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Register a new userTug-of-War in a Double-Nanopore System
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Aniket Bhattacharya
Publication date
2020
fields
Physics
and research's language is
English
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We simulate a tug-of-war (TOW) scenario for a model double-stranded DNA threading through a double nanopore (DNP) system. The DNA, simultaneously captured at both pores is subject to two equal and opposite forces $-vec{f}_L= vec{f}_R$ (TOW), where $vec{f}_L$ and $vec{f}_R$ are the forces applied to the left and the right pore respectively. Even though the net force on the DNA polymer $Delta vec{f}_{LR}=vec{f}_L+ vec{f}_R=0$, the mean first passage time (MFPT) $langle tau rangle$ depends on the magnitude of the TOW forces $ left | f_L right | = left |f_R right | = f_{LR}$. We qualitatively explain this dependence of $langle tau rangle$ on $f_{LR}$ from the known results for the single-pore translocation of a triblock copolymer. We demonstrate that the time of flight (TOF) of a monomer with index $m$ ($langle tau_{LR}(m) rangle$) from one pore to the other exhibits quasi-periodic structure commensurate with the distance between the pores $d_{LR}$. Finally, we study the case $Delta vec{f}_{LR}=vec{f}_L+ vec{f}_R e 0$, and qualitatively reproduce the experimental result of the dependence of the MFPT on $Deltavec{f}_{LR}$. For a moderate bias, the MFPT for the DNP system for a chain length $N$ follows the same scaling ansatz as that of for the single nanopore, $langle tau rangle = left( AN^{1+ u} + eta_{pore}N right) left(Delta f_{LR}right)^{-1}$, where $eta_{pore}$ is the pore friction, which enables us to estimate $langle tau rangle $ for a long chain. Our Brownian dynamics simulation studies provide fundamental insights and valuable information about the details of the translocation speed obtained from $langle tau_{LR}(m) rangle$, and accuracy of the translation of the data obtained in the time-domain to units of genomic distances.
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The potential of a double nanopore system to determine DNA barcodes has been demonstrated experimentally. By carrying out Brownian dynamics simulation on a coarse-grained model DNA with protein tag (barcodes) at known locations along the chain backbone, we demonstrate that due to large variation of velocities of the chain segments between the tags, it is inevitable to under/overestimate the genetic lengths from the experimental current blockade and time of flight data. We demonstrate that it is the tension propagation along the chains backbone that governs the motion of the entire chain and is the key element to explain the non uniformity and disparate velocities of the tags and DNA monomers under translocation that introduce errors in measurement of the length segments between protein tags. Using simulation data we further demonstrate that it is important to consider the dynamics of the entire chain and suggest methods to accurately decipher barcodes. We introduce and validate an interpolation scheme using simulation data for a broad distribution of tag separations and suggest how to implement the scheme experimentally.
We study escape dynamics of a double-stranded DNA (dsDNA) through an idealized double nanopore (DNP) geometry subject to two equal and opposite forces (tug-of-war) using Brownian dynamics (BD) simulation. In addition to the geometrical restrictions imposed on the cocaptured dsDNA segment in between the pores, the presence of tug-of-war forces at each pore results in a variation of the local chain stiffness for the segment of the chain in between the pores which increases the overall stiffness of the chain. We use BD simulation results to understand how the intrinsic chain stiffness and the TOW forces affect the escape dynamics by monitoring the local chain persistence length $ell_p$, the residence time of the individual monomers $W(m)$ in the nanopores, and the chain length dependence of the escape time $langle tau rangle$ and its distribution. Finally, we generalize the scaling theory for the unbiased single nanopore translocation for a fully flexible chain for the escape of a semi-flexible chain through a DNP in presence of TOW forces. We establish that the stiffness dependent part of the escape time is approximately independent of the translocation mechanism so that $langle tau rangle sim ell_p^{2/D+2}$, and therefore the generalized escape time for a semi-flexible chain can be written as $langle tau rangle = AN^alphaell_p^{2/D+2}$. We use BD simulation results to compare the predictions of the scaling theory. Our numerical studies supplemented by scaling analysis provide fundamental insights to design new experiments where a dsDNA moves slowly through a series of graphene nanopores.
This is a preprint of Chapter 2 in the following work: Marta Lewicka, A Course on Tug-of-War Games with Random Noise, 2020, Springer, reproduced with permission of Springer Nature Switzerland AG. We present the basic relation between the linear potential theory and random walks. This fundamental connection, developed by Ito, Doob, Levy and others, relies on the observation that harmonic functions and martingales share a common cancellation property, expressed via mean value properties. It turns out that, with appropriate modifications, a similar observation and approach can be applied also in the nonlinear case, which is of main interest in our Course Notes. Thus, the present Chapter serves as a stepping stone towards gaining familiarity with more complex nonlinear constructions. After recalling the equivalent defining properties of harmonic functions, we introduce the ball walk. This is an infinite horizon discrete process, in which at each step the particle, initially placed at some point $x_0$ in the open, bounded domain $mathcal{D}subsetmathbb{R}^N$, is randomly advanced to a new position, uniformly distributed within the following open ball: centered at the current placement, and with radius equal to the minimum of the parameter $epsilon$ and the distance from the boundary $partialmathcal{D}$. With probability one, such process accumulates on $partialmathcal{D}$ and $u^epsilon(x_0)$ is then defined as the expected value of the given boundary data $F$ at the process limiting position. Each function $u^epsilon$ is harmonic, and if $partialmathcal{D}$ is regular, then each $u^epsilon$ coincides with the unique harmonic extension of $F$ in $mathcal{D}$. One sufficient condition for regularity is the exterior cone condition.
We propose a simple channel-allocation method based on tug-of-war (TOW) dynamics, combined with the time scheduling based on nonlinear oscillator synchronization to efficiently use of the space (channel) and time resources in wireless communications. This study demonstrates that synchronization groups, where each node selects a different channel, are non-uniformly distributed in phase space such that every distance between groups is larger than the area of influence. New type of self-organized spatiotemporal patterns can be formed for resource allocation according to channel rewards.
We study the mean value properties of $mathbf{p}$-harmonic functions on the first Heisenberg group $mathbb{H}$, in connection to the dynamic programming principles of certain stochastic processes. We implement the approach of Peres-Scheffield to provide the game-theoretical interpretation of the sub-elliptic $mathbf{p}$-Laplacian; and of Manfredi-Parviainen-Rossi to characterize its viscosity solutions via the asymptotic mean value expansions.
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