1,492 research outputs found
Anomalous Dynamics of Forced Translocation
We consider the passage of long polymers of length N through a hole in a
membrane. If the process is slow, it is in principle possible to focus on the
dynamics of the number of monomers s on one side of the membrane, assuming that
the two segments are in equilibrium. The dynamics of s(t) in such a limit would
be diffusive, with a mean translocation time scaling as N^2 in the absence of a
force, and proportional to N when a force is applied. We demonstrate that the
assumption of equilibrium must break down for sufficiently long polymers (more
easily when forced), and provide lower bounds for the translocation time by
comparison to unimpeded motion of the polymer. These lower bounds exceed the
time scales calculated on the basis of equilibrium, and point to anomalous
(sub-diffusive) character of translocation dynamics. This is explicitly
verified by numerical simulations of the unforced translocation of a
self-avoiding polymer. Forced translocation times are shown to strongly depend
on the method by which the force is applied. In particular, pulling the polymer
by the end leads to much longer times than when a chemical potential difference
is applied across the membrane. The bounds in these cases grow as N^2 and
N^{1+\nu}, respectively, where \nu is the exponent that relates the scaling of
the radius of gyration to N. Our simulations demonstrate that the actual
translocation times scale in the same manner as the bounds, although influenced
by strong finite size effects which persist even for the longest polymers that
we considered (N=512).Comment: 13 pages, RevTeX4, 16 eps figure
Chaperone-assisted translocation of a polymer through a nanopore
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 between the chaperone and
the chain and the chaperone concentration 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
has a transition from long-tailed distribution to Gaussian distribution with
increasing . rapidly decreases and then almost saturates with
increasing binding energy for short chain, however, it has a minimum for longer
chains at lower chaperone concentration. We also show that has a minimum
as a function of the chaperone concentration. For different , a
nonuniversal dependence of on the chain length is also observed.
These results can be interpreted by characteristic entropic effects for
flexible polymers induced by either crowding effect from high chaperone
concentration or the intersegmental binding for the high binding energy.Comment: 10 pages, to appear in J. Am. Chem. So
Vibrational energy relaxation in proteins
An overview of theories related to vibrational energy relaxation (VER) in
proteins is presented. VER of a selected mode in cytochrome c is studied using
two theoretical approaches. One is the equilibrium simulation approach with
quantum correction factors, and the other is the reduced model approach which
describes the protein as an ensemble of normal modes interacting through
nonlinear coupling elements. Both methods result in estimates of the VER time
(sub ps) for a CD stretching mode in the protein at room temperature. The
theoretical predictions are in accord with the experimental data of Romesberg's
group. A perspective on future directions for the detailed study of time scales
and mechanisms for VER in proteins is presented.Comment: 12 pages, 4 figures, accepted for publication in PNA
Fast DNA translocation through a solid-state nanopore
We report translocation experiments on double-strand DNA through a silicon
oxide nanopore. Samples containing DNA fragments with seven different lengths
between 2000 to 96000 basepairs have been electrophoretically driven through a
10 nm pore. We find a power-law scaling of the translocation time versus
length, with an exponent of 1.26 0.07. This behavior is qualitatively
different from the linear behavior observed in similar experiments performed
with protein pores. We address the observed nonlinear scaling in a theoretical
model that describes experiments where hydrodynamic drag on the section of the
polymer outside the pore is the dominant force counteracting the driving. We
show that this is the case in our experiments and derive a power-law scaling
with an exponent of 1.18, in excellent agreement with our data.Comment: 5 pages, 2 figures. Submitted to PR
Criteria and geological setting for the generic geothermal underground research laboratory, GEOLAB
High flow rate injection and related hydromechanical interaction are the most important factors in reservoir development of Enhanced Geothermal Systems (EGS). GeoLaB, a new generic geothermal underground research laboratory (URL), is proposed for controlled high flow rate experiments (CHFE) to address limited comprehension of coupled processes connected to EGS reservoir flow conditions. As analogue for typical EGS development, CHFE require specific hydromechanical conditions including a connected fracture network in crystalline basement rock, sufficient hydraulic fracture transmissivities, a strike-slip to normal faulting tectonic regime, controllable hydraulic boundary conditions, and hydrothermal alteration fracture fillings that improve conditions for hydromechanical interaction. With the aim to identify most appropriate areas for future site selection, four criteria have been established based on the EGS reference site of Soultz. Two URLs in crystalline basement worldwide approximate the requirements of a new generic GeoLaB and may be used for accompanying experimentation. Besides favourable geological, hydraulic, and stress conditions, the vicinity to long-term EGS production favours the southern Black Forest as potential region for GeoLaB. Therefore, an exemplary site assessment has been carried out at “Wilhelminenstollen” in the southern Black Forest (Germany). New remote sensing, hydrochemical, and geophysical analyses as well as reactivation potential, and stress modelling were added to complement existing geological and hydrogeological information. At this site, reactivation potential analysis reveals two local maxima prone for shear reactivation as strike-slip faults. The highest lineament density is observed for the N110°E strike direction that is associated with both slip and dilation tendency maxima. Clay minerals occur in fractures and the matrix. Local, partly water-bearing fractures, when partly filled with ore minerals, were connected to veins in the tunnel using shallow geophysical methods. Hydrochemical data reveal infiltration of the tunnel water from at least 500 m above the tunnel. The results suggest a crystalline basement with a fracture network that is regionally connected and water-conducting. Hydraulic conductivity in the southern Black Forest granite is estimated to amount to about 4.5·10−8 m s−1 at 500 m depth. The hydraulic boundary conditions exclude unknown drainage. Analyses of the influence of topography on orientation and magnitude of the maximum stress indicate a minimum overburden of about 500 m for regional reactivation to be valid. In conclusion, the southern Black Forest and in particular “Wilhelminenstollen” offers favourable condition for CHFE. Final decision on the GeoLaB site is to be drawn from forthcoming exploration wells
Anisotropic coarse-grained statistical potentials improve the ability to identify native-like protein structures
We present a new method to extract distance and orientation dependent
potentials between amino acid side chains using a database of protein
structures and the standard Boltzmann device. The importance of orientation
dependent interactions is first established by computing orientational order
parameters for proteins with alpha-helical and beta-sheet architecture.
Extraction of the anisotropic interactions requires defining local reference
frames for each amino acid that uniquely determine the coordinates of the
neighboring residues. Using the local reference frames and histograms of the
radial and angular correlation functions for a standard set of non-homologue
protein structures, we construct the anisotropic pair potentials. The
performance of the orientation dependent potentials was studied using a large
database of decoy proteins. The results demonstrate that the new distance and
orientation dependent residue-residue potentials present a significantly
improved ability to recognize native folds from a set of native and decoy
protein structures.Comment: Submitted to "The Journal of Chemical Physics
Dragging a polymer chain into a nanotube and subsequent release
We present a scaling theory and Monte Carlo (MC) simulation results for a
flexible polymer chain slowly dragged by one end into a nanotube. We also
describe the situation when the completely confined chain is released and
gradually leaves the tube. MC simulations were performed for a self-avoiding
lattice model with a biased chain growth algorithm, the pruned-enriched
Rosenbluth method. The nanotube is a long channel opened at one end and its
diameter is much smaller than the size of the polymer coil in solution. We
analyze the following characteristics as functions of the chain end position
inside the tube: the free energy of confinement, the average end-to-end
distance, the average number of imprisoned monomers, and the average stretching
of the confined part of the chain for various values of and for the number
of monomers in the chain, . We show that when the chain end is dragged by a
certain critical distance into the tube, the polymer undergoes a
first-order phase transition whereby the remaining free tail is abruptly sucked
into the tube. This is accompanied by jumps in the average size, the number of
imprisoned segments, and in the average stretching parameter. The critical
distance scales as . The transition takes place when
approximately 3/4 of the chain units are dragged into the tube. The theory
presented is based on constructing the Landau free energy as a function of an
order parameter that provides a complete description of equilibrium and
metastable states. We argue that if the trapped chain is released with all
monomers allowed to fluctuate, the reverse process in which the chain leaves
the confinement occurs smoothly without any jumps. Finally, we apply the theory
to estimate the lifetime of confined DNA in metastable states in nanotubes.Comment: 13pages, 14figure
Does Young's equation hold on the nanoscale? A Monte Carlo test for the binary Lennard-Jones fluid
When a phase-separated binary () mixture is exposed to a wall, that
preferentially attracts one of the components, interfaces between A-rich and
B-rich domains in general meet the wall making a contact angle .
Young's equation describes this angle in terms of a balance between the
interfacial tension and the surface tensions ,
between, respectively, the - and -rich phases and the wall,
. By Monte Carlo simulations
of bridges, formed by one of the components in a binary Lennard-Jones liquid,
connecting the two walls of a nanoscopic slit pore, is estimated from
the inclination of the interfaces, as a function of the wall-fluid interaction
strength. The information on the surface tensions ,
are obtained independently from a new thermodynamic integration method, while
is found from the finite-size scaling analysis of the
concentration distribution function. We show that Young's equation describes
the contact angles of the actual nanoscale interfaces for this model rather
accurately and location of the (first order) wetting transition is estimated.Comment: 6 pages, 6 figure
- …