210 research outputs found
Single molecule experiments in biophysics: exploring the thermal behavior of nonequilibrium small systems
Biomolecules carry out very specialized tasks inside the cell where energies
involved are few tens of k_BT, small enough for thermal fluctuations to be
relevant in many biomolecular processes. In this paper I discuss a few concepts
and present some experimental results that show how the study of fluctuation
theorems applied to biomolecules contributes to our understanding of the
nonequilibrium thermal behavior of small systems.Comment: Proceedings of the 22nd Statphys Conference 2004 (Bangalore,India).
Invited contributio
Extracting Structural Information of a Heteropolymer from Force-Extension Curves
We present a theory for the reverse analysis on the sequence information of a
single H/P two-letter random hetero-polymer (RHP) from its force-extension(f-z)
curves during quasi static stretching. Upon stretching of a self-assembled RHP,
it undergoes several structural transitions. The typical elastic response of a
hetero-polymeric globule is a set of overlapping saw-tooth patterns. With
consideration of the height and the position of the overlapping saw-tooth
shape, we analyze the possibility of extracting the binding energies of the
internal domains and the corresponding block sizes of the contributing
conformations.Comment: 5 figures 7 page
Probing complex RNA structures by mechanical force
RNA secondary structures of increasing complexity are probed combining single
molecule stretching experiments and stochastic unfolding/refolding simulations.
We find that force-induced unfolding pathways cannot usually be interpretated
by solely invoking successive openings of native helices. Indeed, typical
force-extension responses of complex RNA molecules are largely shaped by
stretching-induced, long-lived intermediates including non-native helices. This
is first shown for a set of generic structural motifs found in larger RNA
structures, and then for Escherichia coli's 1540-base long 16S ribosomal RNA,
which exhibits a surprisingly well-structured and reproducible unfolding
pathway under mechanical stretching. Using out-of-equilibrium stochastic
simulations, we demonstrate that these experimental results reflect the slow
relaxation of RNA structural rearrangements. Hence, micromanipulations of
single RNA molecules probe both their native structures and long-lived
intermediates, so-called "kinetic traps", thereby capturing -at the single
molecular level- the hallmark of RNA folding/unfolding dynamics.Comment: 9 pages, 9 figure
Information heat engine: converting information to energy by feedback control
In 1929, Leo Szilard invented a feedback protocol in which a hypothetical
intelligence called Maxwell's demon pumps heat from an isothermal environment
and transduces it to work. After an intense controversy that lasted over eighty
years; it was finally clarified that the demon's role does not contradict the
second law of thermodynamics, implying that we can convert information to free
energy in principle. Nevertheless, experimental demonstration of this
information-to-energy conversion has been elusive. Here, we demonstrate that a
nonequilibrium feedback manipulation of a Brownian particle based on
information about its location achieves a Szilard-type information-energy
conversion. Under real-time feedback control, the particle climbs up a
spiral-stairs-like potential exerted by an electric field and obtains free
energy larger than the amount of work performed on it. This enables us to
verify the generalized Jarzynski equality, or a new fundamental principle of
"information-heat engine" which converts information to energy by feedback
control.Comment: manuscript including 7 pages and 4 figures and supplementary material
including 6 pages and 8 figure
ZnO-Al2O3 and ZnO-TiO2 core-shell nanowire dye-sensitized solar cells
We describe the construction and performance of dye-sensitized solar cells (DSCs) based on arrays of ZnO nanowires coated with thin shells of amorphous Al2O3 or anatase TiO2 by atomic layer deposition. We find that alumina shells of all thicknesses act as insulating barriers that improve cell open-circuit voltage (VOC) only at the expense of a larger decrease in short-circuit current density (JSC). However, titania shells 10-25 nm in thickness cause a dramatic increase in VOC and fill factor with little current falloff, resulting in a substantial improvement in overall conversion efficiency, up to 2.25% under 100 mW cm(-2) AM 1.5 simulated sunlight. The superior performance of the ZnO-TiO2 core-shell nanowire cells is a result of a radial surface field within each nanowire that decreases the rate of recombination in these devices. In a related set of experiments, we have found that TiO2 blocking layers deposited underneath the nanowire films yield cells with reduced efficiency, in contrast to the beneficial use of blocking layers in some TiO2 nanoparticle cells. Raising the efficiency of our nanowire DSCs above 2.5% depends on achieving higher dye loadings through an increase in nanowire array surface area
Unzipping Dynamics of Long DNAs
The two strands of the DNA double helix can be `unzipped' by application of
15 pN force. We analyze the dynamics of unzipping and rezipping, for the case
where the molecule ends are separated and re-approached at constant velocity.
For unzipping of 50 kilobase DNAs at less than about 1000 bases per second,
thermal equilibrium-based theory applies. However, for higher unzipping
velocities, rotational viscous drag creates a buildup of elastic torque to
levels above kBT in the dsDNA region, causing the unzipping force to be well
above or well below the equilibrium unzipping force during respectively
unzipping and rezipping, in accord with recent experimental results of Thomen
et al. [Phys. Rev. Lett. 88, 248102 (2002)]. Our analysis includes the effect
of sequence on unzipping and rezipping, and the transient delay in buildup of
the unzipping force due to the approach to the steady state.Comment: 15 pages Revtex file including 9 figure
Heat release by controlled continuous-time Markov jump processes
We derive the equations governing the protocols minimizing the heat released
by a continuous-time Markov jump process on a one-dimensional countable state
space during a transition between assigned initial and final probability
distributions in a finite time horizon. In particular, we identify the
hypotheses on the transition rates under which the optimal control strategy and
the probability distribution of the Markov jump problem obey a system of
differential equations of Hamilton-Bellman-Jacobi-type. As the state-space mesh
tends to zero, these equations converge to those satisfied by the diffusion
process minimizing the heat released in the Langevin formulation of the same
problem. We also show that in full analogy with the continuum case, heat
minimization is equivalent to entropy production minimization. Thus, our
results may be interpreted as a refined version of the second law of
thermodynamics.Comment: final version, section 2.1 revised, 26 pages, 3 figure
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
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