2,139 research outputs found
Single Stranded DNA Translocation Through A Nanopore: A Master Equation Approach
We study voltage driven translocation of a single stranded (ss) DNA through a
membrane channel. Our model, based on a master equation (ME) approach,
investigates the probability density function (pdf) of the translocation times,
and shows that it can be either double or mono-peaked, depending on the system
parameters. We show that the most probable translocation time is proportional
to the polymer length, and inversely proportional to the first or second power
of the voltage, depending on the initial conditions. The model recovers
experimental observations on hetro-polymers when using their properties inside
the pore, such as stiffness and polymer-pore interaction.Comment: 7 pages submitted to PR
Translocation of a Single Stranded DNA Through a Conformationally Changing Nanopore
We investigate the translocation of a single stranded DNA through a pore
which fluctuates between two conformations, using coupled master equations. The
probability density function of the first passage times (FPT) of the
translocation process is calculated, displaying a triple, double or mono peaked
behavior, depending on the interconversion rates between the conformations, the
applied electric field, and the initial conditions. The cumulative probability
function of the FPT, in a field-free environment, is shown to have two regimes,
characterized by fast and slow timescales. An analytical expression for the
mean first passage time of the translocation process is derived, and provides,
in addition to the interconversion rates, an extensive characterization of the
translocation process. Relationships to experimental observations are
discussed.Comment: 8 pages, 5 figures, Biophys. J., in pres
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
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
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
Applied design thinking in urban air mobility: creating the airtaxi cabin design of the future from a user perspective
In the course of developing digital and future aviation cabin concepts at the
German Aerospace Center, the exploration of user-centered and
acceptance-enhancing methods plays a central role. The challenge here is to
identify the flexible range of requirements of different user groups for a
previously non-existent transport concept, to translate these into a concept
and to generate a rapid evaluation process by the user groups. Therefore, this
paper aims to demonstrate the application of the user-centered Design Thinking
method in the design of cabin for future air taxis. Based on the Design
Thinking approach and its iterative process steps, the direct implementation is
described on the combined airport shuttle and intracity UAM concept. The main
focus is on the identification of key user requirements by means of a focus
group study and the evaluation of initial cabin designs and key ideas by means
of an online survey. Consequently, the creative design process of a digital
prototype will be presented. In addition to an increased awareness and
acceptance among the population towards a novel mode of transportation, the
application of the Design Thinking methodology offers a flexible and
user-centered approach for further testing and simulation scenarios.Comment: 13 page
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
The development of the philosophy os science: From geocentrism to the universe without a center
O presente artigo tem como tema a passagem do geocentrismo a uma concepção do Universo sem centro. Os debates científicos estão atrelados a uma discussão que perdura no campo filosófico há longa data. O que era de se esperar, pois mesmo a filosofia não sendo propriamente uma ciência é considerada a mãe de todas as ciências. Verifica-se que nos terrenos de propriedade das ciências se encontra muito do que um dia era posse da filosofia, entretanto, nem por isso, ela abdicou de todas essas áreas. A exemplo, o que se discute entorno dos métodos de conhecimento, e aí tangenciam-se os métodos e procedimentos científicos, é algo que filosofia e ciências, de modo geral, discutem conjuntamente. Estas discussões, no entanto, nem sempre são pacíficas e harmoniosas, as disputas se revelam e, ora ou outra, combates são travados entre as duas áreas de pesquisa ou, até mesmo, no interior de ambas. Com isso em mente, procura-se expor o processo de desenvolvimento do que é chamado “Filosofia da Ciência”.This article has as its theme the transition from geocentrism to a conception of the Universe without center. Scientific debates are linked to a discussion that has persisted in the philosophical field for a long time. What was to be expected, because even though philosophy is not exactly a science, it is considered the mother of all sciences. It appears that in the lands owned by the sciences is found much of what once was the possession of philosophy, however, however, it has not abdicated all these areas. For example, what is discussed around methods of knowledge, and where scientific methods and procedures are tangent, is something that philosophy and science, in general, discuss together. These discussions, however, are not always peaceful and harmonious, disputes are revealed and, now or then, fighting is fought between the two areas of research or, even, within both. With that in mind, we seek to expose the development process of what we call “Philosophy of Science”
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
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