Chemical Organization Theory Applied to Virus Dynamics (Theorie chemischer Organisationen angewendet auf Infektionsmodelle)

2006 ◽  
Vol 48 (3) ◽  
Author(s):  
Naoki Matsumaru ◽  
Florian Centler ◽  
Pietro Speroni di Fenizio ◽  
Peter Dittrich
Keyword(s):  
Immune Response ◽  
Molecular Species ◽  
Organization Theory ◽  
Reaction Network ◽  
Reaction Networks ◽  
Virus Dynamics ◽  
Abstract Level ◽  
Level I ◽  
New Perspective

SummaryChemical organization theory has been proposed to provide a new perspective to study complex dynamical reaction networks. It decomposes a reaction network into overlapping sub-networks called organizations. An organization is an algebraically closed and self-maintaining set of molecular species. The set of organizations form a hierarchical “organizational structure”, which is here a lattice. In order to evaluate the usefulness of this approach we apply the theory to five models of immune response to HIV infection. We found four different lattices of organizations, which can be used as a first classification of the models. Furthermore, each organization found can be assigned to a functional state of the system. And finally, the lattice of organizations can be used to explain a treatment strategy on a more abstract level, i. e., as a movement from one organization into another.

scholarly journals Molecular Diversity and Network Complexity in Growing Protocells

Life ◽  
2019 ◽  
Vol 9 (2) ◽  
pp. 53
Author(s):  
Atsushi Kamimura ◽  
Kunihiko Kaneko
Keyword(s):  
Molecular Species ◽  
Catalytic Reaction ◽  
Molecular Diversity ◽  
Reaction Network ◽  
Cellular Growth ◽  
Reaction Networks ◽  
Cell Reproduction ◽  
A Cell ◽  
Molecular Components ◽  
Cellular Components

A great variety of molecular components is encapsulated in cells. Each of these components is replicated for cell reproduction. To address the essential role of the huge diversity of cellular components, we studied a model of protocells that convert resources into catalysts with the aid of a catalytic reaction network. As the resources were limited, the diversity in the intracellular components was found to be increased to allow the use of diverse resources for cellular growth. A scaling relation was demonstrated between resource abundances and molecular diversity. In the present study, we examined how the molecular species diversify and how complex catalytic reaction networks develop through an evolutionary course. At some generations, molecular species first appear as parasites that do not contribute to the replication of other molecules. Later, the species turn into host species that contribute to the replication of other species, with further diversification of molecular species. Thus, a complex joint network evolves with this successive increase in species. The present study sheds new light on the origin of molecular diversity and complex reaction networks at the primitive stage of a cell.

scholarly journals Goals as Emergent Autopoietic Processes

2021 ◽  
Vol 9 ◽  
Author(s):  
Tomas Veloz
Keyword(s):  
Organizational Structure ◽  
Recent Work ◽  
Organization Theory ◽  
Reaction Network ◽  
Self Organization ◽  
Reaction Networks ◽  
Modeling Framework ◽  
Emergence Of Life

While the phenomena of reaching a goal is generally represented in the framework of optimization, the phenomena of becoming of a goal is more similar to a “self-organization and emergent” rather than an “optimization and preexisting” process. In this article we provide a modeling framework for the former alternative by representing goals as emergent autopoietic structures. In order to conceptually situate our approach, we first review some of the most remarkable attempts to formally define emergence, and identify that in most cases such definitions rely on a preexisting system to be observed prior and post emergence, being thus inadequate for a formalization of emergent goals corresponding to the becoming of a systems as such (e.g. emergence of life). Next, we review how an implementation of the reaction networks framework, known as Chemical Organization Theory (COT), can be applied to formalize autopoietic structures, providing a basis to operationalize goals as an emergent process. We next revisit the definitions of emergence under the light of our approach, and demonstrate that recent taxonomies developed to classify different forms of emergence can be naturally deduced from recent work aimed to explain the kinds of changes of the organizational structure of a reaction network.

scholarly journals Uncertainty quantification for quantum chemical models of complex reaction networks

2016 ◽  
Vol 195 ◽  
pp. 497-520 ◽  
Author(s):  
Jonny Proppe ◽  
Tamara Husch ◽  
Gregor N. Simm ◽  
Markus Reiher
Keyword(s):  
Free Energy ◽  
Electronic Structure ◽  
State Space ◽  
Time Scales ◽  
Reaction Network ◽  
Reaction Networks ◽  
Multiple Time Scales ◽  
Complex Reaction ◽  
Discrete State ◽  
Continuous State

For the quantitative understanding of complex chemical reaction mechanisms, it is, in general, necessary to accurately determine the corresponding free energy surface and to solve the resulting continuous-time reaction rate equations for a continuous state space. For a general (complex) reaction network, it is computationally hard to fulfill these two requirements. However, it is possible to approximately address these challenges in a physically consistent way. On the one hand, it may be sufficient to consider approximate free energies if a reliable uncertainty measure can be provided. On the other hand, a highly resolved time evolution may not be necessary to still determine quantitative fluxes in a reaction network if one is interested in specific time scales. In this paper, we present discrete-time kinetic simulations in discrete state space taking free energy uncertainties into account. The method builds upon thermo-chemical data obtained from electronic structure calculations in a condensed-phase model. Our kinetic approach supports the analysis of general reaction networks spanning multiple time scales, which is here demonstrated for the example of the formose reaction. An important application of our approach is the detection of regions in a reaction network which require further investigation, given the uncertainties introduced by both approximate electronic structure methods and kinetic models. Such cases can then be studied in greater detail with more sophisticated first-principles calculations and kinetic simulations.

Von den Lesewelten zur Lebenswelt. Überlegungen zu der Frage, warum uns fiktionale Literatur berührt

2018 ◽  
Vol 12 (2) ◽  
pp. 260-278
Author(s):  
Christoph Demmerling
Keyword(s):  
Human Life ◽  
The Novel ◽  
Philosophical Perspective ◽  
Life World ◽  
Anna Karenina ◽  
The Future ◽  
New Perspective ◽  
The One

Abstract The following article argues that fictional texts can be distinguished from non-fictional texts in a prototypical way, even if the concept of the fictional cannot be defined in classical terms. In order to be able to characterize fictional texts, semantic, pragmatic, and reader-conditioned factors have to be taken into account. With reference to Frege, Searle, and Gabriel, the article recalls some proposals for how we might define fictional speech. Underscored in particular is the role of reception for the classification of a text as fictional. I make the case, from a philosophical perspective, for the view that fictional texts represent worlds that do not exist even though these worlds obviously can, and de facto do, contain many elements that are familiar to us from our world. I call these worlds reading worlds and explain the relationship between reading worlds and the life world of readers. This will help support the argument that the encounter with fictional literature can invoke real feelings and that such feelings are by no means irrational, as some defenders of the paradox of fiction would like us to believe. It is the exemplary character of fictional texts that enables us to make connections between the reading worlds and the life world. First and foremost, the article discusses the question of what it is that readers’ feelings are in fact related to. The widespread view that these feelings are primarily related to the characters or events represented in a text proves too simple and needs to be amended. Whoever is sad because of the fate of a fictive character imagines how he or she would fare if in a similar situation. He or she would feel sad as it relates to his or her own situation. And it is this feeling on behalf of one’s self that is the presupposition of sympathy for a fictive character. While reading, the feelings related to fictive characters and content are intertwined with the feelings related to one’s own personal concerns. The feelings one has on his or her own behalf belong to the feelings related to fictive characters; the former are the presupposition of the latter. If we look at the matter in this way, a new perspective opens up on the paradox of fiction. Generally speaking, the discussion surrounding the paradox of fiction is really about readers’ feelings as they relate to fictive persons or content. The question is then how it is possible to have them, since fictive persons and situations do not exist. If, however, the emotional relation to fictive characters and situations is conceived of as mediated by the feelings one has on one’s own behalf, the paradox loses its confusing effect since the imputation of existence no longer plays a central role. Instead, the conjecture that the events in a fictional story could have happened in one’s own life is important. The reader imagines that a story had or could have happened to him or herself. Readers are therefore often moved by a fictive event because they relate what happened in a story to themselves. They have understood the literary event as something that is humanly relevant in a general sense, and they see it as exemplary for human life as such. This is the decisive factor which gives rise to a connection between fiction and reality. The emotional relation to fictive characters happens on the basis of emotions that we would have for our own sake were we confronted with an occurrence like the one being narrated. What happens to the characters in a fictional text could also happen to readers. This is enough to stimulate corresponding feelings. We neither have to assume the existence of fictive characters nor do we have to suspend our knowledge about the fictive character of events or take part in a game of make-believe. But we do have to be able to regard the events in a fictional text as exemplary for human life. The representation of an occurrence in a novel exhibits a number of commonalities with the representation of something that could happen in the future. Consciousness of the future would seem to be a presupposition for developing feelings for something that is only represented. This requires the power of imagination. One has to be able to imagine what is happening to the characters involved in the occurrence being narrated in a fictional text, ›empathize‹ with them, and ultimately one has to be able to imagine that he or she could also be entangled in the same event and what it would be like. Without the use of these skills, it would remain a mystery how reading a fictional text can lead to feelings and how fictive occurrences can be related to reality. The fate of Anna Karenina can move us, we can sympathize with her, because reading the novel confronts us with possibilities that could affect our own lives. The imagination of such possibilities stimulates feelings that are related to us and to our lives. On that basis, we can participate in the fate of fictive characters without having to imagine that they really exist.

scholarly journals Dynamic Creation: Extending the Radical Austrian Approach to Entrepreneurship

2009 ◽  
Vol 31 (1) ◽  
pp. 7-46 ◽  
Author(s):  
Todd H. Chiles ◽  
Christopher S. Tuggle ◽  
Jeffery S. McMullen ◽  
Leonard Bierman ◽  
Daniel W. Greening
Keyword(s):  
Job Search ◽  
Organization Theory ◽  
Future Research ◽  
Creative Processes ◽  
Far From Equilibrium ◽  
Multiple Levels ◽  
New Perspective ◽  
Equilibrium Market ◽  
Heterogeneous Resources ◽  
Novel Products

We develop a new perspective on entrepreneurship as a dynamic, complex, subjective process of creative organizing. Our approach, which we call ‘dynamic creation’, synthesizes core ideas from Austrian ‘radical subjectivism’ with complementary ideas from psychology (empathy), strategy and organization theory (modularity), and complexity theory (self-organization). We articulate conjectures at multiple levels about how such dynamic creative processes as empathizing, modularizing, and self-organizing help organize subjectively imagined novel ideas in entrepreneurs’ minds, heterogeneous resources in their firms, and disequilibrium markets in their environments. In our most provocative claim, we argue that entrepreneurs, by imagining divergent futures and (re)combining heterogeneous resources to create novel products, drive far-from-equilibrium market processes to create not market anarchy but market order. We conclude our exposition of each dynamic creative process by offering one possible direction for future research and articulating additional conjectures that help point the way. Throughout, we draw examples from CareerBuilder—a firm that has played a major role in creating and shaping the online model in the job search/recruiting industry—and its industry rivals (e.g. Monster, Yahoo’s HotJobs) to illustrate selected concepts and relationships in dynamic entrepreneurial creation.

scholarly journals On C-E Translation of Culture-Specific Items from the Perspective of Eco-translatology—A Case Study of Howard Goldblatt’s Red Poppies

2021 ◽  
Vol 3 (1) ◽  
Author(s):  
Xiaojun Zhang
Keyword(s):  
Material Culture ◽  
Chinese Culture ◽  
Three Dimension ◽  
Translation Study ◽  
Wide Range ◽  
Free Translation ◽  
Ecological Culture ◽  
Translation Methods ◽  
New Perspective

<div>This thesis researches the translation of Chinese culture-specific items in <em>Red Poppies</em> from the perspectives of Eco-translatology. Eco-translatology, which was put forward by Chinese scholar Hu Gengshen, adopts some concepts of ecology in translatology and provides a new perspective for translation study and practice. <em>Red Poppies</em> is a novel by Alai whose contents covers a wide range of Tibetan culture and history, which is praised as Tibetan encyclopedia. On one hand, the study focuses on the definition and features of culture-specific items, and their classification of in Red</div><div>Poppies. Based on Nida’s classification of five categories of sub-culture, those culture-specific items are classified into five groups, namely linguistic culture-specific items, material culture-specific items, ecological culture--specific items, social culture-specific items and religious culture-specific items. On the other hand, this thesis explores how Goldblatt deal with those culture-specific items from the perspective of three-dimension transformation in eco-translatology, and it finds translator adopts a combination of foreignization strategy and domestication strategy, and the former plays a dominating role. Besides, various translation methods are adopted such as free translation, transliteration, transliteration plus annotation, and amplification and so on.</div>

Feedback mechanisms in mineral replacement networks: an experimental investigation of the ultramafic model system

2021 ◽  
Author(s):  
Ingvild Aarrestad ◽  
Oliver Plümper ◽  
Desiree Roerdink ◽  
Andreas Beinlich
Keyword(s):  
Reaction Rate ◽  
Energy Transport ◽  
Kinetic Modelling ◽  
Indirect Evidence ◽  
Reaction Network ◽  
Reaction Networks ◽  
Silicate System ◽  
Rock Interaction ◽  
Feedback Mechanisms ◽  
Salinity Effect

&lt;p&gt;The overall rates of multi-component reaction networks are known to be controlled by feedback mechanisms. Feedback mechanisms represent loop systems where the output of the system is conveyed back as input and the system is either accelerated or regulated (positive and negative feedback respectively). In other words, feedback mechanisms control the rate of a reaction network without external influences. Feedback mechanisms are well-studied in a variety of reaction networks (e.g. bio-chemical, atmospheric); however, in fluid-rock interaction systems they are not researched as such. Still, indirect evidence, theoretical considerations and direct observations attest to their existence [e.g. 1, 2, 3]. It remains unknown how mass and energy transport between distinct reaction sites affect the overall reaction rate and outcome through feedback mechanisms. We propose that feedback mechanisms are a missing critical ingredient to understand reaction progress and timescales of fluid-rock interactions. We apply the serpentinization of ultramafic silicates as a relatively simple reaction network to investigate feedback mechanisms during fluid-rock interactions. Recent studies show that theoretical timescale-predictions appear inconsistent with natural observations [e.g. 4, 5]. The ultramafic silicate system is ideal for investigating feedback mechanisms as it is relevant to natural processes, is reactive on timescales that can be explored in the laboratory, and natural peridotite typically consists of less than four phases. Our preliminary observations indicate a feedback between pyroxene dissolution and olivine serpentinization. Olivine serpentinization appears to proceed faster in the presence of pyroxene. Furthermore, the bulk system reaction rate increases with increasing fluid salinity, which is opposite to the salinity effect on the monomineralic olivine system. Dunite (&gt;90% olivine) is rare, which is why it is crucial to explore the more common pyroxene-bearing systems. The salinity effect is important to investigate due to the inevitable increase in fluid salinity from the boiling-induced phase separation and OH-uptake in the formation of serpentine. Here we present preliminary textural and chemical observations, which will subsequently be used for kinetic modelling of feedback.&lt;/p&gt;&lt;p&gt;[1] Ortoleva P., Merino, E., Moore, C. &amp; Chadam, J. (1987). American Journal of Science &lt;strong&gt;287&lt;/strong&gt;, 997-1007.&lt;/p&gt;&lt;p&gt;[2] Centrella, S., Austrheim, H., &amp; Putnis, A. (2015). Lithos &lt;strong&gt;236&amp;#8211;237&lt;/strong&gt;, 245&amp;#8211;255.&lt;/p&gt;&lt;p&gt;[3] Nakatani, T. &amp; Nakamura, M. (2016). Geochemistry, Geophysics, Geosystems &lt;strong&gt;17&lt;/strong&gt;, 3393-3419.&lt;/p&gt;&lt;p&gt;[4] Ingebritsen, S. E. &amp; Manning, C. E. (2010). Geofluids &lt;strong&gt;10&lt;/strong&gt;, 193-205.&lt;/p&gt;&lt;p&gt;[5] Beinlich, A., John, T., Vrijmoed, J.C., Tominaga, M., Magna, T. &amp; Podladchikov, Y.Y. (2020).&amp;#160;Nature Geoscience&amp;#160;&lt;strong&gt;13&lt;/strong&gt;,&amp;#160;307&amp;#8211;311.&lt;/p&gt;

Incidence Structure of Thymus Tumors in the Kharkiv Region and Analysis of Diagnostically Significant Parameters of Immune Response in Patients with Thymomas

2021 ◽  
Vol 6 (5) ◽  
pp. 69-75
Author(s):  
I. V. Belozоrov ◽  
◽  
O. S. Protsenko ◽  
N. O. Remnyova ◽  
L. I. Chumak ◽  
...  
Keyword(s):  
Immune Response ◽  
T Lymphocytes ◽  
Phagocytic Index ◽  
Histological Classification ◽  
Age Group ◽  
Male Population ◽  
The Mean ◽  
The Complement System ◽  
Tumors Of The Thymus

The purpose of the study was to determine the structure of the incidence of thymus tumors in the Kharkiv region, taking into account the histological classification of thymus tumors and to analyze diagnostically significant indicators of the immune response of patients with thymomas. Materials and methods. The medical histories of 158 patients aged 16 to 80 years with diseases of the thymus gland were studied during 2006-2019. The indices of phagocytic activity of granulocytic neutrophils in blood heparinization, phagocytic index, phagocytic number, phagocytosis completion index and activity of proteins of the complement system were analyzed. We also analyzed the indices of the number of T- and B-lymphocytes obtained using monoclonal antibodies (CD2+, CD3+, CD4+, CD8+, CD16+, CD19+) (immunofluorescence method). Results and discussion. The structure of the incidence of tumors of the thymus in the Kharkiv region was determined, taking into account the histological classification of tumors of the thymus and indicators of the immune status of patients with thymomas. The relationship was determined between the indicators of the phagocytic activity of granulocytic neutrophils and the activity of proteins of the complement system, as well as changes in the ratio of the subpopulation composition of T-lymphocytes in patients with different types of thymomas. Lymphoepithelial thymoma is most widespread in male population in the age groups 40-59 and 20-39 years, and the lymphoid thymoma – in male population in the age group 20-39 years and female population in the age group 40-59 years. The significant decrease (p <0.05) in the mean value of the phagocytic index was revealed in group of patients with lymphoid thymomas. The subpopulations of T-lymphocytes CD3+ and CD4+ were significantly reduced (p <0.05) in group of patients with lymphoepithelial thymomas. The subpopulations of T-lymphocytes CD4+ and CD8+ were significantly reduced (p <0.05) in group of patients with lymphoid thymomas. The increasing of the mean values of markers CD16+ and CD19+ (p <0.05) in all study groups indicates that the processes of antibody production in patients with thymomas are activated regardless of the type of thymoma. Conclusion. The structure of thymus pathology in the population of the Kharkiv region is characterized by the predominance of tumor pathology in the general structure of thymus pathology, which is 51.3%. The lymphoepithelial and lymphoid thymomas are the most common tumors of the thymus and were recorded in 64.2% and 30.8% of patients with thymomas, respectively

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