scholarly journals Enhanced polymer capture speed and extended translocation time in pressure-solvation traps

2018 ◽  
Vol 97 (6) ◽  
Author(s):  
Sahin Buyukdagli
Keyword(s):  
Translocation Time

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 Translocation time of a polymer chain through an energy gradient nanopore

2017 ◽  
Vol 12 (3) ◽  
Author(s):  
Meng-Bo Luo ◽  
Shuang Zhang ◽  
Fan Wu ◽  
Li-Zhen Sun
Keyword(s):  
Polymer Chain ◽  
Energy Gradient ◽  
Translocation Time

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.

DYNAMICAL MODES OF POLYMER TRANSLOCATING THROUGH INTERACTING PORE UNDER CHEMICAL POTENTIAL DIFFERENCE

2011 ◽  
Vol 25 (25) ◽  
pp. 3345-3351 ◽  
Author(s):  
WEI-PING CAO ◽  
LI-ZHEN SUN ◽  
CHAO WANG ◽  
MENG-BO LUO
Keyword(s):  
Monte Carlo ◽  
Polymer Chain ◽  
Power Law ◽  
Chemical Potential ◽  
Monte Carlo Technique ◽  
Potential Difference ◽  
Nonequilibrium Process ◽  
Chemical Potential Difference ◽  
Translocation Time

The translocation of polymer chain through an interacting pore under chemical potential difference Δμ is simulated using Monte Carlo technique. Three translocation modes, dependent on the polymer–pore interaction ε and Δμ, are discovered. The translocation process is found to be an nonequilibrium process, which influences the dependence of translocation time τ on ε and Δμ. It is found that τ decreases in a power law relation with the increase of Δμ, and the exponent is dependent on the interaction.

scholarly journals Translocation of a Polymer through a Crowded Channel under Electrical Force

2017 ◽  
Vol 2017 ◽  
pp. 1-7 ◽  
Author(s):  
Tingting Sun ◽  
Yunxin Gen ◽  
Hujun Xie ◽  
Zhouting Jiang ◽  
Zhiyong Yang
Keyword(s):  
Field Strength ◽  
Shape Factor ◽  
Cylindrical Channel ◽  
Protein Translocation ◽  
Scaling Exponent ◽  
Scaling Relation ◽  
Maximum Value ◽  
Translocation Time ◽  
Dynamics Simulations ◽  
Number Of Segments

The translocation of a polymer chain through a crowded cylindrical channel is studied using the Langevin dynamics simulations. The influences of the field strength F, the chain length N, and the crowding extent ρ on the translocation time are evaluated, respectively. Scaling relation τ~F-α is observed. With the crowding extent ρ increasing, the scaling exponent α becomes large. It is found that, for noncrowded channel, translocation probability drops when the field strength becomes large. However, for high-crowded channel, it is the opposite. Moreover, the translocation time and the average translocation time for all segments both have exponential growth with the crowding extent. The investigation of shape factor δ shows maximum value with increasing of the number of segments outside s. At last, the number of segments inside channel Nin in the process of translocation is calculated and a peak is observed. All the information from the study may benefit protein translocation.

scholarly journals Numerical simulation of cell squeezing through a micropore by the immersed boundary method

2017 ◽  
Vol 232 (3) ◽  
pp. 502-514 ◽  
Author(s):  
Jifu Tan ◽  
Salman Sohrabi ◽  
Ran He ◽  
Yaling Liu
Keyword(s):  
Blood Sample ◽  
Tumor Cells ◽  
Circulating Tumor Cells ◽  
Applied Pressure ◽  
Immersed Boundary ◽  
Bending Resistance ◽  
Translocation Time ◽  
Simulation Results ◽  
Membrane Bending ◽  
Young Equation

The deformability of cells has been used as a biomarker to detect circulating tumor cells from patient blood sample using microfluidic devices with microscale pores. Successful separations of circulating tumor cells from a blood sample require careful design of the micropore size and applied pressure. This paper presented a parametric study of cell squeezing through micropores with different size and pressure. Different membrane compressibility modulus was used to characterize the deformability of varying cancer cells. Nucleus effect was also considered. It shows that the cell translocation time through the micropore increases with cell membrane compressibility modulus and nucleus stiffness. Particularly, it increases exponentially as the micropore diameter or pressure decreases. The simulation results such as the cell squeezing shape and translocation time agree well with experimental observations. The simulation results suggest that special care should be taken in applying Laplace–Young equation to microfluidic design due to the nonuniform stress distribution and membrane bending resistance.

scholarly journals Computer simulation of knotted proteins unfold and translocation through nano-pores

2018 ◽  
Author(s):  
M. A. Shahzad
Keyword(s):  
Computer Simulation ◽  
Computational Model ◽  
Coarse Grained ◽  
Kinetic Properties ◽  
Constant Force ◽  
Translocation Mechanism ◽  
Translocation Time ◽  
Knotted Protein ◽  
Knotted Proteins ◽  
Pulling Force

We study the unfold and translocation of knotted protein, YibK and YbeA, through α-hemolysin nano-pore via a coarse grained computational model. We observe that knot of protein unfold in advance before the translocation take place. We also characterized the translocation mechanism by studying the thermodynamical and kinetic properties of the process. In particular, we study the average of translocation time, and the translocation probability as a function of pulling force F acting in the channel. In limit of low pulling inward constant force acting along the axis of the pore, the YibK knotted protein takes longer average translocation time as compare to YbeA knotted protein.

scholarly journals Translocation of structured biomolecule through a vibrating nanopore

2018 ◽  
Author(s):  
M. A. Shahzad
Keyword(s):  
Protein Transport ◽  
Protein Translocation ◽  
Intermediate Frequency ◽  
Global Maximum ◽  
Cylindrical Pore ◽  
Transport Dynamics ◽  
Frequency Regime ◽  
Translocation Time ◽  
Static Channel ◽  
Resonant Activation

ABSTRACTWe study the effect of fluctuating environment in protein transport dynamics. In particular, we investigate the translocation of a structured biomolecule (protein) across a temporally modulated nano-pore. We allow the radius of the cylindrical pore to oscillate harmonically with certain frequency and amplitude about an average radius. The protein is imported inside the pore whose dynamics is influences by the fluctuating nature of the pore. 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, and the frequency of the time dependent radius of the channel. We also examine the distribution of translocation time in the intermediate frequency regime. We observe that the shaking mechanism of pore leads to accelerate the translocation process as compared to the static channel that has a radius equal to the mean radius of oscillating pore. Moreover, the translocation time shows a global maximum as a function of frequency of the oscillating radius, hence revealing a resonant activation phenomenon in the dynamics of protein translocation.

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