PACS 87.15.-v -Biomolecules: structure and physical properties PACS 82.35.Lr -Physical properties of polymers PACS 87.15.A--Theory, modeling, and computer simulationAbstract. -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.

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

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. Numerical simulations are used to demonstrate the validity of the distribution for D=2. Data from laboratory-scale experiments and large-scale quarry blastings of granitic gneiss confirm its validity for D=3. In the experiments the nonzero grain size of rock causes deviation from the ideal model distribution in the small-size limit. The size of the cutoff seems to diverge at the minimum energy sufficient for fragmentation to occur, but the scaling exponent is not universal.

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. Our results suggest that contribution due to fluctuations is important. We construct a minimal model where dynamics is completely excluded to show that close alignment with a full translocation model can be achieved. Our findings set very stringent requirements for a minimal model that is supposed to describe the driven polymer translocation correctly.

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. The side branches have a finite penetration depth as a result of inherent damping. Generic arguments imply that close to the minimum strain (or impact energy) required for fragmentation, the number of fragments of size s scales as s(-(2D-1)/D) f(1) (- (2/lambda)(D) s)+ f(2) (- s(-1 )(0 ) (lambda+ s(1/D) )(D) ), where D is the Euclidean dimension of the space, lambda is the penetration depth, and f(1) and f(2) can be approximated by exponential functions. Simulation results and experiments can both be described by this theoretical fragment-size distribution. The typical largest fragment size s(0) was found to diverge at the minimum strain required for fragmentation as it is inversely related to the density of initially formed cracks. Our results also indicate that scaling of s(0) close to this divergence depends on, e.g., loading conditions, and thus is not universal. At the same time, the density of fragment surface vanishes as L-1, L being the linear dimension of the brittle solid. The results obtained provide an explanation as to why the fragment-size distributions found in nature can have two components, an exponential as well as a power-law component, with varying relative weights.