The Algebraic Computing Structure of Four DNA Bases

2006 ◽  
Author(s):  
Ping Zhu ◽  
Xuqing Tang ◽  
Zhenyuan Xu ◽  
Weihong Guan
Keyword(s):  
Dna Bases ◽  
Algebraic Computing ◽  
Computing Structure

Partition Coefficients of Methylated DNA Bases Obtained from Free Energy Calculations with Molecular Electron Density Derived Atomic Charges.

2018 ◽  
Author(s):  
Alejandro Lara ◽  
Maximiliano Riquelme ◽  
Esteban Vöhringer-Martinez
Keyword(s):  
Electron Density ◽  
Partition Coefficients ◽  
Dna Bases ◽  
Atomic Charges ◽  
Free Energies ◽  
Solvation Model ◽  
Minimal Basis ◽  
Methylated Dna ◽  
Implicit Solvation Model ◽  
Good Agreement

<div> <div> <div> <p>Partition coefficients serve in various areas as pharmacology and environmental sciences to predict the hydrophobicity of different substances. Recently, they have been also used to address the accuracy of force fields for various organic compounds and specifically the methylated DNA bases. In this study atomic charges were derived by different partitioning methods (Hirshfeld and Minimal Basis Iterative Stockholder) directly from the electron density obtained by electronic structure calculations in vac- uum, with an implicit solvation model or with explicit solvation taking the dynamics of the solute and the solvent into account. To test the ability of these charges to describe electrostatic interactions in force fields for condensed phases the original atomic charges of the AMBER99 force field were replaced with the new atomic charges and combined with different solvent models to obtain the hydration and chloroform solvation free energies by molecular dynamics simulations. Chloroform-water partition coefficients derived from the obtained free energies were compared to experimental and previously reported values obtained with the GAFF or the AMBER-99 force field. The results show that good agreement with experimental data is obtained when the polarization of the electron density by the solvent has been taken into account deriving the atomic charges of polar DNA bases and when the energy needed to polarize the electron den- sity of the solute has been considered in the transfer free energy. These results were further confirmed by hydration free energies of polar and aromatic amino acid side chain analogues. Comparison of the two partitioning methods Hirsheld-I and Minimal Basis Iterative Stockholder (MBIS) revealed some deficiencies in the Hirshfeld-I method related to nonexistent isolated anionic nitrogen pro-atoms used in the method. Hydration free energies and partitioning coefficients obtained with atomic charges from the MBIS partitioning method accounting for polarization by the implicit solvation model are in good agreement with the experimental values. </p> </div> </div> </div>

Oxidized DNA Bases in Breast Cancer

2002 ◽  
Author(s):  
Mehul Desai ◽  
Krystyna Frenkel
Keyword(s):  
Breast Cancer ◽  
Dna Bases

scholarly journals Electron transport in DNA bases: An extension of the Geant4-DNA Monte Carlo toolkit

2021 ◽  
Vol 488 ◽  
pp. 70-82
Author(s):  
Sara A. Zein ◽  
Marie-Claude Bordage ◽  
Ziad Francis ◽  
Giovanni Macetti ◽  
Alessandro Genoni ◽  
...  
Keyword(s):  
Monte Carlo ◽  
Electron Transport ◽  
Dna Bases

scholarly journals A single inverse-designed photonic structure that performs parallel computing

2021 ◽  
Vol 12 (1) ◽  
Author(s):  
Miguel Camacho ◽  
Brian Edwards ◽  
Nader Engheta
Keyword(s):  
Wave Equation ◽  
Feedback Loop ◽  
Photonic Structure ◽  
Quantum Devices ◽  
Microwave Frequencies ◽  
Parallel Solution ◽  
Design Build ◽  
Mathematical Problems ◽  
Computing Structure ◽  
Independent Integral

AbstractIn the search for improved computational capabilities, conventional microelectronic computers are facing various problems arising from the miniaturization and concentration of active electronics. Therefore, researchers have explored wave systems, such as photonic or quantum devices, for solving mathematical problems at higher speeds and larger capacities. However, previous devices have not fully exploited the linearity of the wave equation, which as we show here, allows for the simultaneous parallel solution of several independent mathematical problems within the same device. Here we demonstrate that a transmissive cavity filled with a judiciously tailored dielectric distribution and embedded in a multi-frequency feedback loop can calculate the solutions of a number of mathematical problems simultaneously. We design, build, and test a computing structure at microwave frequencies that solves two independent integral equations with any two arbitrary inputs and also provide numerical results for the calculation of the inverse of four 5 x 5 matrices.

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