alexa A unified theoretical framework for fluctuating-charge models in atom-space and in bond-space.
Bioinformatics & Systems Biology

Bioinformatics & Systems Biology

Journal of Proteomics & Bioinformatics

Author(s): Chen J, Hundertmark D, Martnez TJ

Abstract Share this page

Abstract Our previously introduced QTPIE (charge transfer with polarization current equilibration) model [J. Chen and T. J. Martínez, Chem. Phys. Lett. 438, 315 (2007)] is a fluctuating-charge model with correct asymptotic behavior. Unlike most other fluctuating-charge models, QTPIE is formulated in terms of charge-transfer variables and pairwise electronegativities, not atomic charge variables and electronegativities. The pairwise character of the electronegativities in QTPIE allows us to avoid spurious charge transfer when bonds are broken. However, the increased number of variables leads to considerable computational expense and a rank-deficient set of working equations, which is numerically inconvenient. Here, we show that QTPIE can be exactly reformulated in terms of atomic charge variables, leading to a considerable reduction in computational complexity. The transformation between atomic and bond variables is generally applicable to arbitrary fluctuating charge models and uncovers an underlying topological framework that can be used to understand the relation between fluctuating-charge models and the classical theory of electrical circuits. This article was published in J Chem Phys and referenced in Journal of Proteomics & Bioinformatics

Relevant Expert PPTs

Relevant Speaker PPTs

  • David Köhne
    Principles and applications of optical switching assisted imaging and structuring schemes
    PPT Version | PDF Version
  • Dwi Astuti
    Phylogenetic position of Psittacula parakeet bird from Enggano Island, Indonesia based on analyses of cytochrome b gene sequences
    PPT Version | PDF Version
  • Inge Verbrugge
    Radio-immunotherapy of cancer: Therapeutic efficacy, underlying mechanisms and potential applications
    PPT Version | PDF Version
  • Mario Marques da Silva
    MIMO Systems and Applications
    PPT Version | PDF Version
  • Mehdi Shadaram
    Photonic Generation of Millimeter Wave Signals for Wireless Applications
    PPT Version | PDF Version
  • Akbar Vaseghi
    Gold nanoparticles for biomedical applications
    PPT Version | PDF Version
  • Osama O. Ibrahim
    Chemicals structure, properties, regulations and applications of non-nutritive-high intensity sweeteners
    PDF Version
  • Dongmei Li
    Dongmei Li- University-of-Rochester-An-evaluation-of-statistical-methods-for-DNA-methylation-microarray-data-analysis
    PPT Version | PDF Version
  • Pauline Korukundo
    Pauline-Korukundo-Kiira-Motors-Project-Uganda-Development-of-the-KIIRA-EV-SMACK-Supervisory-Control-Firmware
    PPT Version | PDF Version
  • Francis Jeshira Reynoso
    The clinical phenotype of PIGN deficiency and consequences of defective GPI biogenesis
    PPT Version | PDF Version
  • Yosef Yarden
    Classically, the 3’untranslated region (3’UTR) is that region in eukaryotic protein-coding genes from the translation termination codon to the polyA signal. It is transcribed as an integral part of the mRNA encoded by the gene. However, there exists another kind of RNA, which consists of the 3’UTR alone, without all other elements in mRNA such as 5’UTR and coding region. The importance of independent 3’UTR RNA (referred as I3’UTR) was prompted by results of artificially introducing such RNA species into malignant mammalian cells. Since 1991, we found that the middle part of the 3’UTR of the human nuclear factor for interleukin-6 (NF-IL6) or C/EBP gene exerted tumor suppression effect in vivo. Our subsequent studies showed that transfection of C/EBP 3’UTR led to down-regulation of several genes favorable for malignancy and to up-regulation of some genes favorable for phenotypic reversion. Also, it was shown that the sequences near the termini of the C/EBP 3’UTR were important for its tumor suppression activity. Then, the C/EBP 3’UTR was found to directly inhibit the phosphorylation activity of protein kinase CPKC in SMMC-7721, a hepatocarcinoma cell line. Recently, an AU-rich region in the C/EBP 3’UTR was found also to be responsible for its tumor suppression. Recently we have also found evidence that the independent C/EBP 3’UTR RNA is actually exists in human tissues, such as fetal liver and heart, pregnant uterus, senescent fibroblasts etc. Through 1990’s to 2000’s, world scientists found several 3’UTR RNAs that functioned as artificial independent RNAs in cancer cells and resulted in tumor suppression. Interestingly, majority of genes for these RNAs have promoter-like structures in their 3’UTR regions, although the existence of their transcribed products as independent 3’UTR RNAs is still to be confirmed. Our studies indicate that the independent 3’UTR RNA is a novel non-coding RNA species whose function should be the regulation not of the expression of their original mRNA, but of some essential life activities of the cell as a whole.
    PPT Version | PDF Version
  • Hamiyet Unal
    Constitutive activity in the angiotensin ii type 1 receptor: Discovery and applications
    PPT Version | PDF Version
  • Ana de Guzmán Báez
    Gypsum to Gypsum (GtoG): The European life project that aims to transform the gypsum waste market
    PPT Version | PDF Version
  • Constanca Figueiredo
    Generation of HLA Universal Platelets for Regenerative Applications
    PPT Version | PDF Version
  • Tianbiao Leo Liu
    Design and applications of redox active materials for advanced rechargeable batteries
    PPT Version | PDF Version

Recommended Conferences

  • 9th International Conference on Bioinformatics
    October 23-24, 2017 Paris, France
  • 9th International Conference and Expo on Proteomics
    October 23-25, 2017 Paris, France

Relevant Topics

Peer Reviewed Journals
 
Make the best use of Scientific Research and information from our 700 + peer reviewed, Open Access Journals
International Conferences 2017-18
 
Meet Inspiring Speakers and Experts at our 3000+ Global Annual Meetings

Contact Us

 
© 2008-2017 OMICS International - Open Access Publisher. Best viewed in Mozilla Firefox | Google Chrome | Above IE 7.0 version
adwords