Related papers: A Barrier Penetration Model for DNA Double Strand …
The liquid-liquid phase separation of biomolecules is an important process for intracellular organization. Biomolecular sequence combinatorics leads to a large variety of proteins and nucleic acids which can interact to form a diversity of…
Solid-state nanopores are single molecule sensors that measure changes in ionic current as charged polymers such as DNA pass through. Here, we present comprehensive experiments on the length, voltage and salt dependence of the frequency of…
Fragmentation of nuclear system by tunneling is discussed in a molecular dynamics simulation coupled with imaginary time method. In this way we obtain informations on the fragmenting systems at low densities and temperatures. These…
In previous work, we constructed a statistical framework for estimating the rate of clustered ionization from charged particle radiation in DNA. This model is extended to include contributions from secondary electrons. Using a simple…
We study the effect of random forces on a double stranded DNA in unzipping the two strands, analogous to the problem of an adsorbed polymer under a random force. The ground state develops bubbles of various lengths as the random force…
We report a numerical simulation of the phase diagram of a simple model for membrane proteins constrained to move in a plane. In analogy with the corresponding three dimensional models, the liquid-gas transition becomes metastable as the…
A splicing system is a formal model of a recombinant behaviour of sets of double stranded DNA molecules when acted on by restriction enzymes and ligase. In this survey we will concentrate on a specific behaviour of a type of splicing…
We study sequence dependent complexation between oligonucleotides (single strand DNA) and various generation ethylene diamine (EDA) cored poly amido amide (PAMAM) dendrimers through atomistic molecular dynamics simulations accompanied by…
A phase eld approach is developed to model wetting and heterogeneous crystal nucleation of an undercooled pure liquid in contact with a sharp wall. We discuss various choices for the boundary condition at the wall and determine the…
For a model of DNA denaturation, exponents describing the distributions of denaturated loops and unzipped end-segments are determined by exact enumeration and by Monte Carlo simulations in two and three dimensions. The loop distributions…
We study the phase separation of binary lipid mixtures that form bicontinuous cubic phases. The competition between non-uniform Gaussian membrane curvature and line tension leads to a very rich phase diagram, where we observe symmetry…
Memristors based on a double barrier design have been analysed by various nano spectroscopic methods to unveil details about its microstructure and conduction mechanism. The device consists of an AlOx tunnel barrier and a NbOy/Au Schottky…
This paper develops a point-mutation model describing the evolutionary dynamics of a population of adult stem cells. Such a model may prove useful for quantitative studies of tissue aging and the emergence of cancer. We consider two modes…
A model predicting the structure of repulsive, spherically symmetric, monodisperse particles confined between two walls is presented. We study the buckling transition of a single flat layer as the double layer state develops. Experimental…
The barrier formation for metal/organic semiconductor interfaces is analyzed within the Induced Density of Interface States (IDIS) model. Using weak chemisorption theory, we calculate the induced density of states in the organic energy gap…
We propose that supercoiling energizes double-stranded DNA (dsDNA) so as to facilitate thermal fluctuations to an unzipped state. We support this with a model of two elastic rods coupled via forces that represent base pair interactions.…
We evaluate, by means of molecular dynamics simulations employing a realistic DNA coarse-grained model, the phase behaviour and the structural and dynamic properties of tetravalent DNA nanostars, i.e. nanoconstructs completely made of DNA.…
We investigate the salt-dependent current modulation of bundled DNA nanostructures in a nanopore. To this end, we developed four simulation models for a 2x2 origami structure with increasing level of detail: from the mean-field level to an…
Self-consistent field theory is used to determine structural and energetic properties of metastable intermediates and unstable transition states involved in the standard stalk mechanism of bilayer membrane fusion. A microscopic model of…
DNA nanocompartment is a typical DNA-based machine whose function is dependent of molecular collective effect. Fundamental properties of the device have been addressed via electrochemical analysis, fluorescent microscopy, and atomic force…