Related papers: Quantifying the Emergence of Selection Prior to Bi…
The evolution of complexity has been a central theme for Biology and Artificial Life (Bonner, 1988; Bedau et al., 2000). Complexification has been interpreted in different ways: as a process of diversification between evolving units…
Reduction of information entropy along with ever-increasing complexity are among the key signatures of living matter. Understanding the onset of such behavior in early prebiotic world is essential for solving the problem of origins of life.…
Many of the chemical reactions that take place within a living cell are irreversible. Due to evolutionary pressures, the number of allowable reactions within these systems are highly constrained and thus the resulting metabolic networks…
In this paper we explore the eco-evolutionary dynamics of a predator-prey model, where the prey population is structured according to a certain life history trait. The trait distribution within the prey population is the result of interplay…
The problem of the rate and mechanisms of biological evolution was considered. It was shown that species could not be formed due to undirected mutations in characteristic times of about one million years. A mechanism of deterministic…
Most protocols for the high-throughput directed evolution of enzymes rely on random encapsulation to link phenotype and genotype. In order to optimize these approaches, or compare one to another, one needs a measure of their performance at…
Can prelife proceed without cell division? A recently proposed mechanism suggests that transient compartmentalization could have preceded cell division in prebiotic scenarios. Here, we study transient compartmentalization dynamics in the…
Chemical evolution is essential in understanding the origins of life. We present a theory for the evolution of molecule masses and show that small molecules grow by random diffusion and large molecules by a preferential attachment process…
This paper introduces a user-driven evolutionary algorithm based on Quality Diversity (QD) search. During a design session, the user iteratively selects among presented alternatives and their selections affect the upcoming results. We aim…
Motivated by the results of recent laboratory experiments (Yoshida et al. Nature, 424, 303-306 (2003)) as well as many earlier field observations that evolutionary changes can take place in ecosystems over relatively short ecological time…
In the absence of selection, the structure of allelic diversity is described by the elegant sampling formula of Ewens. This formula has helped shape our expectations of empirical patterns of molecular variation. Along with coalescent…
In this lecture I will introduce the concept of galactic chemical evolution, namely the study of how and where the chemical elements formed and how they were distributed in the stars and gas in galaxies. The main ingredients to build models…
Much of uncertainty quantification to date has focused on determining the effect of variables modeled probabilistically, and with a known distribution, on some physical or engineering system. We develop methods to obtain information on the…
Experiment directed simulation is a technique to minimally bias molecular dynamics simulations to match experimentally observed results. The method improves accuracy but does not address the sampling problem of molecular dynamics…
We introduce and study a unified Bayesian framework for extended feature allocations which flexibly captures interactions -- such as repulsion or attraction -- among features and their associated weights. We provide a complete Bayesian…
Evolutionary crystal structure prediction proved to be a powerful approach for studying a wide range of materials. Here, we present a specifically designed algorithm for the prediction of the structure of complex crystals consisting of…
Molecular dynamics simulation is now a widespread approach for understanding complex systems on the atomistic scale. It finds applications from physics and chemistry to engineering, life and medical science. In the last decade, the approach…
Survey respondents may give untruthful answers to sensitive questions when asked directly. In recent years, researchers have turned to the list experiment (also known as the item count technique) to overcome this difficulty. While list…
Observational astronomy is plagued with selection effects that must be taken into account when interpreting data from astronomical surveys. Because of the physical limitations of observing time and instrument sensitivity, datasets are…
The effect of bias on hypothesis formation is characterized for an automated data-driven projection pursuit neural network to extract and select features for binary classification of data streams. This intelligent exploratory process…