Related papers: Sedimentary models of fossil biomolecules, princip…
This article critically examines the methodologies applied in ancient DNA (aDNA) research, particularly those developed by Dr. P\"a\"abo's team, which have significantly influenced the field. The focus is on the challenges of distinguishing…
Fossil DNA preservation varies with depositional environments and diagenesis, producing fragments of heterogeneous origins and degradation states. We use first-principles biomolecular analysis to classify fossil molecular environments into…
The biomolecules in and around a living cell -- proteins, nucleic acids, lipids, carbohydrates -- continuously sample myriad conformational states that are thermally accessible at physiological temperatures. Simultaneously, a given…
A review of the mechanisms of speciation is performed. The mechanisms of the evolution of species, taking into account the feedback of the state of the environment and mechanisms of the emergence of complexity, are considered. It is shown…
The two major approaches to studying macroevolution in deep time are the fossil record and reconstructed relationships among extant taxa from molecular data. Results based on one approach sometimes conflict with those based on the other,…
Palaeoclimate archives contain information on climate variability, trends and mechanisms. Models are developed to explain observations and predict the response of the climate system to perturbations, in particular perturbations associated…
Modeling environmental ecosystems is essential for effective resource management, sustainable development, and understanding complex ecological processes. However, traditional methods frequently struggle with the inherent complexity,…
We introduce a new model for large scale evolution and extinction in which species are organized into food chains. The system evolves by two processes: origination/speciation and extinction. In the model, extinction of a given species can…
Dispersants aid the breakup of crude oil masses and increase the available interfacial surface area for bacteria to degrade insoluble hydrocarbons in the marine environment. However, this common view neglects key aspects of the microscale…
Foraminifera are single-celled marine organisms, which may have a planktic or benthic lifestyle. During their life cycle they construct shells consisting of one or more chambers, and these shells remain as fossils in marine sediments.…
Modeling environmental ecosystems is essential for effective resource management, sustainable development, and understanding complex ecological processes. However, traditional data-driven methods face challenges in capturing inherently…
Computer simulations are an important tool for studying the mechanics of biological evolution. In particular, in silico work with agent-based models provides an opportunity to collect high-quality records of ancestry relationships among…
This paper reviews the new highly interdisciplinary research field studying the behavior of condensed matter systems exposed to radiation. The paper highlights several relevant examples of recent advances in the field and provides a roadmap…
To maintain homeostasis, living cells process information with networks of interacting molecules. Traditional models for cellular information processing have focused on networks of chemical reactions between molecules. Here, we describe how…
We introduce various models for cellulose bio-degradation by micro-organisms. Those models rely on complex chemical mechanisms, involve the structure of the cellulose chains and are allowed to depend on the phenotypical traits of the…
Diffusion probabilistic models have made their way into a number of high-profile applications since their inception. In particular, there has been a wave of research into using diffusion models in the prediction and design of biomolecular…
The study of interactions between biomimetic membranes and micron-sized particles is crucial for understanding various biological processes. Here, we control microparticle spontaneous engulfment by giant lipid vesicles by tuning particle…
Not all activities in living creatures can be explained by classical dynamics. Application of quantum physics in biology helps to study the unexplained phenomena in cells. More detailed research work is needed rather than rejecting the…
The magnitude and variability of Earth's biodiversity have puzzled scientists ever since paleontologic fossil databases became available. We identify and study a model of interdependent species where both endogenous and exogenous impacts…
Geological parameterization entails the representation of a geomodel using a small set of latent variables and a mapping from these variables to grid-block properties such as porosity and permeability. Parameterization is useful for data…