Coarse-grained simulations of stretching entangled DNA using oscillating electric fields.
نویسندگان
چکیده
DNA stretching in entangling media with oscillating electric fields is useful in DNA sequencing. We propose that stretching occurs around hairpin loops at the chain ends, caused by interactions with the medium. Brownian dynamics simulations show that this mechanism explains several experimental observations, including a resonance with varying field frequency.
منابع مشابه
Molecular Dynamics Simulations of Freezing Behavior of Pure Water and 14% Water-NaCl Mixture Using the Coarse-Grained Model
We performed molecular dynamics simulations using the coarse-grained model to study the freezing behavior of pure water and 14% water-salt mixture in a wide range of temperatures for a very long time around 50 nanoseconds. For the salty water, an interface in nanoscale was used. For both systems, the f...
متن کاملAnisotropic Coarse-Grained Model for Proteins Based On Gay–Berne and Electric Multipole Potentials
Gay-Berne anisotropic potential has been widely used to evaluate the non-bonded interactions between coarse-grained particles being described as elliptical rigid bodies. In this paper, we are presenting a coarse-grained model for twenty kinds of amino acids and proteins, based on the anisotropic Gay-Berne and point electric multipole (EMP) potentials. We demonstrate that the anisotropic coarse-...
متن کاملAnalytical rescaling of polymer dynamics from mesoscale simulations.
We present a theoretical approach to scale the artificially fast dynamics of simulated coarse-grained polymer liquids down to its realistic value. As coarse graining affects entropy and dissipation, two factors enter the rescaling: inclusion of intramolecular vibrational degrees of freedom and rescaling of the friction coefficient. Because our approach is analytical, it is general and transfera...
متن کاملStretching and twisting of the DNA duplexes in coarse-grained dynamical models.
Three coarse-grained molecular dynamics models of the double-stranded DNA are proposed and compared in the context of single molecule mechanical manipulation such as twisting and various schemes of stretching-unzipping, shearing, two-strand stretching and stretching of only one strand. The models differ in the number of effective beads (between two and five) representing each nucleotide. They a...
متن کاملMechanical properties of CNT reinforced nano-cellular polymeric nanocomposite foams
Mechanics of CNT-reinforced nano-cellular PMMA nanocomposites are investigated using coarse-grained molecular dynamics simulations. Firstly, static uniaxial stretching of bulk PMMA polymer is simulated and the results are compared with literature. Then, nano-cellular foams with different relative densities are constructed and subjected to static uniaxial stretching and obtained stress-strain cu...
متن کاملذخیره در منابع من
با ذخیره ی این منبع در منابع من، دسترسی به آن را برای استفاده های بعدی آسان تر کنید
برای دانلود متن کامل این مقاله و بیش از 32 میلیون مقاله دیگر ابتدا ثبت نام کنید
ثبت ناماگر عضو سایت هستید لطفا وارد حساب کاربری خود شوید
ورودعنوان ژورنال:
- Chemical communications
دوره 47 1 شماره
صفحات -
تاریخ انتشار 2011