scholarly journals The structure of autocatalytic networks, with application to early biochemistry

2020 ◽  
Author(s):  
Mike Steel ◽  
Joana C. Xavier ◽  
Daniel H. Huson
Keyword(s):  
Mathematical Model ◽  
Living Systems ◽  
Bacterial Metabolism ◽  
The Core ◽  
System Building ◽  
Formal Framework ◽  
The Origin Of Life ◽  
Key Features ◽  
Autocatalytic Networks ◽  
New Algorithms

AbstractMetabolism across all known living systems combines two key features. First, all of the molecules that are required are either available in the environment or can be built up from available resources via other reactions within the system. Second, the reactions proceed in a fast and synchronised fashion via catalysts that are also produced within the system. Building on early work by Stuart Kauffman, a precise mathematical model for describing such self-sustaining autocatalytic systems (RAF theory) has been developed to explore the origins and organisation of living systems within a general formal framework. In this paper, we develop this theory further by establishing new relationships between classes of RAFs and related classes of networks, and developing new algorithms to investigate and visualise RAF structures in detail. We illustrate our results by showing how it reveals further details into the structure of archaeal and bacterial metabolism near the origin of life, and provide techniques to study and visualise the core aspects of primitive biochemistry.

scholarly journals The structure of autocatalytic networks, with application to early biochemistry

2020 ◽  
Vol 17 (171) ◽  
pp. 20200488
Author(s):  
Mike Steel ◽  
Joana C. Xavier ◽  
Daniel H. Huson
Keyword(s):  
Mathematical Model ◽  
Living Systems ◽  
Bacterial Metabolism ◽  
The Core ◽  
System Building ◽  
Formal Framework ◽  
The Origin Of Life ◽  
Key Features ◽  
Autocatalytic Networks ◽  
New Algorithms

Metabolism across all known living systems combines two key features. First, all of the molecules that are required are either available in the environment or can be built up from available resources via other reactions within the system. Second, the reactions proceed in a fast and synchronized fashion via catalysts that are also produced within the system. Building on early work by Stuart Kauffman, a precise mathematical model for describing such self-sustaining autocatalytic systems (RAF theory) has been developed to explore the origins and organization of living systems within a general formal framework. In this paper, we develop this theory further by establishing new relationships between classes of RAFs and related classes of networks, and developing new algorithms to investigate and visualize RAF structures in detail. We illustrate our results by showing how it reveals further details into the structure of archaeal and bacterial metabolism near the origin of life, and provide techniques to study and visualize the core aspects of primitive biochemistry.

scholarly journals Autocatalytic networks in biology: structural theory and algorithms

2019 ◽  
Vol 16 (151) ◽  
pp. 20180808 ◽  
Author(s):  
Mike Steel ◽  
Wim Hordijk ◽  
Joana C. Xavier
Keyword(s):  
Mathematical Analysis ◽  
General Setting ◽  
Structural Theory ◽  
Living Systems ◽  
General Notion ◽  
Graph Theoretic ◽  
Polynomial Time Algorithms ◽  
The Origin Of Life ◽  
Carry Over ◽  
Autocatalytic Networks

Self-sustaining autocatalytic networks play a central role in living systems, from metabolism at the origin of life, simple RNA networks and the modern cell, to ecology and cognition. A collectively autocatalytic network that can be sustained from an ambient food set is also referred to more formally as a ‘reflexively autocatalytic food-generated’ (RAF) set. In this paper, we first investigate a simplified setting for studying RAFs, which is nevertheless relevant to real biochemistry and which allows an exact mathematical analysis based on graph-theoretic concepts. This, in turn, allows for the development of efficient (polynomial-time) algorithms for questions that are computationally intractable (NP-hard) in the general RAF setting. We then show how this simplified setting for RAF systems leads naturally to a more general notion of RAFs that are ‘generative’ (they can be built up from simpler RAFs) and for which efficient algorithms carry over to this more general setting. Finally, we show how classical RAF theory can be extended to deal with ensembles of catalysts as well as the assignment of rates to reactions according to which catalysts (or combinations of catalysts) are available.

scholarly journals Single Cell Mathematical Model Successfully Replicates Key Features of GBM: Go-Or-Grow Is Not Necessary

PLoS ONE ◽  
2017 ◽  
Vol 12 (1) ◽  
pp. e0169434 ◽  
Author(s):  
Elizabeth Scribner ◽  
Hassan M. Fathallah-Shaykh
Keyword(s):  
Mathematical Model ◽  
Single Cell ◽  
Key Features

scholarly journals Mathematical modeling and harmonic analysis of SISFCL

2017 ◽  
Vol 36 (1) ◽  
pp. 258-270
Author(s):  
Debraj Sarkar ◽  
Debabrata Roy ◽  
Amalendu Bikash Choudhury ◽  
Sotoshi Yamada
Keyword(s):  
Mathematical Modeling ◽  
Mathematical Model ◽  
Harmonic Analysis ◽  
Voltage Drop ◽  
Element Model ◽  
Iron Core ◽  
Content Type ◽  
Hysteresis Characteristic ◽  
The Core ◽  
The Mathematical Model

Purpose A saturated iron core superconducting fault current limiter (SISFCL) has an important role to play in the present-day power system, providing effective protection against electrical faults and thus ensuring an uninterrupted supply of electricity to the consumers. Previous mathematical models developed to describe the SISFCL use a simple flux density-magnetic field intensity curve representing the ferromagnetic core. As the magnetic state of the core affects the efficient working of the device, this paper aims to present a novel approach in the mathematical modeling of the device with the inclusion of hysteresis. Design/methodology/approach The Jiles–Atherton’s hysteresis model is utilized to develop the mathematical model of the limiter. The model is numerically solved using MATLAB. To support the validity of model, finite element model (FEM) with similar specifications was simulated. Findings Response of the limiter based on the developed mathematical model is in close agreement with the FEM simulations. To illustrate the effect of the hysteresis, the responses are compared by using three different hysteresis characteristics. Harmonic analysis is performed and comparison is carried out utilizing fast Fourier transform and continuous wavelet transform. It is observed that the core with narrower hysteresis characteristic not only produces a better current suppression but also creates a higher voltage drop across the DC source. It also injects more harmonics in the system under fault condition. Originality/value Inclusion of hysteresis in the mathematical model presents a more realistic approach in the transient analysis of the device. The paper provides an essential insight into the effect of the core hysteresis characteristic on the device performance.

Allais on Transcendental Idealism

2011 ◽  
Vol 16 (3) ◽  
pp. 351-374 ◽  
Author(s):  
Andrew F. Roche
Keyword(s):  
Transcendental Idealism ◽  
Human Beings ◽  
Secondary Qualities ◽  
Relational Properties ◽  
The Core ◽  
Key Features

AbstractLucy Allais argues that we can better understand Kant's transcendental idealism by taking seriously the analogy of appearances to secondary qualities that Kant offers in the Prolegomena. A proper appreciation of this analogy, Allais claims, yields a reading of transcendental idealism according to which all properties that can appear to us in experience are mind-dependent relational properties that inhere in mind-independent objects. In section 1 of my paper, I articulate Allais's position and its benefits, not least of which is its elegant explanation of how the features of objects that appear to us are transcendentally ideal while still being ‘empirically’ real. In section 2, I contend that there are elements of Allais's account that are problematic, yet also inessential, to what I view to be the core contribution of her analysis. These elements are the views that the properties that appear to human beings are not really distinct from properties that things have ‘in themselves’ and that Kant embraced a relational account of perception. In section 3, I return to the core of Allais's reading and argue that, despite its multiple virtues, it cannot make sense of key features of Kant's idealism.

VuFind

2013 ◽  
pp. 73-99 ◽  
Author(s):  
Demian Katz ◽  
Andrew Nagy
Keyword(s):  
Open Source ◽  
Search Engine ◽  
Relational Database ◽  
Data Retrieval ◽  
Similarity Analysis ◽  
The Core ◽  
Front End ◽  
Informative Case ◽  
Key Features

Apache Solr, an open source Java-based search engine, forms the core of many Library 2.0 products. The use of an index in place of a relational database allows faster data retrieval along with key features like faceting and similarity analysis that are not practical in the previous generation of library software. The popular VuFind discovery tool was built to provide a library-friendly front-end for Solr’s powerful searching capabilities, and its development provides an informative case study on the use of Solr in a library setting. VuFind is just one of many library packages using Solr, and examples like Blacklight, Summon, and the eXtensible Catalog project show other possible approaches to its use.

Hostile hospitality and the criminalization of civil society actors aiding border crossers in Greece

2020 ◽  
pp. 026377582095870
Author(s):  
Laura Schack ◽  
Ashley Witcher
Keyword(s):  
Civil Society ◽  
Field Research ◽  
State Policies ◽  
Research Data ◽  
Search And Rescue ◽  
Constitutive Relationship ◽  
The Core ◽  
Police Harassment ◽  
Key Features ◽  
Border Crossers

Civil society actors aiding border crossers in Europe have been subject to systematic criminalization through prosecutions and attempted prosecutions, extensive police harassment, public scapegoating, and the imposition of bureaucratic barriers. We seek to explain why this is occurring through the analysis of field research data, collected in Greece between 2017 and 2019, through the lens of Derrida’s concept of “hostile hospitality”. We develop a theoretical framework with three key features: first, the demarcation between insider and outsider which lies at the core of notions of hospitality; second, the constitutive relationship between hostility and hospitality which is closely related to notions of sovereignty; and third, the primacy of state definitions of hospitality, which subordinate private and collective hospitality practices. This explanatory framework guides the analysis of two case studies from our fieldwork: the criminalization of solidarity initiatives providing accommodation in squats in Athens and Pikpa camp on Lesvos, and the criminalization of boat-spotting and search and rescue activities on Lesvos. We conclude that civil society actors aiding border crossers in Greece are criminalized because they challenge and interfere with state policies and practices of hostile hospitality.

Panspermia in the context of the timing of the origin of life and microbial phylogeny

2007 ◽  
Vol 6 (3) ◽  
pp. 249-254 ◽  
Author(s):  
M.A. Line
Keyword(s):  
Origin Of Life ◽  
Deep Level ◽  
Bacterial Metabolism ◽  
Phylogenetic Studies ◽  
Radiation Resistant ◽  
Physical Information ◽  
Insufficient Time ◽  
Microbial Genomic ◽  
The Origin Of Life ◽  
Life On Earth

AbstractThe synthesis of physical information on early Earth (or Mars) with recent knowledge arising from microbial genomic, proteomic and phylogenetic studies, strongly indicates that there was insufficient time (∼600 000 years) for life to arise and evolve to reach the biochemical complexity evident within the Last Common Community (LCC). If recent strong evidence of fossil cyanobacteria in carbonaceous meteorites is accepted, then the LCC would have existed prior to the origin of life on Earth and the planet would then have been seeded with representatives of the three domains once it became habitable. The existence of intermittently active cyanobacteria in comets opens the possibility for the evolution of microaerobic bacterial metabolism, elements of which appear at a deep level of the microbial phylogeny, at or below the depth of the LCC. It is also notable from a panspermia perspective that recent phylogenetic evidence indicates that the Gram-positive lineage (representatives of which are endowed with long-lived radiation-resistant spores) lies at the deepest level of domain Bacteria, with Archaea and Eukarya evolving from this lineage probably before 3.6 Gigayears ago (Gya).

General discussion after session V

1988 ◽  
Vol 325 (1587) ◽  
pp. 611-618 ◽  
Keyword(s):  
Origin Of Life ◽  
Time Perspective ◽  
Applied Mathematics ◽  
Building Blocks ◽  
Living Systems ◽  
Organic Chemical ◽  
General Terms ◽  
The Earth ◽  
The Origin Of Life ◽  
Emergence Of Life

N. C. Wickramasinghe ( Department of Applied Mathematics and Astronomy, University College, Cardiff, U. K. ). The question of the origin of life is, of course, one of the most important scientific questions and it is also one of the most difficult. One is inevitably faced here with a situation where there are very few empirical facts of direct relevance and perhaps no facts relating to the actual transition from organic material to material that can even remotely be described as living. The time perspective of events that relate to this problem has already been presented by Dr Chang. Uncertainty still persists as to the actual first moment of the origin or the emergence of life on the Earth. At some time between 3800 and 3300 Ma BP the first microscopic living systems seem to have emerged. There is a definite moment in time corresponding to a sudden appearance of cellular-type living systems. Now, traditionally the evolution of carbonaceous compounds which led to the emergence of life on Earth could be divided into three principal steps and I shall just remind you what those steps are. The first step is the production of chemical building blocks that lead to the origin of the organic molecules necessary as a prerequisite for the evolution of life. Step two can be described in general terms as prebiotic evolution, the arrangement of these chemical units into some kind of sequence of precursor systems that come almost up to life but not quite; and then stage three is the early biological evolution which actually effects the transition from proto-cellular organic-type forms into truly cellular living systems. The transition is from organic chemistry, prebiotic chemistry to biochemistry. Those are the three principal stages that have been defined by traditional workers in the field, the people who, as Dr Chang said, have had the courage to make these queries and attempt to answer them. Ever since the classic experiments where organic materials were synthesized in the laboratory a few decades back, it was thought that the first step, the production of organic chemical units, is important for the origin of life on the Earth, and that this had to take place in some location on the Earth itself.

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