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Natural models for evolution on networks

George B. Mertzios, Sotiris Nikoletseas, Christoforos Raptopoulos, Paul G. Spirakis
2013 Theoretical Computer Science  
Apart from being important on its own, this new evolutionary model appears to be useful also in the abstract modeling of control mechanisms over invading populations in networks.  ...  Recently, this approach has been generalized in (Lieberman et al., Nature, 433:312-316, 2005) by arranging individuals on the nodes of a network (in general, directed).  ...  Spirakis wishes to thank Josep Díaz, Leslie Ann Goldberg, and Maria Serna, for many inspiring discussions on the model of [19] .  ... 
doi:10.1016/j.tcs.2012.11.032 fatcat:uexgc6cplnc4rk2ujtsgfo3s3a

Natural Models for Evolution on Networks [article]

George B. Mertzios, Sotiris Nikoletseas, Christoforos Raptopoulos, Paul G. Spirakis
2012 arXiv   pre-print
Apart from being important on its own, this new evolutionary model appears to be useful also in the abstract modeling of control mechanisms over invading populations in networks.  ...  Recently, this approach has been generalized in LHN by arranging individuals on the nodes of a network.  ...  Spirakis wishes to thank Josep Diaz, Leslie Ann Goldberg, and Maria Serna, for many inspiring discussions on the model of [16] .  ... 
arXiv:1102.3426v3 fatcat:wwa6lnlbdfbbnpeyvg23zfrmuu

Natural Models for Evolution on Networks [chapter]

George B. Mertzios, Sotiris Nikoletseas, Christoforos Raptopoulos, Paul G. Spirakis
2011 Lecture Notes in Computer Science  
Apart from being important on its own, this new evolutionary model appears to be useful also in the abstract modeling of control mechanisms over invading populations in networks.  ...  Recently, this approach has been generalized in (Lieberman et al., Nature, 433:312-316, 2005) by arranging individuals on the nodes of a network (in general, directed).  ...  Spirakis wishes to thank Josep Díaz, Leslie Ann Goldberg, and Maria Serna, for many inspiring discussions on the model of [19] .  ... 
doi:10.1007/978-3-642-25510-6_25 fatcat:ibn3xwokwfgofiaz4msvi62yf4

Modeling and Simulation of Opinion Natural Reversal Dynamics with Opinion Leader Based on HK Bounded Confidence Model

Renbin Xiao, Tongyang Yu, Jundong Hou
2020 Complexity  
on the individual's view choice behavior into account based on the Hegselmann and Krause (HK) bounded confidence model.  ...  Opinion natural reversals are important and common phenomena in network management.  ...  Traditionally, the evolution models regarding opinion diffusion and public opinion are mostly based on regular or random networks.  ... 
doi:10.1155/2020/7360302 fatcat:3xe2b5tg2ffknmmcvitontg7im

Network Evolution of Logistics Service Effect of Port Infrastructure in Coastal China

Jihong Chen, Haoqiang Li, Tianxiao Zheng, Zheng Wan
2020 IEEE Access  
INDEX TERMS Complex network, port infrastructure, BBV model, port logistics, network evolution.  ...  This study builds a BBV(Barrat, Barthélemy and Vespignani model) weighted network evolution model to analysis the complex network evolution laws of the service effect of typical seaports in coastal China  ...  ACKNOWLEDGMENT The authors are solely responsible for all the views and analyses in this article.  ... 
doi:10.1109/access.2020.2975364 fatcat:y652y75tnzhztpknoqowoyfcdi

Quantum Genetics and Quantum Automata Models of Quantum-Molecular Evolution Involved in the Evolution of Organisms and Species

I. Baianu
2012 Nature Precedings  
This was followed by a report on quantum and abstract, symbolic computation based on the theory of categories, functors and natural transformations (Baianu, 1971b; 1977; 1987; 2004; Baianu et al, 2004  ...  Molecular models in terms of categories, functors and natural transformations were then formulated for uni-molecular chemical transformations, multi-molecular chemical and biochemical transformations  ... 
doi:10.1038/npre.2012.7083.1 fatcat:auzs33diyngbvfmobjmpnimf4y

Quantum Genetics and Quantum Automata Models of Quantum-Molecular Evolution Involved in the Evolution of Organisms and Species

I. Baianu
2012 Nature Precedings  
This was followed by a report on quantum and abstract, symbolic computation based on the theory of categories, functors and natural transformations (Baianu, 1971b; 1977; 1987; 2004; Baianu et al, 2004  ...  Molecular models in terms of categories, functors and natural transformations were then formulated for uni-molecular chemical transformations, multi-molecular chemical and biochemical transformations  ... 
doi:10.1038/npre.2012.7083.2 fatcat:zumjsftqzjb5bi6px3sac7hdlm

Are There Laws of Genome Evolution?

Eugene V. Koonin, Philip E. Bourne
2011 PLoS Computational Biology  
The universals of genome evolution can be accounted for by simple mathematical models similar to those used in statistical physics, such as the birth-death-innovation model.  ...  These universals include the log-normal distribution of the evolutionary rates of orthologous genes; the power law-like distributions of paralogous family size and node degree in various biological networks  ...  Koonin thanks Yuri Wolf for critical reading of the manuscript and helpful comments.  ... 
doi:10.1371/journal.pcbi.1002173 pmid:21901087 pmcid:PMC3161903 fatcat:u6nl6cfewnfn7e5baq45b3njgm

Simulating protein evolution in sequence and structure space

Yu Xia, Michael Levitt
2004 Current Opinion in Structural Biology  
Simulating protein evolution with simplified and all-atom models has shed light on the evolutionary dynamics of protein populations, the nature of evolved sequences and structures, and the extent to which  ...  Finally, evolutionary-like simulations with all-atom models, in particular computational protein design, have helped identify the dominant selection pressures on naturally occurring protein sequences and  ...  Acknowledgements We thank Tanya Raschke for helpful comments. YX thanks Mark Gerstein for support.  ... 
doi:10.1016/j.sbi.2004.03.001 pmid:15093835 fatcat:kyk5wzv47vd27dq6bm5jranapq

Making the right connections: biological networks in the light of evolution

Christopher G. Knight, John W. Pinney
2009 Bioessays  
Our understanding of how evolution acts on biological networks remains patchy, as is our knowledge of how that action is best identified, modelled and understood.  ...  analogies for biological networks themselves.  ...  Acknowledgments: Thanks to Michael Stumpf for a critical reading of this manuscript. J. W. P. is supported by a University Research Fellowship from the Royal Society and C. G.  ... 
doi:10.1002/bies.200900043 pmid:19722181 pmcid:PMC2962804 fatcat:chzqfl5uzrhklexi3ptuq7dclm

Towards Merging Models of Information Spreading and Dynamic Phenomena in Social Networks [chapter]

Erick Stattner, Martine Collard, Nicolas Vidot
2013 Communications in Computer and Information Science  
Our results provide promising results on how and why network dynamics is a strong parameter to integrate in requirements for information spreading modelling.  ...  We present an approach that merges two models: model of information diffusion through social networks and model of network evolution.  ...  For this, we focus on changes that occur on network structure, by studying the evolution of main network properties.  ... 
doi:10.1007/978-3-642-35879-1_62 fatcat:zjg4pwmjfjcnpjj7db3zz7lnwy

Varying environments can speed up evolution

N. Kashtan, E. Noor, U. Alon
2007 Proceedings of the National Academy of Sciences of the United States of America  
It is therefore of interest to look for generic ways, compatible with natural conditions, in which evolution in simulations can be speeded.  ...  Here, we study the impact of temporally varying goals on the speed of evolution, defined as the number of generations needed for an initially random population to achieve a given goal.  ...  It is therefore of interest to look for generic ways, compatible with natural conditions, in which evolution in simulations can be speeded.  ... 
doi:10.1073/pnas.0611630104 pmid:17698964 pmcid:PMC1948871 fatcat:lgjhxk4lwfc6doacagbnh43eq4

Chaotic Behavior of Traffic-Flow Evolution with Two Departure Intervals in Two-Link Transportation Network

Shixu Liu, Lidan Guo, Said M. Easa, Wensi Chen, Hao Yan, Yingnuo Tang
2018 Discrete Dynamics in Nature and Society  
Combining historical information and real-time information, a dynamic evolution model of traffic flow with a study period divided into two intervals is proposed for a simple two-link network.  ...  Then, the evolution of network traffic flow is investigated using numerical experiments.  ...  Discrete Dynamics in Nature and Society  ... 
doi:10.1155/2018/1605717 fatcat:52ybn5riazgejgc35fxmnsdifu

How Social Network Structure Affects The Dynamics Of Evolution Of Cooperation?

Mohammad Akbarpour, Reza Nasiri Mahalati, Caro Lucas
2008 Zenodo  
On a graph, cooperators can evolve by forming network bunches [2, 3, 4]. In a research, Ohtsuki et al used the idea of iterated prisoners- dilemma on a graph to model an evolutionary game.  ...  If natural selection favors selfish individuals, then what mechanism is at work that we see so many cooperative behaviors? One answer is the effect of network structure.  ...  ACKNOWLEDGMENT The authors would like to thank Masoud Tavazoei and Mohammad Hassan Ghaed for their contributions to this research.  ... 
doi:10.5281/zenodo.1081652 fatcat:odm6l7qkgvbzrbndzarpyqhyci

BioJazz:in silicoevolution of cellular networks with unbounded complexity using rule-based modeling

Song Feng, Julien F. Ollivier, Peter S. Swain, Orkun S. Soyer
2015 Nucleic Acids Research  
As natural evolution at the level of network dynamics is difficult to study, in silico evolution of network models can provide important insights.  ...  Unlike previous tools for in silico evolution, BioJazz allows for the evolution of cellular networks with unbounded complexity by combining rule-based modeling with an encoding of networks that is akin  ...  ACKNOWLEDGEMENT We thank Vincent Danos for insightful discussions.  ... 
doi:10.1093/nar/gkv595 pmid:26101250 pmcid:PMC4627059 fatcat:tgxyfh6nrjenhfldxnmssecrae
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