400 research outputs found
Molecular Chemical Engines: Pseudo-Static Processes and the Mechanism of Energy Transduction
We propose a simple theoretical model for a molecular chemical engine that
catalyzes a chemical reaction and converts the free energy released by the
reaction into mechanical work. Binding and unbinding processes of reactant and
product molecules to and from the engine are explicitly taken into account. The
work delivered by the engine is calculated analytically for infinitely slow
(``pseudo-static'') processes, which can be reversible (quasi-static) or
irreversible, controlled by an external agent. It is shown that the work larger
than the maximum value limited by the second law of thermodynamics can be
obtained in a single cycle of operation by chance, although the statistical
average of the work never exceeds this limit and the maximum work is delivered
if the process is reversible. The mechanism of the energy transductionis also
discussed.Comment: 8 pages, 3 figues, submitted to J. Phys. Soc. Jp
Efficiency of Energy Transduction in a Molecular Chemical Engine
A simple model of the two-state ratchet type is proposed for molecular
chemical engines that convert chemical free energy into mechanical work and
vice versa. The engine works by catalyzing a chemical reaction and turning a
rotor. Analytical expressions are obtained for the dependences of rotation and
reaction rates on the concentrations of reactant and product molecules, from
which the performance of the engine is analyzed. In particular, the efficiency
of energy transduction is discussed in some detail.Comment: 4 pages, 4 fugures; title modified, figures 2 and 3 modified, content
changed (pages 1 and 4, mainly), references adde
Extrapolation-CAM Theory for Critical Exponents
By intentionally underestimating the rate of convergence of
exact-diagonalization values for the mass or energy gaps of finite systems, we
form families of sequences of gap estimates. The gap estimates cross zero with
generically nonzero linear terms in their Taylor expansions, so that
for each member of these sequences of estimates. Thus, the Coherent Anomaly
Method can be used to determine . Our freedom in deciding exactly how to
underestimate the convergence allows us to choose the sequence that displays
the clearest coherent anomaly. We demonstrate this approach on the
two-dimensional ferromagnetic Ising model, for which . We also use it
on the three-dimensional ferromagnetic Ising model, finding , in good agreement with other estimates.Comment: 21 pages, Submitted to Journal of Physics A; new section added
discussing rate of convergence and relation to Finite-Size Scalin
The ATP-waiting conformation of rotating F1-ATPase revealed by single-pair fluorescence resonance energy transfer
F1-ATPase is an ATP-driven rotary motor in which a rod-shaped gamma subunit rotates inside a cylinder made of alpha3beta3 subunits. To elucidate the conformations of rotating F1, we measured fluorescence resonance energy transfer (FRET) between a donor on one of the three betas and an acceptor on gamma in single F1 molecules. The yield of FRET changed stepwise at low ATP concentrations, reflecting the stepwise rotation of gamma. In the ATP-waiting state, the FRET yields indicated a gamma position approximately 40 degrees counterclockwise (= direction of rotation) from that in the crystal structures of mitochondrial F1, suggesting that the crystal structures mimic a metastable state before product release
Bose-Einstein condensation in multilayers
The critical BEC temperature of a non interacting boson gas in a
layered structure like those of cuprate superconductors is shown to have a
minimum , at a characteristic separation between planes . It is
shown that for , increases monotonically back up to the ideal
Bose gas suggesting that a reduction in the separation between planes,
as happens when one increases the pressure in a cuprate, leads to an increase
in the critical temperature. For finite plane separation and penetrability the
specific heat as a function of temperature shows two novel crests connected by
a ridge in addition to the well-known BEC peak at associated with the
3D behavior of the gas. For completely impenetrable planes the model reduces to
many disconnected infinite slabs for which just one hump survives becoming a
peak only when the slab widths are infinite.Comment: Four pages, four figure
Catalysis and rotation of F-1 motor: Cleavage of ATP at the catalytic site occurs in 1 ms before 40 degrees substep rotation
F-1, a water-soluble portion of FoF1-ATP synthase, is an ATIP hydrolysis-driven rotary motor. The central gamma-subunit rotates in the alpha(3)beta(3) cylinder by repeating the following four stages of rotation: ATP-binding dwell, rapid 801 substep rotation, interim dwell, and rapid 40degrees substep rotation. At least two 1-ms catalytic events occur in the interim dwell, but it is still unclear which steps in the ATPase cycle, except for ATIP binding, correspond to these events. To discover which steps, we analyzed rotations of F-1 subcomplex (alpha(3)beta(3)gamma) from thermophilic Bacillus PS3 under conditions where cleavage of ATIP at the catalytic site is decelerated: hydrolysis of ATP by the catalytic-site mutant F, and hydrolysis of a slowly hydrolyzable substrate ATPgammaS (adenosine 5'-[gamma-thio]triphosphate) by wild-type F-1. In both cases, interim dwells were extended as expected from bulk phase kinetics, confirming that cleavage of ATP takes place during the interim dwell. Furthermore, the results of ATPgammaS hydrolysis by the mutant F-1 ensure that cleavage of ATIP most likely corresponds to one of the two 1-ms events and not some other faster undetected event. Thus, cleavage of ATP on F-1 occurs in 1 ms during the interim dwell, and we call this interim dwell catalytic dwell
Direct Observation of the Myosin Va Recovery Stroke That Contributes to Unidirectional Stepping along Actin
Myosins are ATP-driven linear molecular motors that work as cellular force
generators, transporters, and force sensors. These functions are driven by
large-scale nucleotide-dependent conformational changes, termed
âstrokesâ; the âpower strokeâ is the force-generating
swinging of the myosin light chainâbinding âneckâ domain
relative to the motor domain âheadâ while bound to actin; the
ârecovery strokeâ is the necessary initial motion that primes, or
âcocks,â myosin while detached from actin. Myosin Va is a processive
dimer that steps unidirectionally along actin following a âhand over
handâ mechanism in which the trailing head detaches and steps forward
âŒ72 nm. Despite large rotational Brownian motion of the detached head about
a free joint adjoining the two necks, unidirectional stepping is achieved, in
part by the power stroke of the attached head that moves the joint forward.
However, the power stroke alone cannot fully account for preferential forward
site binding since the orientation and angle stability of the detached head,
which is determined by the properties of the recovery stroke, dictate actin
binding site accessibility. Here, we directly observe the recovery stroke
dynamics and fluctuations of myosin Va using a novel, transient caged
ATP-controlling system that maintains constant ATP levels through stepwise
UV-pulse sequences of varying intensity. We immobilized the neck of monomeric
myosin Va on a surface and observed real time motions of bead(s) attached
site-specifically to the head. ATP induces a transient swing of the neck to the
post-recovery stroke conformation, where it remains for âŒ40 s, until ATP
hydrolysis products are released. Angle distributions indicate that the
post-recovery stroke conformation is stabilized by â„5
kBT of energy. The high kinetic
and energetic stability of the post-recovery stroke conformation favors
preferential binding of the detached head to a forward site 72 nm away. Thus,
the recovery stroke contributes to unidirectional stepping of myosin Va
Direct Observation of Strand Passage by DNA-Topoisomerase and Its Limited Processivity
Type-II DNA topoisomerases resolve DNA entanglements such as supercoils, knots and catenanes by passing one segment of DNA duplex through a transient enzyme-bridged double-stranded break in another segment. The ATP-dependent passage reaction has previously been demonstrated at the single-molecule level, showing apparent processivity at saturating ATP. Here we directly observed the strand passage by human topoisomerase IIα, after winding a pair of fluorescently stained DNA molecules with optical tweezers for 30 turns into an X-shaped braid. On average 0.51±0.33 ”m (11±6 turns) of a braid was unlinked in a burst of reactions taking 8±4 s, the unlinked length being essentially independent of the enzyme concentration between 0.25â37 pM. The time elapsed before the start of processive unlinking decreased with the enzyme concentration, being âŒ100 s at 3.7 pM. These results are consistent with a scenario where the enzyme binds to one DNA for a period of âŒ10 s, waiting for multiple diffusional encounters with the other DNA to transport it across the break âŒ10 times, and then dissociates from the binding site without waiting for the exhaustion of transportable DNA segments
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