As challenging the coarse-grained simulation to predict the free energy of ss/dsDNA precisely using a new thermostat strategy, the stability of ss/dsDNA strand and nanoparticle delivery ratchet system corresponding to stimuli like thermal gradient and fixation rigidity are investigated.

The new thermostat, which is modified by internal heat diffusion along the molecule instead of Langevin equation by Koh et al.\[arXiv:1910.02880, 2019\] has shown that the Coarse-Grained molecular dynamics (CGMD) simulation can dictate the subtle nonlinearity of free thermal vibration of SWCNT. The same method is applied to oxDNA \[Šulc, P. et al., J. Chem. Phys. 137,  2012\], the coarse-grained model which has analyzed DNA origami and theoretical dynamics research on DNA molecular systems. The suggested thermostat algorithm offers very neat level of total energy, which indicates the system has a minimized level of influence from random force from Langevin thermostat. By adapting new thermostat, ss/dsDNA could be less affected by random noise. It means the motion of coarse-grained particle from the thermal energy including the thermal fluctuations inside the particle is directly assumed as the consequence in macroscopic scale. This should be identical to the dynamics from the free energy landscape of the system. More the replicated model precisely dictates the free energy landscape of original model, more delicate dynamics of the system could be revealed. Although the Gaussian distribution assures the influence of the artificially mimicked thermal noise to be irrelevant in overall dynamic characteristics, it can also distort the view of the pathways which can be altered by small artificial randomness. If unnecessary randomness can be reduced, such trial would offer the possibility to observe and the motion characteristics of DNA itself separately from the influence of random fluctuations so that it would provide interesting perspectives on twist-bend coupling. \[Nomidis, S. K. et al. Phys. Rev. E, 2019\]

 

Brownian ratchet system with nanoparticle as suggested by Park et al.\[ Park, S., Song, J. & Kim, J. S.. Sci. Adv. 5, 2019\] is one of the possible candidates that can offer the interesting perspectives on free energy landscape of dsDNA and its twist-bend coupling. It is designed to be a one-way ratchet to deliver nanoscale nanoparticle on sequence engineered dsDNA to change NP-DNA binding energy gradually so that NP can move along the strand to one direction. The changing salt concentration is used to switching the activation of the binding energy. With the preciseness that new thermostat can dictates, the different stimuli for ratchet system has tried which can alter the activation of binding energy threshold for more effective ratchet system and the influence of twist-bend mode of dsDNA is examined.  


Free Energy Landscape for Twist-Bending Coupling of ss/dsDNA and Its Influence on DNA-NP Brownian Ratchet System

Division / Sponsors: 
Aerospace, Bioengineering, Applied Mechanics, Design Engineering Division, Advanced Energy Systems, Manufacturing Engineering Division, Noise Control and Acoustics, Nondestructive Evaluation, Diagnosis, and Prognosis (NDPD), Nuclear Engineering Division, Process Industries Division, Fluids Engineering, Heat Transfer, Materials, Microelectromechanical Systems, Safety Engineering and Risk Analysis, Computers & Information in Engineering


Paper Proceedings: https://asmedigitalcollection.asme.org/IMECE/IMECE2020/volume/84478

IMECE2020 - Virtual Conference

Supporting the need among researchers worldwide for additional online and multimedia content, ASME now offers the ASME Conference Video Collection. This platform will collect and provide long-term access to conference presentation videos, encompassing all technology areas within ASME's technical conference and events program. About 30,000-40,000 engineers across all mechanical engineering and related disciplines participate in ASME conferences each year. This includes authors of approximately 6,000 to 8,000 technical papers published by ASME, the majority of whom also submit video presentations for our virtual conferences. The video collection will be available as an add-on to existing product packages or as a separate subscription.