Sequencing of semiflexible polymers of varying bending rigidity using patterned pores

Kumar, Rajneesh; Chaudhuri, Abhishek; Kapri, Rajeev

doi:10.1063/1.5036529

Cited by 20 publications

(25 citation statements)

References 84 publications

(84 reference statements)

Supporting

Mentioning

Contrasting

Order By: Relevance

“…The residence times of the monomers in the pore exhibit less variability in the case of a neutral wall because the absence of a force pushing them toward or away from the wall results in their trajectories being largely similar to one another. the results of Kumar et al, [20] who reported w 2 (s) to increase with the strength of the monomer-pore attraction. They also found that the sharp change in w 2 (s) observed for the end monomers diminishes as the driving force increases.…”

Section: Effect Of Polymer-pore Interactionssupporting

confidence: 54%

“…[17][18][19] The last two strategies are the focus of the present computational study. Although the effect of polymer-pore interactions upon the translocation time has been investigated in previous simulation studies, [13,16,20] the pore was idealized as having a planar or cylindrical geometry in most such cases. The effect of the polymer-pore interactions may be very different in pores with more complicated geometries.…”

Section: Doi: 101002/mats202000042mentioning

confidence: 99%

See 1 more Smart Citation

Polyelectrolyte Translocation through a Corrugated Nanopore

Nagarajan

Chen

2020

Macro Theory & Simulations

View full text Add to dashboard Cite

The problem of slowing down the rate of DNA translocation through a nanopore so as to facilitate detection of the genetic information remains a major challenge. In this study, the effectiveness of employing corrugated nanopores to reduce the polymer translocation velocity is investigated using dissipative particle dynamics (DPD) simulations. The average translocation time, <τ>, increases with the pore length and extent of variation of the pore cross‐sectional area. A systematic comparison of <τ> between flat and corrugated nanopores with walls that are either neutral or attractive for the polymer is performed. The value of <τ> for a corrugated nanopore with an attractive wall is 158% greater than that for a flat pore with a neutral wall. The extent of increase in <τ> obtained by manipulating either the geometry of the pore or the nature of its interaction with the polymer alone is significantly smaller. This is because the combined effect of monomer‐pore interactions and the spatial variation of the electric field strength significantly slows down the entry and escape of the chain from the pore.

show abstract

Section: Effect Of Polymer-pore Interactionssupporting

confidence: 54%

Section: Doi: 101002/mats202000042mentioning

confidence: 99%

Polyelectrolyte Translocation through a Corrugated Nanopore

Nagarajan

Chen

2020

Macro Theory & Simulations

View full text Add to dashboard Cite

show abstract

“…We first considered PA chains composed of N = 20 monomers carrying either types of charges +1 or −1. We enumerated all possible 2 20 sequences, and for each sequence 100 independent trials for translocation were conducted. To explore the influence of the sequence length, we also tested the translocation times for N = 40, for which we created 10 7 independent random sequences.…”

Section: Model: Monte Carlo Simulationmentioning

confidence: 99%

“…Translocation dynamics of negatively charged particles [14] and polymers (polyelectrolytes) through the α-hemolysin has been addressed [15][16][17]. Simulation studies include the influence of pore charge [18], heterogeneity in charge distribution [19], polymer rigidity [20], solvent conditions [21] and temperature [8]. The structure of the α-hemolysin pore is known at the scale of single residues.…”

Section: Introductionmentioning

confidence: 99%

Translocation, Rejection and Trapping of Polyampholytes

et al. 2022

View full text Add to dashboard Cite

Polyampholytes (PA) are a special class of polymers comprising both positive and negative monomers along their sequence. Most proteins have positive and negative residues and are PAs. Proteins have a well-defined sequence while synthetic PAs have a random charge sequence. We investigated the translocation behavior of random polyampholyte chains through a pore under the action of an electric field by means of Monte Carlo simulations. The simulations incorporated a realistic translocation potential profile along an extended asymmetric pore and translocation was studied for both directions of engagement. The study was conducted from the perspective of statistics for disordered systems. The translocation behavior (translocation vs. rejection) was recorded for all 220 sequences comprised of N = 20 charged monomers. The results were compared with those for 107 random sequences of N = 40 to better demonstrate asymptotic laws. At early times, rejection was mainly controlled by the charge sequence of the head part, but late translocation/rejection was governed by the escape from a trapped state over an antagonistic barrier built up along the sequence. The probability distribution of translocation times from all successful attempts revealed a power-law tail. At finite times, there was a population of trapped sequences that relaxed very slowly (logarithmically) with time. If a subensemble of sequences with prescribed net charge was considered the power-law decay was steeper for a more favorable net charge. Our findings were rationalized by theoretical arguments developed for long chains. We also provided operational criteria for the translocation behavior of a sequence, explaining the selection by the translocation process. From the perspective of protein translocation, our findings can help rationalize the behavior of intrinsically disordered proteins (IDPs), which can be modeled as polyampholytes. Most IDP sequences have a strong net charge favoring translocation. Even for sequences with those large net charges, the translocation times remained very dispersed and the translocation was highly sequence-selective.

show abstract

“…The carbon atom has a unique ability to participate in robust covalent bonds with the other carbon atoms in various hybridization states, namely, sp, sp 2 , and sp 3 . This property enables them to form different types of structures, namely, long chain polymers and beautiful structured allotropes [1][2][3] and is one of great importance in organic and biochemistry. [4] Over the past few decades, carbon nanoparticles have received a great interest from biologists, chemists, and physicists.…”

Section: Introductionmentioning

confidence: 99%

Dynamics of the mixtures of fullerene‐60 and aromatic solvents: A molecular dynamics approach

Singh

2020

J of Physical Organic Chem

View full text Add to dashboard Cite

The dynamics of the fullerene molecule (C 60) in the different aromatic solvents has been probed using all-atom molecular dynamics simulation. For this study, the four aromatic solvents, (1) 1-chloronaphthalene, (2) 1-methylnaphthalene, (3) 1,2,4-trimethylbenzene, and (4) chlorobenzene, have been used. The 1-chloronaphthalene is important due to the high solubility (51 g/L) of the fullerene in it. The rest of the three solvents have the decreasing order of

show abstract

Sequencing of semiflexible polymers of varying bending rigidity using patterned pores

Cited by 20 publications

References 84 publications

Polyelectrolyte Translocation through a Corrugated Nanopore

Polyelectrolyte Translocation through a Corrugated Nanopore

Translocation, Rejection and Trapping of Polyampholytes

Dynamics of the mixtures of fullerene‐60 and aromatic solvents: A molecular dynamics approach

Contact Info

Product

Resources

About