Discrete Breathers in a Realistic Coarse-Grained Model of Proteins

We report the results of molecular dynamics simulations of an off-lattice protein model featuring a physical force-field and amino-acid sequence. We show that localized modes of nonlinear origin (discrete breathers) emerge naturally as continuations of a subset of high-frequency normal modes residing at specific sites dictated by the native fold. In the case of the small $\beta$-barrel structure that we consider, localization occurs on the turns connecting the strands. At high energies, discrete breathers stabilize the structure by concentrating energy on few sites, while their collapse marks the onset of large-amplitude fluctuations of the protein. Furthermore, we show how breathers develop as energy-accumulating centres following perturbations even at distant locations, thus mediating efficient and irreversible energy transfers. Remarkably, due to the presence of angular potentials, the breather induces a local static distortion of the native fold. Altogether, the combination of this two nonlinear effects may provide a ready means for remotely controlling local conformational changes in proteins.Comment: Submitted to Physical Biolog

how much more and how much better?

Funding Information: We thank two autonomous reviewers and the team of Climate Policy editors for their excellent comments and suggestions. We are thankful for the financial support of the German Federal Ministry of Economic Cooperation and Development (BMZ) for this research. The research was done independently, BMZ had no role in the preparation, analysis or writing of this article or its outcomes. Publisher Copyright: © 2022 The Author(s). Published by Informa UK Limited, trading as Taylor & Francis Group.Formal deliberations for the new collective quantified goal on climate finance began at COP26 in Glasgow. This Perspectives article aims to inform this process by discussing the potential size and nature of is post-2025 target. We argue that the climate finance system around the current target to mobilise US$100 billion per year to support developing countries has been fraught with difficulties, and that it would be ineffective to simply increase the climate finance target without addressing these difficulties. Therefore, we identify and discuss five priority elements for negotiations: the relation to Article 2.1(c) of the Paris Agreement; the adaptation-mitigation balance; financial instruments; mobilising private finance; and ‘new and additional’ finance. To increase transparency, accountability, and trust in climate finance under the UNFCCC and to simultaneously allow for the mobilisation of finance at scale, we suggest setting a sub-target for grants. In combination with additional (sub)target(s), this could define an overall new collective quantified goal that is better suited to serve the challenging dual role of mobilising finance at scale and transferring resources to developing countries. Key policy insights: Ambiguous definitions of climate finance and the US$100 billion target allow for multiple interpretations, reducing transparency and trust between countries. Climate finance targets can be interpreted in a dual and sometimes contrasting way: mobilising investment at scale and transferring resources from developed to developing countries. Recognising this duality may help to find common ground for a post-2025 climate finance target. Increasing the climate finance target may prove ineffective without further clarity on private finance mobilisation, the relation to Art. 2.1(c), and other priority elements. More detailed assessments of needs, priorities, costs, and support are needed to inform the post-2025 target and assess climate finance provision effectiveness. A sub-target for grants could increase accountability, trust, and transparency, and target the needs of the most vulnerable developing countries. Negotiations on the post-2025 climate finance target could also consider additional aspects such as access to and prioritisation of finance, and loss and damage.publishersversionpublishe

Climate change adaptation among female-led micro, small, and medium enterprises in semiarid areas: a case study from Kenya

This chapter contributes to the literature on private sector adaptation by empirically exploring how female-led micro, small, and medium enterprise (MSMEs) in Kenya’s semiarid lands (SALs) experience and respond to climate risk. The chapter argues that strong sociocultural orientations around gender roles and resource use and access not only confine female-led MSMEs to sectors that experience higher exposure to climate risk – most notably agriculture – but also trigger more pronounced barriers to building resilience within their businesses, including reduced access to land, capital, markets, new technology, and educational opportunities. Faced by these barriers, female entrepreneurs may pursue unsustainable forms of coping, as part of which business activity is scaled back through reduced profits, loss of business, and the sale of valuable business assets. Such strategies may help enterprises to cope in the short term but may undermine longer-term MSME adaptive capacity. Social networks, such as women’s groups and table banking initiatives, appear to be crucial adaptation tools. Additionally, a strong dependency exists between household resilience and business resilience, implying that building resilience at the household level could support adaptive capacity among female-led MSMEs. Supporting the adaptive capacity of women in business should be a policy priority

Perceived stressors of climate vulnerability across scales in the Savannah zone of Ghana: a participatory approach

Smallholder farmers in sub-Saharan Africa are confronted with climatic and non-climatic stressors. Research attention has focused on climatic stressors, such as rainfall variability, with few empirical studies exploring non-climatic stressors and how these interact with climatic stressors at multiple scales to affect food security and livelihoods. This focus on climatic factors restricts understanding of the combinations of stressors that exacerbate the vulnerability of farming households and hampers the development of holistic climate change adaptation policies. This study addresses this particular research gap by adopting a multi-scale approach to understand how climatic and non-climatic stressors vary, and interact, across three spatial scales (household, community and district levels) to influence livelihood vulnerability of smallholder farming households in the Savannah zone of northern Ghana. This study across three case study villages utilises a series of participatory tools including semi-structured interviews, key informant interviews and focus group discussions. The incidence, importance, severity and overall risk indices for stressors are calculated at the household, community, and district levels. Results show that climatic and non-climatic stressors were perceived differently; yet, there were a number of common stressors including lack of money, high cost of farm inputs, erratic rainfall, cattle destruction of crops, limited access to markets and lack of agricultural equipment that crossed all scales. Results indicate that the gender of respondents influenced the perception and severity assessment of stressors on rural livelihoods at the community level. Findings suggest a mismatch between local and district level priorities that have implications for policy and development of agricultural and related livelihoods in rural communities. Ghana’s climate change adaptation policies need to take a more holistic approach that integrates both climatic and non-climatic factors to ensure policy coherence between national climate adaptation plans and District development plans

Noise and Robustness in Phyllotaxis

A striking feature of vascular plants is the regular arrangement of lateral organs on the stem, known as phyllotaxis. The most common phyllotactic patterns can be described using spirals, numbers from the Fibonacci sequence and the golden angle. This rich mathematical structure, along with the experimental reproduction of phyllotactic spirals in physical systems, has led to a view of phyllotaxis focusing on regularity. However all organisms are affected by natural stochastic variability, raising questions about the effect of this variability on phyllotaxis and the achievement of such regular patterns. Here we address these questions theoretically using a dynamical system of interacting sources of inhibitory field. Previous work has shown that phyllotaxis can emerge deterministically from the self-organization of such sources and that inhibition is primarily mediated by the depletion of the plant hormone auxin through polarized transport. We incorporated stochasticity in the model and found three main classes of defects in spiral phyllotaxis – the reversal of the handedness of spirals, the concomitant initiation of organs and the occurrence of distichous angles – and we investigated whether a secondary inhibitory field filters out defects. Our results are consistent with available experimental data and yield a prediction of the main source of stochasticity during organogenesis. Our model can be related to cellular parameters and thus provides a framework for the analysis of phyllotactic mutants at both cellular and tissular levels. We propose that secondary fields associated with organogenesis, such as other biochemical signals or mechanical forces, are important for the robustness of phyllotaxis. More generally, our work sheds light on how a target pattern can be achieved within a noisy background

The Geometric and Dynamic Essence of Phyllotaxis

We present a dynamic geometric model of phyllotaxis based on two postulates, primordia formation and meristem expansion. We find that Fibonacci, Lucas, bijugate and multijugate are all variations of the same unifying phenomenon and that the difference lies in the changes in position of initial primordia. We explore the set of all initial positions and color-code its points depending on the phyllotactic pattern that arises

Implementing REDD+ at the national level: Stakeholder engagement and policy coherences between REDD+ rules and Kenya’s sectoral policies

Effective implementation of rules on reduced emission from avoided deforestation and forest degradation (REDD+) depends on the compatibility between these rules and existing sectoral policies associated with forests. This paper applies content analysis of policy documents, semi-structured interviews and case study analysis to examine the interplay between REDD+ rules and Kenyan sectorial policies and local socioeconomic settings. Results reveal that the preparation of national REDD+ strategies in Kenya is usefully coordinated by the Kenyan forestry sector drawing on the sector’s policy mandate and past experiences in forest management. This sectoral mainstreaming however degenerates into negative vertical policy interplay caused by poor consultations with key sectors outside the forestry sector e.g. lands and agriculture and further exacerbated by sectoral competition for climate finance. Analysis of REDD+ coherences with sectoral policies revealed that forest polices on reforestation and decentralisation are coherent with REDD+ rules (horizontal interplay) but this coherence is impeded by limited implementation of these measures e.g. poor support and coordination of Community Forest Associations. Lack of coherence was mainly observed between REDD+ rules and resettlement and agricultural mechanisation policies prescribed in the lands and agriculture policies. Agricultural mechanisation and resettlement policies are synonymous with deforestation especially through illegal and politically motivated agricultural or settlement expansions into Kenya’s forest areas. At the local level, REDD+ showed potential to positively influence local livelihoods but the aforementioned national institutional gaps and strict carbon standards and prices lead to negative trade-offs between carbon sequestration and alternative livelihoods. The paper advocates for strong multi-stakeholder consultative mechanism so that both Kenyan policy and socioeconomic settings can support effective REDD+ implementation