Polymer ejection from strong spherical confinement

We examine the ejection of an initially strongly confined flexible polymer from a spherical capsid through a nanoscale pore. We use molecular dynamics for unprecedentedly high initial monomer densities. We show that the time for an individual monomer to eject grows exponentially with the number of ejected monomers. By measurements of the force at the pore we show this dependence to be a consequence of the excess free energy of the polymer due to confinement growing exponentially with the number of monomers initially inside the capsid. This growth relates closely to the divergence of mixing energy in the Flory-Huggins theory at large concentration. We show that the pressure inside the capsid driving the ejection dominates the process that is characterized by the ejection time growing linearly with the lengths of different polymers. Waiting time profiles would indicate that the superlinear dependence obtained for polymers amenable to computer simulations results from a finite-size effect due to the final retraction of polymers' tails from capsids.Comment: 6 pages, 9 figures, accepted for publication in Phys. Rev. E, increased readability from previous versio

Chaperone-assisted translocation of flexible polymers in three dimensions

Polymer translocation through a nanometer-scale pore assisted by chaperones binding to the polymer is a process encountered in vivo for proteins. Studying the relevant models by computer simulations is computationally demanding. Accordingly, previous studies are either for stiff polymers in three dimensions or flexible polymers in two dimensions. Here, we study chaperone-assisted translocation of flexible polymers in three dimensions using Langevin dynamics. We show that differences in binding mechanisms, more specifically, whether a chaperone can bind to a single or multiple sites on the polymer, lead to substantial differences in translocation dynamics in three dimensions. We show that the single-binding mode leads to dynamics that is very much like that in the constant-force driven translocation and accordingly mainly determined by tension propagation on the cis side. We obtain $\beta \approx 1.26$ for the exponent for the scaling of the translocation time with polymer length. This fairly low value can be explained by the additional friction due to binding particles. The multiple-site binding leads to translocation whose dynamics is mainly determined by the trans side. For this process we obtain $\beta \approx 1.36$. This value can be explained by our derivation of $\beta = 4/3$ for constant-bias translocation, where translocated polymer segments form a globule on the trans side. Our results pave the way for understanding and utilizing chaperone-assisted translocation where variations in microscopic details lead to rich variations in the emerging dynamics.Comment: 10 pages, 12 figure

Dynamics of polymer ejection from capsid

Polymer ejection from a capsid through a nanoscale pore is an important biological process with relevance to modern biotechnology. Here, we study generic capsid ejection using Langevin dynamics. We show that even when the ejection takes place within the drift-dominated region there is a very high probability for the ejection process not to be completed. Introducing a small aligning force at the pore entrance enhances ejection dramatically. Such a pore asymmetry is a candidate for a mechanism by which a viral ejection is completed. By detailed high-resolution simulations we show that such capsid ejection is an out-of-equilibrium process that shares many common features with the much studied driven polymer translocation through a pore in a wall or a membrane. We find that the escape times scale with polymer length, $\tau \sim N^\alpha$. We show that for the pore without the asymmetry the previous predictions corroborated by Monte Carlo simulations do not hold. For the pore with the asymmetry the scaling exponent varies with the initial monomer density (monomers per capsid volume) $\rho$ inside the capsid. For very low densities $\rho \le 0.002$ the polymer is only weakly confined by the capsid, and we measure $\alpha = 1.33$, which is close to $\alpha = 1.4$ obtained for polymer translocation. At intermediate densities the scaling exponents $\alpha = 1.25$ and $1.21$ for $\rho = 0.01$ and $0.02$, respectively. These scalings are in accord with a crude derivation for the lower limit $\alpha = 1.2$. For the asymmetrical pore precise scaling breaks down, when the density exceeds the value for complete confinement by the capsid, $\rho \gtrapprox 0.25$. The high-resolution data show that the capsid ejection for both pores, analogously to polymer translocation, can be characterized as a multiplicative stochastic process that is dominated by small-scale transitions.Comment: 10 pages, 6 figure

Critical evaluation of the computational methods used in the forced polymer translocation

In forced polymer translocation, the average translocation time, $\tau$, scales with respect to pore force, $f$, and polymer length, $N$, as $\tau \sim f^{-1} N^{\beta}$. We demonstrate that an artifact in Metropolis Monte Carlo method resulting in breakage of the force scaling with large $f$ may be responsible for some of the controversies between different computationally obtained results and also between computational and experimental results. Using Langevin dynamics simulations we show that the scaling exponent $\beta \le 1 + \nu$ is not universal, but depends on $f$. Moreover, we show that forced translocation can be described by a relatively simple force balance argument and $\beta$ to arise solely from the initial polymer configuration

Event distributions of polymer translocation

We present event distributions for the polymer translocation obtained by extensive Langevin dynamics simulations. Such distributions have not been reported previously and they provide new understanding of the stochastic characteristics of the process. We extract at a high length scale resolution distributions of polymer segments that continuously traverse through a nanoscale pore. The obtained log-normal distributions together with the characteristics of polymer translocation suggest that it is describable as a multiplicative stochastic process. In spite of its clear out-of-equilibrium nature the forced translocation is surprisingly similar to the unforced case. We find forms for the distributions almost unaltered with a common cut-off length. We show that the individual short-segment and short-time movements inside the pore give the scaling relations $\tau \sim N^\alpha$ and $\tau \sim f^{-\beta}$ for the polymer translocation.Comment: Second revision. 7 pages, 8 figure

Superconducting NbN microstrip detectors

Superconducting NbN strip transmission line counters and coupling circuits were processed on silicon wafers using thin film techniques, and they were characterized with several methods to verify the design principles. The stripline circuits, designed using microwave design rules, were simulated using a circuit design tool enhanced to include modelling of the superconducting lines. The strips, etched out of the 282 nm thick top NbN film with resistivity 284 µ?cm at 20 K, have critical temperatures in the range 12 to 13 K and a critical current density approximately Jc(0) = 3.3·105 A/cm2. The linearized heat transfer coefficient between the strip and the substrate is approximately 1.1·105 W/(m2K) and the healing length is about 1.6 µm between 3 and 5 K temperatures. Traversing 5 MeV a-particles caused the strips to quench. No events due to electrons could be detected in agreement with the predicted signal amplitude which is below the noise threshold of our wideband circuitry. The strip bias current and hence the signal amplitude were limited due to a microbridge at the isolator step of the impedance transformer

Dynamics of forced biopolymer translocation

We present results from our simulations of biopolymer translocation in a solvent which explain the main experimental findings. The forced translocation can be described by simple force balance arguments for the relevant range of pore potentials in experiments and biological systems. Scaling of translocation time with polymer length varies with pore force and friction. Hydrodynamics affects this scaling and significantly reduces translocation times.Comment: Published in: http://www.iop.org/EJ/article/0295-5075/85/5/58006/epl_85_5_58006.htm