Related papers: Kinetic Selection of Template Polymer with Complex…
The search for high-affinity aptamers for targets such as proteins, small molecules, or cancer cells remains a formidable endeavor. Systematic Evolution of Ligands by EXponential Enrichment (SELEX) offers an iterative process to discover…
Templated copying is the central operation by which biology produces complex molecules. Cells copy sequence information from DNA to RNA and on into proteins, which are the molecules responsible for the function and regulation of cellular…
Using molecular dynamics simulations we examine the dynamics of a family of model polymers with varying chain length and torsional potential barriers. We focus on features of the dynamics of polymers that are seen experimentally but absent…
We discuss a problem of cyclization of a polymer molecule, which is an important example of reaction in a system showing strongly non-Markovian behavior on the timescales of interest. We show that the knowledge of the joint three-time…
Abstract polymer models are systems of weighted objects, called polymers, equipped with an incompatibility relation. An important quantity associated with such models is the partition function, which is the weighted sum over all sets of…
Active processes in living systems generate nonequilibrium forces that deform embedded passive macromolecules. To understand how such dynamics influence polymer conformation, we study a flexible passive chain in an active nematic fluid.…
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…
Synthetic and biological living polymers are self-assembling chains whose chain length distributions (CLDs) are dynamic. We show these dynamics are ultrasensitive: even a small perturbation (e.g. temperature jump) non-linearly distorts the…
We show that in a particular model of catalytic reaction systems, known as the binary polymer model, there is a mathematical invariance between two versions of the model: (1) random catalysis and (2) template-based catalysis. In particular,…
Semi-flexible polymers in crowded environments exhibit complex dynamics that play a crucial role in various biological and material design processes. Based on the classic reptation theory, it is generally believed that semiflexible polymers…
Some recent results on the rotational dynamics of polymers are reviewed and extended. We focus here on the relaxation of a polymer, either flexible or semiflexible, initially wrapped around a rigid rod. We also study the steady polymer…
Dimerization and subsequent aggregation of polymers and biopolymers often occur under nonequilibrium conditions. When the initial state of the polymer is not collapsed or the final folded native state, the dynamics of dimerization can…
The habitat of microorganisms is typically complex and viscoelastic. A natural question arises: Do polymers in a suspension of active swimmers enhance chaotic motion or promote orientational order? We address this issue by performing…
The discerning behavior of living systems relies on accurate interactions selected from the lot of molecular collisions occurring in the cell. To ensure the reliability of interactions, binding partners are classically envisioned as finely…
A central challenge in the origin of life is understanding how catalytic peptide-like polymers and information-bearing nucleic acid-like polymers emerged as an interde-pendent system. This study constructs a primordial cognitive model…
The aims of this paper are to propose, construct and analyse microscopic kinetic models for the emergence of long chains of RNA from monomeric beta-D-ribonucleotide precursors in prebiotic circumstances. Our theory starts out from similar…
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…
We investigated the Karman vortex behind a circular cylinder in a polymer solution by a molecular dynamics simulation. The vortex characteristics are distinctly different for short and long polymers. The solution with the long polymer…
Biopolymer length regulation is a complex process that involves a large number of subprocesses acting simultaneously across multiple spatial and temporal scales. An illustrative example important for genomic stability is the length…
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…