Molecular models of DNA

About: Molecular models of DNA is a research topic. Over the lifetime, 300 publications have been published within this topic receiving 16805 citations.

Hierarchical multiscale simulation of DNA condensation

Abstract: DNA condensation at mesoscale level, induced by multivalent ions is of substantial importance for packing of DNA in vivo with many applications in biology, biotechnology and polymer physics. Rigorous modeling of this process with all-atom molecular dynamics (MD) simulations is presently impossible due to size and time scale limitations. Here, we present a hierarchical approach for systematic multiscale coarse-grained (CG) simulations of DNA condensation induced by the three-valent cobalt(III)-hexammine (CoHex3+). On the basis of all-atom MD simulations, we extract solvent-mediated effective potentials for a CG model of DNA and simulate DNA aggregation in the presence of CoHex3+. Further coarse-graining to a super-CG DNA model enables simulations of DNA condensation at mesoscale level. Modeling a 10 kbp-long DNA molecule results in formation of a toroid with distinct hexagonal packing in agreement with Cryo-EM observations. The approach uses no adjustable parameters and is applied on DNA up to megabase dimensions. It may be generalized to modeling chromatin up to chromosome size.

DNA Transcription Mechanism with a Moving Enzyme

Abstract: Previous numerical investigations of an one-dimensional DNA model with an extended modified coupling constant by transcripting enzyme are integrated to longer time and demonstrated explicitly the trapping of breathers by DNA chains with realistic parameters obtained from experiments. Furthermore, collective coordinate method is used to explain a previously observed numerical evidence that breathers placed far from defects are difficult to trap, and the motional effect of RNA-polymerase is investigated.

A DNA model for solving the hierarchical clustering problem

Abstract: The hierarchical clustering algorithm is one of the clustering algorithms used widely. The typical character of the hierarchical clustering algorithm is to find the “shortest” patterns. But it is not to ensure that to find the global optimal result by adding the shortest pattern each time. In this paper, we use DNA computing to solve this problem. Because during the ligation of the DNA strands, the bio-reaction's character is to combine all the possible single DNA strands into the shortest double DNA strand. We propose a DNA model with the coding strategy and DNA computing algorithm for the hierarchical clustering problem. we use this algorithm to solve the real problem — the retailer's region partition problem. Although we use the computer to simulate the bio-chemical reactions, we will execute this algorithm in the biological lab in the near future.

Pair-wise Key Pre-distribution Scheme Based on Extended DNA Model

Abstract: A DNA model based pair-wise key establishment scheme is analyzed and the result shows that the resilience of the scheme is poorCombining DNA model with the idea of multiple key pool,an extended DNA model based pair-wise key establishment scheme is proposedThe gray degree of the variable is changed form 2 toThe nodes select multi-DNA strands as its key ring and use the code of some oligonucleotide in some DNA strand as their actual pair-wise keyThe key connectivity,security and overhead of the scheme are discussedThe analysis shows that the overhead of computation and communication of the new scheme is little and the security is greatly improved compared with the original DNA model scheme

Implications of the quantum DNA model for information sciences

Abstract: The DNA molecule can be modeled as a quantum logic processor, and this model has been supported by pilot research that experimentally demonstrated non-local communication between cells in separated cell cultures. This modeling and pilot research have important implications for information sciences, providing a potential architecture for quantum computing that operates at room temperature and is scalable to millions of qubits, and including the potential for an entanglement communication system based upon the quantum DNA architecture. Such a system could be used to provide non-local quantum key distribution that could not be blocked by any shielding or water depth, would be simultaneous over any distance, and could not be electromagnetically interfered with or eavesdropped upon. The quantum DNA model also has implications for artificial neural networks and can provide architecture for a system of quantum random number generation.