Related papers: A mathematical model for DNA
It is shown that information transmission inside a cell can occur by means of mechanical waves transmitted through DNA. The propagation of the waves is strongly dependent on the shape of the DNA thus proteins that change the shape of DNA…
The cell cycle is an orderly sequence of events which ultimately lead to the division of a single cell into two daughter cells. In the case of DNA damage by radiation or chemicals, the damage checkpoints in the $G_{1}$ and $G_{2}$ phases of…
Chemical reactions can be induced at a distance due to the propagation of electromagnetic signals during intermediate chemical stages. Although it is well known at optical frequencies, e.g. photosynthetic reactions, electromagnetic signals…
The lack of molecular-level understanding for the electronic excitation response of DNA to charged particle radiation, such as high-energy protons, remains a fundamental scientific bottleneck in advancing proton and other ion beam cancer…
Ion-induced DNA damage is an important effect underlying ion-beam cancer therapy. This paper introduces the methodology of modeling DNA damage induced by a shock wave caused by a projectile ion. Specifically, it is demonstrated how single-…
This paper describes the model for DNA in MATLAB taking into account all of component atoms. In this model, it is possible to generate sequences with length 10000 basis pairs available for introducing all types of sequences. Once the…
Electronic properties of DNA are believed to play a crucial role in many phenomena in living organisms, for example the location of DNA lesions by base excision repair (BER) glycosylases and the regulation of tumor-suppressor genes such as…
A mechanism of double strand breaking (DSB) in DNA due to the action of two electrons is considered. These are the electrons produced in the vicinity of DNA molecules due to ionization of water molecules with a consecutive emission of two…
A general theoretical framework is put forth to organize and understand various observed phenomena and mathematical relationships in the field of molecular biology. By modeling each cell in eukaryotic organisms as a processor having a…
We studied the electrical conductivity of DNA molecules with conducting atomic force microscopy as a function of the chemical nature of the substrate surfaces, the nature of the electrical contact, and the number of DNA molecules (from a…
This paper introduces the use of cable dynamics models as a means to explore the mechanics of DNA on long-length scales. It is on these length scales that DNA forms twisted and curved three-dimensional shapes known as supercoils and loops.…
Radiation damage is considered to be the major problem that still prevents imaging an individual biological molecule for structural analysis. So far, all known mapping techniques using sufficient short wave-length radiation, be it X-rays or…
We propose a multi-scale approach to understand the physics related to ion-beam cancer therapy. It allows the calculation of the probability of DNA damage as a result of irradiation of tissues with energetic ions, up to 430 MeV/u. This…
The DNA molecule, apart from carrying the genetic information, plays a crucial role in a variety of biological processes and find applications in drug design, nanotechnology and nanoelectronics. The molecule undergoes significant structural…
The effective DNA-DNA interaction force is calculated by computer simulations with explicit tetravalent counterions and monovalent salt. For overcharged DNA molecules, the interaction force shows a double-minimum structure. The positions…
Quantum effects are mainly used for the determination of molecular shapes in molecular biology, but quantum information theory may be a more useful tool to understand the physics of life. Organic molecules and quantum circuits/protocols can…
Measurements of electron transfer rates as well as of charge transport characteristics in DNA produced a number of seemingly contradictory results, ranging from insulating behaviour to the suggestion that DNA is an efficient medium for…
A mathematical model of genome degradation is proposed that takes into account a variable rate of mutation and increasing number of cells in a developing human organism. The model explains known properties of cancer development, in…
This paper is devoted to the analysis of the complex damage of DNA irradiated by ions. The analysis and assessment of complex damage is important because cells in which it occurs are less likely to survive because the DNA repair mechanisms…
Our understanding of radiation induced cellular damage has greatly improved over the past decades. Despite this progress, there are still many obstacles to fully understanding how radiation interacts with biologically relevant cellular…