Related papers: Nucleation and growth in one dimension, part II: A…
Motivated by a recent application of the Kolmogorov-Johnson-Mehl-Avrami (KJMA) model to the study of DNA replication, we consider the one-dimensional version of this model. We generalize previous work to the case where the nucleation rate…
We present a calculation technique for modeling inhomogeneous DNA replication kinetics, where replication factors such as initiation rates or fork speeds can change with both position and time. We can use our model to simulate data sets…
Kinetics of the first order phase transition is investigated. In some rather wide spread situations the property of avalanche growth of the objects of a new phase doesn't take place. This radically complicates the theoretical description of…
A kinetic theory is developed for exonuclease-deficient DNA polymerases, based on the experimental observation that the rates depend not only on the newly incorporated nucleotide, but also on the previous one, leading to the growth of…
Nucleation and growth is the dominant relaxation mechanism driving first order phase transitions. In two-dimensional at systems nucleation has been applied to a wide range of problems in physics, chemistry and biology. Here we study…
We formulate a kinetic model of DNA replication that quantitatively describes recent results on DNA replication in the in vitro system of Xenopus laevis prior to the mid-blastula transition. The model describes well a large amount of…
We study irreversible dimer nucleation on top of terraces during epitaxial growth in one and two dimensions, for all values of the step-edge barrier. The problem is solved exactly by transforming it into a first passage problem for a random…
Dynamic models are widely used to mathematically describe biological phenomena that evolve over time. One important area of application is leukaemia research, where leukaemia cells are genetically modified in preclinical studies to explore…
We study theoretically the in vitro evolution of a DNA sequence by binding to a transcription factor. Using a simple model of protein-DNA binding and available binding constants for the Mnt protein, we perform large-scale, realistic…
A DNA polymerase (DNAP) replicates a template DNA strand. It also exploits the template as the track for its own motor-like mechanical movement. In the polymerase mode it elongates the nascent DNA by one nucleotide in each step. But,…
Being a dual purpose enzyme, the DNA polymerase is responsible for elongation of the newly formed DNA strand as well as cleaving the erroneous growth in case of a misincorporation. The efficiency of replication depends on the coordination…
Replication of genetic material is an important process for all living organisms. Origins of replication initiate the copying of DNA at many points on a chromosome, and it is the distribution of these points that is relevant here, as it…
We study the time dependence of the grain size distribution N(r,t) during crystallization of a d-dimensional solid. A partial differential equation including a source term for nuclei and a growth law for grains is solved analytically for…
The growth-fragmentation equation arises in many different contexts, ranging from cell division, protein polymerization, biopolymers, neurosciences etc. Direct observation of temporal dynamics being often difficult, it is of main interest…
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.
We study statistical properties of the Kolmogorov-Avrami-Johnson-Mehl nucleation-and-growth model in one dimension. We obtain exact results for the gap density as well as the island distribution. When all nucleation events occur…
Kinetic theory and thermodynamics are applied to DNA polymerases with exonuclease activity, taking into account the dependence of the rates on the previously incorportated nucleotide. The replication fidelity is shown to increase…
We review statistical-mechanical theories of single-molecule micromanipulation experiments on nucleic acids. First, models for describing polymer elasticity are introduced. We then review how these models are used to interpret…
We investigate the evolution of tumor growth relying on a nonlinear model of partial differential equations which incorporates mechanical laws for tissue compression combined with rules for nutrients availability and drug application.…
Biological cells replicate their genomes in a well-planned manner. The DNA replication program of an organism determines the timing at which different genomic regions are replicated, with fundamental consequences for cell homeostasis and…