and the DSSA can become very small causing considerable computational overheads. In order to overcome the limit of small step sizes, various τ-leap strategies have been suggested for improving computational performance of the SSA. In this paper, we present a binomial τ- DSSA method that extends the τ-leap idea to the delay setting and avoids drawing insufficient numbers of reactions, a common shortcoming of existing binomial τ-leap methods that becomes evident when dealing with complex chemical interactions. The resulting inaccuracies are most evident in the delayed case, even when considering reaction products as potential reactants within the same time step in which they are produced. Moreover, we extend the framework to account for multicellular systems with different degrees of intercellular communication. We apply these ideas to two important genetic regulatory models, namely, the hes1 gene, implicated as a molecular clock, and a Her1/Her 7 model for coupled oscillating cells.

Oscillatory regulation of Hes1: Discrete stochastic delay modelling and simulation

Discrete stochastic simulations are a powerful tool for understanding the dynamics of chemical kinetics when there are small-to-moderate numbers of certain molecular species. In this paper we introduce delays into the stochastic simulation algorithm, thus mimicking delays associated with transcription and translation. We then show that this process may well explain more faithfully than continuous deterministic models the observed sustained oscillations in expression levels of hes1 mRNA and Hes1 protein.

Computational approaches for modelling intrinsic noise and delays in genetic regulatory networks

This chapter focuses on the interactions and roles between delays and intrinsic noise effects within cellular pathways and regulatory networks. We address these aspects by focusing on genetic regulatory networks that share a common network motif, namely the negative feedback loop, leading to oscillatory gene expression and protein levels. In this context, we discuss computational simulation algorithms for addressing the interplay of delays and noise within the signaling pathways based on biological data. We address implementational issues associated with efficiency and robustness. In a molecular biology setting we present two case studies of temporal models for the Hes1 gene (Monk, 2003; Hirata et al., 2002), known to act as a molecular clock, and the Her1/Her7 regulatory system controlling the periodic somite segmentation in vertebrate embryos (Giudicelli and Lewis, 2004; Horikawa et al., 2006).

‘It’s about finding a way’ : children, sites of opportunity, and building everyday peace in Colombia

The multiple forms of violence associated with protracted conflict disproportionately affect young people. Literature on conflict-affected children often focuses on the need to provide stability and security through institutions such as schools but rarely considers how young people themselves see these sites as part of their everyday lives. The enduring, pervasive, and complex nature of Colombia’s conflict means many young Colombians face the challenges of poverty, persistent social exclusion, and violence. Such conditions are exacerbated in ‘informal’ barrio communities such as los Altos de Cazucá, just south of the capital Bogotá. Drawing on field research in this community, particularly through interviews conducted with young people aged 10 to 17 this article explores how young people themselves understand the roles of the local school and ngo in their personal conceptualisations of the violence in their everyday lives. The evidence indicates that children use spaces available to them opportunistically and that these actions can and should be read as contributing to local, everyday forms of peacebuilding. The ways in which institutional spaces are understood and used by young people as ‘sites of opportunity’ challenges the assumed illegitimacy of young people’s voices and experiences in these environments.

An embodied everyday peace in the midst of violence

Orthodox notions of peace built on liberal institutionalism have been critiqued for their lack of attention to the local and the people who populate these structures. The concept of an ‘everyday peace’ seeks to take into account the agency and activity of those frequently marginalised or excluded and use these experiences as the basis for a more responsive way of understanding peace. Further, reconceptualising and complicating a notion of ‘everyday peace’ as embodied recognises marginalised people as competent commentators and observers of their world, and capable of engaging with the practices, routines and radical events that shape their everyday resistances and peacebuilding. Peace, in this imagining, is not abstract, but built through everyday practices amidst violence. Young people, in particular, are often marginalised or rendered passive in discussions of the violences that affect them. In recognising this limited engagement, this paper responds through drawing on fieldwork conducted with conflict-affected young people in a peri-urban barrio community near Colombia’s capital Bogota to forward a notion of an embodied everyday peace. This involves exploring the presence and voices of young people as stakeholders in a negotiation of what it means to build peace within daily experience in the context of local and broader violence and marginalisation. By centring young people’s understandings of and contributions within the everyday, this paper responds to the inadequacies of liberal peacebuilding narratives, and forwards a more complex rendering of everyday peace as embodied.

Stochastic linear multistep methods for the simulation of chemical kinetics

In this paper, we introduce the Stochastic Adams-Bashforth (SAB) and Stochastic Adams-Moulton (SAM) methods as an extension of the tau-leaping framework to past information. Using the theta-trapezoidal tau-leap method of weak order two as a starting procedure, we show that the k-step SAB method with k >= 3 is order three in the mean and correlation, while a predictor-corrector implementation of the SAM method is weak order three in the mean but only order one in the correlation. These convergence results have been derived analytically for linear problems and successfully tested numerically for both linear and non-linear systems. A series of additional examples have been implemented in order to demonstrate the efficacy of this approach.

Efficient simulation of stochastic chemical kinetics with the Stochastic Bulirsch-Stoer extrapolation method

Background Biochemical systems with relatively low numbers of components must be simulated stochastically in order to capture their inherent noise. Although there has recently been considerable work on discrete stochastic solvers, there is still a need for numerical methods that are both fast and accurate. The Bulirsch-Stoer method is an established method for solving ordinary differential equations that possesses both of these qualities. Results In this paper, we present the Stochastic Bulirsch-Stoer method, a new numerical method for simulating discrete chemical reaction systems, inspired by its deterministic counterpart. It is able to achieve an excellent efficiency due to the fact that it is based on an approach with high deterministic order, allowing for larger stepsizes and leading to fast simulations. We compare it to the Euler τ-leap, as well as two more recent τ-leap methods, on a number of example problems, and find that as well as being very accurate, our method is the most robust, in terms of efficiency, of all the methods considered in this paper. The problems it is most suited for are those with increased populations that would be too slow to simulate using Gillespie’s stochastic simulation algorithm. For such problems, it is likely to achieve higher weak order in the moments. Conclusions The Stochastic Bulirsch-Stoer method is a novel stochastic solver that can be used for fast and accurate simulations. Crucially, compared to other similar methods, it better retains its high accuracy when the timesteps are increased. Thus the Stochastic Bulirsch-Stoer method is both computationally efficient and robust. These are key properties for any stochastic numerical method, as they must typically run many thousands of simulations.