Related papers: A Barrier Penetration Model for DNA Double Strand …
A method to approximate transmission probabilities for a nonseparable multidimensional barrier is applied to a waveguide model. The method uses complex barrier-crossing orbits to represent reaction probabilities in phase space and is…
Motivated by empirical observations of algebraic duplicated sequence length distributions in a broad range of natural genomes, we analytically formulate and solve a class of simple discrete duplication/substitution models that generate…
The double-well potential is a good example, where we can compute the splitting in the bound state energy of the system due to the tunneling effect with various methods, namely WKB or instanton calculations. All these methods are…
The interaction between nano- or micro-sized particles and cell membranes is of crucial importance in many biological and biomedical applications such as drug and gene delivery to cells and tissues. During their cellular uptake, the…
Membranes are present in all cells and tissues. Mathematical models of cells and tissues need a compact mathematical description of membranes with a resolution of about 1 nm. Membranes isolate cells because ions have difficulty penetrating…
In recent years significant attention has been attracted to proposals which utilize DNA for nanotechnological applications. Potential applications of these ideas range from the programmable self-assembly of colloidal crystals, to biosensors…
The basic physics of nucleation in solid \hl{single-crystal} nanoparticles is revealed by a phase-field theory that includes surface energy, chemical reactions and coherency strain. In contrast to binary fluids, which form arbitrary contact…
A very simple model for cell swelling by osmosis is introduced, resulting in a parabolic free boundary problem. In case of radially symmetric initial conditions, it is shown that the model can be viewed as a gradient flow involving entropy,…
We study pairs of interacting self-avoiding walks on the 3d simple cubic lattice. They have a common origin and are allowed to overlap only at the same monomer position along the chain. The latter overlaps are indeed favored by an energetic…
Under supercoiling constraints, naked DNA, such as a large part of bacterial DNA, folds into braided structures called plectonemes. The double-helix can also undergo local structural transitions, leading to the formation of denaturation…
Functionalization of nanoparticles or colloids is increasingly being used to develop customizable "atoms". Functionalization by attaching single strands of DNA allows for direct control of the binding between nanoparticles, since…
By extending the classical Peyrard-Bishop model, we are able to obtain a fully analytical description for the mechanical resistance of DNA under stretching at variable values of temperature, number of base pairs and intrachains and…
A new kind of invasion percolation is introduced in order to take into account the inertia of the invader fluid. The inertia strength is controlled by the number N of pores (or steps) invaded after the perimeter rupture. The new model…
Charge transfer in a DNA duplex chain is studied by constructing a system with virtual electrodes connected at the ends of each DNA strand. The systeym is described by the tight-binding model and its transport is analyzed by the transfer…
Two separate algorithms for calculating the intermediate states, using cellular automata and the initial conditions in the rate matrix for the diffusion-collision model are introduced. They enable easy and fast calculations of the folding…
Breakage-Fusion-Bridge cycles in cancer arise when a broken segment of DNA is duplicated and an end from each copy joined together. This structure then `unfolds' into a new piece of palindromic DNA. This is one mechanism responsible for the…
The effect of secondary structure on DNA duplex formation is poorly understood. We use a coarse-grained model of DNA to show that specific 3- and 4-base pair hairpins reduce hybridization rates by factors of 2 and 10 respectively, in good…
According to the experimental evidence damage induced by densely ionizing radiation in mammalian cells is distributed along the DNA molecule in the form of clusters. The most critical constituent of DNA damage are double-strand breaks…
Nucleation is the rate-determining step in the kinetics of many self-assembly processes. However, the importance of nucleation in the kinetics of DNA-origami self-assembly, which involves both the binding of staple strands and the folding…
A high activity of reactions can be confined in a model cell with a semipermeable membrane in the Schl\"ogl model. It is interpreted as a model of primitive metabolism in a cell. We study two generalized models to understand the creation of…