26 papers · ranked by Valyu relevance
Winston Campeau, Andrew M. Simons, Brett Stevens, Marcos Gomes Eleuterio da Luz
'Marcos Gomes Eleuterio da Luz'] Lévy flight is a type of random walk that characterizes the behaviour of many natural phenomena studied across a multiplicity of academic disciplines; within biology specifically, the behaviour of fish, birds, insects, mollusks, bacteria, plants, slime molds, t-cells, and human…
Manasa Josyula
—Evolution is the theory that plants and animals today have come from kinds that have existed in the past. Scientists such as Charles Darwin and Alfred Wallace dedicate their life to observe how species interact with their environment, grow, and change. We are able to predict future changes as well as simulate the…
Paul Banse, Santiago F Elena, Guillaume Beslon
Viruses evolve by periods of relative stasis interleaved with sudden, rapid series of mutation fixations, known as evolutionary bursts. These bursts can be triggered by external factors, such as environmental changes, antiviral therapies, or spill-overs from reservoirs into novel host species. However, it has also been…
Juliette Luiselli, David P. Parsons, Romain Gallé, Paul Banse + 2 more
Aevol is a forward-in-time simulator of genome architecture. It simulates a population of individuals, each with an explicit genome whose sequence and architecture can be modified by various mutational operators, including substitutions, indels, and large-scale chromosomal rearrangements. This enables performing in…
Roberto Latorre, Miguel Brun-Usan, Gloria Fernández-Lázaro, Tzen-Yuh Chiang
Microevolution and macroevolution describe evolutionary change at different scales: short-term genetic and phenotypic variation within populations, and long-term patterns of diversification and extinction. Despite their interconnected nature, they have often been studied separately, and the reciprocal causal links…
Martin Bagic, Arian Šajina, William John Bradshaw, Dario Riccardo Valenzano + 1 more
Nature presents a staggering diversity of life history strategies, ranging from rapid to slow onset of sexual maturity, short or long life, low or high number of offspring, and much more. Each species-specific life history trait reflects on the one hand specific adaptations to unique environments, e.g., nutrient…
Bert Wang-Chak Chan
Inspired by biological and cultural evolution, there have been many attempts to explore and elucidate the necessary conditions for openendedness in artificial intelligence and artificial life. Using a continuous cellular automata called Lenia as the base system, we built largescale evolutionary simulations using…
Tyler Millhouse, Melanie Moses, Melanie Mitchell
In July of 2021, the Santa Fe Institute hosted a workshop on evolutionary computation as part of its Foundations of Intelligence in Natural and Artificial Systems project. This project seeks to advance the field of artificial intelligence by promoting interdisciplinary research on the nature of intelligence. The…
Maurice HT Ling
Genetic algorithm (GA) is inspired by biological evolution of genetic organisms by optimizing the genotypic combinations encoded within each individual with the help of evolutionary operators, suggesting that GA may be a suitable model for studying real-life evolutionary processes. This paper describes the design of a…
Alexander O. Gusev, Leonid M. Martyushev, Robert Niven, Hisashi Ozawa
'Hisashi Ozawa'] The simplest evolutionary model for catching prey by an agent (predator) is considered. The simulation is performed on the basis of a software-emulated Intel i8080 processor. Maximizing the number of catches is chosen as the objective function. This function is associated with energy dissipation and…
Lillian T. Tatka, Lucian P. Smith, Herbert M. Sauro
Evolutionary algorithms, a class of optimization techniques inspired by biological evolution, have emerged as powerful tools for the optimization of complex systems, including the evolution of mass-action chemical reaction networks. This work explores the application of evolutionary algorithms in this domain…
Quentin Fernandez de Grado, Antoine Frénoy
Mutation is the ultimate mechanism that produces genetic novelty, and thus a central ingredient of evolution. Mutation rates are therefore thought to be tuned by natural selection, for example to optimize a delicate balance between the generation of adaptive diversity and the accumulation of deleterious mutations. As…
Gordon Irlam
The creation-mutation-selection model makes predictions regarding the fitness of asexual and sexual populations in an environment that includes both positive and negative selection. However, for the asexual case, the model predictions depend upon the variance or skewness of the population log fitness distribution…
Boaz Shvartzman, Yoav Ram, Roger Dimitri Kouyos
In evolutionary models, mutations are exogenously introduced by the modeler, rather than endogenously introduced by the replicator itself. We present a new deep-learning based computational model, the self-replicating artificial neural network (SeRANN). We train it to (i) copy its own genotype, like a biological…
Conor Houghton
A challenging simulation of evolutionary dynamics based on a three-state cellular automaton is used as a test of how cooperation can drive the evolution of complex traits. Building on the approach of Wolfram (2025), the fitness of a cellular automaton is determined by the number of updates it endures before returning…
Michael R. King
Introduction Conway’s Game of Life (GOL), and related cellular automata (CA) models, have served as interesting simulations of complex behaviors resulting from simple rules of interactions between neighboring cells, that sometime resemble the growth and reproduction of living things. Thus, CA has been applied towards…
Aedan Brown, Sarah Datta, Pankaj Mehta, Brian Cleary
Population genetics has been successful in explaining how drift, selection, and mutation shape allele frequencies. However, we still lack an understanding of how biological and evolutionary constraints arising from genotype-phenotype maps shape evolutionary dynamics. To explore this question, we developed a new…
Authors not listed
Compositionally complex materials, e.g. high-entropy alloys/oxides, have long been of research interest for their unique mechanical and functional properties thanks to the synergistic effects between the large number of components. More recently, they have emerged as a promising platform for the development of novel…
Michael Remington, Rulon W. Clark, Ryan Hanscom, Timothy E. Higham + 1 more
Evolutionary game theory boasts a rich history of application in the study of phenotypic evolution and behavioral strategies. Complementing this, agent-based modeling offers a powerful simulation framework that allows for explicit modeling and parameterization of individual agents within a virtual environment. The…
Anuraag Bukkuri, Kenneth J. Pienta, Sarah R. Amend, Robert H. Austin + 2 more
'Emma U. Hammarlund' 'Joel S. Brown'] Title: Abstract Evolvability is the capacity of a population to generate heritable variation that can be acted upon by natural selection. This ability influences the adaptations and fitness of individual organisms. By viewing this capacity as a trait, evolvability is subject to…
Liudmyla Vasylenko, Adi Livnat
At the fundamental conceptual level, two alternatives have traditionally been considered for how mutations arise and how evolution happens: 1) random mutation and natural selection, and 2) Lamarckism. Recently, the theory of Interaction-based Evolution (IBE) has been proposed, according to which mutations are neither…
Anupam Ojha, Saumya Thakur, Surl-Hee Ahn, Rommie Amaro
Recent advances in computational power and algorithms have made molecular dynamics (MD) simulations reach greater timescales. However, for observing conformational transitions associated with biomolecular processes, MD simulations still have limitations. Several enhanced sampling techniques seek to address this…
Robert Worden
In 1995 I wrote a paper 'A Speed Limit for Evolution' – whose main result was that evolution must proceed rather slowly, in accordance with the earlier views and intuitions of many authors. The abstract of the paper said: 'An upper bound on the speed of evolution is derived. The bound concerns the amount of genetic…
Sebastian Brickel, Andrey O. Demkiv, Rory M. Crean, Gaspar P. Pinto + 1 more
The exploration of chemical systems occurs on complex energy landscapes. Comprehensively sampling rugged energy landscapes with many local minima is a common problem for molecular dynamics simulations. These multiple local minima trap the dynamic system, preventing efficient sampling. This is a particular challenge for…
Authors not listed
Stochastic Simulation Algorithms (SSA) are a cornerstone in simulating Free Radical Polymerization (FRP) due to their accuracy and reliability. However, computational inefficiency remains a challenge for large-scale and complex polymerization systems. This work introduces a novel stochastic simulation algorithm…
Authors not listed
Electrochemiluminescence (ECL) is a vital analytical technique widely used in immunosensing and emerging applica-tions in biological imaging. Traditional ECL simulations rely on finite element methods, which provide valuable insights into reaction dynamics and spatial distribution of species. However, such methods are…