scholarly journals Non-monotonous polymer translocation time across corrugated channels: Comparison between Fick-Jacobs approximation and numerical simulations

2016 ◽  
Vol 145 (11) ◽  
pp. 114904 ◽  
Author(s):  
Valentino Bianco ◽  
Paolo Malgaretti
Keyword(s):  
Numerical Simulations ◽  
Translocation Time ◽  
Polymer Translocation

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.

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.

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 Theoretical Modeling of Polymer Translocation: From the Electrohydrodynamics of Short Polymers to the Fluctuating Long Polymers

Polymers ◽  
2019 ◽  
Vol 11 (1) ◽  
pp. 118 ◽  
Author(s):  
Sahin Buyukdagli ◽  
Jalal Sarabadani ◽  
Tapio Ala-Nissila
Keyword(s):  
Driving Force ◽  
Polymer Dynamics ◽  
Polymer Model ◽  
Theoretical Formulation ◽  
Dna Mobility ◽  
Monovalent Salt ◽  
Translocation Velocity ◽  
Translocation Time ◽  
Polymer Translocation ◽  
Polymer Fluctuations

The theoretical formulation of driven polymer translocation through nanopores is complicated by the combination of the pore electrohydrodynamics and the nonequilibrium polymer dynamics originating from the conformational polymer fluctuations. In this review, we discuss the modeling of polymer translocation in the distinct regimes of short and long polymers where these two effects decouple. For the case of short polymers where polymer fluctuations are negligible, we present a stiff polymer model including the details of the electrohydrodynamic forces on the translocating molecule. We first show that the electrohydrodynamic theory can accurately characterize the hydrostatic pressure dependence of the polymer translocation velocity and time in pressure-voltage-driven polymer trapping experiments. Then, we discuss the electrostatic correlation mechanisms responsible for the experimentally observed DNA mobility inversion by added multivalent cations in solid-state pores, and the rapid growth of polymer capture rates by added monovalent salt in α -Hemolysin pores. In the opposite regime of long polymers where polymer fluctuations prevail, we review the iso-flux tension propagation (IFTP) theory, which can characterize the translocation dynamics at the level of single segments. The IFTP theory is valid for a variety of polymer translocation and pulling scenarios. We discuss the predictions of the theory for fully flexible and rodlike pore-driven and end-pulled translocation scenarios, where exact analytic results can be derived for the scaling of the translocation time with chain length and driving force.

Two-dimensional diffusion model for the biopolymers dynamics at nanometer scale

Open Physics ◽  
2009 ◽  
Vol 7 (3) ◽  
Author(s):  
Viorel Paun
Keyword(s):  
Electric Field ◽  
External Electric Field ◽  
Electric Field Intensity ◽  
Nanometer Scale ◽  
Linear Polymers ◽  
Two Dimensional ◽  
Physical Behavior ◽  
Dimensional Diffusion ◽  
Translocation Time ◽  
Polymer Translocation

AbstractIn this paper the driven transport of linear polymers through a nanopore is presented. Biopolymer physical behavior in an external electric field is modeled and its motion is simulated using the Langevin impulse integrator method. Within fairly large limits, the polymer translocation time is inversely proportional with the electric field intensity and directly proportional with the polymer chain length.

Polymer Translocation Time

2021 ◽  
pp. 11534-11542
Author(s):  
Yuyuan Lu ◽  
Zhenhua Wang ◽  
Lijia An ◽  
An-Chang Shi
Keyword(s):  
Translocation Time ◽  
Polymer Translocation

scholarly journals Polymer translocation through nano-pores: influence of pore and polymer deformation

2018 ◽  
Author(s):  
M. A. Shahzad
Keyword(s):  
Thermal Fluctuations ◽  
Coarse Grained ◽  
Free Energy Barrier ◽  
Transport Dynamics ◽  
Polymer Deformation ◽  
Cellular Environment ◽  
Small Pore ◽  
Drastic Increase ◽  
Translocation Time ◽  
Polymer Translocation

We have simulated polymer translocation across the a α-hemolysin nano-pore via a coarse grained computational model for both the polymer and the pore. We simulate the translocation process by allowing the protein cross a free-energy barrier from a metastable state, in the presence of thermal fluctuations. The deformation in the channel, which we model by making the radius of pore change from large to small size, can be originated by the random and non-random (systematic) cellular environment, drive out the polymer out of equilibrium during the transport dynamics. We expect that in more realistic conditions, effects originating on the translocation phenomena due to the deformability of the nano-pore can either decrease or increase the transport time of biomolecule passing through the channel. Deformation in channel can occurred because the structure of α-hemolysin channel is not completely immobile, hence a small pore deformation can be occurred during translocation process. We also discuss the effects of polymer deformation on the translocation process, which we achieve by varying the value of the empirical and dihedral potential constants. We investigate the dynamic and thermodynamical properties of the translocation process by revealing the statistics of translocation time as a function of the pulling inward force acting along the axis of the pore under the influence of small and large pore. We observed that a pore with small size can speed down the polymer translocation process, especially at the limit of small pulling force. A drastic increase in translocation time at the limit of low force for small pore clearly illustrate the strong interaction between the transport polymer and pore. Our results can be of fundamental importance for those experiments on DNA-RNA sorting and sequencing and drug delivery mechanism for anti-cancer therapy.

Saturation mechanism and generated viscosity in gravito-turbulent accretion disks

2020 ◽  
Vol 640 ◽  
pp. A53
Author(s):  
L. Löhnert ◽  
S. Krätschmer ◽  
A. G. Peeters
Keyword(s):  
Growth Rate ◽  
Numerical Simulations ◽  
Accretion Disks ◽  
Gravitational Instability ◽  
Turbulent Viscosity ◽  
Radial Distance ◽  
Maximum Growth ◽  
Wave Number ◽  
Radiative Cooling ◽  
Mixing Length

Here, we address the turbulent dynamics of the gravitational instability in accretion disks, retaining both radiative cooling and irradiation. Due to radiative cooling, the disk is unstable for all values of the Toomre parameter, and an accurate estimate of the maximum growth rate is derived analytically. A detailed study of the turbulent spectra shows a rapid decay with an azimuthal wave number stronger than ky−3, whereas the spectrum is more broad in the radial direction and shows a scaling in the range kx−3 to kx−2. The radial component of the radial velocity profile consists of a superposition of shocks of different heights, and is similar to that found in Burgers’ turbulence. Assuming saturation occurs through nonlinear wave steepening leading to shock formation, we developed a mixing-length model in which the typical length scale is related to the average radial distance between shocks. Furthermore, since the numerical simulations show that linear drive is necessary in order to sustain turbulence, we used the growth rate of the most unstable mode to estimate the typical timescale. The mixing-length model that was obtained agrees well with numerical simulations. The model gives an analytic expression for the turbulent viscosity as a function of the Toomre parameter and cooling time. It predicts that relevant values of α = 10−3 can be obtained in disks that have a Toomre parameter as high as Q ≈ 10.

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