767 research outputs found
Hysteretic Optimization For Spin Glasses
The recently proposed Hysteretic Optimization (HO) procedure is applied to
the 1D Ising spin chain with long range interactions. To study its
effectiveness, the quality of ground state energies found as a function of the
distance dependence exponent, , is assessed. It is found that the
transition from an infinite-range to a long-range interaction at
is accompanied by a sharp decrease in the performance . The transition is
signaled by a change in the scaling behavior of the average avalanche size
observed during the hysteresis process. This indicates that HO requires the
system to be infinite-range, with a high degree of interconnectivity between
variables leading to large avalanches, in order to function properly. An
analysis of the way auto-correlations evolve during the optimization procedure
confirm that the search of phase space is less efficient, with the system
becoming effectively stuck in suboptimal configurations much earlier. These
observations explain the poor performance that HO obtained for the
Edwards-Anderson spin glass on finite-dimensional lattices, and suggest that
its usefulness might be limited in many combinatorial optimization problems.Comment: 6 pages, 9 figures. To appear in JSTAT. Author website:
http://www.bgoncalves.co
Picosecond fluctuating protein energy landscape mapped by pressure–temperature molecular dynamics simulation
Microscopic statistical pressure fluctuations can, in principle, lead to corresponding fluctuations in the shape of a protein energy landscape. To examine this, nanosecond molecular dynamics simulations of lysozyme are performed covering a range of temperatures and pressures. The well known dynamical transition with temperature is found to be pressure-independent, indicating that the effective energy barriers separating conformational substates are not significantly influenced by pressure. In contrast, vibrations within substates stiffen with pressure, due to increased curvature of the local harmonic potential in which the atoms vibrate. The application of pressure is also shown to selectively increase the damping of the anharmonic, low-frequency collective modes in the protein, leaving the more local modes relatively unaffected. The critical damping frequency, i.e., the frequency at which energy is most efficiently dissipated, increases linearly with pressure. The results suggest that an invariant description of protein energy landscapes should be subsumed by a fluctuating picture and that this may have repercussions in, for example, mechanisms of energy dissipation accompanying functional, structural, and chemical relaxation
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
Model Independent Form Factors for Spin Independent Neutralino-Nucleon Scattering from Elastic Electron Scattering Data
Theoretical calculations of neutralino-nucleon interaction rates with various
nuclei are of great interest to direct dark matter searches such as CDMS,
EDELWEISS, ZEPLIN, and other experiments since they are used to establish upper
bounds on the WIMP-proton cross section. These interaction rates and cross
sections are generally computed with standard, one or two parameter
model-dependent nuclear form factors, which may not exactly mirror the actual
form factor for the particular nucleus in question. As is well known, elastic
electron scattering can allow for very precise determinations of nuclear form
factors and hence nuclear charge densities for spherical or near-spherical
nuclei. We use charge densities derived from elastic electron scattering data
to calculate model independent, analytic form factors for various target nuclei
important in dark matter searches, such as Si, Ge, S, Ca and others. We have
found that for nuclear recoils in the range of 1-100 keV significant
differences in cross sections and rates exist when the model independent form
factors are used: at 30 keV nuclear recoil the form factors squared differ by a
factor of 1.06 for Si, 1.11 for Ca, 1.27 for Ge, and 1.92
for Xe. We show the effect of different form factors on the upper limit
on the WIMP-proton cross section obtained with a hypothetical Ge
detector during a 100 kg-day effective exposure. Helm form factors with various
parameter choices differ at most by 10--20% from the best (Fourier Bessel) form
factor, and can approach it to better than 1% if the parameters are chosen to
mimic the actual nuclear density.Comment: 20 pages, 8 figure
Folding, Design and Determination of Interaction Potentials Using Off-Lattice Dynamics of Model Heteropolymers
We present the results of a self-consistent, unified molecular dynamics study
of simple model heteropolymers in the continuum with emphasis on folding,
sequence design and the determination of the interaction parameters of the
effective potential between the amino acids from the knowledge of the native
states of the designed sequences.Comment: 8 pages, 3 Postscript figures, uses RevTeX. Submitted to Physical
Review Letter
Thermodynamics of protein folding: a random matrix formulation
The process of protein folding from an unfolded state to a biologically
active, folded conformation is governed by many parameters e.g the sequence of
amino acids, intermolecular interactions, the solvent, temperature and chaperon
molecules. Our study, based on random matrix modeling of the interactions,
shows however that the evolution of the statistical measures e.g Gibbs free
energy, heat capacity, entropy is single parametric. The information can
explain the selection of specific folding pathways from an infinite number of
possible ways as well as other folding characteristics observed in computer
simulation studies.Comment: 21 Pages, no figure
Glassy Dynamics of Protein Folding
A coarse grained model of a random polypeptide chain, with only discrete
torsional degrees of freedom and Hookean springs connecting pairs of
hydrophobic residues is shown to display stretched exponential relaxation under
Metropolis dynamics at low temperatures with the exponent , in
agreement with the best experimental results. The time dependent correlation
functions for fluctuations about the native state, computed in the Gaussian
approximation for real proteins, have also been found to have the same
functional form. Our results indicate that the energy landscape exhibits
universal features over a very large range of energies and is relatively
independent of the specific dynamics.Comment: RevTeX, 4 pages, multicolumn, including 5 figures; larger
computations performed, error bars improve
Transapical aortic implantation of autologous marrow stromal cell-based tissue-engineered heart valves: first experiences in the systemic circulation
Establishing the entatic state in folding metallated Pseudomonas aeruginosa azurin
Understanding how the folding of proteins establishes their functional characteristics at the molecular level challenges both theorists and experimentalists. The simplest test beds for confronting this issue are provided by electron transfer proteins. The environment provided by the folded protein to the cofactor tunes the metal's electron transport capabilities as envisioned in the entatic hypothesis. To see how the entatic state is achieved one must study how the folding landscape affects and in turn is affected by the metal. Here, we develop a coarse-grained functional to explicitly model how the coordination of the metal (which results in a so-called entatic or rack-induced state) modifies the folding of the metallated Pseudomonas aeruginosa azurin. Our free-energy functional-based approach directly yields the proper nonlinear extra-thermodynamic free energy relationships for the kinetics of folding the wild type and several point-mutated variants of the metallated protein. The results agree quite well with corresponding laboratory experiments. Moreover, our modified free-energy functional provides a sufficient level of detail to explicitly model how the geometric entatic state of the metal modifies the dynamic folding nucleus of azurin
Prospective measurement of the width of cerebrospinal fluid spaces by cranial ultrasound in neurologically healthy children aged 0-19 months
BACKGROUND
Ultrasound (US) is often the first method used to look for brain or cerebrospinal fluid (CSF) space pathologies. Knowledge of normal CSF width values is essential. Most of the available US normative values were established over 20 years ago, were obtained with older equipment, and cover only part of the age spectrum that can be examined by cranial US. This prospective study aimed to determine the normative values of the widths of the subarachnoid and internal CSF spaces (craniocortical, minimal and maximal interhemispheric, interventricular, and frontal horn) for high-resolution linear US probes in neurologically healthy infants and children aged 0-19 months and assess whether subdural fluid collections can be delineated.
METHODS
Two radiologists measured the width of the CSF spaces with a conventional linear probe and an ultralight hockey-stick probe in neurologically healthy children not referred for cranial or spinal US.
RESULTS
This study included 359 neurologically healthy children (n = 178, 49.6%; n = 181, 50.4%) with a median age of 46.0 days and a range of 1-599 days. We constructed prediction plots, including the 5th, 50th, and 95th percentiles, and an interactive spreadsheet to calculate normative values for individual patients. The measurements of the two probes and the left and right sides did not differ, eliminating the need for separate normative values. No subdural fluid collection was detected.
CONCLUSION
Normative values for the widths of the subarachnoid space and the internal CSF spaces are useful for evaluating intracranial pathology, especially when determining whether an increase in the subarachnoid space width is abnormal
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