Modification of surface properties by polymer adsorption is a widely used technique to tune interactions in molecular experiments such as nanopore sensing. Here, we investigate how the ionic current noise through solid-state nanopores reflects the adsorption of short, neutral polymers to the pore surface. The power spectral density of the noise shows a characteristic change upon adsorption of polymer, the magnitude of which is strongly dependent on both polymer length and salt concentration. In particular, for short polymers at low salt concentrations no change is observed, despite verification of comparable adsorption in these systems using quartz crystal microbalance measurements. We propose that the characteristic noise is generated by the movement of polymers on and off the surface and perform simulations to assess the feasibility of this model. Excellent agreement with experimental data is obtained using physically motivated simulation parameters, providing deep insight into the shape of the adsorption potential and underlying processes. This paves the way towards using noise spectral analysis for in situ characterisation of functionalised nanopores.
We present a new concept for the separation of DNA molecules by contour length that combines a nanofluidic ratchet, nanopore translocation and pulsed fields. Using Langevin Dynamics simulations, we show that it is possible to design pulsed field sequences to ratchet captured semiflexible molecules in such a way that only short chains successfully translocate, effectively transforming the nanopore process into a low pass molecular filter. We also show that asymmetric pulses can significantly enhance the device efficiency. The process itself can be performed with many pores in parallel, and it s…
The translocation time of a polymer chain through an interaction energy gradient nanopore was studied by Monte Carlo simulations and the Fokker-Planck equation with double-absorbing boundary conditions. Both the simulation and calculation revealed three different behaviors for polymer translocation. These behaviors can be explained qualitatively from free-energy landscapes obtained for polymer translocation at different parameters. Results show that the translocation time of a polymer chain through a nanopore can be tuned by suitably designing the interaction energy gradient.
We study unbiased translocation of a flexible polymer chain through a membrane pore under the influence of active noise and steric exclusion using Langevin dynamics simulations. The active noise is incorporated by introducing nonchiral and chiral active particles on one or both sides of the membrane. Translocation of the polymer into either side of the pore is assisted by an effective pulling due to particle activity and is hindered by an effective pushing due to steric repulsions between the polymer and active particles. As a result of the competition between these effective forces, we find a…
Polymer translocation through a nanopore in a membrane investigated theoretically. Recent experiments on voltage-driven DNA and RNA translocations through a nanopore indicate that the size and geometry of the pore are important factors in polymer dynamics. A theoretical approach is presented which explicitly takes into account the effect of the nanopore length and diameter for polymer motion across the membrane. It is shown that the length of the pore is crucial for polymer translocation dynamics. The present model predicts that for realistic conditions (long nanopores and large external field…
DNA capture with high fidelity is an essential part of nanopore translocation. We report several important aspects of the capture process and subsequent translocation of a model DNA polymer through a solid-state nanopore in presence of an extended electric field using the Brownian dynamics simulation that enables us to record statistics of the conformations at every stage of the translocation process. By releasing the equilibrated DNAs from different equipotentials, we observe that the capture time distribution depends on the initial starting point and follows a Poisson process. The field grad…
The statistical theory of polymers tethered around the inner surface of a cylindrical channel has traditionally employed the assumption that the equilibrium density of the polymers is independent of the azimuthal coordinate. However, simulations have shown that this rotational symmetry can be broken when there are attractive interactions between the polymers. We investigate the phases that emerge in these circumstances, and we quantify the effect of the symmetry assumption on the phase behavior of the system. In the absence of this assumption, one can observe large differences in the equilibri…
Motivated by DNA electrophoresis near a nanopore, we consider the flow field around an "elongated jet", a long thin source which injects momentum into a liquid. This solution qualitatively describes the electro-osmotic flow around a long rigid polymer, where due to electrohydrodynamic coupling, the solvent receives momentum from the electric field. Based on the qualitative behavior of the elongated jet solution, we develop a coarse-grained scheme which reproduces the known theoretical results regarding the electrophoretic behavior of a long rigid polymer and a polymer coil in a uniform field, …
Using Langevin dynamics simulations, we investigate the dynamics of polymer translocation into a circular nanocontainer through a nanopore under a driving force $F$. We observe that the translocation probability initially increases and then saturates with increasing $F$, independent of $ϕ$, which is the average density of the whole chain in the nanocontainer. The translocation time distribution undergoes a transition from a Gaussian distribution to an asymmetric distribution with increasing $ϕ$. Moreover, we find a nonuniversal scaling exponent of the translocation time as chain length, depend…
We study the effect of physical confinement on the capillary infiltration of polymers into cylindrical nanopores using molecular dynamics simulations. In particular, we probe whether the critical contact angle above which capillary rise infiltration ceases to occur changes for long chain polymers, possibly due to loss of conformation entropy induced by chain confinement. Surprisingly, the critical contact angle does not strongly depend on the length of polymer chains and stays constant for large N. A free energy model is developed to show that the critical angle for infiltration depends strong…
We investigate the problem of polymer translocation through a nanopore in the absence of an external driving force. To this end, we use the two-dimensional (2D) fluctuating bond model with single-segment Monte Carlo moves. To overcome the entropic barrier without artificial restrictions, we consider a polymer which is initially placed in the middle of the pore, and study the escape time required for the polymer to completely exit the pore on either end. In particular, we examined the effect of the pore length on the escape time.
Polymer-coated pores play a crucial role in nucleo-cytoplasmic transport and in a number of biomimetic and nanotechnological applications. Here we present Monte Carlo and Density Functional Theory approaches to identify different collective phases of end-grafted polymers in a nanopore and to study their relative stability as a function of intermolecular interactions. Over a range of system parameters that is relevant for nuclear pore complexes, we observe two distinct phases: one with the bulk of the polymers condensed at the wall of the pore, and the other with the polymers condensed along it…
Flexible chains (linear or branched) can be forced to enter into a narrow capillary by using a hydrodynamic flow. Here, we correct our earlier description of this problem by considering the progressive nature of the suction process. We find that the critical current for penetration, $J\_c$, is controlled by the entry of a single blob of the capillary size, and that its scaling structure is the same for branched and linear chains.
The motion of polymers with inhomogeneous structure through nanopores is discussed theoretically. Specifically, we consider the translocation dynamics of polymers consisting of double-stranded and single-stranded blocks. Since only the single-stranded chain can go through the nanopore the double-stranded segment has to unzip before the translocation. Utilizing a simple analytical model, translocation times are calculated explicitly for different polymer orientations, i.e., when the single-stranded block enters the pore first and when the double-stranded segment is a leading one. The dependence…
We use a combination of computer simulations and iso-flux tension propagation (IFTP) theory to investigate translocation dynamics of a flexible linear polymer through a nanopore into an environment composed of repulsive active rods in 2D. We demonstrate that the rod activity induces a crowding effect on the polymer, leading to a time-dependent net force that facilitates translocation into the active environment. Incorporating this force into the IFTP theory for pore-driven translocation allows us to characterise translocation dynamics in detail and derive a scaling form for the average translo…
We investigate the translocation dynamics of a folded linear polymer which is pulled through a nanopore by an external force. To this end, we generalize the iso-flux tension propagation (IFTP) theory for end-pulled polymer translocation to include the case of two segments of the folded polymer traversing simultaneously trough the pore. Our theory is extensively benchmarked with corresponding Molecular Dynamics (MD) simulations. The translocation process for a folded polymer can be divided into two main stages. In the first stage, both branches are traversing the pore and their dynamics is coup…
The threading of a polymer chain through a small pore is a classic problem in polymer dynamics and underlies nanopore sensing technology. However important experimental aspects of the polymer motion in a solid-state nanopore, such as an accurate measurement of the velocity variation during translocation, have remained elusive. In this work we analysed the translocation through conical quartz nanopores of a 7 kbp DNA double-strand labelled with six markers equally spaced along its contour. These markers, constructed from DNA hairpins, give direct experimental access to the translocation dynamic…
We review recent progress on the theory of dynamics of polymer translocation through a nanopore based on the iso-flux tension propagation (IFTP) theory. We investigate both pore-driven translocation of flexible and a semi-flexible polymers, and the end-pulled case of flexible chains by means of the IFTP theory and extensive molecular dynamics (MD) simulations. The validity of the IFTP theory can be quantified by the waiting time distributions of the monomers which reveal the details of the dynamics of the translocation process. The IFTP theory allows a parameter-free description of the translo…
We investigate the translocation of stiff polymers in the presence of binding particles through a nanopore by two-dimensional Langevin dynamics simulations. We find that the mean translocation time shows a minimum as a function of the binding energy $ε$ and the particle concentration $ϕ$, due to the interplay of the force from binding and the frictional force. Particularly, for the strong binding the translocation proceeds with a decreasing translocation velocity induced by a significant increase of the frictional force. In addition, both $ε$ and $ϕ$ have an notable impact on the distribution …
The alteration of the dielectric membrane properties by membrane engineering techniques such as carbon nanotube (CNT) coating opens the way to novel molecular transport strategies for biosensing purposes. In this article, we predict a macromolecular transport mechanism enabling the dielectric manipulation of the polymer translocation dynamics in dielectric membrane pores confining mixed electrolytes. In the giant permittivity regime of these engineered membranes governed by attractive polarization forces, multivalent ions adsorbed by the membrane nanopore trigger a monovalent ion separation an…
We predict streaming current inversion with multivalent counterions in hydrodynamically driven polymer translocation events from a correlation-corrected charge transport theory including charge fluctuations around mean-field electrostatics. In the presence of multivalent counterions, electrostatic many-body effects result in the reversal of the DNA charge. The attraction of anions to the charge-inverted DNA molecule reverses the sign of the ionic current through the pore. Our theory allows for a comprehensive understanding of the complex features of the resulting streaming currents. The underl…
Solid-state nanopores are single molecule sensors that measure changes in ionic current as charged polymers such as DNA pass through. Here, we present comprehensive experiments on the length, voltage and salt dependence of the frequency of double-stranded DNA translocations through conical quartz nanopores with mean opening diameter 15 nm. We observe an entropic barrier limited, length dependent translocation frequency at 4M LiCl salt concentration and a drift-dominated, length independent translocation frequency at 1M KCl salt concentration. These observations are described by a unifying conv…
Using two dimensional Langevin dynamics simulations, we investigate the dynamics of polymer translocation into a fluidic channel with diameter $R$ through a nanopore under a driving force $F$. Due to the crowding effect induced by the partially translocated monomers, the translocation dynamics is significantly altered in comparison to an unconfined environment, namely, we observe a nonuniversal dependence of the translocation time $τ$ on the chain length $N$. $τ$ initially decreases rapidly and then saturates with increasing $R$, and a dependence of the scaling exponent $α$ of $τ$ with $N$ on …
The effect of the microscopic structure of a pore on polymer translocation is studied using Langevin dynamics simulation, and the consequence of introducing patterned stickiness inside the pore is investigated. It is found that the translocation process is extremely sensitive to the detailed structure of such patterns with faster than exponential dependence of translocation times on the stickiness of the pore. The stochastic nature of the translocation process leads to discernable differences between how polymers with different sequences go through specifically patterned pores. This notion is …
The transport of polymers with folded configurations across membrane pores is investigated theoretically by analyzing simple discrete stochastic models. The translocation dynamics is viewed as a sequence of two events: motion of the folded segment through the channel followed by the linear part of the polymer. The transition rates vary for the folded and linear segments because of different interactions between the polymer molecule and the pore. It is shown that the translocation time depends non-monotonously on the length of the folded segment for short polymers and weak external fields, whil…
The optical polarimetry technique is used to explore molecular ordering of nematic liquid crystals 5FPFFPP3 embedded in parallel cylindrical channels of alumina membranes with pore walls covered by a SE-1211 polymer film enhancing normal anchoring. A chemical film deposition from organic solution apparently results in inhomogeneous coverage with local islands on the channels walls. Accordingly, a coexistence of differently ordered LC regions (nanodomains), characterized by positive and negative anisotropy, results in a weak effective (average) optical birefringence. Repeated polymer deposition…
Here using LAMMPS molecular dynamics (MD) software, we simulate polymer translocation in 2 dimensions. We do the simulations for weak and moderate forces and for different pore diameters. Our results show that in both non-equilibrium and equilibrium initial conditions, translocation time will always increase by increasing binding energy and or increasing pore diameter. Moreover, scaling exponent of time versus force is -0.9531 in accordance to our predecessors. The comparison between equilibrium and non-equilibrium initial condition shows that the translocation time is very sensitive to the in…
The conformational behavior of a polymer in a critical binary solvent confined in a porous medium is studied. The size of the polymer in bulk, which is mainly governed by the correlation length of the solvent density fluctuations, depends on the proximity to the critical point of the binary mixture. We find that in contrast to the bulk behavior, the conformational properties of the polymer in a porous medium depends strongly on the pore size. The latter controls the correlation length of the solvent density fluctuations and thus determines the polymer size.
The translocation of a polymer through a pore in a membrane separating fluids of different viscosities is studied via several computational approaches. Starting with the polymer halfway, we find that as a viscosity difference across the pore is introduced, translocation will predominately occur towards one side of the membrane. These results suggest an intrinsic pumping mechanism for translocation across cell walls which could arise whenever the fluid across the membrane is inhomogeneous. Somewhat surprisingly, the sign of the preferred direction of translocation is found to be strongly depend…
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 transloc…
I did off-lattice 3D Monte Carlo simulations for polymer translocation through a narrow pore at low external field, trying to be as close to a direct approach as possible. The process was found non equilibrium globally, but dynamics of the monomers close to the pore (the fold) was found close to quasi equilibrium. I observed a tension (or pressure) buildup near the pore, and subdiffusion for the displacement of the middle monomer in the pore, as reported in the literature. I did not find the distribution of the reaction coordinate after some time of free diffusion predicted by the fractional d…
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 ch…
We study the adsorption of homogeneous or heterogeneous polymers onto heterogeneous planar surfaces with exponentially decaying site-site correlations, using a variational reference system approach. As a main result, we derive simple equations for the adsorption-desorption transition line. We show that the adsorption threshold is the same for systems with quenched and annealed disorder. The results are discussed with respect to their implications for the physics of molecular recognition.
We consider the translocation dynamics of a polymer chain forced through a nanopore by an external force on its head monomer on the trans side. For a proper theoretical treatment we generalize the iso-flux tension propagation (IFTP) theory to include friction arising from the trans side subchain. The theory reveals a complicated scenario of multiple scaling regimes depending on the configurations of the cis and the trans side subchains. In the limit of high driving forces $f$ such that the trans subchain is strongly stretched, the theory is in excellent agreement with molecular dynamics simula…
The behavior of annealed branched polymers near adsorbing surfaces plays a fundamental role in many biological and industrial processes. Most importantly single stranded RNA in solution tends to fold up and self-bind to form a highly branched structure. Using a mean field theory, we both perturbatively and numerically examine the adsorption of branched polymers on surfaces of several different geometries in a good solvent. Independent of the geometry of the wall, we observe that as branching density increases, surface tension decreases. However, we find a coupling between the branching density…
Monte Carlo (MC) simulations are used to study the dynamics of polymer translocation through a nanopore in the limit where the translocation rate is sufficiently slow that the polymer maintains a state of conformational quasi-equilibrium. The system is modeled as a flexible hard-sphere chain that translocates through a cylindrical hole in a hard flat wall. In some calculations, the nanopore is connected at one end to a spherical cavity. Translocation times are measured directly using MC dynamics simulations. For sufficiently narrow pores, translocation is sufficiently slow that the mean transl…
We investigate the voltage-driven translocation of an inhomogeneously charged polymer through a nanopore by utilizing discrete and continuous stochastic models. As a simplified illustration of the effect of charge distribution on translocation, we consider the translocation of a polymer with a single charged site in the presence and absence of interactions between the charge and the pore. We find that the position of the charge that minimizes the translocation time in the absence of pore--polymer interactions is determined by the entropic cost of translocation, with the optimum charge position…
The translocation of a macromolecule through a nanometer-sized pore is an interesting process with important applications in the development of biosensors for single--molecule analysis and in drug delivery and gene therapy. We have carried out a molecular dynamics simulation study of electrophoretic translocation of a charged polymer through an artificial nanopore to explore the feasibility of semiconductor--based nanopore devices for ultra--fast DNA sequencing. The polymer is represented by a simple bead--spring model designed to yield an appropriate coarse-grained description of the phosphat…
We determine the scaling exponents of polymer translocation (PT) through a nanopore by extensive computer simulations of various microscopic models for chain lengths extending up to N=800 in some cases. We focus on the scaling of the average PT time $τ\sim N^α$ and the mean-square change of the PT coordinate $<s^2(t)> \sim t^β$. We find $α=1+2ν$ and $β=2/α$ for unbiased PT in 2D and 3D. The relation $αβ=2$ holds for driven PT in 2D, with crossover from $α\approx 2ν$ for short chains to $α\approx 1+ν$ for long chains. This crossover is, however, absent in 3D where $α= 1.42 \pm 0.01$ and $αβ\app…
We study the translocation dynamics of a polymer chain threaded through a nanopore by an external force. By means of diverse methods (scaling arguments, fractional calculus and Monte Carlo simulation) we show that the relevant dynamic variable, the translocated number of segments $s(t)$, displays an {\em anomalous} diffusive behavior even in the {\em presence} of an external force. The anomalous dynamics of the translocation process is governed by the same universal exponent $α= 2/(2ν+2 - γ_1)$, where $ν$ is the Flory exponent and $γ_1$ - the surface exponent, which was established recently fo…
We investigate polymer translocation through a nanopore under a pulling force using Langevin dynamics simulations. We concentrate on the influence of the chain length $N$ and the pulling force $F$ on the translocation time $τ$. The distribution of $τ$ is symmetric and narrow for strong $F$. We find that $τ\sim N^{2}$ and translocation velocity $v\sim N^{-1}$ for both moderate and strong $F$. For infinitely wide pores, three regimes are observed for $τ$ as a function of $F$. With increasing $F$, $τ$ is independent of $F$ for weak $F$, and then $τ\sim F^{-2+ν^{-1}}$ for moderate $F$, where $ν$ i…
The translocation dynamics of a polymer chain through a nanopore in the absence of an external driving force is analyzed by means of scaling arguments, fractional calculus, and computer simulations. The problem at hand is mapped on a one dimensional {\em anomalous} diffusion process in terms of reaction coordinate $s$ (i.e. the translocated number of segments at time $t$) and shown to be governed by an universal exponent $α= 2/(2ν+2-γ_1)$ whose value is nearly the same in two- and three-dimensions. The process is described by a {\em fractional} diffusion equation which is solved exactly in the…
We study the translocation of a flexible polymer through a pore in a membrane induced by its adsorption on \trans side of the membrane. When temperature $T$ is higher than $T_c$, the adsorption-desorption transition temperature, attractive interaction between polymer and membrane plays little role in affecting polymer conformation, leading to translocation time that scales as $τ\sim L^3$ where $L$ is the polymer contour length. When $T < T_c$, however, the translocation time undergoes a sharp crossover to $τ\sim L^2$ for sufficiently long polymers, following the second order conformational (ad…
We investigate the translocation of a stiff polymer consisting of M monomers through a nanopore in a membrane, in the presence of binding particles (chaperones) that bind onto the polymer, and partially prevent backsliding of the polymer through the pore. The process is characterized by the rates: k for the polymer to make a diffusive jump through the pore, q for unbinding of a chaperone, and the rate q kappa for binding (with a binding strength kappa); except for the case of no binding kappa=0 the presence of the chaperones give rise to an effective force that drives the translocation process…
Using Langevin dynamics simulations, we investigate the dynamics of chaperone-assisted translocation of a flexible polymer through a nanopore. We find that increasing the binding energy $ε$ between the chaperone and the chain and the chaperone concentration $N_c$ can greatly improve the translocation probability. Particularly, with increasing the chaperone concentration a maximum translocation probability is observed for weak binding. For a fixed chaperone concentration, the histogram of translocation time $τ$ has a transition from long-tailed distribution to Gaussian distribution with increas…
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…
We develop a theory for polymer translocation driven by a time-dependent force through an oscillating nanopore. To this end, we extend the iso-flux tension propagation theory (IFTP) [Sarabadani \textit{et al., J. Chem. Phys.}, 2014, \textbf{141}, 214907] for such a setup. We assume that the external driving force in the pore has a component oscillating in time, and the flickering pore is similarly described by an oscillating term in the pore friction. In addition to numerically solving the model, we derive analytical approximations that are in good agreement with the numerical simulations. Our…
The structural properties of polymers adsorbed onto a surface have been widely investigated using self-consistent mean-field theories. Recently, analytical mean-field theories have been applied to study polymer adsorption on curved surfaces but all in the context of the ground state dominance approximation in which the polymer chain length (N) is essentially infinite. Using an expression for the free energy by Semenov, we determine leading order (in 1/N) corrections due to the finiteness of the polymer chain length on surface tension, spontaneous curvature, and rigidity constants.
We consider the influence of electrostatic forces on driven translocation dynamics of a flexible polyelectrolyte being pulled through a nanopore by an external force on the head monomer. To this end, we augment the iso-flux tension propagation (IFTP) theory with electrostatics for a negatively charged biopolymer pulled through a nanopore embedded in a similarly charged anionic membrane. We show that for the realistic case such as a single-stranded DNA, the translocation dynamics at low salt where screening is weak and at finite negative membrane charge is unexpectedly accelerated despite the l…
Low-energy structures of a hybrid system consisting of a polymer and an attractive nanowire substrate as well as the thermodynamics of the adsorption transition are studied by means of Monte Carlo computer simulations. Depending on structural and energetic properties of the substrate, we find different adsorbed polymer conformations, amongst which are spherical droplets attached to the wire and monolayer tubes surrounding it. We identify adsorption temperatures and the type of the transition between adsorbed and desorbed structures depending on the substrate attraction strength.
The adsorption of a single polymer to a flat surface in shear is investigated using Brownian hydrodynamics simulations and scaling arguments. Competing effects are disentangled: in the absence of hydrodynamic interactions, shear drag flattens the chain and thus enhances adsorption. Hydrodynamic lift on the other hand gives rise to long-ranged repulsion from the surface which preempts the surface-adsorbed state via a discontinuous desorption transition, in agreement with theoretical arguments. Chain flattening is dominated by hydrodynamic lift, so overall, shear flow weakens the adsorption of f…
Adsorption of polymers to surfaces is crucial for understanding many fundamental processes in nature. Recent experimental studies indicate that the adsorption dynamics is dominated by non-equilibrium effects. We investigate the adsorption of a single polymer of length $N$ to a planar solid surface in the absence of hydrodynamic interactions. We find that for weak adsorption energies the adsorption time scales $ \sim N^{(1+2ν)/(1+ν)}$, where $ν$ is the Flory exponent for the polymer. We argue that in this regime the single chain adsorption is closely related to a field-driven polymer translocat…
We study the driven translocation of a semi-flexible polymer through a nanopore by means of a modified version of the iso-flux tension propagation theory (IFTP), and extensive molecular dynamics (MD) simulations. We show that in contrast to fully flexible chains, for semi-flexible polymers with a finite persistence length $\tilde{\ell}_p$ the {\it trans} side friction must be explicitly taken into account to properly describe the translocation process. In addition, the scaling of the end-to-end distance $R_N$ as a function of the chain length $N$ must be known. To this end, we first derive a s…
We have performed chain-growth simulations of minimalistic hybrid lattice models for polymers interacting with interfaces of attractive solid substrates in order to gain insights into the conformational transitions of the polymers in the adsorption process. Primarily focusing on the dependence of the conformational behavior on temperature and solubility we obtained pseudophase diagrams with a detailed structure of conformational subphases. In the study of hydrophobic-polar peptides in the vicinity of different types of substrates, we found a noticeable substrate specificity of the assembly of …
We investigate the dynamics of polymer translocation through a nanopore using two-dimensional Langevin dynamics simulations. In the absence of external driving force, we consider a polymer which is initially placed in the middle of the pore and study the escape time $τ_e$ required for the polymer to completely exit the pore on either side. The distribution of the escape times is wide and has a long tail. We find that $τ_e$ scales with the chain length $N$ as $τ_e \sim N^{1+2ν}$, where $ν$ is the Flory exponent. For driven translocation, we concentrate on the influence of the friction coefficie…
We discuss the adsorption of semiflexible polymers to a planar attractive wall and focus on the questions of the adsorption threshold for polymers of {\it finite} length and their loop and tail distributions using both Monte-Carlo simulations and analytical arguments. For the adsorption threshold, we find three regimes: (i) a flexible or Gaussian regime if the persistence length is smaller than the adsorption potential range, (ii) a semiflexible regime if the persistence length is larger than the potential range, and (iii) for finite polymers, a novel crossover to a rigid rod regime if the def…
We present a lattice model for helicity induction on an optically inactive polymer due to the adsorption of exogenous chiral amine molecules. The system is mapped onto a one-dimensional Ising model characterized by an on-site polymer helicity variable and an amine occupancy one. The equilibrium properties are analyzed at the limit of strong coupling between helicity induction and amine adsorption and that of non-interacting adsorbant molecules. We discuss our results in view of recent experimental results.
