Related papers: Evolutionary Algorithms Simulating Molecular Evolu…
We have presented the basic knowledge on the structure of molecules coding the genetic information, mechanisms of transfer of this information from DNA to proteins and phenomena connected with replication of DNA. In particular, we have…
Life occurs in concentrated `Ringer Solutions' derived from seawater that Lesser Blum studied for most of his life. As we worked together, Lesser and I realized that the questions asked of those solutions were quite different in biology…
Foundation models (FMs) have recently opened up new frontiers in the field of artificial life (ALife) by providing powerful tools to automate search through ALife simulations. Previous work aligns ALife simulations with natural language…
Proteins are the fundamental macromolecules that play diverse and crucial roles in all living matter and have tremendous implications in healthcare, manufacturing, and biotechnology. Their functions are largely determined by the sequences…
One of the defining features of living systems is their adaptability to changing environmental conditions. This requires organisms to extract temporal and spatial features of their environment, and use that information to compute the…
Polymerases are protein enzymes that move along nucleic acid chains and catalyze template-based polymerization reactions during gene transcription and replication. The polymerases also substantially improve transcription or replication…
Recently, it has been proven that evolutionary algorithms produce good results for a wide range of combinatorial optimization problems. Some of the considered problems are tackled by evolutionary algorithms that use a representation which…
In living systems, we often see the emergence of the ingredients necessary for computation -- the capacity for information transmission, storage, and modification -- begging the question of how we may exploit or imitate such biological…
Life is confronted with computation problems in a variety of domains including animal behavior, single-cell behavior, and embryonic development. Yet we currently do not know of a naturally existing biological system that is capable of…
Molecular evolution is the process of simulating the natural evolution of molecules in chemical space to explore potential molecular structures and properties. The relationships between similar molecules are often described through…
Biology stores information and computes at the molecular scale, yet the ways in which it does so are often distinct from human-engineered computers. Mapping biological computation onto architectures familiar to computer science remains an…
Abbreviated Abstract: The objective of Evolutionary Computation is to solve practical problems (e.g. optimization, data mining) by simulating the mechanisms of natural evolution. This thesis addresses several topics related to adaptation…
Enzymes are on the front lines of evolution. All living organisms rely on highly efficient, specific enzymes for growth, sustenance, and reproduction; and many diseases are a consequence of a mutation on an enzyme that affects its catalytic…
Genetic algorithms are modeled after the biological evolutionary processes that use natural selection to select the best species to survive. They are heuristics based and low cost to compute. Genetic algorithms use selection, crossover, and…
We investigate the ability of a genetic algorithm to design cellular automata that perform computations. The computational strategies of the resulting cellular automata can be understood using a framework in which ``particles'' embedded in…
We study theoretically the in vitro evolution of a DNA sequence by binding to a transcription factor. Using a simple model of protein-DNA binding and available binding constants for the Mnt protein, we perform large-scale, realistic…
Evolution and learning are two of the fundamental mechanisms by which life adapts in order to survive and to transcend limitations. These biological phenomena inspired successful computational methods such as evolutionary algorithms and…
Protein evolution underpins life, and understanding its behavior as a system is of great importance. However, our current models of protein evolution are arguably too simplistic to allow quantitative interpretation and prediction of…
Evolutionary Computation (EC) has emerged as a powerful field of Artificial Intelligence, inspired by nature's mechanisms of gradual development. However, EC approaches often face challenges such as stagnation, diversity loss, computational…
Designing safe and sustainable chemicals is critical to combat chemical pollution in our environment. Machine learning (ML) methods have been developed to aid with de novo molecule design. However, data on the environmental impacts of…