Related papers: A mathematical model for DNA
We have presented the basic knowledge on the structure of molecules coding the genetic information, mechanisms of transfer of this information from DNA to proteins and phenomena connected with replication of DNA. In particular, we have…
In this work we numerically calculate the electric current through three kinds of DNA sequences (telomeric, \lambda-DNA, and p53-DNA) described by different heuristic models. A bias voltage is applied between two zig-zag edged graphene…
Molecular biology explains function of molecules by their geometrical and electronical structures that are mainly determined by utilization of quantum effects in chemistry. However, further quantum effects are not thought to play any…
Development of a tumor is known to be a result of accumulation of DNA changes in somatic cells. However, the processes of how DNA changes are produced and how they accumulate in somatic cells are not clear. DNA changes include two types:…
A strict method is used to calculate the current-voltage characteristics of a double-stranded DNA. A more reliable model considering the electrostatic potential drop along an individual DNA molecular wire between the contacts is considered…
We propose an inclusive approach for calculating characteristics of secondary electrons produced by ions/protons in tissue-like media. This approach is based on an analysis of the projectile's interaction with the medium on the microscopic…
Extrachromosomal DNA (ecDNA) can drive oncogene amplification, gene expression and intratumor heterogeneity, representing a major force in cancer initiation and progression. The phenomenon becomes even more intricate as distinct types of…
Purpose: To present a closed formalism calculating charged particle radiation damage induced in DNA. The formalism is valid for all types of charged particles and due to its closed nature is suited to provide fast conversion of dose to…
First principle calculations of charge transfer in DNA molecules are computationally expensive given that charge carriers migrate in interaction with intra- and inter-molecular atomic motion. Screening sequences, e.g. to identify excellent…
It is well known that the structural deformations (stressed states) of DNA molecule play a crucial role in its biological functions including gene expression. For instance, looping in DNA (often mediated by protein binding) is a crucial…
In solution, DNA is a highly charged macromolecule which bears a unit of negative charge on each phosphate of its sugar-phosphate backbone. Although partially compensated by counterions adsorbed at or condensed near it, DNA still produces a…
We present a very simple model for the study of charge transport in a molecule patterned on B-DNA. In this model we use a discrete non-linear Schr\"{o}dinger equation to describe electrons propagating along the sugar-phosphate backbone of…
A dynamical model is presented for chiral change in DNA molecules. The model is an extension of the conventional elastic model which incorporates the structure of base pairs and uses a spinor representation for the DNA configuration…
Understanding how the electronic excitation of DNA changes in response to different high-energy particles is central to advancing ion beam cancer therapy. While protons have been the predominant ion of choice in beam cancer therapy, heavier…
Using high-quality gas phase electron scattering calculations and multiple scattering theory, we attempt to gain insights on the radiation damage to DNA induced by secondary low-energy electrons in the condensed phase, and to bridge the…
The scientific community shows a great interest in the study of DNA damage induction, DNA damage repair and the biological effects on cells and cellular systems after exposure to ionizing radiation. Several in-silico methods have been…
Recent theoretical predictions on DNA mechanical separation induced by pulling forces are numerically tested within a model in which self-avoidance for DNA strands is fully taken into account. DNA strands are described by interacting pairs…
Nucleic acids, like DNA and RNA, are molecules that are present in any life form. Their most notable function is to encode biological information. Why then would a physicist be interested in these molecules? As we will see, DNA is an…
The cellular phenotype is described by a complex network of molecular interactions. Elucidating network properties that distinguish disease from the healthy cellular state is therefore of critical importance for gaining systems-level…
The structure of DNA Binding Proteins enables a strong interaction with their specific target site on DNA. However, recent single molecule experiment reported that proteins can diffuse on DNA. This suggests that the interactions between…