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These notes are devoted to the statistical mechanics of directed polymers interacting with one-dimensional spatial defects. We are interested in particular in the situation where frozen disorder is present. These polymer models undergo a…
The process of morphogenesis, which can be defined as an evolution of the form of an organism, is one of the most intriguing mysteries in the life sciences. It is clear, that gene expression patterns cannot explain the development of the…
In this work, we develop model for neuronal degeneration based on polymer chain folding dynamics and their connectivity in various scale. In the first phase, we just developed the model and numerical simulation need to be complete in order…
The interplay between bacterial chromosome organization and functions such as transcription and replication can be studied in increasing detail using novel experimental techniques. Interpreting the resulting quantitative data, however, can…
A model to describe the arising of new structures in an initial homogeneous biological system is proposed. The essay is motivated by the intention to work on a non-equilibrium situation grouping together several mechanisms and processes as:…
Chromatin is known to be organized into multiple domains of varying sizes and compaction. While these domains are often imagined as static structures, they are highly dynamic and show cell-to-cell variability. Since processes such as gene…
Cells crawling through tissues migrate inside a complex fibrous environment called the extracellular matrix (ECM), which provides signals regulating motility. Here we investigate one such well-known pathway, involving mutually antagonistic…
We study the impact of mutations (changes in amino acid sequence) on the thermodynamics of simple protein-like heteropolymers consisting of N monomers, representing the amino acid sequence. The sequence is designed to fold into its native…
We study the dynamics of a polymer when it is quenched from a $\theta$ solvent into a good or bad solvent by means of a Langevin equation. The variation of the radius of gyration is studied as a function of time. For the first stage of…
Abnormal cortical folding patterns may be related to neurodevelopmental disorders such as lissencephaly and polymicrogyria. In this context, computational modeling is a powerful tool to provide a better understanding of the early brain…
Polymer models are a widely used tool to study the prebiotic formation of metabolism at the origins of life. Counts of the number of reactions in these models are often crucial in probabilistic arguments concerning the emergence of…
Electropolymerization is a bottom-up materials engineering process of micro and nano-scale that utilizes electrical signals to deposit conducting dendrites' morphologies by a redox reaction in the liquid phase. It resembles synaptogenesis…
A theoretical framework for evaluating the approximate energy and dynamic properties associated with the folding of DNA into nucleosomes and chromatin is presented. For this purpose experimentally determined elastic constants of linear DNA…
The folding transition of biopolymers from the coil to compact structures has attracted wide research interest in the past and is well studied in polymer physics. Recent seminal works on DNA in confined devices have shown that these long…
The organization of interphase chromosomes in a number of species is starting to emerge thanks to advances in a variety of experimental techniques. However, much less is known about the dynamics, especially in the functional states of…
The 3D organisation of the genome in interphase cells is not a randomly folded polymer. Rather, experiments show that chromosomes arrange into a network of 3D compartments that correlate with biological processes, such as transcription,…
This short paper presents an abstract, tunable model of genomic structural change within the cell lifecycle and explores its use with simulated evolution. A well-known Boolean model of genetic regulatory networks is extended to include…
The role of active stress on the conformational dynamics of a polymer has drawn significant interest due to its potential applications in understanding the energy landscape of protein structures, buckling of biopolymers, genomic spatial…
Discrete dynamical systems defined by the iteration of a polynomial map of the unit simplex to itself appear in the context of population genetic systems evolving under mutation, recombination and weak selection. Although exceptional…
We investigated the viscoelastic response of model interphase chromosomes by tracking the three-dimensional motion of hundreds of dispersed Brownian particles of sizes ranging from the thickness of the chromatin fiber up to slightly above…