The fitness landscape—the mapping between genotypes and fitness—determines properties of the process of adaptation. Several small genotypic fitness landscapes have recently been built by selecting a ...handful of beneficial mutations and measuring fitness of all combinations of these mutations. Here, we generate several testable predictions for the properties of these small genotypic landscapes under Fisher's geometric model of adaptation. When the ancestral strain is far from the fitness optimum, we analytically compute the fitness effect of selected mutations and their epistatic interactions. Epistasis may be negative or positive on average depending on the distance of the ancestral genotype to the optimum and whether mutations were independently selected, or coselected in an adaptive walk. Simulations show that genotypic landscapes built from Fisher's model are very close to an additive landscape when the ancestral strain is far from the optimum. However, when it is close to the optimum, a large diversity of landscape with substantial roughness and sign epistasis emerged. Strikingly, small genotypic landscapes built from several replicate adaptive walks on the same underlying landscape were highly variable, suggesting that several realizations of small genotypic landscapes are needed to gain information about the underlying architecture of the fitness landscape.
The coal mine production industry is a complex sociotechnical system with interactive relationships among several risk factors. Currently, causation analysis of gas explosion accidents is mainly ...focused on the aspects of human error and equipment fault, while neglecting the interactive relationships among risk factors. A new method is proposed through risk coupling. First, the meaning of risk coupling of a gas explosion is defined, and types of risk coupling are classified. Next, the coupled relationship and coupled effects among risk factors are explored through combining the interpretative structural modeling (ISM) and the NK model. Twenty‐eight representative risk factors and 16 coupled types of risk factors are obtained through analysis of 332 gas explosion accidents in coal mines in China. Through the application of the combined ISM–NK model, an eight‐level hierarchical model of risk coupling of a gas explosion accident is established, and the coupled degrees of different types of risk coupling are assessed. The hierarchical model reveals that two of the 28 risk factors, such as state policies, laws, and regulations, are the root risk factors for gas explosions; nine of the 28 risk factors, such as flame from blasting, electric spark, and local gas accumulation, are direct causes of gas explosions; whereas 17 of the risk factors, such as three‐violation actions, ventilation system, and safety management, are indirect ones. A quantitative analysis of the NK model shows that the probability of gas explosion increases with the increasing number of risk factors. Compared with subjective risk factors, objective risk factors have a higher probability of causing gas explosion because of risk coupling.
Trade-offs in antibody repertoires to complex antigens Childs, Lauren M.; Baskerville, Edward B.; Cobey, Sarah
Philosophical transactions of the Royal Society of London. Series B. Biological sciences,
09/2015, Letnik:
370, Številka:
1676
Journal Article
Recenzirano
Odprti dostop
Pathogens vary in their antigenic complexity. While some pathogens such as measles present a few relatively invariant targets to the immune system, others such as malaria display considerable ...antigenic diversity. How the immune response copes in the presence of multiple antigens, and whether a trade-off exists between the breadth and efficacy of antibody (Ab)-mediated immune responses, are unsolved problems. We present a theoretical model of affinity maturation of B-cell receptors (BCRs) during a primary infection and examine how variation in the number of accessible antigenic sites alters the Ab repertoire. Naive B cells with randomly generated receptor sequences initiate the germinal centre (GC) reaction. The binding affinity of a BCR to an antigen is quantified via a genotype–phenotype map, based on a random energy landscape, that combines local and distant interactions between residues. In the presence of numerous antigens or epitopes, B-cell clones with different specificities compete for stimulation during rounds of mutation within GCs. We find that the availability of many epitopes reduces the affinity and relative breadth of the Ab repertoire. Despite the stochasticity of somatic hypermutation, patterns of immunodominance are strongly shaped by chance selection of naive B cells with specificities for particular epitopes. Our model provides a mechanistic basis for the diversity of Ab repertoires and the evolutionary advantage of antigenically complex pathogens.
To explore the niche improvement path of photovoltaic agriculture in China, a niche influencing factor system was constructed first. Then, this study innovatively combined the DEMATEL and analytic ...network process (DANP) method and the NK model, which can correct the defects of the traditional NK model. Based on the above method, the influence coefficients and index weight of each niche factor were calculated, and the niche fitness landscape of photovoltaic agriculture was constructed. Finally, according to the fitness landscape map of each combination state, the optimal configuration state of niche influencing factors of photovoltaic agriculture and the optimal niche improvement path of photovoltaic agriculture were explored. We found that the interaction between the six niche influencing factors determines the niche fitness of photovoltaic agriculture, and the changes in the niche fitness and the niche improvement of photovoltaic agriculture are coordinated. It was proposed that the optimal niche improvement path of photovoltaic agriculture in China is "technological innovation → policy formulation → resource allocation → economic improvement → social recognition → environmental protection", and the research conclusions were further explained and discussed.
We discuss fitness landscapes and how they can be modified to account for co-evolution. We are interested in using the landscape as a way to model rational decision making in a toy economic system. ...We develop a model very similar to the Tangled Nature Model of Christensen et al. that we call the Tangled Decision Model. This is a natural setting for our discussion of co-evolutionary fitness landscapes. We use a Monte Carlo step to simulate decision making and investigate two different decision making procedures.
•Construction of multi-species model, single species landscape and system landscape.•Monte-Carlo Step as model of decision making.•Rational decisions do not lead to equilibrium.•Mixture of local and global decisions produce better optimised systems.
Purpose
This paper aims to introduce a joint DEMATEL and NK methodology to develop a process model for introducing and implementing relational supply chain practices for low-carbon supply chains. ...Using this process model as a guide, insights into specific practices and how to implement these relational practices to achieve competitive advantage across organizations are introduced.
Design/methodology/approach
Low-carbon cooperation practices framework based on the relational view is developed. A methodology based on DEMATEL and the NK model is used to construct a sequential process model for introducing and implementing these relational practices. Empirical data from three manufacturing organizations in China are utilized to validate the model.
Findings
Initial results provide a sequence of relational practices for guiding those organizations and their suppliers for healthy and low-carbon development. Interdependencies between relational practices are analyzed and evaluated from four aspects. Insights into the broader application of the methodology and initial results from both a research and managerial perspective are presented, especially with consideration of the China, an emerging economy, context.
Research limitations/implications
The methodology remains relatively abstract in nature, yet the tool can provide very useful interpretations and information for both researchers and practitioners.
Practical implications
This paper stipulates that in addition to internal operational practices, the relational practices between buyer and supplier may be equally important to achieve a low-carbon outcome, especially in supply chain setting. This paper also shows that not only the relational practice itself but also the implementation sequence of the relational practices can relate to performance. According to the authors’ initial results, organizations in this study should first develop product development cooperation, then exchange carbon knowledge and implement effective governance and last build a trust relationship with its suppliers for low-carbon cooperation.
Originality/value
This is one of the few approaches that directly evaluates and identifies the interdependencies among relational practices and to construct a process model for introducing and implementing low-carbon supply chain cooperation. It is also the first time that the NK model has been integrated with DEMATEL. Focusing on Chinese supply chain carbon emissions concerns is also a unique perspective.
Research on the interactions among activities in firms and the extent to which these interactions help create and sustain competitive advantage has rapidly expanded in recent years. In this research, ...the two most common approaches have been the complementarity framework, as developed by Milgrom and Roberts (1990), and the NK-model (Kauffman, 1993) for simulation studies. This paper provides an introduction to these approaches, summarizes key results, and points to an aspect of interactions that has not found much attention because neither of the two approaches is well-suited to address it: contextual interactions, i.e., interactions that are influenced by other activity choices made by a firm. We provide a number of examples of contextual interactions drawn from in-depth studies of individual firms and outline suggestions for future research.
Spin glasses and complexity Stein, Daniel L; Stein, Daniel L; Newman, Charles M
2013., 20130115, 2013, Letnik:
4
eBook
Spin glasses are disordered magnetic systems that have led to the development of mathematical tools with an array of real-world applications, from airline scheduling to neural networks.Spin Glasses ...and Complexityoffers the most concise, engaging, and accessible introduction to the subject, fully explaining what spin glasses are, why they are important, and how they are opening up new ways of thinking about complexity.
This one-of-a-kind guide to spin glasses begins by explaining the fundamentals of order and symmetry in condensed matter physics and how spin glasses fit into--and modify--this framework. It then explores how spin-glass concepts and ideas have found applications in areas as diverse as computational complexity, biological and artificial neural networks, protein folding, immune response maturation, combinatorial optimization, and social network modeling.
Providing an essential overview of the history, science, and growing significance of this exciting field, Spin Glasses and Complexityalso features a forward-looking discussion of what spin glasses may teach us in the future about complex systems. This is a must-have book for students and practitioners in the natural and social sciences, with new material even for the experts.
While much is understood about the general pattern of industry dynamics, a critical element underlying these dynamics, the rate of the expansion of individual firms, has been largely overlooked. We ...argue that the rate at which firms can reliably increase their scale of operations is a critical factor in understanding the structure of industries. Further, success at scaling-up the firm's operations provides a dynamic-isolating mechanism that insulates established firms from new competition. We show that the bases of profitability in the industry (monopoly-like profits stemming from the restriction of output, efficiency rents based on firm-specific productivity differences, or transitory Schumpeterian profits) can be traced to the scale adjustment process. We explore these issues in a computational model of industry dynamics.
The similarity between product architecture and organization design has become known as the “mirroring hypothesis”. We present a theoretical model of new product development using the NK-model, in ...which we represent organization design with varying degrees of mirroring. The main result holds that perfectly mirroring organizations only perform well in designing products with many components and low complexity, while imperfectly mirroring organizations do better in designing product with few components and high complexity. Our theoretical model can inform future empirical research, which hitherto lacked a common representation framework for organization design.
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