Multidimensional replica-exchange method for free-energy calculations

We have developed a new simulation algorithm for free-energy calculations. The method is a multidimensional extension of the replica-exchange method. While pairs of replicas with different temperatures are exchanged during the simulation in the original replica-exchange method, pairs of replicas with different temperatures and/or different parameters of the potential energy are exchanged in the new algorithm. This greatly enhances the sampling of the conformational space and allows accurate calculations of free energy in a wide temperature range from a single simulation run, using the weighted histogram analysis method.Comment: 13 pages, (ReVTeX), 9 figures. J. Chem. Phys. 113 (2000), in pres

Proof of the generalized Lieb-Wehrl conjecture for integer indices larger than one

Gnutzmann and Zyczkowski have proposed the Renyi-Wehrl entropy as a generalization of the Wehrl entropy, and conjectured that its minimum is obtained for coherent states. We prove this conjecture for the Renyi index q=2,3,... in the cases of compact semisimple Lie groups. A general formula for the minimum value is given.Comment: 8 pages, typos fixed, published versio

Moments of generalized Husimi distributions and complexity of many-body quantum states

We consider generalized Husimi distributions for many-body systems, and show that their moments are good measures of complexity of many-body quantum states. Our construction of the Husimi distribution is based on the coherent state of the single-particle transformation group. Then the coherent states are independent-particle states, and, at the same time, the most localized states in the Husimi representation. Therefore delocalization of the Husimi distribution, which can be measured by the moments, is a sign of many-body correlation (entanglement). Since the delocalization of the Husimi distribution is also related to chaoticity of the dynamics, it suggests a relation between entanglement and chaos. Our definition of the Husimi distribution can be applied not only to the systems of distinguishable particles, but also to those of identical particles, i.e., fermions and bosons. We derive an algebraic formula to evaluate the moments of the Husimi distribution.Comment: published version, 33 pages, 7 figre

Regulation of CD1 Antigen-presenting Complex Stability

For major histocompatibility complex class I and II molecules, the binding of specific peptide antigens is essential for assembly and trafficking and is at the center of their quality control mechanism. However, the role of lipid antigen binding in stabilization and quality control of CD1 heavy chain (HC).beta(2)-microglobulin (beta(2)m) complexes is unclear. Furthermore, the distinct trafficking and loading routes of CD1 proteins take them from mildly acidic pH in early endososmal compartments (pH 6.0) to markedly acidic pH in lysosomes (pH 5.0) and back to neutral pH of the cell surface (pH 7.4). Here, we present evidence that the stability of each CD1 HC.beta(2)m complex is determined by the distinct pH optima identical to that of the intracellular compartments in which each CD1 isoform resides. Although stable at acidic endosomal pH, complexes are only stable at cell surface pH 7.4 when bound to specific lipid antigens. The proposed model outlines a quality control program that allows lipid exchange at low endosomal pH without dissociation of the CD1 HC.beta(2)m complex and then stabilizes the antigen-loaded complex at neutral pH at the cell surface

Signals of tree volume and temperature in a high-resolution record of pollen accumulation rates in northern Finland

International audiencePollen accumulation rates (PARs) provide a potential proxy for quantitative tree volume (m3 ha 1) reconstruction with reliable absolute pollen productivity estimates (APPEs). We obtained APPEs for pine, spruce and birch at their range limits in northern Finland under two temperature periods ('warm' and 'cold') based on long-term pollen trap and tree volume records within a 14-km radius of each trap. APPEs (mean SE; 108 grains m 3 a 1) tend to be higher for the 'warm' periods (pine 123.8 24.4, birch 528.0 398.4, spruce 434.3 113.7) compared with the 'cold' periods (pine 95.5 37.3, birch 317.3 282.6, spruce 119.6 37.6), although the difference is only significant for spruce. Using an independent temperature record and the APPEs obtained, we reconstruct a low-frequency record of pine volume changes over the last 1000 years at Palomaa mire, where a high-resolution record of Pinus PARs is available. Five phases are distinguished in the reconstruction: moderate pine volume, AD 1080-1170; high volume, AD 1170-1340; low volume, AD 1340-1630; very low volume, AD 1630-1810; and rising pine volume, AD 1810- 1950. These phases do not coincide with periods of high or low June-July-August temperatures, and thus appear to reflect regional variations in tree volume, while high-frequency changes within each time-period block show variations in PARs in response to temperatur

Genetic analysis of porcine H3N2 viruses originating in southern China

From immunological and phylogenetic analyses of H3 influenza viruses isolated from pigs and ducks in the People's Republic of China (China), Hong Kong, Taiwan and Japan, between 1968 and 1982, we arrived at the following conclusions. The H3 haemagglutinin and N2 neuraminidase genes from swine isolates can be segregated into four mammalian lineages, including: (i) the earliest human strains; (ii) early swine strains including Hong Kong isolates from 1976-1977; (iii) an intermediate strain between the early swine and recent human strains; and (iv) recent human strains. In this study we found an unusual swine strain (sw/Hong Kong/127/82) belonging to the third lineage which behaved like those of the early swine-like lineage in the haemagglutination inhibition test; but neuraminidase inhibition profiles with monoclonal antibodies indicated that this virus is related to late human strains. On the basis of pairwise comparisons of complete or partial nucleotide sequences the genes encoding the three polymerase proteins (PB2, PB1, PA), the nucleoprotein, the membrane protein and possibly the nonstructural proteins of sw/Hong Kong/127/82 are of the swine H1N1 lineage, whereas genes encoding the two surface glycoproteins belong to the human H3N2 lineage. In contrast, all RNA segments of one swine isolate (sw/Hong Kong/81/78) are similar to those of recent human H3N2 viruses. This study indicated that frequent interspecies infections between human and swine hosts appeared to occur during 1976-82. Although the evolutionary rates of human (0.0122/site/year), swine (0.0127/site/year) and avian (0.0193/site/year) virus genes are similar when based upon synonymous substitutions, nonsynonymous substitutions indicated that viral genes derived from human and swine viruses evolved about three times faster (0.0026-0.0027/site/year) than those of avian viruses (0.0008/site/year). Furthermore, the evolutionary mechanism by which human and swine H3 haemagglutinin genes evolve at a similar rate, based on nonsynonymous substitutions, appeared to be quite different from previous evidence which showed that human H1 haemagglutinin genes evolved three times faster than those of swine viruses. However, comparison of the number of nonsynonymous substitutions in the antigenic sites (A-E) of haemagglutinin molecules demonstrated that swine viruses evolve at a rate that is about one fifth to one tenth that of human viruses, reflecting the conservative nature of the antigenic structure in the former.published_or_final_versio