Related papers: Kinetic model of DNA replication in eukaryotic org…
This study presents a theoretical model for a self-replicating mechanical system inspired by biological processes within living cells and supported by computer simulations. The model decomposes self-replication into core components, each of…
When it is viewed at the scale of a base pair, DNA appears as a nonlinear lattice. Modelling its properties is a fascinating goal. The detailed experiments that can be performed on this system impose constraints on the models and can be…
A key problem in computational biology is discovering the gene expression changes that regulate cell fate transitions, in which one cell type turns into another. However, each individual cell cannot be tracked longitudinally, and cells at…
Gene expression is a central process to any form of life. It involves multiple temporal and functional scales that extend from specific protein-DNA interactions to the coordinated regulation of multiple genes in response to intracellular…
Capturing intricate biological phenomena often requires multiscale modeling where coarse and inexpensive models are developed using limited components of expensive and high-fidelity models. Here, we consider such a multiscale framework in…
Biological organisms adapt to changes by processing informations from different sources, most notably from their ancestors and from their environment. We review an approach to quantify these informations by analyzing mathematical models of…
The linear-quadratic (LQ) model to describe the survival of irradiated cells may be the most frequently used biomathematical model in radiotherapy. There has been an intense debate on the mechanistic origin of the LQ model. An interesting…
We introduce a generic, purely mechanical model for environment sensitive motion of mammalian cells that is applicable to chemotaxis, haptotaxis, and durotaxis as modes of motility. It is able to theoretically explain all relevant…
The significant role of epigenetic mechanisms within natural systems has become increasingly clear. This paper uses a recently presented abstract, tunable Boolean genetic regulatory network model to explore aspects of epigenetics. It is…
The idea of the inheritance of biological processes, such as the developmental process or the life cycle of an organism, has been discussed in the biology literature, but formal mathematical descriptions and plausible data analysis…
Transcription is the first step of gene expression, in which a particular segment of DNA is copied to RNA by the enzyme RNA polymerase (RNAP). Despite many details of the complex interactions between DNA and RNA synthesis disclosed…
We model and simulate the stepping dynamics of the kinesin motor including electric and mechanical forces, environmental noise, and the complicated potentials produced by tracking and neighboring protofilaments. Our dynamical model supports…
We propose a dynamical model for non-specific DNA-protein interaction, which is based on the 'bead-spring' model previously developed by other groups, and investigate its properties using Brownian Dynamics simulations. We show that the…
Does quantum dynamics play a role in DNA replication? What type of tests would reveal that? Some statistical checks that distinguish classical and quantum dynamics in DNA replication are proposed.
The regulatory mechanisms driving progression of the yeast cell cycle appears to be comprised of an interacting network of transcription factors (TFs), cyclin-dependent kinases (CDK) and ubiquitin ligases. From a systems perspective the…
Based on previously published experimental observations and mathematical models for Hes1, p53 and NF-kB gene expression, we improve these models through a distributed delay formulation of the time lag between transcription factor binding…
Despite growth being fundamental to all aspects of cell biology, we do not yet know its organizing principles in eukaryotic cells. Classic models derived from the bacteria E. coli posit that protein-synthesis rates are set by mass-action…
We study a simple model of DNA evolution in a growing population of cells. Each cell contains a nucleotide sequence which randomly mutates at cell division. Cells divide according to a branching process. Following typical parameter values…
The first level of folding of DNA in eukaryotes is provided by the so called '10 nm chromatin fibre', where DNA wraps around histone proteins (approx. 10 nm in size) to form nucleosomes, which go on to create a zig zagging bead on a string…
Gene assembly in ciliates is one of the most involved DNA processings going on in any organism. This process transforms one nucleus (the micronucleus) into another functionally different nucleus (the macronucleus). We continue the…