67 research outputs found
Controlling DNA capture and propagation through artificial nanopores
Electrophorescing blopolymers across nanopores modulates the ionic current through the pore, revealing the polymer's diameter, length, and conformation. The rapidity of polymer translocation (similar to 30 000 bp/ms) in this geometry greatly limits the information that can be obtained for each base. Here we show that the translocation speed of lambda-DNA through artificial nanopores can be reduced using. optical tweezers. DNAs coupled to optically trapped beads were presented to nanopores. DNAs initially placed up to several micrometers from the pore could be captured. Subsequently, the optical tweezers reduced translocation speeds to 150 bp/ms, about 200-fold slower than free DNA. Moreover, the optical tweezers allowed us to "floss" single polymers back and forth through the pore. The combination of controlled sample presentation, greatly slowed translocation speeds, and repeated electrophoresis of single DNAs removes several barriers to using artificial nanopores for sequencing, haplotyping, and characterization of protein-DNA interactions
Fabrication of 10 nm diameter hydrocarbon nanopores
The addition of carbon to samples, during transmission electron microscope imaging, presents a barrier to accurate analysis; the controlled deposition of hydrocarbons by a focused electron beam can be a useful technique for local nanometer-scale sculpting of material. Here we use hydrocarbon deposition to form nanopores from larger focused ion beam holes in silicon nitride membranes. Using this method, we close 100ā200 nm diameter holes to diameters of 10 nm and below, with deposition rates of 0.6 nm/min. I-V characteristics of electrolytic flow through these nanopores agree quantitatively with a one dimensional model at all examined salt concentrations
Lower bounds on dissipation upon coarse graining
By different coarse-graining procedures we derive lower bounds on the total
mean work dissipated in Brownian systems driven out of equilibrium. With
several analytically solvable examples we illustrate how, when, and where the
information on the dissipation is captured.Comment: 11 pages, 8 figure
Efficiency of Free Energy Transduction in Autonomous Systems
We consider the thermodynamics of chemical coupling from the viewpoint of
free energy transduction efficiency. In contrast to an external
parameter-driven stochastic energetics setup, the dynamic change of the
equilibrium distribution induced by chemical coupling, adopted, for example, in
biological systems, is inevitably an autonomous process. We found that the
efficiency is bounded by the ratio between the non-symmetric and the
symmetrized Kullback-Leibler distance, which is significantly lower than unity.
Consequences of this low efficiency are demonstrated in the simple two-state
case, which serves as an important minimal model for studying the energetics of
biomolecules.Comment: 4 pages, 4 figure
A nonequilibrium extension of the Clausius heat theorem
We generalize the Clausius (in)equality to overdamped mesoscopic and
macroscopic diffusions in the presence of nonconservative forces. In contrast
to previous frameworks, we use a decomposition scheme for heat which is based
on an exact variant of the Minimum Entropy Production Principle as obtained
from dynamical fluctuation theory. This new extended heat theorem holds true
for arbitrary driving and does not require assumptions of local or close to
equilibrium. The argument remains exactly intact for diffusing fields where the
fields correspond to macroscopic profiles of interacting particles under
hydrodynamic fluctuations. We also show that the change of Shannon entropy is
related to the antisymmetric part under a modified time-reversal of the
time-integrated entropy flux.Comment: 23 pages; v2: manuscript significantly extende
Entropy production for mechanically or chemically driven biomolecules
Entropy production along a single stochastic trajectory of a biomolecule is
discussed for two different sources of non-equilibrium. For a molecule
manipulated mechanically by an AFM or an optical tweezer, entropy production
(or annihilation) occurs in the molecular conformation proper or in the
surrounding medium. Within a Langevin dynamics, a unique identification of
these two contributions is possible. The total entropy change obeys an integral
fluctuation theorem and a class of further exact relations, which we prove for
arbitrarily coupled slow degrees of freedom including hydrodynamic
interactions. These theoretical results can therefore also be applied to driven
colloidal systems. For transitions between different internal conformations of
a biomolecule involving unbalanced chemical reactions, we provide a
thermodynamically consistent formulation and identify again the two sources of
entropy production, which obey similar exact relations. We clarify the
particular role degenerate states have in such a description
Single-molecule experiments in biological physics: methods and applications
I review single-molecule experiments (SME) in biological physics. Recent
technological developments have provided the tools to design and build
scientific instruments of high enough sensitivity and precision to manipulate
and visualize individual molecules and measure microscopic forces. Using SME it
is possible to: manipulate molecules one at a time and measure distributions
describing molecular properties; characterize the kinetics of biomolecular
reactions and; detect molecular intermediates. SME provide the additional
information about thermodynamics and kinetics of biomolecular processes. This
complements information obtained in traditional bulk assays. In SME it is also
possible to measure small energies and detect large Brownian deviations in
biomolecular reactions, thereby offering new methods and systems to scrutinize
the basic foundations of statistical mechanics. This review is written at a
very introductory level emphasizing the importance of SME to scientists
interested in knowing the common playground of ideas and the interdisciplinary
topics accessible by these techniques. The review discusses SME from an
experimental perspective, first exposing the most common experimental
methodologies and later presenting various molecular systems where such
techniques have been applied. I briefly discuss experimental techniques such as
atomic-force microscopy (AFM), laser optical tweezers (LOT), magnetic tweezers
(MT), biomembrane force probe (BFP) and single-molecule fluorescence (SMF). I
then present several applications of SME to the study of nucleic acids (DNA,
RNA and DNA condensation), proteins (protein-protein interactions, protein
folding and molecular motors). Finally, I discuss applications of SME to the
study of the nonequilibrium thermodynamics of small systems and the
experimental verification of fluctuation theorems. I conclude with a discussion
of open questions and future perspectives.Comment: Latex, 60 pages, 12 figures, Topical Review for J. Phys. C (Cond.
Matt
The CMS High Level Trigger
At the Large Hadron Collider at CERN the proton bunches cross at a rate of
40MHz. At the Compact Muon Solenoid experiment the original collision rate is
reduced by a factor of O (1000) using a Level-1 hardware trigger. A subsequent
factor of O(1000) data reduction is obtained by a software-implemented High
Level Trigger (HLT) selection that is executed on a multi-processor farm. In
this review we present in detail prototype CMS HLT physics selection
algorithms, expected trigger rates and trigger performance in terms of both
physics efficiency and timing.Comment: accepted by EPJ Nov 200
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