3 research outputs found
Activated sampling in complex materials at finite temperature: the properly-obeying-probability activation-relaxation technique
While the dynamics of many complex systems is dominated by activated events,
there are very few simulation methods that take advantage of this fact. Most of
these procedures are restricted to relatively simple systems or, as with the
activation-relaxation technique (ART), sample the conformation space
efficiently at the cost of a correct thermodynamical description. We present
here an extension of ART, the properly-obeying-probability ART (POP-ART), that
obeys detailed balance and samples correctly the thermodynamic ensemble.
Testing POP-ART on two model systems, a vacancy and an interstitial in
crystalline silicon, we show that this method recovers the proper
thermodynamical weights associated with the various accessible states and is
significantly faster than MD in the diffusion of a vacancy below 700 K.Comment: 10 pages, 3 figure
Amplitude and Frequency Spectrum of Thermal Fluctuations of A Translocating RNA Molecule
Using a combination of theory and computer simulations, we study the
translocation of an RNA molecule, pulled through a solid-state nanopore by an
optical tweezer, as a method to determine its secondary structure. The
resolution with which the elements of the secondary structure can be determined
is limited by thermal fluctuations. We present a detailed study of these
thermal fluctuations, including the frequency spectrum, and show that these
rule out single-nucleotide resolution under the experimental conditions which
we simulated. Two possible ways to improve this resolution are strong
stretching of the RNA with a back-pulling voltage across the membrane, and
stiffening of the translocated part of the RNA by biochemical means.Comment: Significantly expanded compared to previous version, 13 pages, 4
figures, to appear in J. Phys.: Condens. Matte
Pore-blockade Times for Field-Driven Polymer Translocation
We study pore blockade times for a translocating polymer of length ,
driven by a field across the pore in three dimensions. The polymer performs
Rouse dynamics, i.e., we consider polymer dynamics in the absence of
hydrodynamical interactions. We find that the typical time the pore remains
blocked during a translocation event scales as ,
where is the Flory exponent for the polymer. In line with our
previous work, we show that this scaling behaviour stems from the polymer
dynamics at the immediate vicinity of the pore -- in particular, the memory
effects in the polymer chain tension imbalance across the pore. This result,
along with the numerical results by several other groups, violates the lower
bound suggested earlier in the literature. We discuss why
this lower bound is incorrect and show, based on conservation of energy, that
the correct lower bound for the pore-blockade time for field-driven
translocation is given by , where is the viscosity of
the medium surrounding the polymer.Comment: 14 pages, 6 figures, slightly shorter than the previous version; to
appear in J. Phys.: Cond. Ma