1,046 research outputs found
Determination of Interaction Potentials of Amino Acids from Native Protein Structures: Test on Simple Lattice Models
We propose a novel method for the determination of the effective interaction
potential between the amino acids of a protein. The strategy is based on the
combination of a new optimization procedure and a geometrical argument, which
also uncovers the shortcomings of any optimization procedure. The strategy can
be applied on any data set of native structures such as those available from
the Protein Data Bank (PDB). In this work, however, we explain and test our
approach on simple lattice models, where the true interactions are known a
priori. Excellent agreement is obtained between the extracted and the true
potentials even for modest numbers of protein structures in the PDB.
Comparisons with other methods are also discussed.Comment: 24 pages, 4 figure
Superradiance and exciton delocalization in bacterial photosynthetic light-harvesting systems.
LH-2 complexes of Rhodobacter sphaeroides and on the isolated B820 subunit of Rhodospirillum rubrum. From these measurements the superradiance is calculated, which is related to the delocalization of excitations in these complexes. In the B820 preparation we find a radiative rate that is 30 % higher than that of monomeric bacteriochlorophyll, in agreement with a dimer model of this subunit. At room temperature both LH-1 and LH-2 are superradiant relative to monomeric Bchl-a with enhancement factors of 3.8 and 2.8, respectively. In LH-2 the radiative rate does not change significantly upon lowering the temperature to 4 K. LH-1 however exhibits a strong temperature dependence, giving rise to a 2.4 times higher radiative rate at 4 K relative to room temperature. From modeling of the superradiance using a Hamiltonian based on the LH-2 structure and including site inhomogeneity, we conclude that the ratio of inhomogeneity over the coupling betwee
Long-lived charge-separated states in bacterial reaction centers isolated from Rhodobacter sphaeroides
AbstractWe studied the accumulation of long-lived charge-separated states in reaction centers isolated from Rhodobacter sphaeroides, using continuous illumination, or trains of single-turnover flashes. We found that under both conditions a long-lived state was produced with a quantum yield of about 1%. This long-lived species resembles the normal P+Q− state in all respects, but has a lifetime of several minutes. Under continuous illumination the long-lived state can be accumulated, leading to close to full conversion of the reaction centers into this state. The lifetime of this accumulated state varies from a few minutes up to more than 20 min, and depends on the illumination history. Surprisingly, the lifetime and quantum yield do not depend on the presence of the secondary quinone, QB. Under oxygen-free conditions the accumulation was reversible, no changes in the normal recombination times were observed due to the intense illumination. The long-lived state is responsible for most of the dark adaptation and hysteresis effects observed in room temperature experiments. A simple method for quinone extraction and reconstitution was developed
Three-pulse photon echo measurements on LH1 and LH2 complexes of Rhodobacter sphaeroides: A nonlinear spectroscopic probe of energy transfer.
Three-pulse echo peak shift measurements were performed on the B875 and B850 bands of detergent-isolated LH1 and LH2 complexes at room temperature. The peak shifts are much larger and decay much faster than typically observed for dye molecules in solution. Simulations of the peak shifts based on the optical transition frequency correlation function,M(t), are presented. M(t) includes contributions from rapid protein fluctuations, vibrational motion, and energy transfer. The model reproduces the room temperature absorption spectra of B850 and B875, shows that the coupling of electronic and nuclear degrees of freedom is much weaker than for dyes in solution, and identifies contributions to the line shapes that may be important to the energy transfer processes. The implications of these results for the extent of electronic delocalization in LH1 and LH2 are also discussed. Although the role of coherence transfer still needs to be understood, the results are shown to be consistent with the use of weak-coupling excitation transfer models of B850 and B875. I
A Novel Perspective on Interference Control and Distraction in ADHD
Sergeant, J.A. [Promotor]Oosterlaan, J. [Promotor
Cluster derivation of Parisi's RSB solution for disordered systems
We propose a general scheme in which disordered systems are allowed to
sacrifice energy equi-partitioning and separate into a hierarchy of ergodic
sub-systems (clusters) with different characteristic time-scales and
temperatures. The details of the break-up follow from the requirement of
stationarity of the entropy of the slower cluster, at every level in the
hierarchy. We apply our ideas to the Sherrington-Kirkpatrick model, and show
how the Parisi solution can be {\it derived} quantitatively from plausible
physical principles. Our approach gives new insight into the physics behind
Parisi's solution and its relations with other theories, numerical experiments,
and short range models.Comment: 7 pages 5 figure
Survey propagation for the cascading Sourlas code
We investigate how insights from statistical physics, namely survey
propagation, can improve decoding of a particular class of sparse error
correcting codes. We show that a recently proposed algorithm, time averaged
belief propagation, is in fact intimately linked to a specific survey
propagation for which Parisi's replica symmetry breaking parameter is set to
zero, and that the latter is always superior to belief propagation in the high
connectivity limit. We briefly look at further improvements available by going
to the second level of replica symmetry breaking.Comment: 14 pages, 5 figure
Spectra of Modular and Small-World Matrices
We compute spectra of symmetric random matrices describing graphs with
general modular structure and arbitrary inter- and intra-module degree
distributions, subject only to the constraint of finite mean connectivities. We
also evaluate spectra of a certain class of small-world matrices generated from
random graphs by introducing short-cuts via additional random connectivity
components. Both adjacency matrices and the associated graph Laplacians are
investigated. For the Laplacians, we find Lifshitz type singular behaviour of
the spectral density in a localised region of small values. In the
case of modular networks, we can identify contributions local densities of
state from individual modules. For small-world networks, we find that the
introduction of short cuts can lead to the creation of satellite bands outside
the central band of extended states, exhibiting only localised states in the
band-gaps. Results for the ensemble in the thermodynamic limit are in excellent
agreement with those obtained via a cavity approach for large finite single
instances, and with direct diagonalisation results.Comment: 18 pages, 5 figure
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