相关论文: Package models and the information crisis of prebi…

A fundamental problem in protobiological dynamics is to understand how chemically generated polymers can form persistent sequence distributions before the emergence of replication. We study deterministic polymer growth in which each finite…

For prebiotic chemistry to succeed in producing a starting metastable, autocatalytic and reproducing system subject to evolutionary selection it must satisfy at least two apparently contradictory requirements: Because such systems are rare,…

A critical issue in the evolution of software models is change propagation: given a primary change that is made to a model in order to meet a new or changed requirement, what additional secondary changes are needed to maintain consistency…

Templated copolymerization, in which information stored in the sequence of a heteropolymer template is copied into another polymer product, is the mechanism behind all known methods of genetic information transfer. A key aspect of templated…

Cumulative resource constraints can model scarce resources in scheduling problems or a dimension in packing and cutting problems. In order to efficiently solve such problems with a constraint programming solver, it is important to have…

Pattern formation in biological tissues plays an important role in the development of living organisms. Since the classical work of Alan Turing, a pre-eminent way of modelling has been through reaction-diffusion mechanisms. More recently,…

Antibiotic resistance presents a growing global health crisis, demanding new therapeutic strategies that target novel bacterial mechanisms. Recent advances in protein structure prediction and machine learning-driven molecule generation…

This thesis broadly concerns the origins of life problem, pursuing a joint approach that combines general philosophical/conceptual reflection on the problem along with more detailed and formal scientific modelling work oriented in the…

The solution to science's replication crisis is a new ecosystem in which scientists sell what they learn from their research. In each pairwise transaction, the information seller makes (loses) money if he turns out to be correct…

We investigate Eigen's model for the evolution of the genetic code of microorganisms using a novel method based on population dynamics analysis. This model, for a given number of offspring, determines long-term survival as a function of the…

The web of data has brought forth the need to preserve and sustain evolving information within linked datasets; however, a basic requirement of data preservation is the maintenance of the datasets' structural characteristics as well. As…

Biological information processing as implemented by regulatory and signaling networks in living cells requires sufficient specificity of molecular interaction to distinguish signals from one another, but much of regulation and signaling…

Quantitative population modelling is an invaluable tool for identifying the cascading effects of ecosystem management and interventions. Ecosystem models are often constructed by assuming stability and coexistence in ecological communities…

Living systems can be understood as organized entities that capture, transform, and reproduce information. Classical gene-centered models explain adaptation through frequency changes driven by differential fitness, yet they often overlook…

Protocells are supposed to have played a key role in the self-organizing processes leading to the emergence of life. Existing models either (i) describe protocell architecture and dynamics, given the existence of sets of collectively…

Evolution of life on earth was governed, primarily, by natural selection, with major contribution of other evolutionary processes, such as neutral variation, exaptation, and gene duplication. However, for biological evolution to take off, a…

Understanding the pattern formation in communities has been at the center of attention in various fields. Here we introduce a novel model, called an "information-particle model," which is based on the reaction-diffusion model and the…

Partial Information Decomposition (PID) represents multivariate mutual information via antichain-lattice that aims to specify which source groups can recover which informational components of a target. For three or more sources, widely…

Protein is linked to almost every life process. Therefore, analyzing the biological structure and property of protein sequences is critical to the exploration of life, as well as disease detection and drug discovery. Traditional protein…

The scientific community believes in the theory of evolution with a passion that rivals that of any religious belief. This passion extends beyond the irrefutable evidence of the fossil record to the familiar claims of survival of the…