Related papers: On the Growth Rate of Non-Enzymatic Molecular Repl…
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…
We propose a new simple model for DNA denaturation bases on the pendulum model of Englander\cite{A1} and the microscopic model of Peyrard {\it et al.},\cite{A3} so called "combined model". The main parameters of our model are: the coupling…
We present models of electrodeposition of ZnO films with organic additives, with focus on the growth of hybrid films with eosin Y. First we propose a rate equation model which assumes that the additives form branches with an exposed part…
The theory of multistate template-directed reversible copolymerization is developed by extending the method based on iterated function systems to matrices, taking into account the possibility of multiple activation states instead of a…
Cell proliferation and diffusion can be modeled through reaction-diffusion systems describing the space-time evolution of a density variable. In this work, we present non-linear transformations of heat equation solutions to model cellular…
Inspired by recent experiments on DNA replication, we apply a one-dimensional nucleation-and-growth model to DNA-replication kinetics, focusing on how to extract the time-dependent nucleation rate I(t) and growth speed v from data. We…
Thermodynamical properties of canonical and grand-canonical ensembles of the half-filled two-site Hubbard model have been discussed within the framework of the nonextensive statistics (NES). For relating the physical temperature $T$ to the…
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…
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…
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…
A recombination reaction model for high-temperature chemical kinetics is derived from ab initio simulations data. A kinetic recombination rate model is derived using a recently developed ab initio state-specific dissociation model and the…
In the replica-exchange molecular dynamics method, where constant-temperature molecular dynamics simulations are performed in each replica, one usually rescales the momentum of each particle after replica exchange. This rescaling method had…
We calculate the electron recombination rates with target ions W$^{q+}$, $q = 18$ -- $25$, as functions of electron energy and electron temperature (i.e. the rates integrated over the Maxwellian velocity distribution). Comparison with…
Template matching is widely used for many applications in image and signal processing and usually is time-critical. Traditional methods usually focus on how to reduce the search locations by coarse-to-fine strategy or full search combined…
In the growth of bacterial colonies, a great variety of complex patterns are observed in experiments, depending on external conditions and the bacterial species. Typically, existing models employ systems of reaction-diffusion equations or…
The thermodynamical property of a small cluster including $M$ Hubbard dimers, each of which is described by the two-site Hubbard model, has been discussed within the nonextensive statistics (NES). We have calculated the temperature…
We study bulk recombination in a medium with energetic disorder by using the multiple trapping (MT) model under continuous irradiation with excitation light. Charge densities are shown to obey power law as a function of the intensity of…
It is a long-standing question in origin-of-life research whether the information content of replicating molecules can be maintained in the presence of replication errors. Extending standard quasispecies models of non-enzymatic replication,…
In biology experiments, oligonucleotide microarrays are contacted with a solution of long nucleic acid (NA) targets. The hybridized probes thus carry long tails. When the surface density of the oligonucleotide probes is high enough, the…
We study the self-similar behavior of the exchange-driven growth model, which describes a process in which pairs of clusters, consisting of an integer number of monomers, interact through the exchange of a single monomer. The rate of…