25 papers · ranked by Valyu relevance
Miguel Arenas, Fran Lewitter
This is an original PLoS Computational Biology tutorial. This study is intended for evolutionary biologists interested in strategies for the simulation of molecular data under diverse evolutionary scenarios. It begins with a brief background on simulation approaches and describes some of the most important simulators…
Bérénice Batut, David P Parsons, Stephan Fischer, Guillaume Beslon + 1 more
'Carole Knibbe'] Comparative genomics has revealed that some species have exceptional genomes, compared to their closest relatives. For instance, some species have undergone a strong reduction of their genome with a drastic reduction of their genic repertoire. Deciphering the causes of these atypical trajectories can…
Adrien Henry, Mathieu Hemery, Paul François, Dina Schneidman
Molecular networks are at the core of most cellular decisions, but are often difficult to comprehend. Reverse engineering of network architecture from their functions has proved fruitful to classify and predict the structure and function of molecular networks, suggesting new experimental tests and biological…
P. Spivakovsky, P. Lio, M. S. Clark
We present a new software tool in R, the PhylSim package, which allows the user to simulate trait evolution on a phylogeny, while varying the speciation rate and evolutionary model over the course of the simulation. In particular, the user can specify any number of regimes, with a different speciation rate for each…
Antonio Carvajal-Rodríguez
The importance of simulation software in current and future evolutionary and genomic studies is just confirmed by the recent publication of several new simulation tools. The forward-in-time simulation strategy has, therefore, re-emerged as a complement of coalescent simulation. Additionally, more efficient coalescent…
Louis Gauthier, Rémicia Di Franco, Adrian W.R. Serohijos
Simulating protein evolution with realistic constraints from population genetics is essential in addressing problems in molecular evolution, from understanding the forces shaping the evolutionary landscape to the clinical challenges of antibiotic resistance, viral evolution and cancer. To address this need, we present…
Remi Matthey-Doret
SimBit is a general purpose and high performance forward-in-time population genetics simulator. SimBit has been designed to be able to model a wide diversity of complex scenarios from a simple set of commands that are very flexible. SimBit also comes with a R wrapper that simplifies the management of an entire research…
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…
Alexander Alexander, Khazatsky, Albert Yu, Zihao Zhao + 1 more
'Gabe Zuckerman'] We model evolution of plants in a world, made up of different locations, with multiple environments (mutually exclusive and collectively exhaustive subsets of locations). Each environment (landmass) has temperature, rainfall, and other attributes that directly affect plant growth and reproduction.…
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…
Daniel Nichol, Peter Jeavons, Robert A. Bonomo, Philip K. Maini + 4 more
'Jerome L. Paul' 'Robert A. Gatenby' 'Alexander R.A. Anderson' 'Jacob G. Scott'] The evolutionary process has been modelled in many ways using both stochastic and deterministic models. We develop an algebraic model of evolution in a population of asexually reproducing organisms in which we represent a stochastic walk…
Dehua Hang, Eric Torng, Charles Ofria, Thomas M Schmidt
Background Maximum parsimony is one of the most commonly used and extensively studied phylogeny reconstruction methods. While current evaluation methodologies such as computer simulations provide insight into how well maximum parsimony reconstructs phylogenies, they tell us little about how well maximum parsimony…
Alexey A. Shadrin, Dmitri V. Parkhomchuk
How mutations accumulate in genomes is the central question of molecular evolution theories. However, our understanding of this process is far from complete. Drake’s rule is a notoriously universal property of genomes from microbes to mammals-the number of (functional) mutations per-genome per-generation is…
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…
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…
Edith Invernizzi, Graeme D Ruxton
The metaphor of fitness landscapes is common in evolutionary biology, as a way to visualise the change in allele or phenotypic frequencies of a population under selection. Understanding how different factors in the evolutionary process affect the trajectory of the population across the landscape is of interest to both…
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…
Lisandro Milocco, Isaac Salazar-Ciudad
A fundamental aim of post-genomic 21st century biology is to understand the genotype-phenotype map (GPM) or how specific genetic variation relates to specific phenotypic variation (1). Quantitative genetics approximates such maps using linear models, and has developed methods to predict the response to selection in a…
Vaibhav Madhok
We propose a faster algorithm for individual based simulations for adaptive dynamics based on a simple modification to the standard Gillespie Algorithm for simulating stochastic birth death processes. We provide an analytical explanation that shows that simulations based on the modified algorithm, in the deterministic…
Joel Lehman, Risto Miikkulainen, Genlou Sun
Extinction events impact the trajectory of biological evolution significantly. They are often viewed as upheavals to the evolutionary process. In contrast, this paper supports the hypothesis that although they are unpredictably destructive, extinction events may in the long term accelerate evolution by increasing…
Jan H. Jensen
This paper presents a comparison of a graph-based genetic algorithm (GB-GA) and machine learning (ML) results for the optimisation of logP values with a constraint for synthetic accessibility and shows that GA is as good or better than the ML approaches for this particular property. The molecules found by GB-GA bear…
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…
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…
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…