Artificial Chemistry and Molecular Darwinian Evolution in silico

2003 ◽  
Vol 68 (1) ◽  
pp. 139-177 ◽  
Author(s):  
Vladimír Kvasnička ◽  
Jiří Pospíchal
Keyword(s):  
Graph Theory ◽  
Molecular Level ◽  
Stable State ◽  
Chemical Reactor ◽  
Darwinian Evolution ◽  
Simplified Model ◽  
Asymptotically Stable ◽  
Artificial Chemistry ◽  
Neutral Mutations ◽  
Binary Strings

A simplified model of Darwinian evolution at the molecular level is studied by applying the methods of artificial chemistry. A chemical reactor (chemostat) contains molecules that are represented by binary strings, the strings being capable of replication with a probability proportional to their fitness. Moreover, the process of replication is not fully precise, sporadic mutations may produce new offspring strings, which are slightly different from their parent templates. The dynamics of such an autoreplicating system is described by Eigen's differential equations. These equations have a unique asymptotically stable state, which corresponds to those strings that have the highest rate constants (fitness). Fitness of binary string is calculated as a graph-theory similarity between a folding (phenotype) of respective string and the so-called required folding. The presented method offers a detailed view of mechanisms of the molecular Darwinian evolution, in particular of the meaning and importance of neutral mutations.

The Interaction of Reactions and Transport Part II: Combined Reactors and Exchangers

2007 ◽  
Vol 5 (1) ◽  
Author(s):  
Stuart W. Churchill
Keyword(s):  
Indirect Effects ◽  
Molecular Level ◽  
Chemical Reactor ◽  
Complex Behavior ◽  
Geometrical Configuration ◽  
Direct Effects ◽  
Optimal Conditions ◽  
Chemical Reactors ◽  
And Performance ◽  
Transport Part

The interactions between chemical reactions and transport may be divided into direct effects, for example on the molecular level, and indirect effects, for example those arising from the geometrical configuration of the integrated reactor/exchanger. Attention herein is focused on the latter, although in many instances the direct effects must be accounted for as well. Particular attention is given to the identification of behavior that does not arise in chemical reactors not connected to an exchanger or in exchangers not connected to a chemical reactor, as well as to optimal conditions and configurations of combined reactors and exchangers. Generalizations are difficult to formulate for such complex behavior and equipment, necessitating a primary reliance on illustrative examples. However, some general conclusions are drawn concerning the occurrence, identification, and performance of interactive designs.

Artificial Chemistry and Replicator Theory of Coevolution of Genes and Memes

2007 ◽  
Vol 72 (2) ◽  
pp. 223-251 ◽  
Author(s):  
Vladimír Kvasnička ◽  
Jiří Pospíchal
Keyword(s):  
Computer Simulations ◽  
Present Model ◽  
Gene Interaction ◽  
Darwinian Evolution ◽  
M Gene ◽  
Artificial Chemistry ◽  
Different Types

A simple replication theory of coevolution of genes and memes is proposed. A population composed of pairs of genes and memes, the so-called m-genes, is postulated as a subject of Darwinian evolution. Three different types of operations over m-genes are introduced: Replication (an m-gene is replicated with mutations onto an offspring m-gene), interaction (a memetic transfer from a donor to an acceptor), and extinction (an m-gene is eliminated). Computer simulations of the present model allow to identify different mechanisms of gene and meme coevolution.

scholarly journals Enhanced Specificity Mutations Perturb Allosteric Signaling in CRISPR-Cas9

2021 ◽  
Author(s):  
Łukasz Nierzwicki ◽  
Kyle W. East ◽  
Uriel N. Morzan ◽  
Pablo R. Arantes ◽  
Victor S. Batista ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Graph Theory ◽  
Genome Editing ◽  
Dna Cleavage ◽  
Molecular Level ◽  
Signal Transmission ◽  
Dna Recognition ◽  
Solution Nmr ◽  
Catalytic Sites

ABSTRACTCRISPR-Cas9 is a molecular tool with transformative genome editing capabilities. At the molecular level, an intricate allosteric signaling is critical for DNA cleavage, but its role in the specificity enhancement of the Cas9 endonuclease is poorly understood. Here, solution NMR is combined with multi-microsecond molecular dynamics and graph theory-derived models to probe the allosteric role of key enhancement specificity mutations. We show that the mutations responsible for increasing the specificity of Cas9 alter the allosteric structure of the catalytic HNH domain, impacting the signal transmission from the DNA recognition region to the catalytic sites for cleavage. Specifically, the K855A mutation strongly disrupts the HNH domain allosteric structure, exerting the highest perturbation on the signaling transfer, while K810A and K848A result in more moderate effects on the allosteric intercommunication. This differential perturbation of the allosteric signaling reflects the different capabilities of the single mutants to increase Cas9 specificity, with the mutation achieving the highest specificity also strongly perturbing the signaling transfer. These outcomes reveal that the allosteric regulation is critical for the specificity enhancement of the Cas9 enzyme, and are valuable to harness the signaling network to improve the system’s specificity.

scholarly journals Maximizing cooperation in the prisoner’s dilemma evolutionary game via optimal control

2020 ◽  
Author(s):  
P.K. Newton ◽  
Y. Ma
Keyword(s):  
Optimal Control ◽  
Prisoner's Dilemma ◽  
Evolutionary Game ◽  
Optimal Schedule ◽  
Stable State ◽  
Prisoner’S Dilemma ◽  
Payoff Matrix ◽  
Optimal Timing ◽  
Initial Population ◽  
Asymptotically Stable

The prisoner’s dilemma (PD) game offers a simple paradigm of competition between two players who can either cooperate or defect. Since defection is a strict Nash equilibrium, it is an asymptotically stable state of the replicator dynamical system that uses the PD payoff matrix to define the fitness landscape of two interacting evolving populations. The dilemma arises from the fact that the average payoff of this asymptotically stable state is sub-optimal. Coaxing the players to cooperate would result in a higher payoff for both. Here we develop an optimal control theory for the prisoner’s dilemma evolutionary game in order to maximize cooperation (minimize the defector population) over a given cycle-time T, subject to constraints. Our two time-dependent controllers are applied to the off-diagonal elements of the payoff matrix in a bang-bang sequence that dynamically changes the game being played by dynamically adjusting the payoffs, with optimal timing that depends on the initial population distributions. Over multiple cycles nT (n > 1), the method is adaptive as it uses the defector population at the end of the nth cycle to calculate the optimal schedule over the n + 1st cycle. The control method, based on Pontryagin’s maximum principle, can be viewed as determining the optimal way to dynamically alter incentives and penalties in order to maximize the probability of cooperation in settings that track dynamic changes in the frequency of strategists, with potential applications in evolutionary biology, economics, theoretical ecology, and other fields where the replicator system is used.PACS numbers02.50.Le; 02.30.Yy; 05.45.-a; 87.23.Kg; 87.23.Cc

scholarly journals The Evolution of Citizen Participation and Regulatory Success

2017 ◽  
Vol 9 (6) ◽  
pp. 179
Author(s):  
Ken-Ichi Akao ◽  
Geumsoo Kim
Keyword(s):  
Citizen Participation ◽  
Regulatory Agency ◽  
Evolutionary Game ◽  
Stable State ◽  
Asymptotically Stable ◽  
Initial State ◽  
Private Monitoring ◽  
Relative Share

In an evolutionary game setting we have shown that either perfect compliance or perfect non-compliance with a regulation can evolve as an asymptotically stable state. However, this depends critically on the size of a defector’s additional payoff when there is no private monitoring to a cooperator’s payoff, relative to his expected fine from an enforcer’s monitoring. As an enforcer’s willingness to monitor voluntarily gets affected by their relative share of the population to the defectors’, the society could be stuck in the neighborhood of the initial state if many defectors already exist and a little larger than enforcers, even though the regulatory agency has a strong policy in its enforcement.

scholarly journals A new characterization and a recognition algorithm of Lucas cubes

2013 ◽  
Vol Vol. 15 no. 3 (Graph Theory) ◽  
Author(s):  
Andrej Taranenko
Keyword(s):  
Graph Theory ◽  
Interconnection Networks ◽  
Linear Time ◽  
Recognition Algorithm ◽  
Induced Subgraphs ◽  
Fibonacci Cube ◽  
Vertex Set ◽  
International Audience ◽  
Binary Strings

Graph Theory International audience Fibonacci and Lucas cubes are induced subgraphs of hypercubes obtained by excluding certain binary strings from the vertex set. They appear as models for interconnection networks, as well as in chemistry. We derive a characterization of Lucas cubes that is based on a peripheral expansion of a unique convex subgraph of an appropriate Fibonacci cube. This serves as the foundation for a recognition algorithm of Lucas cubes that runs in linear time.

Preparatory Procedures for Electron Microscopic Analysis at the Molecular Level of Resolution

1978 ◽  
Vol 36 (3) ◽  
pp. 516-520
Author(s):  
F.J. Sjostrand
Keyword(s):  
Electron Microscope ◽  
Molecular Level ◽  
Microscopic Analysis ◽  
Resolving Power ◽  
Cellular Structures ◽  
Electron Microscopic ◽  
Systematic Analysis ◽  
Technical Developments ◽  
Thin Sectioning ◽  
Obvious Reason

In the 1940's and 1950's electron microscopy conferences were attended with everybody interested in learning about the latest technical developments for one very obvious reason. There was the electron microscope with its outstanding performance but nobody could make very much use of it because we were lacking proper techniques to prepare biological specimens. The development of the thin sectioning technique with its perfectioning in 1952 changed the situation and systematic analysis of the structure of cells could now be pursued. Since then electron microscopists have in general become satisfied with the level of resolution at which cellular structures can be analyzed when applying this technique. There has been little interest in trying to push the limit of resolution closer to that determined by the resolving power of the electron microscope.

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