Related papers: Universal Sequence Replication, Reversible Polymer…
The building of minimal self-reproducing systems with a physical embodiment (generically called protocells) is a great challenge, with implications for both theory and applied sciences. Although the classical view of a living protocell…
Evolutionary and ecosystem dynamics are often treated as different processes --operating at separate timescales-- even if evidence reveals that rapid evolutionary changes can feed back into ecological interactions. A recent long-term field…
Biomolecular condensates formed through the phase separation of proteins and nucleic acids are widely observed, offering a fundamental means of organizing intracellular materials in a membrane-less fashion. Traditionally, these condensates…
Proteins, essential to biological systems, perform functions intricately linked to their three-dimensional structures. Understanding the relationship between protein structures and their amino acid sequences remains a core challenge in…
Prior to the origin of simple cellular life, the building blocks of RNA (nucleotides) had to form and polymerize in favourable environments on the early Earth. At this time, meteorites and interplanetary dust particles delivered organics…
Loop formation in long molecules occurs many places in nature, from solutions of carbon nanotubes to polymers inside a cell. In this article, we review theoretical studies of the static and dynamic properties of polymer loops. For example,…
Self-assembled linear structures like giant cylindrical micelles or discotic molecules in solution stacked in flexible columns are systems reminiscent of polydisperse polymer solutions.These supramolecular polymers have an equilibrium…
Letting free polymers diffuse from solution into a crosslinked polymer gel is often a crucial processing step in the synthesis of multiphase polymer-based gels, e.g., core-shell microgels. Here we use coarse-grained molecular dynamics…
The emergence of replicases that can replicate themselves is a central issue in the origin of life. Recent experiments suggest that such replicases can be realized if an RNA polymerase ribozyme is divided into fragments short enough to be…
The emergent spatial patterns generated by growing bacterial colonies have been the focus of intense study in physics during the last twenty years. Both experimental and theoretical investigations have made possible a clear qualitative…
The evolution of enzyme production is studied analytically using ideas of the group selection theory for the evolution of altruistic behavior. In particular, we argue that the mathematical formulation of Wilson's structured deme model ({\it…
The functioning of machines typically requires a concerted action of their parts. This requirement also holds for molecular motors that drive vital cellular processes and imposes constraints on their conformational changes as well as the…
Locomotion is essential for living cells. It enables bacteria and algae to explore space for food, cancer to spread, and immune system to fight infections. Motile cells display trajectories of intriguing complexity, from regular (e.g.…
Applying machine learning to biological sequences - DNA, RNA and protein - has enormous potential to advance human health, environmental sustainability, and fundamental biological understanding. However, many existing machine learning…
It is generally recognized that a distinguishing feature of life is its peculiar capability to avoid equilibration. The origin of this capability and its evolution along the timeline of abiogenesis is not yet understood. We propose to study…
Polymers are high-molecular-weight compounds constructed by the covalent bonding of numerous identical or similar monomers so that their 3D structures are complex yet exhibit unignorable regularity. Typically, the properties of a polymer,…
While machine learning has transformed polymer design by enabling rapid property prediction and candidate generation, translating these designs into experimentally realizable materials remains a critical challenge. Traditionally, the…
Biological polymers, such as intrinsically disordered proteins, play a central role in cellular biology, including mediating phase separation and controlling activity of biological condensates. The physical properties and functions of…
Systems of "living" polymers are ubiquitous in industry and are traditionally realised using surfactants. Here I review the state-of-the-art of living polymers and discuss non-equilibrium extensions that may be realised with advanced…
Molecular phenotypes are important links between genomic information and organismic functions, fitness, and evolution. Complex phenotypes, which are also called quantitative traits, often depend on multiple genomic loci. Their evolution…