scholarly journals Mineral self-organization in anoxic conditions: a window into early Earth geochemistry and prebiotic chemical reactions

2021 ◽  
Author(s):  
Electra Kotopoulou ◽  
Alexander Van Driessche ◽  
Alejandro Fernandez-Martinez ◽  
Marco di Michiel
Keyword(s):  
Chemical Reactions ◽  
Self Organization ◽  
Early Earth ◽  
Anoxic Conditions ◽  
Prebiotic Chemical

Carbonaceous chondrites: tracers of the prebiotic chemical evolution of the Solar System

2005 ◽  
Vol 4 (1) ◽  
pp. 13-17 ◽  
Author(s):  
Anja C. Andersen ◽  
Henning Haack
Keyword(s):  
Amino Acids ◽  
Solar System ◽  
Direct Result ◽  
Early Earth ◽  
Carbonaceous Chondrites ◽  
Subsequent Evolution ◽  
Prebiotic Chemical ◽  
Unique Source ◽  
Sugar Derivatives ◽  
Source Of Information

The astrobiological relevance of carbonaceous chondrites is reviewed. It is argued that the primitive meteorites called carbonaceous chondrites provide a unique source of information about the materials and conditions in the Solar System during the earliest phases of its history, and its subsequent evolution. Presolar dust grains extracted from the carbonaceous chondrites provide direct information on the previous generations of stars that provided the materials present for planet formation. The organic material found in carbonaceous chondrites consist of amino acids, carboxylic acids and sugar derivatives. Part of the amino acids found show L-enantiomeric excesses, which indicates that homochirality on Earth could be a direct result of input from meteoritic material to the early Earth.

scholarly journals From cartoons to quantitative models in Golgi transport

2020 ◽  
Author(s):  
D. Nicolas Quiros ◽  
Luis S. Mayorga
Keyword(s):  
Golgi Apparatus ◽  
Mathematical Models ◽  
Chemical Reactions ◽  
Molecular Interactions ◽  
Cell Biology ◽  
Lipid Transport ◽  
Self Organization ◽  
Agent Based ◽  
Cellular Processes ◽  
Golgi Transport

ABSTRACTCell biology is evolving to become a more formal and quantitative science. In particular, several mathematical models have been proposed to address Golgi self-organization and protein and lipid transport. However, most scientific articles about the Golgi apparatus are still using static cartoons to represent their findings that miss the dynamism of this organelle. In this report, we show that schematic drawings of Golgi trafficking can be easily translated into an Agent-Based Model (ABM) using the Repast platform. The simulations generate an active interplay among cisternae and vesicles rendering quantitative predictions about Golgi stability and transport of soluble and membrane-associated cargoes. The models can incorporate complex networks of molecular interactions and chemical reactions by association with COPASI, a software that handles Ordinary Differential Equations. The strategy described provides a simple, flexible, and multiscale support to analyze Golgi transport. The simulations can be used to address issues directly linked to the mechanism of transport or as a way to incorporate the complexity of trafficking to other cellular processes that occur in dynamic organelles.

BASICS OF THE THEORY OF SELF-ORGANIZATION

2021 ◽  
Author(s):  
Igor Kudryavtsev
Keyword(s):  
Graduate Students ◽  
Differential Equations ◽  
Chemical Reactions ◽  
Natural Sciences ◽  
Basic Knowledge ◽  
Self Organization ◽  
Unified Approach ◽  
Physical Chemical ◽  
Basic Ideas

The tutorial reviews the basic ideas and concepts of the theory of self-organization. Numerous examples of physical, chemical, biological, social and other systems are given, which are characterized by the nonlinearity of the phenomena under consideration and which can be described within the framework of a unified approach. The presentation includes the basics of thermodynamics and of the theory of differential equations. The simplest schemes of chemical reactions were used for modeling. The manual is focused primarily on students and graduate students of humanitarian specialities with basic knowledge in the field of natural sciences.

DIFFUSIVE INSTABILITIES AND CHEMICAL REACTIONS

2002 ◽  
Vol 12 (11) ◽  
pp. 2307-2332 ◽  
Author(s):  
P. BORCKMANS ◽  
G. DEWEL ◽  
A. DE WIT ◽  
E. DULOS ◽  
J. BOISSONADE ◽  
...  
Keyword(s):  
Chemical Reactions ◽  
Reaction Diffusion ◽  
Dissipative Structures ◽  
Steady States ◽  
Experimental Results ◽  
Self Organization ◽  
Chemical Systems ◽  
Theoretical Predictions ◽  
Temporal And Spatial

Diffusive instabilities provide the engine for an ever increasing number of dissipative structures. In this class autocatalytic chemical systems are prone to generate temporal and spatial self-organization phenomena. The development of open spatial reactors and the subsequent discovery in 1989 of the stationary reaction–diffusion patterns predicted by Turing [1952] have triggered a large amount of research. This review aims at a comparison between theoretical predictions and experimental results obtained with various type of reactors in use. The differences arising from the use of reactions exhibiting either bistability of homogeneous steady states or a single one in a CSTR are emphasized.

scholarly journals Goal Directedness, Chemical Organizations, and Cybernetic Mechanisms

Entropy ◽  
2021 ◽  
Vol 23 (8) ◽  
pp. 1039
Author(s):  
Evo Busseniers ◽  
Tomas Veloz ◽  
Francis Heylighen
Keyword(s):  
Chemical Reactions ◽  
Negative Feedback ◽  
Organization Theory ◽  
The Self ◽  
Self Organization ◽  
Reaction Networks ◽  
Reference Levels ◽  
The Origin Of Life ◽  
Goal Directedness ◽  
Theoretical Results

In this article, we attempt at developing a scenario for the self-organization of goal-directed systems out of networks of (chemical) reactions. Related scenarios have been proposed to explain the origin of life starting from autocatalytic sets, but these sets tend to be too unstable and dependent on their environment to maintain. We apply instead a framework called Chemical Organization Theory (COT), which shows mathematically under which conditions reaction networks are able to form self-maintaining, autopoietic organizations. We introduce the concepts of perturbation, action, and goal based on an operationalization of the notion of change developed within COT. Next, we incorporate the latter with notions native to the theory of cybernetics aimed to explain goal directedness: reference levels and negative feedback among others. To test and refine these theoretical results, we present some examples that illustrate our approach. We finally discuss how this could result in a realistic, step-by-step scenario for the evolution of goal directedness, thus providing a theoretical solution to the age-old question of the origins of purpose.

scholarly journals Far from Equilibrium Maximal Principle Leading to Matter Self-Organization

2009 ◽  
Vol 5 (3) ◽  
pp. 753-783
Author(s):  
Piero Chiarelli
Keyword(s):  
Free Energy ◽  
Energy Dissipation ◽  
Entropy Production ◽  
Chemical Reactions ◽  
Space Velocity ◽  
Maximum Energy ◽  
Self Organization ◽  
Minimum Entropy ◽  
Minimum Entropy Production ◽  
Far From Equilibrium

In this work an extremal principle driving the far from equilibrium evolution of a system of structureless particles is derived by using the stochastic quantum hydrodynamic analogy. For a classical phase (i.e., the quantum correlations decay on a distance smaller than the mean inter-molecular distance) the far from equilibrium kinetic equation can be cast in the form of a Fokker-Plank equation whose phase space velocity vector maximizes the dissipation of the energy-type function, named here, stochastic free energy.Near equilibrium the maximum stochastic free energy dissipation (SFED) is shown to be compatible with the Prigogine’s principle of minimum entropy production. Moreover, in quasi-isothermal far from equilibrium states, the theory shows that, in the case of elastic molecular collisions and in absence of chemical reactions, the maximum SFED reduces to the maximum free energy dissipation.When chemical reactions or relevant thermal gradients are present, the theory highlights that the Sawada enunciation of maximum free energy dissipation can be violated.The proposed model depicts the Prigogine’s principle of minimum entropy production near-equilibrium and the far from equilibrium Sawada’s principle of maximum energy dissipation as two complementary principia of a unique theory where the latter one is a particular case of the more general one of maximum stochastic free energy dissipation.Following the tendency to reach the highest rate of SFED, a system relaxing to equilibrium goes through states with higher order so that the matter self-organization becomes possible.

scholarly journals Exploring the Emergence of RNA Nucleosides and Nucleotides on the Early Earth

Life ◽  
2018 ◽  
Vol 8 (4) ◽  
pp. 57 ◽  
Author(s):  
Annabelle Biscans
Keyword(s):  
Amino Acids ◽  
Chemical Reactions ◽  
Early Earth ◽  
Evolution Of Life ◽  
Cellular Components

Understanding how life began is one of the most fascinating problems to solve. By approaching this enigma from a chemistry perspective, the goal is to define what series of chemical reactions could lead to the synthesis of nucleotides, amino acids, lipids, and other cellular components from simple feedstocks under prebiotically plausible conditions. It is well established that evolution of life involved RNA which plays central roles in both inheritance and catalysis. In this review, we present historically important and recently published articles aimed at understanding the emergence of RNA nucleosides and nucleotides on the early Earth.

Elements of the radiation-induced structural self-organization in materials

1988 ◽  
Vol 3 (4) ◽  
pp. 640-644 ◽  
Author(s):  
C. Abromeit ◽  
H. Wollenberger
Keyword(s):  
Stability Analysis ◽  
Chemical Reactions ◽  
Open System ◽  
Rate Equation ◽  
Linear Stability Analysis ◽  
Self Organization ◽  
Solute Fluxes ◽  
Minimum Requirements ◽  
Radiation Induced ◽  
Defect Reactions

A crystal irradiated by energetic particles is an open system capable of self-organization. The minimum requirements for self-organization of the microstructure (defect sinks) are derived by a linear stability analysis based upon a rate equation treatment of the defect reactions. The selected description eases the application also for proper chemical reactions. Coupling of defect fluxes to solute fluxes and resulting compositional self-organization in alloys is also considered

scholarly journals Microfluidic trapping of vesicles reveals membrane-tension dependent FtsZ cytoskeletal re-organisation

2019 ◽  
Author(s):  
Kristina A. Ganzinger ◽  
Adrián Merino-Salomón ◽  
Daniela A. García-Soriano ◽  
A. Nelson Butterfield ◽  
Thomas Litschel ◽  
...  
Keyword(s):  
Cell Division ◽  
Synthetic Biology ◽  
Surface Area ◽  
Chemical Reactions ◽  
Microfluidic Chip ◽  
Self Organization ◽  
Membrane Tension ◽  
Area Minimization ◽  
Z Ring ◽  
Membrane Bound

AbstractThe geometry of reaction compartments can affect the outcome of chemical reactions. Synthetic biology commonly uses giant unilamellar vesicles (GUVs) to generate cell-sized, membrane-bound reaction compartments. However, these liposomes are always spherical due to surface area minimization. Here, we have developed a microfluidic chip to trap and reversibly deform GUVs into rod- or cigar-like shapes, including a constriction site in the trap mimicking the membrane furrow in cell division. When we introduce into these GUVs the bacterial tubulin homologue FtsZ, the primary protein of the bacterial Z ring, we find that FtsZ organization changes from dynamic rings to elongated filaments upon GUV deformation, and that these FtsZ filaments align preferentially with the short GUV axis, in particular at the membrane neck. In contrast, pulsing Min oscillations in GUVs remained largely unaffected. We conclude that microfluidic traps are a useful tool for deforming GUVs into non-spherical membrane shapes, akin to those seen in cell division, and for investigating the effect of confinement geometry on biochemical reactions, such as protein filament self-organization.

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