scholarly journals Some aspects of a two-pore translocation problem

2021 ◽  
Vol 2122 (1) ◽  
pp. 012003
Author(s):  
Aniket Bhattacharya
Keyword(s):  
Brownian Dynamics ◽  
Coarse Grained ◽  
Mean First Passage Times ◽  
Chain Stiffness ◽  
Flexible Polymer ◽  
Simulation Results ◽  
The Right ◽  
Polymer Segment ◽  
Semi Flexible Polymer ◽  
Passage Times

Abstract We report Brownian dynamics (BD) simulation results for a coarse-grained (CG) model semi-flexible polymer threading through two nanopores. Particularly we study a “tug-of-war” situation where equal and opposite forces are applied on each pore to avoid folds for the polymer segment in between the pores. We calculate mean first passage times (MFPT) through the left and the right pores and show how the MFPT decays as a function of the off-set voltage between the pores. We present results for several bias voltages and chain stiffness. Our BD simulation results validate recent experimental results and offer avenues to further explore various aspects of multi-pore translocation problem using BD simulation strategies which we believe will provide insights to design new experiments.

scholarly journals A Coarse Grained Model for DNA and Polymer Packaging: Statics and Dynamics

2005 ◽  
Vol 6 (2) ◽  
pp. 115-117 ◽  
Author(s):  
I. Ali ◽  
D. Marenduzzo ◽  
C. Micheletti ◽  
J. M. Yeomans
Keyword(s):  
Coarse Grained ◽  
Viral Capsids ◽  
Coarse Grained Model ◽  
Flexible Polymer ◽  
Numerical Characterization ◽  
Bacteriophage Genome ◽  
Statics And Dynamics ◽  
Dynamical Features ◽  
Semi Flexible Polymer

We present a numerical characterization of the statics and dynamics of the packaging of a semi-flexible polymer inside a sphere. The study is motivated by recent experiments on the packaging of DNA inside viral capsids. It is found that the force required to confine the coarse-grained polymer is in fair agreement with that found in experiments for the packaging of the phi29 bacteriophage genome. Despite its schematic nature, the model is capable of reproducing the most salient dynamical features of packaging experiments such as the presence of pauses during individual packaging processes and the trend of the resisting force as a function of chain packed fraction.

Monte Carlo simulation on the dynamics of a semi-flexible polymer in the presence of nanoparticles

2018 ◽  
Vol 20 (41) ◽  
pp. 26333-26343 ◽  
Author(s):  
Yi Peng ◽  
Huan Zhang ◽  
Xiao-Wei Huang ◽  
Jian-Hua Huang ◽  
Meng-Bo Luo
Keyword(s):  
Monte Carlo Simulation ◽  
Monte Carlo ◽  
Polymer Dynamics ◽  
Polymer Nanoparticle ◽  
Chain Stiffness ◽  
Flexible Polymer ◽  
Semi Flexible Polymer

Polymer dynamics vary non-monotonically with chain stiffness at strong polymer–nanoparticle attraction: stiff polymers can move faster than flexible ones.

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.

scholarly journals Water supply network with zonation system in Golo Wua dan Golo Watu Village, Manggarai District

2020 ◽  
Vol 4 (1) ◽  
Author(s):  
Teguh Taruna Utama
Keyword(s):  
Drinking Water ◽  
Water Supply ◽  
Distribution Network ◽  
Water Sources ◽  
Pipe Diameter ◽  
Water Supply Network ◽  
Minimum Pressure ◽  
Simulation Results ◽  
Pressure Resistance ◽  
The Right

Drinking water sources in Manggarai Regency are mostly supplied from springs. Golo Wua and Golo Watu are two villages in Manggarai Regency that utilize springs. About 12.06 liters/second of drinking water are needed by residants in those villages. This study addresses to forecast the demand of drinking water. This study found that pressure values in manual calculations range from 1.85 meters to 84.22 meters. The minimum pressure requirements from BPP-SPAM is 7 meters (0.7 bar). While the simulation results using the EPANET program, the pressure value is at 1.90 meters up to 84.22 meters. Therefore, the pipe diameter selection is appropriate and the pressure meets the requirements of the BPP-SPAM. Difference between pressure values less than 5% indicates that the selection is the right pipe diameter. Choosing the right pipe diameter will optimize the distribution network in the villages of Golo Wua and Golo Watu. The selected pipe is HDPE type. Selected pipe diameter 1½"; 2"; 2½”; 3"; 4 and 5". The pipe has a pressure resistance of up to 125 meters.

scholarly journals Forensic igneous petrology: locating the source quarry for the “black granite" Titanic headstones in Halifax, Nova Scotia, Canada

2017 ◽  
Vol 53 ◽  
pp. 087-114
Author(s):  
D. Barrie Clarke ◽  
Christopher R.M. McFarlane ◽  
David Hamilton ◽  
David Stevens
Keyword(s):  
Nova Scotia ◽  
New Brunswick ◽  
Coarse Grained ◽  
Chemical Compositions ◽  
Dimension Stone ◽  
Forensic Evidence ◽  
Igneous Petrology ◽  
Temporal Properties ◽  
Textural Parameters ◽  
The Right

In Halifax, Nova Scotia, 149 victims of the 1912 sinking of the Titanic lie beneath petrologically identical "black granite" headstones. Those headstones, supplied by the White Star Line, arrived in Halifax in late 1912, but no known historical document reveals their source. They consist of medium- to coarse-grained olivine-bearing gabbro, with cumulus phases consisting of randomly oriented euhedral plagioclase laths, corroded olivine, and titaniferous magnetite, and intercumulus material consisting of augite with reaction rims of hornblende, both of which are variably altered to actinolite and biotite. Three types of forensic evidence [quantitative – radiometric age of 422.1 ± 1.3 Ma (n = 17), mean olivine FeO/(FeO + MgO) values ranging from 0.43 to 0.46, augite rim trace- element compositions (35 elements), and whole-rock chemical compositions (48 elements), including statistical analysis of all these data showing no significant differences between the headstones and their putative source quarry; qualitative – mineral assemblages, modal proportions, textural parameters, style and degree of alteration; and circumstantial – regional reputation, quarrying history, local logistics, regional transportation, McGrattan marker] connect the Titanic headstones to the Saint George Batholith in southwestern New Brunswick. Precise matching of any dimension stone to its source quarry is problematic, because that material connects only to a void in the quarry. Ideally, all physical-chemical-temporal properties of the dimension stone and source quarry should match, both quantitatively and qualitatively, but in reality only the ages must almost certainly match. Thus it is remotely possible for the right quarry to mismatch most of the properties of the dimension stone, and for a wrong quarry to match most of the properties of the dimension stone. However, in the case of the Titanic headstones, the cumulative weight of all the quantitative, qualitative, and circumstantial evidence, combined with a process of elimination and application of Ockham’s razor, indicate that the Charles Hanson quarry near Bocabec, southwestern New Brunswick, is the likely source for the gabbroic Titanic headstones in Halifax, Nova Scotia.

scholarly journals Study on the Effect of Heat-Input on the Thickness of the Heat-Affected Zone of the SUS316L Steel Welded Joint by Numerical Simulation

2021 ◽  
Vol 31 (5) ◽  
pp. 68-74
Keyword(s):  
Numerical Simulation ◽  
Heat Affected Zone ◽  
Heat Input ◽  
Welded Joint ◽  
Plate Thickness ◽  
Great Influence ◽  
Thickness Direction ◽  
Welding Joint ◽  
Simulation Results ◽  
The Right

The thickness of the heat-affected zone (HAZ) has a great influence on the strength of the welded joint, so one of the important tasks is to control the HAZ to a small enough level, through using the suitable heat-input (qd). In this study, the authors use SYSWELD software to compute and build a relationship between the heat-input and the thickness of the heat-affected zone in the plate thickness direction to find the right heat-input for researched welding joint. The simulation results show that when welding the root pass with qd > 552 J/mm and the cap pass with 754 J/mm < qd < 1066 J/mm, the thickness of HAZ were increased with a function almost linearly.

scholarly journals Analysis of suspension bridge tunnel-type anchorage construction on the stability of surrounding rock

2020 ◽  
Vol 198 ◽  
pp. 02006
Author(s):  
Nana Li ◽  
Yongqiang Zhou ◽  
Yanqiang Zhao ◽  
Guiju Li
Keyword(s):  
Suspension Bridge ◽  
Surrounding Rock ◽  
Construction Process ◽  
Analysis Model ◽  
Stability Of Surrounding Rock ◽  
Numerical Software ◽  
Left And Right ◽  
Simulation Results ◽  
The Stability ◽  
The Right

In order to study the interaction between the left and right tunnels of suspension bridge tunnel-type anchorage, the finite difference numerical software is used to analyze the mechanical properties of the surrounding rock during the construction process. A numerical analysis model based on FLAC3D is established to analyze the stress, displacement and plastic zone changes of the surrounding rock of right tunnel anchor cavern during the construction of left tunnel anchor cavern. The right tunnel anchor cavern is excavated firstly, and then the left tunnel anchor cavern is excavated. The numerical simulation results show that the main displacement of the right tunnel occurs in the construction stage of the anchor plug body and the rear anchor cavern of the left tunnel. During the excavation of the left tunnel, the plastic zones of the left and right tunnel anchor caverns are only connected above the middle of the waist wall. Therefore, it is suggested that during the construction process, especially in the excavation stage of the anchor plug body and the rear anchor cavern, the area above the middle of the tunnel waist wall should be strengthened in time to ensure the construction safety.

scholarly journals Dilute Solution Structure of Bottlebrush Polymers

2019 ◽  
Author(s):  
Sarit Dutta ◽  
Matthew A. Wade ◽  
Dylan J. Walsh ◽  
Damien Guironnet ◽  
Simon A. Rogers ◽  
...  
Keyword(s):  
Brownian Dynamics ◽  
Solution Structure ◽  
Coarse Grained ◽  
Poly Lactic Acid ◽  
Linear Polymers ◽  
Molecular Architecture ◽  
Wide Range ◽  
Conformational Properties ◽  
Atomistic Structure ◽  
Insight Into

<div>Bottlebrush polymers are a class of macromolecules that has recently found use</div><div>in a wide variety of materials, ranging from lubricating brushes and</div><div>nanostructured coatings to elastomeric gels that exhibit structural color. These</div><div>polymers are characterized by dense branches extending from a central backbone,</div><div>and thus have properties distinct from linear polymers. It remains a challenge</div><div>to specifically understand conformational properties of these molecules, due to</div><div>the wide range of architectural parameters that can be present in a system, and</div><div>thus there is a need to accurately characterize and model these molecules. In</div><div>this paper, we use a combination of viscometry, light scattering, and computer</div><div>simulations to gain insight into the conformational properties of dilute</div><div>bottlebrush polymers. We focus on a series of model bottlebrushes consisting of</div><div>a poly(norbornene) (PNB) backbone with poly(lactic acid) (PLA) side chains. We</div><div>demonstrate that intrinsic viscosity and hydrodynamic radius are experimental</div><div>observations \emph{sensitive} to molecular architecture, exhibiting distinct</div><div>differences with different choices of branch and backbone lengths. Informed by</div><div>the atomistic structure of this PNB-PLA system, we rationalize a coarse-grained</div><div>simulation model that we evaluate using a combination of Brownian Dynamics and</div><div>Monte Carlo simulations. We show that this exhibits quantitative matching to</div><div>experimental results, enabling us to characterize the overall shape of the</div><div>bottlebrush via a number of metrics that can be extended to more general</div><div>bottlebrush architectures.</div>

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