Related papers: A Barrier Penetration Model for DNA Double Strand …
We investigate the computing power of a restricted class of DNA strand displacement structures: those that are made of double strands with nicks (interruptions) in the top strand. To preserve this structural invariant, we impose…
We present a simple model for deep bed filtration, where particles suspended in a fluid are trapped while passing through a porous filter. A steady state of the model is reached when filter can not trap additional particles. We find the…
The tunneling probability between two leads connected by a molecule, a chain, a film, or a bulk polarizable insulator is investigated within a model of an electron tunneling from lead A to a state higher in energy, describing the barrier,…
The emergence of longer information-carrying and functional nucleotide polymers from random short strands was a major stepping stone at the dawn of life. But the formation of those polymers under temperature oscillation required some form…
We derive a theory that describes homogeneous nucleation of grain boundary (GB) phases. Our analysis takes account of the energy resulting from the GB phase junction, the line defect separating two different GB structures, which is…
The understanding of mechanisms that control epigenetic changes is an important research area in modern functional biology. Epigenetic modifications such as DNA methylation are in general very stable over many cell divisions. DNA…
The denaturation dynamics of a long double-stranded DNA is studied by means of a model of the Poland-Scheraga type. We note that the linking of the two strands is a locally conserved quantity, hence we introduce local updates that respect…
With the rapid advent of biomedical and biotechnological innovations, a deep understanding of the nature of interaction between nanomaterials and cell membranes, tissues, and organs, has become increasingly important. Active penetration of…
We present a Monte Carlo study of a model protein with 54 amino acids that folds directly to its native three-helix-bundle state without forming any well-defined intermediate state. The free-energy barrier separating the native and unfolded…
Model of biological effects of ionizing particles, especially of protons and other ions, is proposed. The model is based on distinguishing the single-particle and collective effects of the underlying radiobiological mechanism. The…
We use self-consistent field theory to determine structural and energetic properties of intermediates and transition states involved in bilayer membrane fusion. In particular, we extend our original calculations from those of the standard…
We calculate the spectrum of torsional vibrations of a double-stranded structure that models the double helix of the DNA. We come to the conclusion that within the framework of the model elementary excitations may display an asymmetry as…
We study voltage driven translocation of a single stranded (ss) DNA through a membrane channel. Our model, based on a master equation (ME) approach, investigates the probability density function (pdf) of the translocation times, and shows…
We identify a nontrivial 4-state Landau-Zener model for which transition probabilities between any pair of diabatic states can be determined analytically and exactly. The model describes an experimentally accessible system of two…
We discuss how to construct open membranes in the recently proposed matrix model of M theory. In order to sustain an open membrane, two boundary terms are needed in the construction. These boundary terms are available in the system of the…
The statistical physics of homogeneous DNA is investigated by the imaginary time path integral formalism. The base pair stretchings are described by an ensemble of paths selected through a macroscopic constraint, the fulfillement of the…
Double-strand breaks (DSBs) in DNA are naturally occurring destructive events in all organisms that may lead to genome instability. Cells employ various repair methods known as non-homologous end joining (NHEJ), microhomology mediated end…
Structural changes in giant DNA induced by the addition of the flexible polymer PEG were examined by the method of single-DNA observation. In dilute DNA conditions, individual DNA assumes a compact state via a discrete coil-globule…
When double-stranded DNA molecules are heated, or exposed to denaturing agents, the two strands get separated. The statistical physics of this process has a long history, and is commonly described in term of the Poland-Scheraga (PS) model.…
A multiscale approach is used to simulate the translocation of DNA through a nanopore. Within this scheme, the interactions of the molecule with the surrounding fluid (solvent) are explicitly taken into account. By generating polymers of…