Dynamics of driven translocation of semiflexible polymers.

We study translocation of semiflexible polymers driven by force f_{d} inside a nanometer-scale pore using our three-dimensional Langevin dynamics model. We show that the translocation time τ increases with increasing bending rigidity κ. Similarly, the exponent β for the scaling of τ with polymer length N,τ∼N^{β}, increases with increasing κ as well as with increasing f_{d}.

Rigidity-induced scale invariance in polymer ejection from capsid.

While the dynamics of a fully flexible polymer ejecting a capsid through a nanopore has been extensively studied, the ejection dynamics of semiflexible polymers has not been properly characterized. Here we report results from simulations of ejection dynamics of semiflexible polymers ejecting from spherical capsids. Ejections start from strongly confined polymer conformations of constant initial monomer density.

Quantification of tension to explain bias dependence of driven polymer translocation dynamics.

Motivated by identifying the origin of the bias dependence of tension propagation, we investigate methods for measuring tension propagation quantitatively in computer simulations of driven polymer translocation. Here, the motion of flexible polymer chains through a narrow pore is simulated using Langevin dynamics. We measure tension forces, bead velocities, bead distances, and bond angles along the polymer at all stages of translocation with unprecedented precision.

Uniform description of polymer ejection dynamics from capsid with and without hydrodynamics.

We use stochastic rotation dynamics (SRD) to examine the dynamics of the ejection of an initially strongly confined flexible polymer from a spherical capsid with and without hydrodynamics. The results obtained using stochastic rotation dynamics (SRD) are compared to similar Langevin simulations. Inclusion of hydrodynamic modes speeds up the ejection but also allows the part of the polymer outside the capsid to expand closer to equilibrium.

Driven polymer translocation in good and bad solvent: Effects of hydrodynamics and tension propagation.

We investigate the driven polymer translocation through a nanometer-scale pore in the presence and absence of hydrodynamics both in good and bad solvent. We present our results on tension propagating along the polymer segment on the cis side that is measured for the first time using our method that works also in the presence of hydrodynamics. For simulations we use stochastic rotation dynamics, also called multiparticle collision dynamics.

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.

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.

Criteria for minimal model of driven polymer translocation.

While the characteristics of the driven translocation for asymptotically long polymers are well understood, this is not the case for finite-sized polymers, which are relevant for real-world experiments and simulation studies. Most notably, the behavior of the exponent α, which describes the scaling of the translocation time with polymer length, when the driving force fp in the pore is changed, is under debate. By Langevin dynamics simulations of regular and modified translocation models using the freely jointed-chain polymer model we find that a previously reported incomplete model, where the trans side and fluctuations were excluded, gives rise to characteristics that are in stark contradiction with those of the complete model, for which α increases with fp.

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.

Sedimentation of knotted polymers.

We investigate the sedimentation of knotted polymers by means of stochastic rotation dynamics, a molecular dynamics algorithm that takes hydrodynamics fully into account. We show that the sedimentation coefficient s, related to the terminal velocity of the knotted polymers, increases linearly with the average crossing number n(c) of the corresponding ideal knot. This provides direct computational confirmation of this relation, postulated on the basis of sedimentation experiments by Rybenkov et al.

Thermal conduction and interface effects in nanoscale Fermi-Pasta-Ulam conductors.

We perform classical nonequilibrium molecular dynamics simulations to calculate heat flow through a microscopic junction connecting two larger reservoirs. In contrast to earlier papers, we also include the reservoirs in the simulated region to study the effect of the bulk-nanostructure interfaces and the bulk conductance. The scalar Fermi-Pasta-Ulam (FPU) model is used to describe the effects of anharmonic interactions in a simple manner.

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.

Pore-polymer interaction reveals nonuniversality in forced polymer translocation.

We present a numerical study of forced polymer translocation by using two separate pore models. Both of them have been extensively used in previous forced translocation studies. We show that variations in the pore model affect the forced translocation characteristics significantly in the biologically relevant range of the pore force, i.

Unforced polymer translocation compared to the forced case.

We present results for unforced polymer translocation from simulations using Langevin dynamics in two dimensions (2D) to four dimensions and stochastic rotation dynamics supporting hydrodynamic modes in three dimensions (3D). We compare our results to forced translocation and a simplified model where the polymer escapes from an infinite pore. The simple model shows that the scaling behavior of unforced translocation is independent of the dimension of the side to which the polymer is translocating.

Biodegradable protections for nucleoside 5'-monophosphates: comparative study on the removal of O-acetyl and O-acetyloxymethyl protected 3-hydroxy-2,2-bis(ethoxycarbonyl)propyl groups.

The applicability of 3-acetyloxy-2,2-bis(ethoxycarbonyl)propyl and 3-acetyloxymethoxy-2,2-bis(ethoxycarbonyl)propyl groups as biodegradable phosphate protecting groups for nucleoside 5'-monophosphates has been studied in a HEPES buffer at pH 7.5. Enzymatic deacetylation with porcine carboxyesterase triggers the removal of the resulting 3-hydroxy-2,2-bis(ethoxycarbonyl)propyl and 3-hydroxymethoxy-2,2-bis(ethoxycarbonyl)propyl groups by retro-aldol condensation and consecutive half acetal hydrolysis and retro-aldol condensation, respectively.

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 approximately f;{-1}N;{beta} . We demonstrate that an artifact in the 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 View Article and Find Full Text PDF

Analysis of DNA elasticity.

With a model that incorporates hydrodynamics directly, we show that flow experiments can be used for detecting some characteristics of the DNA elasticity which manifest themselves clearly at large length scales but cannot be observed by mechanical forcing experiments even at very small length scales. By systematic analysis, the conclusiveness of different experimental methods is evaluated. For the wormlike chain, confirmed as the correct model for DNA, we find an underlying scaling relation between its extension and flow velocity of the form L(p) approximately v(0.

Dimensional effects in dynamic fragmentation of brittle materials.

It has been shown previously that dynamic fragmentation of brittle D -dimensional objects in a D -dimensional space gives rise to a power-law contribution to the fragment-size distribution with a universal scaling exponent 2-1/D . We demonstrate that in fragmentation of two-dimensional brittle objects in three-dimensional space, an additional fragmentation mechanism appears, which causes scale-invariant secondary breaking of existing fragments. Due to this mechanism, the power law in the fragment-size distribution has now a scaling exponent of approximately 1.

Exponential and power-law mass distributions in brittle fragmentation.

Generic arguments, a minimal numerical model, and fragmentation experiments with gypsum disk are used to investigate the fragment-size distribution that results from dynamic brittle fragmentation. Fragmentation is initiated by random nucleation of cracks due to material inhomogeneities, and its dynamics are pictured as a process of propagating cracks that are unstable against side-branch formation. The initial cracks and side branches both merge mutually to form fragments.

Universal dynamic fragmentation in D dimensions.

A generic model is introduced for brittle fragmentation in D dimensions, and this model is shown to lead to a fragment-size distribution with two distinct components. In the small fragment-size limit a scale-invariant size distribution results from a crack branching-merging process. At larger sizes the distribution becomes exponential as a result of a Poisson process, which introduces a large-scale cutoff.

Comment on "Scaling behavior in explosive fragmentation".

We discuss the data analysis and the conclusions based upon the analysis given in the paper by Diehl et al. [Phys. Rev.