Results 41 to 50 of about 698,311 (125)

QuantumDNA: A Python Package for Analyzing Quantum Charge Dynamics in DNA and Exploring Its Biological Relevance [PDF]

arXiv
The study of DNA charge dynamics is a highly interdisciplinary field that bridges physics, chemistry, biology, and medicine, and plays a critical role in processes such as DNA damage detection, protein-DNA interactions, and DNA-based nanotechnology. However, despite significant advances in each of these areas, knowledge often remains inaccessible to ...
arxiv  

Detection of Epigenomic Network Community Oncomarkers [PDF]

arXiv, 2015
In this paper we propose network methodology to infer prognostic cancer biomarkers based on the epigenetic pattern DNA methylation. Epigenetic processes such as DNA methylation reflect environmental risk factors, and are increasingly recognised for their fundamental role in diseases such as cancer.
arxiv  

Can Specific THz Fields Induce Collective Base-Flipping in DNA? A Stochastic Averaging and Resonant Enhancement Investigation Based on a New Mesoscopic Model [PDF]

arXiv
We study the metastability, internal frequencies, activation mechanism, energy transfer, and the collective base-flipping in a mesoscopic DNA via resonance with specific electric fields. Our new mesoscopic DNA model takes into account not only the issues of helicity and the coupling of an electric field with the base dipole moments, but also includes ...
arxiv  

Flexible Cancer-Associated Chromatin Configuration (CACC) Might Be the Fundamental Reason Why Cancer Is So Difficult to Cure [PDF]

arXiv, 2019
We once proposed that cell-type-associated chromatin configurations determine cell types and that cancer cell type is determined by cancer-associated chromatin configuration (CACC). In this paper, we hypothesize that flexible cell-type-associated chromatin configuration is associated with cell potency and has an advantage over inflexible one in ...
arxiv  

DNA Fragments in Crude Oil Reveals Earth's Hidden History [PDF]

arXiv
This groundbreaking research extracted DNA from petroleum using nanoparticle affinity bead technology, yielding 3,159,020 petroleum DNA (pDNA) sequences, primarily environmental DNA. While most original in situ DNA (oriDNA) was lost, ancient DNA (aDNA) from petroleum offers an important source of ecological and evolutionary information, surpassing ...
arxiv  

Built to evolve [PDF]

arXiv, 2005
We study the probabilities of evolution based on random mutations and natural selection. We conclude that evolution to multicellular eukaryots, or even prokaryots, is unlikely to be the result of only random mutations. Complex organisms have evolved through several mechanisms besides random mutations, namely DNA recombination, adaptive mutations, and ...
arxiv  

Intermediate coherent-incoherent charge transport: DNA as a case study [PDF]

J. Phys. Chem. C 120 (42), 23951-23962 (2016), 2016
We study an intermediate quantum coherent-incoherent charge transport mechanism in metal-molecule-metal junctions using B\"uttiker's probe technique. This tool allows us to include incoherent effects in a controlled manner, and thus to study situations in which partial decoherence affects charge transfer dynamics.
arxiv  

DNA Hash Pooling and its Applications [PDF]

arXiv, 2007
In this paper we describe a new technique for the comparison of populations of DNA strands. Comparison is vital to the study of ecological systems, at both the micro and macro scales. Existing methods make use of DNA sequencing and cloning, which can prove costly and time consuming, even with current sequencing techniques.
arxiv  

Double-Strand Break Clustering: An Economical and Effective Strategy for DNA Repair [PDF]

arXiv
In mammalian cells, repair centers for DNA double-strand breaks (DSBs) have been identified. However, previous researches predominantly rely on methods that induce specific DSBs by cutting particular DNA sequences. The clustering and its spatiotemporal properties of non-specifically DSBs, especially those induced by environmental stresses such as ...
arxiv  

Modelling the proliferation of transposable elements in populations under environmental stress [PDF]

arXiv, 2016
In this article, we investigate the evolution of sexual diploid populations which are hosts for active TE families. Our purpose is to explore the relationship between the environmental change, that influences such population and activity of those TEs that are present in genomes.
arxiv