Related papers: Gene Copy Number and Cell Cycle Arrest
Cancer is a term that denotes a group of diseases caused by abnormal growth of cells that can spread in different parts of the body. According to the World Health Organization (WHO), cancer is the second major cause of death after…
A common approach to quantifying DNA involves repeated cycles of DNA amplification. This approach, employed by the polymerase chain reaction (PCR), produces outputs that are corrupted by amplification noise, making it challenging to…
Oxidative DNA single strand breaks arise continuously in cells and defects in their repair have been implicated in neurological disease. While much progress has been made in understanding how chromosomal single strand breaks are repaired…
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…
The origin of heredity is studied as a recursive state in a replicating proto-cell consisting of many molecule species in mutually catalyzing reaction networks. Protocells divide when the number of molecules, increasing due to replication,…
Genetic recombination can produce heterogeneous phylogenetic histories within a set of homologous genes. Delineating recombination events is important in the study of molecular evolution, as inference of such events provides a clearer…
Single molecule DNA experiments often generate data from force versus extension measurements involving the tethering of a microsphere to one end of a single DNA molecule while the other is attached to a substrate. We show that the…
We present a detailed kinetic model for the Polymerase Chain Reaction, and model the probability of replication in terms of the physical parameters of the problem. Applying the theory of branching processes, we show the existance of a new…
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…
How a nano-searcher finds its nano-target is a general problem in non-equilibrium statistical physics. It becomes vital when the searcher is a damaged DNA fragment trying to find its counterpart on the intact homologous chromosome. If the…
Signaling pathways serve to communicate information about extracellular conditions into the cell, to both the nucleus and cytoplasmic processes to control cell responses. Genetic mutations in signaling network components are frequently…
For efficient application of protons and light ions in radiotherapy, detailed knowledge and realistic models of the corresponding radiobiological mechanism are necessary. Basic characteristics of this mechanism have been represented within…
Renaturation of complementary single strands of DNA is one of the important processes that requires better understanding in the view of molecular biology and biological physics. Here we develop a stochastic dynamical model on the DNA…
Specific activator and repressor transcription factors which bind to specific regulator DNA sequences, play an important role in gene activity control. Interactions between genes coding such transcription factors should explain the…
The molecular network in an organism consists of transcription/translation regulation, protein-protein interactions/modifications and a metabolic network, together forming a system that allows the cell to respond sensibly to the multiple…
The mitotic cell cycle governs DNA replication and cell division. The effectiveness of radiotherapy and chemotherapy depends on cell-cycle position, with increased resistance during DNA replication and mitosis. Thus, accurate mathematical…
This paper proposes that eukaryotic cells, under severe genotoxic stress, can commit genoautotomy (genome 'self-injury') that involves cutting and releasing single-stranded DNA (ssDNA) fragments from double-stranded DNA and leaving ssDNA…
We present a theoretical agent-based model of cell evolution under the action of cytotoxic treatments, such as radioteraphy or chemoteraphy. The major features of cell cycle and proliferation, cell damage and repair, and chemical diffusion…
The cell cycle duration is a variable cellular phenotype that underlies long-term population growth and age structures. By analyzing the stationary solutions of a branching process with heritable cell division times, we demonstrate…
The phage $\lambda$ infection of an \textit{E. coli} cell has become a paradigm for understanding the molecular processes involved in gene expression and cell signaling. This system provides an example of a genetic switch, as cells with…