Adaptive resolution simulation of an atomistic DNA molecule in MARTINI salt solution
نویسندگان
چکیده
منابع مشابه
Adaptive resolution simulation of a DNA molecule in salt solution.
We present a multiscale simulation of a DNA molecule in 1 M NaCl salt solution environment, employing the adaptive resolution simulation approach that allows the solvent molecules, i.e., water and ions, to change their resolution from atomistic to coarse-grained and vice versa adaptively on-the-fly. The region of high resolution moves together with the DNA center-of-mass so that the DNA itself ...
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We present an adaptive resolution simulation of protein G in multiscale water. We couple atomistic water around the protein with mesoscopic water, where four water molecules are represented with one coarse-grained bead, farther away. We circumvent the difficulties that arise from coupling to the coarse-grained model via a 4-to-1 molecule coarse-grain mapping by using bundled water models, i.e.,...
متن کاملSupporting Information for Adaptive resolution simulation of MARTINI solvents
The Langevin thermostat does not reproduce the correct hydrodynamics, i.e., the hydrodynamic interactions are unphysically screened. To correctly describe hydrodynamic interactions, we have to use the DPD thermostat1,2 instead. The DPD thermostat satisfies Newton’s third law by construction and owing to mass, momentum and temperature conservation, hydrodynamics is also properly reproduced.3 We ...
متن کاملAdaptive resolution simulation of salt solutions
We present an adaptive resolution simulation of aqueous salt (NaCl) solutions at ambient conditions using the adaptive resolution scheme. Our multiscale approach concurrently couples the atomistic and coarse-grained models of the aqueous NaCl, where water molecules and ions change their resolution while moving from one resolution domain to the other. We employ standard extended simple point cha...
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We review recent advances in the DNA sequencing method based on measurements of transverse electrical currents. Device configurations proposed in the literature are classified according to whether the molecular fingerprints appear as the major (Mode I) or perturbing (Mode II) current signals. Scanning tunneling microscope and tunneling electrode gap configurations belong to the former category,...
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ژورنال
عنوان ژورنال: The European Physical Journal Special Topics
سال: 2016
ISSN: 1951-6355,1951-6401
DOI: 10.1140/epjst/e2016-60117-8