scholarly journals Coarse-Grained Brownian Dynamics Simulation of Rule-Based Models

2013 ◽  
pp. 64-77 ◽  
Author(s):  
Michael Klann ◽  
Loïc Paulevé ◽  
Tatjana Petrov ◽  
Heinz Koeppl
Keyword(s):  
Brownian Dynamics ◽  
Dynamics Simulation ◽  
Coarse Grained ◽  
Brownian Dynamics Simulation ◽  
Rule Based

scholarly journals Prediction of solution properties and dynamics of RNAs by means of Brownian dynamics simulation of coarse-grained models: Ribosomal 5S RNA and phenylalanine transfer RNA

2015 ◽  
Vol 8 (1) ◽  
Author(s):  
Aarón Ayllón Benítez ◽  
José Ginés Hernández Cifre ◽  
Francisco Guillermo Díaz Baños ◽  
José García de la Torre
Keyword(s):  
Brownian Dynamics ◽  
Transfer Rna ◽  
Dynamics Simulation ◽  
Coarse Grained ◽  
Solution Properties ◽  
Brownian Dynamics Simulation ◽  
5S Rna

scholarly journals DNA barcodes using a double nanopore system

2021 ◽  
Vol 11 (1) ◽  
Author(s):  
Swarnadeep Seth ◽  
Aniket Bhattacharya
Keyword(s):  
Brownian Dynamics ◽  
Dynamics Simulation ◽  
Coarse Grained ◽  
Dna Barcodes ◽  
Brownian Dynamics Simulation ◽  
Simulation Data ◽  
Broad Distribution ◽  
Coarse Grained Model ◽  
Protein Tag ◽  
Protein Tags

AbstractThe potential of a double nanopore system to determine DNA barcodes has been demonstrated experimentally. By carrying out Brownian dynamics simulation on a coarse-grained model DNA with protein tag (barcodes) at known locations along the chain backbone, we demonstrate that due to large variation of velocities of the chain segments between the tags, it is inevitable to under/overestimate the genetic lengths from the experimental current blockade and time of flight data. We demonstrate that it is the tension propagation along the chain’s backbone that governs the motion of the entire chain and is the key element to explain the non uniformity and disparate velocities of the tags and DNA monomers under translocation that introduce errors in measurement of the length segments between protein tags. Using simulation data we further demonstrate that it is important to consider the dynamics of the entire chain and suggest methods to accurately decipher barcodes. We introduce and validate an interpolation scheme using simulation data for a broad distribution of tag separations and suggest how to implement the scheme experimentally.

Brownian Dynamics Simulation of the Dynamics of Stretched DNA

2014 ◽  
Author(s):  
Ikenna D. Ivenso ◽  
Todd D. Lillian
Keyword(s):  
Single Molecule ◽  
Brownian Dynamics ◽  
Magnetic Bead ◽  
Dynamics Simulation ◽  
Coarse Grained ◽  
Brownian Dynamics Simulation ◽  
Dna Molecule ◽  
Flexible Polymer ◽  
Dynamics Simulations ◽  
And Function

DNA is a long flexible polymer and is involved in several fundamental cellular processes such as transcription, replication and chromosome packaging. These processes induce forces and torques in the DNA which deform it. These deformations in turn affect the structure and function of DNA. However, understanding of the dynamic response of DNA to the various forces that act on it is still far from complete. Several experiments have been carried out to study these responses most of which use a micron sized magnetic bead attached to the DNA molecule to both manipulate it and to observe its dynamics. One limitation of this approach is that the dynamics of the DNA molecule has mostly been characterized “indirectly” by observing the dynamics of the magnetic bead. It is also reasonable to expect that, because of the size of the bead relative to that of the DNA, the magnetic bead dynamics will obscure that of the DNA. We adapt existing coarse-grained Brownian dynamics models of DNA to develop a model capable of representing the dynamics of DNA without any of the artifacts inherent to the experiments. This model accounts for bending, torsion, extension, electrostatics, hydrodynamics and the random thermal forces acting on DNA in an electrolyte solution. We then carry out Brownian dynamics simulations with our model to benchmark with well established theoretical results of a stretched polymer in solution. Finally, we employ our model to predict the relaxation time scale for single molecule experiments which sets the framework for future studies in which we plan to further shed light on the dynamics of DNA over long length and time scales.

Brownian Dynamics Simulations of Polymer Behavior in Nanofluidic and Microfluidic Systems

2007 ◽  
Author(s):  
Satish Kumar
Keyword(s):  
Brownian Dynamics ◽  
Simulation Method ◽  
Transport Processes ◽  
Design Tool ◽  
Dynamics Simulation ◽  
Coarse Grained ◽  
Contour Length ◽  
Brownian Dynamics Simulation ◽  
Polyelectrolyte Adsorption ◽  
Dynamics Simulations

Brownian dynamics (BD) is a stochastic simulation method that can quantitatively describe the non-equilibrium behavior of long polymers (∼1 micron contour length) over long time scales (∼1 s). With the increasing use of nanofluidic and microfluidic devices for the handling of biopolymers such as DNA, BD has the potential to be a powerful design tool for the separation and transport processes carried out in these devices. As a coarse-grained simulation method, BD also serves as a natural bridge between atomistic and continuum modeling. In this talk, an introduction to the Brownian dynamics simulation method will be given along with simulation results for some applications of current interest. The introduction will review basic molecular models for polymers (bead-rod, bead-spring) and the stochastic differential equations used to describe their dynamics. The applications will focus on polyelectrolyte adsorption and electrophoresis.

Brownian dynamics simulation of diffusion‐influenced bimolecular reactions

1984 ◽  
Vol 80 (4) ◽  
pp. 1517-1524 ◽  
Author(s):  
Scott H. Northrup ◽  
Stuart A. Allison ◽  
J. Andrew McCammon
Keyword(s):  
Brownian Dynamics ◽  
Dynamics Simulation ◽  
Brownian Dynamics Simulation ◽  
Bimolecular Reactions
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