758 research outputs found
High resolution frequency selective photochemistry of phycobilisomes at cryogenic temperatures
LOOKING INTO THE ENERGY LANDSCAPE OF MYOGLOBIN
Using the haem group of myoglobin as a probe in optical experiments makes it possible to study its conformational fluctuations in real time. Results of these experiments can be directly interpreted in terms of the structure of the potential energy surface of the protein. The current view is that proteins have rough energy landscapes comprising a large number of minima which represent conformational substates, and that these substates are hierarchically organized. Here, we show that the energy landscape is characterized by a number of discrete distributions of;barrier heights each representing a tier within a hierarchy of conformational substates. Furthermore, we provide evidence that the energy surface is self-similar and offer suggestions for a characterization of the protein fluctuations
External Inversion, Internal Inversion, and Reflection Invariance
Having in mind that physical systems have different levels of structure we
develop the concept of external, internal and total improper Lorentz
transformation (space inversion and time reversal). A particle obtained from
the ordinary one by the application of internal space inversion or time
reversal is generally a different particle. From this point of view the
intrinsic parity of a nuclear particle (`elementary particle') is in fact the
external intrinsic parity, if we take into account the internal structure of a
particle. We show that non-conservation of the external parity does not
necessarily imply non-invariance of nature under space inversion. The
conventional theory of beta-decay can be corrected by including the internal
degrees of freedom to become invariant under total space inversion, though not
under the external one.Comment: 15 pages. An early proposal of "mirror matter", published in 1974.
This is an exact copy of the published paper. I am posting it here because of
the increasing interest in the "exact parity models" and its experimental
consequence
Structurally specific thermal fluctuations identify functional sites for DNA transcription
We report results showing that thermally-induced openings of double stranded
DNA coincide with the location of functionally relevant sites for
transcription. Investigating both viral and bacterial DNA gene promoter
segments, we found that the most probable opening occurs at the transcription
start site. Minor openings appear to be related to other regulatory sites. Our
results suggest that coherent thermal fluctuations play an important role in
the initiation of transcription. Essential elements of the dynamics, in
addition to sequence specificity, are nonlinearity and entropy, provided by
local base-pair constraints
Anomalous relaxation and self-organization in non-equilibrium processes
We study thermal relaxation in ordered arrays of coupled nonlinear elements
with external driving. We find, that our model exhibits dynamic
self-organization manifested in a universal stretched-exponential form of
relaxation. We identify two types of self-organization, cooperative and
anti-cooperative, which lead to fast and slow relaxation, respectively. We give
a qualitative explanation for the behavior of the stretched exponent in
different parameter ranges. We emphasize that this is a system exhibiting
stretched-exponential relaxation without explicit disorder or frustration.Comment: submitted to PR
Heat exchange between two interacting nanoparticles beyond the fluctuation-dissipation regime
We show that the observed non-monotonic behavior of the thermal conductance
between two nanoparticles when they are brought into contact is originated by
an intricate phase space dynamics. Here it is assumed that this dynamics
results from the thermally activated jumping through a rough energy landscape.
A hierarchy of relaxation times plays the key role in the description of this
complex phase space behaviour. Our theory enables us to analyze the heat
transfer just before and at the moment of contact.Comment: 4 pages, 1 figure, approved for publication in Physical Review
Letter
Fractal Analysis of Protein Potential Energy Landscapes
The fractal properties of the total potential energy V as a function of time
t are studied for a number of systems, including realistic models of proteins
(PPT, BPTI and myoglobin). The fractal dimension of V(t), characterized by the
exponent \gamma, is almost independent of temperature and increases with time,
more slowly the larger the protein. Perhaps the most striking observation of
this study is the apparent universality of the fractal dimension, which depends
only weakly on the type of molecular system. We explain this behavior by
assuming that fractality is caused by a self-generated dynamical noise, a
consequence of intermode coupling due to anharmonicity. Global topological
features of the potential energy landscape are found to have little effect on
the observed fractal behavior.Comment: 17 pages, single spaced, including 12 figure
The Goldbeter-Koshland switch in the first-order region and its response to dynamic disorder
In their classical work (Proc. Natl. Acad. Sci. USA, 1981, 78:6840-6844),
Goldbeter and Koshland mathematically analyzed a reversible covalent
modification system which is highly sensitive to the concentration of
effectors. Its signal-response curve appears sigmoidal, constituting a
biochemical switch. However, the switch behavior only emerges in the
"zero-order region", i.e. when the signal molecule concentration is much lower
than that of the substrate it modifies. In this work we showed that the
switching behavior can also occur under comparable concentrations of signals
and substrates, provided that the signal molecules catalyze the modification
reaction in cooperation. We also studied the effect of dynamic disorders on the
proposed biochemical switch, in which the enzymatic reaction rates, instead of
constant, appear as stochastic functions of time. We showed that the system is
robust to dynamic disorder at bulk concentration. But if the dynamic disorder
is quasi-static, large fluctuations of the switch response behavior may be
observed at low concentrations. Such fluctuation is relevant to many biological
functions. It can be reduced by either increasing the conformation
interconversion rate of the protein, or correlating the enzymatic reaction
rates in the network.Comment: 23 pages, 4 figures, accepted by PLOS ON
Reaction rate for two--neutron capture by He
Recent investigations suggest that the neutrino--heated hot bubble between
the nascent neutron star and the overlying stellar mantle of a type--II
supernova may be the site of the r--process. In the preceding --process
building up the elements to , the He(2n,)He--
and He(,n)Be--reactions bridging the instability gap at
and could be of relevance. We suggest a mechanism for
He(2n,)He and calculate the reaction rate within the
+n+n approach. The value obtained is about a factor 1.6 smaller than
the one obtained recently in the simpler direct--capture model, but is at least
three order of magnitude enhanced compared to the previously adopted value. Our
calculation confirms the result of the direct--capture calculation that under
representative conditions in the --process the reaction path proceeding
through He is negligible compared to He(n,)Be.Comment: 13 pages, 4 postscript figures, to appear in "Zeitschrift f. Physik
A", changed internet address and filename, the uuencoded postscript file
including the figures is available at
ftp://is1.kph.tuwien.ac.at/pub/ohu/twoneutron.u
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