arXiv subjects

Tapio Ala-Nissila

Publications and source records attributed to Tapio Ala-Nissila.

At least 127 records · Page 7Linked to original sources

arXiv2012

Polymer translocation under time-dependent driving forces: resonant activation induced by attractive polymer-pore interactions

We study the driven translocation of polymers under time-dependent driving forces using $N$-particle Langevin dynamics simulations. We consider the force to be either sinusoidally oscillating in time or dichotomic noise with exponential correlation time, to mimic both plausible experimental setups and naturally occurring biological conditions. In addition, we consider both the case of purely repulsive polymer-pore interactions and the case with additional attractive polymer-pore interactions, typically occurring inside biological pores. We find that the nature of the interaction fundamentally affects the translocation dynamics. For the non-attractive pore, the translocation time crosses over to a fast translocation regime as the frequency of the driving force decreases. In the attractive pore case, because of a free energy well induced inside the pore, the translocation time can be a minimum at the optimal frequency of the force, the so-called resonant activation. In the latter case, we examine the effect of various physical parameters on the resonant activation, and explain our observations using simple theoretical arguments.

cond-mat.soft↗

arXiv2012

Influence of non-universal effects on dynamical scaling in driven polymer translocation

We study the dynamics of driven polymer translocation using both molecular dynamics (MD) simulations and a theoretical model based on the non-equilibrium tension propagation on the {\it cis} side subchain. We present theoretical and numerical evidence that the non-universal behavior observed in experiments and simulations are due to finite chain length effects that persist well beyond the relevant experimental and simulation regimes. In particular, we consider the influence of the pore-polymer interactions and show that they give a major contribution to the non-universal effects. In addition, we present comparisons between the theory and MD simulations for several quantities, showing extremely good agreement in the relevant parameter regimes. Finally, we discuss the potential limitations of the present theories.

cond-mat.soft↗

arXiv2012

Scaling theory of driven polymer translocation

We present a theoretical argument to derive a scaling law between the mean translocation time $τ$ and the chain length $N$ for driven polymer translocation. This scaling law explicitly takes into account the pore-polymer interactions, which appear as a correction term to asymptotic scaling and are responsible for the dominant finite size effects in the process. By eliminating the correction-to-scaling term we introduce a rescaled translocation time and show, by employing both the Brownian Dynamics Tension Propagation theory [Ikonen {\it et al.}, Phys. Rev. E {\bf 85}, 051803 (2012)] and molecular dynamics simulations that the rescaled exponent reaches the asymptotic limit in a range of chain lengths that is easily accessible to simulations and experiments. The rescaling procedure can also be used to quantitatively estimate the magnitude of the pore-polymer interaction from simulations or experimental data. Finally, we also consider the case of driven translocation with hydrodynamic interactions (HIs). We show that by augmenting the BDTP theory with HIs one reaches a good agreement between the theory and previous simulation results found in the literature. Our results suggest that the scaling relation between $τ$ and $N$ is retained even in this case.

cond-mat.soft↗

arXiv2012

Hydrodynamic forces on steady and oscillating porous particles

We derive new analytical results for the hydrodynamic force exerted on a sinusoidally oscillating porous shell and a sphere of uniform density in the Stokes limit. The coupling between the spherical particle and the solvent is done using the Debye-Bueche-Brinkman (DBB) model, i.e. by a frictional force proportional to the local velocity difference between the permeable particle and the solvent. We compare our analytical results and existing dynamic theories to Lattice-Boltzmann simulations of full Navier-Stokes equations for the oscillating porous particle. We find our analytical results to agree with simulations over a broad range of porosities and frequencies.

physics.flu-dyn↗

arXiv2012

Hydrodynamic Effects on Confined Polymers

We consider the statics and dynamics of a flexible polymer confined between parallel plates both in the presence and absence of hydrodynamic interactions. The hydrodynamic interactions are described at the level of the fluctuating, compressible Navier-Stokes equation. We consider two cases: (i) confinement for both the solvent and the polymer, and (ii) confinement for the polymer only (in a 3D solvent), which is experimentally feasible, for instance, by (optical) trapping. We find a continuous transition from 2D to 3D dynamic scaling as a function of decreasing degree of confinement within the de Gennes and the weak-confinement regimes. We demonstrate that, in the presence of hydrodynamics, the polymer's center-of-mass diffusion coefficient in the direction parallel to the walls scales differently as a function of the level of confinement in cases (i) and (ii). We also find that in the commonly used Langevin dynamics description, the polymer swells more parallel to the walls than in the presence of hydrodynamics, and the planar diffusion coefficient shows scaling behavior similar to case (ii) rather than case (i). In addition, we quantify the differences in the static structure factor of the polymer between cases (i) and (ii), and between case (i) and Langevin dynamics.

cond-mat.soft↗

arXiv2012

Electrostatic correlations in inhomogeneous charged fluids beyond loop expansion

Electrostatic correlation effects in inhomogeneous symmetric electrolytes are investigated within a previously developed electrostatic self-consistent (SC) theory (R.R. Netz and H. Orland, Eur. Phys.J. E 11, 301 (2003)). To this aim, we introduce two computational approaches that allow to solve the SC equations beyond the loop expansion. Both approaches can handle the case of dielectrically discontinuous boundaries where the one-loop theory is known to fail. By comparing the theoretical results obtained from these schemes with the results of the MC simulations that we ran for ions at neutral single dielectric interfaces as well as with previous MC data for charged interfaces, we first show that the weak coupling (WC) Debye-Huckel (DH) theory remains quantitatively accurate up to the bulk ion density rhob=0.01 M, whereas the SC theory exhibits a good quantitative accuracy up to rhob=0.2 M. Then, we derive from the perturbative SC scheme the one-loop theory of asymmetrically partitioned salt systems around a dielectrically homogeneous charged surface. It is shown that correlation effects originate in these systems from a competition between the salt screening loss at the interface driving the ions to the bulk region, and the interfacial counterion screening excess attracting them towards the surface. In the case of weak surface charges, the interfacial salt screening loss is the dominant effect. As a result, correlations decrease the MF density of both coions and counterions. With increasing surface charge, the surface-attractive counterion screening excess starts to dominate, and correlation effects amplify in this regime the MF density of both type of ions. We also show that at a characteristic value of the electrostatic coupling parameter, electrostatic correlations result in a charge inversion effect.

cond-mat.soft↗

arXiv2012

Unifying model of driven polymer translocation

We present a Brownian dynamics model of driven polymer translocation, in which non-equilibrium memory effects arising from tension propagation (TP) along the cis side subchain are incorporated as a time-dependent friction. To solve the effective friction, we develop a finite chain length TP formalism, expanding on the work of Sakaue [Sakaue, PRE 76, 021803 (2007)]. The model, solved numerically, yields results in excellent agreement with molecular dynamics simulations in a wide range of parameters. Our results show that non-equilibrium TP along the cis side subchain dominates the dynamics of driven translocation. In addition, the model explains the different scaling of translocation time w.r.t chain length observed both in experiments and simulations as a combined effect of finite chain length and pore-polymer interactions.

cond-mat.soft↗

arXiv2012

Dipolar depletion effect on the differential capacitance of carbon based materials

The remarkably low experimental values of the capacitance data of carbon based materials in contact with water solvent needs to be explained from a microscopic theory in order to optimize the efficiency of these materials. We show that this experimental result can be explained by the dielectric screening deficiency of the electrostatic potential, which in turn results from the interfacial solvent depletion effect driven by image dipole interactions. We show this by deriving from the microscopic system Hamiltonian a non-mean-field dipolar Poisson-Boltzmann equation. This can account for the interaction of solvent molecules with their electrostatic image resulting from the dielectric discontinuity between the solvent medium and the substrate. The predictions of the extended dipolar Poisson-Boltzmann equation for the differential capacitance are compared with experimental data and good agreement is found without any fitting parameters.

cond-mat.soft↗

arXiv2010

Polymer Translocation Induced by a Bad Solvent

We employ 3D Langevin Dynamics simulations to study the dynamics of polymer chains translocating through a nanopore in presence of asymmetric solvent conditions. Initially a large fraction ($>$ 50%) of the chain is placed at the \textit{cis} side in a good solvent while the $trans$ segments are placed in a bad solvent that causes the chain to collapse and promotes translocation from the $cis$ to the $trans$ side. In particular, we study the ratcheting effect of a globule formed at the \textit{trans} side created by the translocated segment, and how this ratchet drives the system towards faster translocation. Unlike in the case of unbiased or externally forced translocation where the mean first passage time $\langle τ\rangle $ is often characterized by algebraic scaling as a function of the chain length $N$ with a single scaling exponent $α$, and the histogram of the mean first passage time $P(τ/\langleτ\rangle)$ exhibits scaling, we find that scaling is not well obeyed. For relatively long chains we find $\langle τ\rangle \sim N^α$ where $α\approx 1$ for $\varepsilon/k_{B}T > 1$. In this limit, we also find that translocation proceeds with a nearly constant velocity of the individual beads(monomers), which is attributed to the coiling of the globule. We provide an approximate theory assuming rotat ional motion restricted on a 2D disc to demonstrate that there is a crossover from diffusive behavior of the center of mass for short chains to a single file translocation for long chains, where the average translocation time scales linearly with the chain length $N$.

cond-mat.soft↗

arXiv2009

Driven polymer translocation through nanopores: slow versus fast dynamics

We investigate the dynamics of polymer translocation through nanopores under external driving by 3D Langevin Dynamics simulations, focusing on the scaling of the average translocation time $τ$ versus the length of the polymer, $τ\sim N^α$. For slow translocation, i.e., under low driving force and/or high friction, we find $α\approx 1+ν\approx 1.588$ where $ν$ denotes the Flory exponent. In contrast, $α\approx 1.37$ is observed for fast translocation due to the highly deformed chain conformation on the trans side, reflecting a pronounced non-equilibrium situation. The dependence of the translocation time on the driving force is given by $τ\sim F^{-1}$ and $τ\sim F^{-0.80}$ for slow and fast translocation, respectively. These results clarify the controversy on the magnitude of the scaling exponent $α$ for driven translocation.

cond-mat.soft↗

arXiv2009

Polymer translocation out of confined environments

We consider the dynamics of polymer translocation out of confined environments. Analytic scaling arguments lead to the prediction that the translocation time scales like $τ\sim N^{β+ν_{2D}}R^{1+(1-ν_{2D})/ν}$ for translocation out of a planar confinement between two walls with separation $R$ into a 3D environment, and $τ\sim N^{β+1}R$ for translocation out of two strips with separation $R$ into a 2D environment. Here, $N$ is the chain length, $ν$ and $ν_{2D}$ are the Flory exponents in 3D and 2D, and $β$ is the scaling exponent of translocation velocity with $N$, whose value for the present choice of parameters is $β\approx 0.8$ based on Langevin dynamics simulations. These scaling exponents improve on earlier predictions.

cond-mat.soft↗

arXiv2009

Three-dimensional "Mercedes-Benz" model for water

In this paper we introduce a three-dimensional version of the Mercedes-Benz model to describe water molecules. In this model van der Waals interactions and hydrogen bonds are given explicitly through a Lennard-Jones potential and a Gaussian orientation-dependent terms, respectively. At low temperature the model freezes forming Ice-I and it reproduces the main peaks of the experimental radial distribution function of water. In addition to these structural properties, the model also captures the thermodynamical anomalies of water: the anomalous density profile, the negative thermal expansivity, the large heat capacity and the minimum in the isothermal compressibility.

cond-mat.soft↗

arXiv2008

Scaling exponents of Forced Polymer Translocation through a nano-pore

We investigate several scaling properties of a translocating homopolymer through a thin pore driven by an external field present inside the pore only using Langevin Dynamics (LD) simulation in three dimension (3D). Specifically motivated by several recent theoretical and numerical studies that are apparently at odds with each other, we determine the chain length dependence of the scaling exponents of the average translocation time, the average velocity of the center of mass, $ $, the effective radius of gyration during the translocation process, and the scaling exponent of the translocation coordinate ($s$-coordinate) as a function of the translocation time. We further discuss the possibility that in the case of driven translocation the finite pore size and its geometry could be responsible that the veclocity scaling exponent is less than unity and discuss the dependence of the scaling exponents on the pore geometry for the range of $N$ studied here.

cond-mat.soft↗

arXiv2008

Dynamics of DNA translocation through an attractive nanopore

We investigate the dynamics of DNA translocation through a nanopore driven by an external force using Langevin dynamics simulations in two dimensions (2D) to study how the translocation dynamics depend on the details of the DNA sequences. We consider a coarse-grained model of DNA built from two bases $A$ and $C$, having different base-pore interactions, {\textit e.g.}, a strong (weak) attractive force between the pore and the base $A$ ($C$) inside the pore. From a series of studies on hetero-DNAs with repeat units $A_mC_n$, we find that the translocation time decreases exponentially as a function of the volume fraction $f_C$ of the base $C$. %($ε_{pC} < ε_{pA}$). For longer $A$ sequences with $f_C \le 0.5$, the translocation time strongly depends on the orientation of DNA, namely which base enters the pore first. Our studies clearly demonstrate that for a DNA of certain length $N$ with repeat units $A_mC_n$, the pattern exhibited by the waiting times of the individual bases and their periodicity can unambiguously determine the values of $m$, $n$ and $N$ respectively. Therefore, a prospective experimental realization of this phenomenon may lead to fast and efficient sequence detection technic.

cond-mat.soft↗

arXiv2008

Translocation Dynamics with Attractive Nanopore-Polymer Interactions

Using Langevin dynamics simulations, we investigate the influence of polymer-pore interactions on the dynamics of biopolymer translocation through nanopores. We find that an attractive interaction can significantly change the translocation dynamics. This can be understood by examining the three components of the total translocation time $τ\approx τ_1+τ_2+τ_3$ corresponding to the initial filling of the pore, transfer of polymer from the \textit{cis} side to the \textit{trans} side, and emptying of the pore, respectively. We find that the dynamics for the last process of emptying of the pore changes from non-activated to activated in nature as the strength of the attractive interaction increases, and $τ_3$ becomes the dominant contribution to the total translocation time for strong attraction. This leads to a new dependence of $τ$ as a function of driving force and chain length. Our results are in good agreement with recent experimental findings, and provide a possible explanation for the different scaling behavior observed in solid state nanopores {\it vs.} that for the natural $α$-hemolysin channel.

cond-mat.soft↗

arXiv2007

Sequence dependence of DNA translocation through a nanopore

We investigate the dynamics of DNA translocation through a nanopore using 2D Langevin dynamics simulations, focusing on the dependence of the translocation dynamics on the details of DNA sequences. The DNA molecules studied in this work are built from two types of bases $A$ and $C$, which has been shown previously to have different interactions with the pore. We study DNA with repeating blocks $A_nC_n$ for various values of $n$, and find that the translocation time depends strongly on the {\em block length} $2n$ as well as on the {\em orientation} of which base entering the pore first. Thus, we demonstrate that the measurement of translocation dynamics of DNA through nanopore can yield detailed information about its structure. We have also found that the periodicity of the block sequences are contained in the periodicity of the residence time of the individual nucleotides inside the pore.

cond-mat.soft↗

arXiv2007

Comment on ``Passage Times for Unbiased Polymer Translocation through a Narrow Pore''

One of the most fundamental quantities associated with polymer translocation through a nanopore is the translocation time $τ$ and its dependence on the chain length $N$. Our simulation results based on both the bond fluctuation Monte Carlo and Molecular Dynamics methods confirm the original prediction $τ\sim N^{2ν+1}$, which scales in the same manner as the Rouse relaxation time of the chain except for a larger prefactor, and invalidates other scaling claims.

cond-mat.soft↗

arXiv2007

Influence of polymer-pore interactions on translocation

We investigate the influence of polymer-pore interactions on the translocation dynamics using Langevin dynamics simulations. An attractive interaction can greatly improve translocation probability. At the same time, it also increases translocation time slowly for weak attraction while exponential dependence is observed for strong attraction. For fixed driving force and chain length the histogram of translocation time has a transition from Gaussian distribution to long-tailed distribution with increasing attraction. Under a weak driving force and a strong attractive force, both the translocation time and the residence time in the pore show a non-monotonic behavior as a function of the chain length. Our simulations results are in good agreement with recent experimental data.

cond-mat.soft↗