Polymer translocation of linear polymer and ring polymer influenced by crowding

2019 ◽  
Vol 33 (26) ◽  
pp. 1950318
Author(s):  
Qu-Cheng Gao ◽  
Zhuo-Yi Li ◽  
Yi-Wei Xu ◽  
Chen Guo ◽  
Ji-Xuan Hou
Keyword(s):  
Hard Sphere ◽  
Linear Polymer ◽  
Radius Of Gyration ◽  
Complex Environment ◽  
Surrounding Environment ◽  
The Monte Carlo Method ◽  
Ring Polymer ◽  
Translocation Time ◽  
Polymer Translocation ◽  
Crowded Environment

The transport of biomolecules across bio-membranes occurs in a complex environment where the fluid on both sides of the membrane contains many inclusions. The Monte Carlo method and the hard-sphere (HS) model are used to simulate the translocation of linear polymer and ring polymer through a nanopore in a crowded environment. We compare the results of linear polymer and ring polymer and find that the ring polymer is more sensitive to the surrounding environment. Moreover, the influences of the nanopore and the inclusions to the translocation are studied and our results show that the nanopore changes the translocation time and the inclusions change the translocation tendency to the random side of the membrane. Here, the radius of gyration is described as a balance.

scholarly journals Translocation through a narrow pore under a pulling force

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Mohammadreza Niknam Hamidabad ◽  
Rouhollah Haji Abdolvahab
Keyword(s):  
Interaction Energy ◽  
External Force ◽  
Center Of Mass ◽  
Three Dimensional ◽  
Major Effect ◽  
Translocation Time ◽  
Polymer Translocation ◽  
Pulling Force ◽  
External Forces ◽  
Polymer Shape

AbstractWe employ a three-dimensional molecular dynamics to simulate a driven polymer translocation through a nanopore by applying an external force, for four pore diameters and two external forces. To see the polymer and pore interaction effects on translocation time, we studied nine interaction energies. Moreover, to better understand the simulation results, we investigate polymer center of mass, shape factor and the monomer spatial distribution through the translocation process. Our results reveal that increasing the polymer-pore interaction energy is accompanied by an increase in the translocation time and decrease in the process rate. Furthermore, for pores with greater diameter, the translocation becomes faster. The shape analysis of the polymer indicates that the polymer shape is highly sensitive to the interaction energy. In great interactions, the monomers come close to the pore from both sides. As a result, the translocation becomes fast at first and slows down at last. Overall, it can be concluded that the external force does not play a major role in the shape and distribution of translocated monomers. However, the interaction energy between monomer and nanopore has a major effect especially on the distribution of translocated monomers on the trans side.

Synthesis and Properties of Regular Star Polybutadienes with 32 Arms

1992 ◽  
Vol 65 (2) ◽  
pp. 303-314 ◽  
Author(s):  
L-L. Zhou ◽  
N. Hadjichristidis ◽  
P. M. Toporowski ◽  
J. Roovers
Keyword(s):  
Molecular Weight ◽  
Coupling Agent ◽  
Hard Sphere ◽  
Star Polymers ◽  
Radius Of Gyration ◽  
Linear Polymers ◽  
Solution Properties ◽  
Mean Square ◽  
Dilute Solution ◽  
Dilute Solution Properties

Abstract A dendrimer carbosilane containing 32 Si—Cl bonds in the perimeter has been prepared and has been used as a coupling agent to prepare 32-arm star polybutadienes. The dilute-solution properties 〈RG2〉, A2, [η], and D0 have been measured in one good solvent and in one ¸ -solvent. The dimensions of the 32-arm star polymers are compared with those of linear polymers at constant molecular weight. It is shown that the 32-arm star polybutadiene has the characteristic properties of a hard-sphere molecule in dilute solution. The equivalent hard-sphere radii calculated from A2, D0 and [η] are identical and 1.29 times larger than the root mean-square radius of gyration. The Daoud—Cotton scaling model for stars is also tested.

scholarly journals Dielectric Trapping of Biopolymers Translocating through Insulating Membranes

Polymers ◽  
2018 ◽  
Vol 10 (11) ◽  
pp. 1242 ◽  
Author(s):  
Sahin Buyukdagli ◽  
Jalal Sarabadani ◽  
Tapio Ala-Nissila
Keyword(s):  
Electrostatic Interactions ◽  
Screening Parameter ◽  
Dielectric Contrast ◽  
Polymer Interactions ◽  
Translocation Time ◽  
Drift Force ◽  
Polymer Translocation ◽  
Drift Behavior ◽  
Low Permittivity ◽  
Salt Screening

Sensitive sequencing of biopolymers by nanopore-based translocation techniques requires an extension of the time spent by the molecule in the pore. We develop an electrostatic theory of polymer translocation to show that the translocation time can be extended via the dielectric trapping of the polymer. In dilute salt conditions, the dielectric contrast between the low permittivity membrane and large permittivity solvent gives rise to attractive interactions between the c i s and t r a n s portions of the polymer. This self-attraction acts as a dielectric trap that can enhance the translocation time by orders of magnitude. We also find that electrostatic interactions result in the piecewise scaling of the translocation time τ with the polymer length L. In the short polymer regime L ≲ 10 nm where the external drift force dominates electrostatic polymer interactions, the translocation is characterized by the drift behavior τ ∼ L 2 . In the intermediate length regime 10 nm ≲ L ≲ κ b − 1 where κ b is the Debye–Hückel screening parameter, the dielectric trap takes over the drift force. As a result, increasing polymer length leads to quasi-exponential growth of the translocation time. Finally, in the regime of long polymers L ≳ κ b − 1 where salt screening leads to the saturation of the dielectric trap, the translocation time grows linearly as τ ∼ L . This strong departure from the drift behavior highlights the essential role played by electrostatic interactions in polymer translocation.

A Review on Snake Robot Locomotion, Modelling, and Controlling in Challenging Environment

2020 ◽  
Vol 17 (2) ◽  
pp. 558-569
Author(s):  
Areej Ghazi Abdulshaheed ◽  
Mohamed Bin Hussein ◽  
Mohd Azuwan Mat Dzahir ◽  
Shaharil Mad Saad ◽  
Rohani Othman
Keyword(s):  
Detection System ◽  
Obstacle Detection ◽  
Complex Environment ◽  
Snake Robot ◽  
Robot Locomotion ◽  
Surrounding Environment ◽  
Different Types ◽  
Common Strategy ◽  
Challenging Environment ◽  
Robot Body

The flexibility of the snake robot body and its ability to adapt to different types of terrain attracted the attention of researchers to the great possibilities of its application in inspection, rescue, and searching tasks. These tasks require the robot to have the ability to navigate smartly in a complex environment (CE), which is considered to be one of the most critical challenges in the robotics field. The robot should be able to sense the surrounding environment and overcome different types of obstacles. In this paper, we have presented a review of the different type of snake robot locomotion and the controlling strategies in an environment with obstacles. We focus on avoidance obstacle locomotion as it is considered to be the most common strategy for dealing with obstacles. In addition, various types of modeling and controlling of locomotion with the presence of obstacles are discussed. Finally, a recommendation on the introduction of an obstacle detection system (ODS) and sensor fusion technology is given.

Numerical simulation on polymer translocation into crowded environment with nanoparticles

2016 ◽  
Vol 294 (8) ◽  
pp. 1351-1357 ◽  
Author(s):  
Qing-Bao Ren ◽  
Song-Hua Ma ◽  
Ya-Jiang Chen ◽  
Li-Zhen Sun ◽  
Wei-Ping Cao
Keyword(s):  
Numerical Simulation ◽  
Polymer Translocation ◽  
Crowded Environment

scholarly journals Friction between ring polymer brushes

Soft Matter ◽  
2015 ◽  
Vol 11 (16) ◽  
pp. 3139-3148 ◽  
Author(s):  
Aykut Erbaş ◽  
Jarosław Paturej
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Polymer Brushes ◽  
Polymer Brush ◽  
Linear Polymer ◽  
Coarse Grained ◽  
Ring Polymer ◽  
Dynamics Simulations ◽  
Scaling Arguments ◽  
Coarse Grained Molecular Dynamics

Friction between ring polymer brush bilayers sliding past each other is studied using extensive coarse-grained molecular dynamics simulations and scaling arguments, and the results are compared to the friction between bilayers of linear polymer brushes.

scholarly journals Cancellation of Auxetic Properties in F.C.C. Hard Sphere Crystals by Hybrid Layer-Channel Nanoinclusions Filled by Hard Spheres of Another Diameter

Materials ◽  
2021 ◽  
Vol 14 (11) ◽  
pp. 3008
Author(s):  
Jakub W. Narojczyk ◽  
Krzysztof W. Wojciechowski ◽  
Jerzy Smardzewski ◽  
Attila R. Imre ◽  
Joseph N. Grima ◽  
...  
Keyword(s):  
Elastic Properties ◽  
Hard Sphere ◽  
Hard Spheres ◽  
Large Diameter ◽  
Hybrid Layer ◽  
Simple Modification ◽  
Periodic Arrays ◽  
Tetragonal System ◽  
The Monte Carlo Method ◽  
The Subject

The elastic properties of f.c.c. hard sphere crystals with periodic arrays of nanoinclusions filled by hard spheres of another diameter are the subject of this paper. It has been shown that a simple modification of the model structure is sufficient to cause very significant changes in its elastic properties. The use of inclusions in the form of joined (mutually orthogonal) layers and channels showed that the resulting tetragonal system exhibited a complete lack of auxetic properties when the inclusion spheres reached sufficiently large diameter. Moreover, it was very surprising that this hybrid inclusion, which can completely eliminate auxeticity, was composed of components that, alone, in these conditions, enhanced the auxeticity either slightly (layer) or strongly (channel). The study was performed with computer simulations using the Monte Carlo method in the isothermal-isobaric (NpT) ensemble with a variable box shape.

scholarly journals Association equilibria for proteins interacted with crowders of short-range attraction in crowded environment

2017 ◽  
Vol 31 (03) ◽  
pp. 1750007
Author(s):  
Jiachen Wei ◽  
Fan Song
Keyword(s):  
Hard Sphere ◽  
Relative Size ◽  
Macromolecular Crowding ◽  
Globular Proteins ◽  
Coarse Grained ◽  
Protein Solution ◽  
Ideal Behavior ◽  
Coarse Grained Model ◽  
Association Equilibria ◽  
Crowded Environment

Based on a very simple coarse-grained colloidal model, here we implement an effective hard-sphere theory and numerical simulation to capture the general features of the association equilibria for globular proteins in crowded environment. We measure the activity coefficient, i.e., the deviation from ideal behavior of protein solution, and the crowding factor, i.e., the contribution of crowders to the association equilibria, for proteins in macromolecular crowding. The results show that the association balance in macromolecular crowding depends sensitively on the magnitude of protein–crowder attraction and the relative size of reactant to crowding agent. Since our coarse-grained model is irrelevant to the microscopic details of the molecules, it can be applied to the control of the association equilibria of many globular proteins such as bovine serum albumin, crystallin and lysozyme.

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