3,725 research outputs found
Generalized-ensemble Monte carlo method for systems with rough energy landscape
We present a novel Monte Carlo algorithm which enhances equilibrization of
low-temperature simulations and allows sampling of configurations over a large
range of energies. The method is based on a non-Boltzmann probability weight
factor and is another version of the so-called generalized-ensemble techniques.
The effectiveness of the new approach is demonstrated for the system of a small
peptide, an example of the frustrated system with a rugged energy landscape.Comment: Latex; ps-files include
Expression of the insulin-like growth factor-II/mannose-6-phosphate receptor in multiple human tissues during fetal life and early infancy
The insulin like growth factor-II/mannose-6-phosphate (IGF-II/M6P) receptor has been detected in many cells and tissues. In the rat, there is a dramatic developmental regulation of IGF-II/M6P receptor expression, the receptor being high in fetal and neonatal tissues and declining thereafter. We have systematically studied the expression of the human IGF-II/M6P receptor protein in tissues from 10 human fetuses and infants (age 23 weeks gestation to 24 months postnatal). We have asked 1) whether there is differential expression among different organs, and 2) whether or not the human IGF-II/M6P receptor is developmentally regulated from 23 weeks gestation to 24 months postnatal. Protein was extracted from human tissues using a buffer containing 2% sodium dodecyl sulfate and 2% Triton X-100. Aliquots of the protein extracts were analyzed by sodium dodecyl sulfate- polyacrylamide gel electrophoresis and immunoblotting using an anti-IGF- II/M6P receptor antiserum (no. 66416) and 125I-protein A or an immunoperoxidase stain. IGF-II/M6P receptor immunoreactivity was detected in all tissues studied with the highest amount of receptor being expressed in heart, thymus, and kidney and the lowest receptor content being measured in brain and muscle. The receptor content in ovary, testis, lung, and spleen was intermediate. The apparent molecular weight of the IGF-II/M6P receptor (220,000 kilos without reduction of disulfide bonds) varied among the different tissues: in brain the receptor was of lower molecular weight than in other organs. Immunoquantitation experiments employing 125I-protein A and protein extracts from human kidney at different ages revealed a small, albeit not significant, difference of the receptor content between fetal and postnatal tissues: as in other species, larger amounts of receptor seemed to be present in fetal than in postnatal organs. In addition, no significant difference of the receptor content between human fetal liver and early postnatal liver was measured employing 125I-protein A- immunoquantitation in three fetal and five postnatal liver tissue samples. The distribution of IGF-binding protein (IGEBP) species, another abundant and major class of IGF binding principles, was also measured in human fetal and early postnatal lung, liver, kidney, muscle, and brain using Western ligand blotting with 125I-IGF-II: as with IGF-II/M6P receptor immunoreactivity there was differential expression of the different classes of IGFBPs in the various organs
Partition Function Zeros and Finite Size Scaling of Helix-Coil Transitions in a Polypeptide
We report on multicanonical simulations of the helix-coil transition of a
polypeptide. The nature of this transition was studied by calculating partition
function zeros and the finite-size scaling of various quantities. Estimates for
critical exponents are presented.Comment: RevTex, 4 eps-files; to appear in Phys. Rev. Le
Structure of the Energy Landscape of Short Peptides
We have simulated, as a showcase, the pentapeptide Met-enkephalin
(Tyr-Gly-Gly-Phe-Met) to visualize the energy landscape and investigate the
conformational coverage by the multicanonical method. We have obtained a
three-dimensional topographic picture of the whole energy landscape by plotting
the histogram with respect to energy(temperature) and the order parameter,
which gives the degree of resemblance of any created conformation with the
global energy minimum (GEM).Comment: 17 pages, 4 figure
Multicanonical Study of the 3D Ising Spin Glass
We simulated the Edwards-Anderson Ising spin glass model in three dimensions
via the recently proposed multicanonical ensemble. Physical quantities such as
energy density, specific heat and entropy are evaluated at all temperatures. We
studied their finite size scaling, as well as the zero temperature limit to
explore the ground state properties.Comment: FSU-SCRI-92-121; 7 pages; sorry, no figures include
Determining the crystal-field ground state in rare earth Heavy Fermion materials using soft-x-ray absorption spectroscopy
We infer that soft-x-ray absorption spectroscopy is a versatile method for
the determination of the crystal-field ground state symmetry of rare earth
Heavy Fermion systems, complementing neutron scattering. Using realistic and
universal parameters, we provide a theoretical mapping between the polarization
dependence of Ce spectra and the charge distribution of the Ce
states. The experimental resolution can be orders of magnitude larger than the
crystal field splitting itself. To demonstrate the experimental
feasibility of the method, we investigated CePdSi, thereby settling an
existing disagreement about its crystal-field ground state
Multi-Overlap Simulations for Transitions between Reference Configurations
We introduce a new procedure to construct weight factors, which flatten the
probability density of the overlap with respect to some pre-defined reference
configuration. This allows one to overcome free energy barriers in the overlap
variable. Subsequently, we generalize the approach to deal with the overlaps
with respect to two reference configurations so that transitions between them
are induced. We illustrate our approach by simulations of the brainpeptide
Met-enkephalin with the ECEPP/2 energy function using the global-energy-minimum
and the second lowest-energy states as reference configurations. The free
energy is obtained as functions of the dihedral and the root-mean-square
distances from these two configurations. The latter allows one to identify the
transition state and to estimate its associated free energy barrier.Comment: 12 pages, (RevTeX), 14 figures, Phys. Rev. E, submitte
Monte Carlo simulation and global optimization without parameters
We propose a new ensemble for Monte Carlo simulations, in which each state is
assigned a statistical weight , where is the number of states with
smaller or equal energy. This ensemble has robust ergodicity properties and
gives significant weight to the ground state, making it effective for hard
optimization problems. It can be used to find free energies at all temperatures
and picks up aspects of critical behaviour (if present) without any parameter
tuning. We test it on the travelling salesperson problem, the Edwards-Anderson
spin glass and the triangular antiferromagnet.Comment: 10 pages with 3 Postscript figures, to appear in Phys. Rev. Lett
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