bluuebunny/crossref_metadata_2025 huggingface dataset:
Exceptional pairs of amino acid neighbors in α‐helices
Authors: Goliaei Bahram , Minuchehr Zarrin
Published: February 2003

Amino acids seem to have specific preferences for various locations in α‐helices. These specific preferences, called singlet local propensity (SLP), have been determined by calculating the preference of occurrence of each amino acid in different positions of the α‐helix. We have studied the occurrence of amino acids, single or pairs, in different positions, singlet or doublet, of α‐helices in a database of 343 non‐homologous proteins representing a unique superfamily from the SCOP database with a resolution better than 2.5 Å from the Protein Data Bank. The preference of single amino acids for various locations of the helix was shown by the relative entropy of each amino acid with respect to the background. Based on the total relative entropy of all amino acids occurring in a single position, the Ncap position was found to be the most selective position in the α‐helix. A rigorous statistical analysis of amino acid pair occurrences showed that there are exceptional pairs for which, the observed frequency of occurrence in various doublet positions of the α‐helix is significantly different from the expected frequency of occurrence in that position. The doublet local propensity (DLP) was defined as the preference of occurrences of amino acid pairs in different doublet positions of the α‐helix. For most amino acid pairs, the observed DLP (DLPO) was nearly equal to the expected DLP (DLPE), which is the product of the related SLPs. However, for exceptional pairs of amino acids identified above, the DLPO and DLPE values were significantly different. Based on the relative values of DLPO and DLPE, exceptional amino acid pairs were divided into two categories. Those, for which the DLPO values are higher than DLPE, should have a strong tendency to pair together in the specified position. For those pairs which the DLPO values are less than DLPE, there exists a hindrance in neighboring of the two amino acids in that specific position of the α‐helix. These cases have been identified and listed in various tables in this paper. The amount of mutual information carried by the exceptional pairs of amino acids was significantly higher than the average mutual information carried by other amino acid pairs. The average mutual information conveyed by amino acid pairs in each doublet position was found to be very small but non‐zero.
Evidence for glycosylphosphatidylinositol (GPI)‐anchored eosinophil‐derived neurotoxin (EDN) on human granulocytes
Authors: Debierre-Grockiego Françoise , Desaint Corinne , Fuentes Vincent , Poussin Mathilde , Socié Gérard , Azzouz Nahid , Schwarz Ralph T. , Prin Lionel , Gouilleux-Gruart Valérie
Published: February 2003

Eosinophil‐derived neurotoxin (EDN) is one of the four basic proteins stored in specific eosinophil granules. Here we demonstrate that EDN can also be detected at the surface of granulocytes. Reduction of EDN membrane expression after phosphatidylinositol‐specific phospholipase C treatment suggests that a glycosylphosphatidylinositol (GPI) anchor is involved in the membrane association of EDN. The presence of a GPI anchor was confirmed by a lower expression of membrane EDN on granulocytes from patients with paroxysmal nocturnal hemoglobinuria which present cells lacking GPI anchor proteins. Furthermore, metabolic labeling with GPI anchor components supports biochemical evidence of GPI anchoring of EDN.
Analytical model for determination of parameters of helical structures in solution by small angle scattering: comparison of RecA structures by SANS
Authors: Lebedev D.V. , Baitin D.M. , Islamov A.Kh. , Kuklin A.I. , Shalguev V.Kh. , Lanzov V.A. , Isaev-Ivanov V.V.
Published: February 2003

The filament structures of the self‐polymers of RecA proteins from Escherichia coli and Pseudomonas aeruginosa, their complexes with ATPγS, phage M13 single‐stranded DNA (ssDNA) and the tertiary complexes RecA::ATPγS::ssDNA were compared by small angle neutron scattering. A model was developed that allowed for an analytical solution for small angle scattering on a long helical filament, making it possible to obtain the helical pitch and the mean diameter of the protein filament from the scattering curves. The results suggest that the structure of the filaments formed by these two RecA proteins, and particularly their complexes with ATPγS, is conservative.
Preliminary characterisation of mechanoresponsive regions of the c‐fos promoter in bone cells
Authors: Peake Matthew A. , El Haj Alicia J.
Published: February 2003

Preliminary analysis of the mechanisms involved in induction of stretch‐mediated transcriptional activity in the c‐fos promoter of bone has been undertaken using a series of c‐fos promoter–reporter constructs. UMR‐106 osteoblastic cells transfected with reporter constructs were subjected to cyclical physiological loading. The major determinants in the resulting transcriptional mechanoactivation are within the sequence between −356 and −151 which contains the serum response element and a consensus shear stress response element. Elements beyond this region also play a role as deletion of this region does not eliminate mechanoinduction. These results suggest that the mechanical induction of c‐fos in osteoblastic bone cells is mediated by multiple response elements.
Increasing D4Z4 repeat copy number compromises C2C12 myoblast differentiation
Authors: Yip Darren J. , Picketts David J.
Published: February 2003

Facioscapulohumeral muscular dystrophy (FSHD) is an autosomal dominant myopathy associated with deletions of a subtelomeric repeat (D4Z4). A reduction in D4Z4 copy number coincides with increased expression of neighboring 4q35 genes, implying a normal repressive role for the repeats. Here we examine the effect of increasing D4Z4 repeat number on reporter gene activity in C2C12 cells. Repeat size had only a minor cis‐effect on reporter gene activity but greatly compromised myotube formation. This latter trans‐effect did not result from expression of a gene within the repeat (DUX4) but likely results from squelching of the D4Z4 recognition complex.
Tissue‐specific expression, heat inducibility, and biological roles of two hsp16 genes in Caenorhabditis elegans
Authors: Shim Jaegal , Im Seol Hee , Lee Junho
Published: February 2003

In this report we have examined two new heat shock protein (HSP16) proteins in the nematode Caenorhabditis elegans encoded by the open reading frames F08H9.3 and F08H9.4. The F08H9.3 and F08H9.4 genes are oriented in the same direction next to each other on the chromosome, not sharing any promoter region, unlike other hsp16 genes that share common promoters in pairs. The F08H9.3 and F08H9.4 proteins were expressed in a tissue‐specific manner, unlike the other four HSP16 proteins. F08H9.3 was expressed in the pharynx, and F08H9.4 in the excretory canal and a few neuronal cells. While F08H9.3 was weakly induced by heat shock only in the same tissue as under the normal condition, F08H9.4 was newly induced in the intestine. RNA interference experiments showed that these two proteins are required for survival under the heat shock condition.
Role of iron and ferritin in TNFα‐induced apoptosis in HeLa cells
Authors: Cozzi Anna , Levi Sonia , Corsi Barbara , Santambrogio Paolo , Campanella Alessandro , Gerardi Gianmario , Arosio Paolo
Published: February 2003

We found that tumor necrosis factor α (TNFα)‐induced apoptosis in HeLa cells was accompanied by a ∼2‐fold increase in H‐ and L‐ferritin and a decrease in transferrin receptor, two indices of increased iron availability. Iron supplementation and overexpression of H‐ferritin or its mutant with an inactivated ferroxidase center reduced by about ∼50% the number of apoptotic cells after TNFα‐treatment, while overexpression of L‐ferritin was ineffective. The data indicate that H‐ferritin has an anti‐apoptotic activity unrelated to its ferroxidase activity and to its capacity to modify cellular iron metabolism.
Hypertonic activation of phospholemman in solitary rat hepatocytes in primary culture
Authors: Kirschner Udo , Van Driessche Willy , Werner Andreas , Wehner Frank
Published: February 2003

Under hypertonic conditions, solitary rat hepatocytes in primary culture shrink and subsequently exhibit a distinct regulatory volume increase (RVI). Reverse‐transcribed polymerase chain reaction and 5′ and 3′ RACE (rapid amplification of cDNA ends) techniques reveal that these cells express phospholemman (PLM). In whole‐cell recordings, the hypertonic activation of a channel is observed that resembles PLM with respect to unitary conductance (600–700 pS), gating pattern, and non‐selectivity for Na+ over K+. In Xenopus oocytes expressing hepatocyte PLM, hypertonic stress induces a non‐selective cation conductance and noise analysis reveals the activation of a channel with a unitary conductance of approximately 700 pS. These results suggest a role of PLM in the RVI of rat hepatocytes.
Involvement of three pathogenicity factors of Erwinia amylovora in the oxidative stress associated with compatible interaction in pear
Authors: Venisse Jean-Stéphane , Barny Marie-Anne , Paulin Jean-Pierre , Brisset Marie-Noëlle
Published: February 2003

Erwinia amylovora, the causal agent of fire blight of Maloideae, induces in its susceptible host plants an oxidative burst as does an incompatible pathogen. In this paper we present evidence that the elicitation of this phenomenon is the result of the combined action of two Hrp effectors of the bacteria, HrpN and DspA. We also confirmed that desferrioxamine, the siderophore of E. amylovora, is necessary for the bacteria to tolerate high levels of hydrogen peroxide. Two other pathogenicity factors of the bacteria, the HrpW effector and the capsule, do not seem to play any role in the elicitation of the oxidative burst nor in the protection of the bacteria.
Molecular cloning and characterization of TPP36 and its isoform TPP32, novel substrates of Abl tyrosine kinase
Authors: Tsuchiya Kiichiro , Kawano Youhei , Kojima Toshiyuki , Nagata Kisaburo , Takao Toshifumi , Okada Masato , Shinohara Hisaaki , Maki Kazushige , Toyama-Sorimachi Noriko , Miyasaka Nobuyuki , Watanabe Mamoru , Karasuyama Hajime
Published: February 2003

We have molecularly cloned TPP36, a novel 36 kDa protein with 281 amino acids that was identified as a protein phosphorylated in B progenitor cells following stimulation with pervanadate/H2O2. Analysis with anti‐TPP36 antiserum revealed that TPP36 was expressed ubiquitously and had an isoform with 236 amino acids, designated TPP32. TPP36/32 were localized mainly in cytoplasm despite the presence of a typical nuclear localization signal sequence. These proteins were phosphorylated preferentially by Abl among a panel of tyrosine kinases examined. Phosphorylation of tyrosine 120 in TPP36/32 led to an apparent mobility shift in sodium dodecyl sulfate–polyacrylamide gel electrophoresis, suggesting conformational change in the phosphorylated protein. Thus, TPP36/32 appear to be novel substrates of Abl tyrosine kinase.
Transfer RNA modification: influence on translational frameshifting and metabolism
Authors: Björk Glenn R , Durand Jérôme M.B , Hagervall Tord G , Leipuvien≐ Ramun≐ , Lundgren Hans K , Nilsson Kristina , Chen Peng , Qian Qiang , Urbonavičius Jaunius
Published: February 2003

Transfer RNA modification improves the rate of aa‐tRNA selection at the A‐site and the fitness in the P‐site and thereby prevents frameshifting according to a new model how frameshifting occurs [Qian et al. (1998) Mol. Cell 1, 471–482]. Evidence that the presence of various modified nucleosides in tRNA also influences central metabolism, thiamine metabolism, and bacterial virulence is reviewed.
Protein kinases in control of the centrosome cycle
Authors: Mayor Thibault , Meraldi Patrick , Stierhof York-Dieter , Nigg Erich A. , Fry Andrew M.
Published: February 2003

The centrosome is the major microtubule nucleating center of the animal cell and forms the two poles of the mitotic spindle upon which chromosomes are segregated. During the cell division cycle, the centrosome undergoes a series of major structural and functional transitions that are essential for both interphase centrosome function and mitotic spindle formation. The localization of an increasing number of protein kinases to the centrosome has revealed the importance of protein phosphorylation in controlling many of these transitions. Here, we focus on two protein kinases, the polo‐like kinase 1 and the NIMA‐related kinase 2, for which recent data indicate key roles during the centrosome cycle.
Learning from the genome sequence of Mycobacterium tuberculosis H37Rv
Authors: Cole Stewart T
Published: February 2003

Mycobacterium tuberculosis, the scourge of humanity, is one of the most successful and scientifically challenging pathogens of all time. To catalyse the conception of new prophylactic and therapeutic interventions against tuberculosis, and to enhance our understanding of the biology of the tubercle bacillus, the complete genome sequence of the most widely used strain, H37Rv, has been determined. Bioinformatic analysis led to the identification of ∼4000 genes in the 4.41 Mb genome sequence and provided fresh insight into the biochemistry, physiology, genetics and immunology of this much‐feared bacterium. Genomic information is centralised in TubercuList (http://www.pasteur.fr/Bio/TubercuList/).
Vaginal fluid pH as a screening test for vaginitis
Authors: Thinkhamrop J. , Lumbiganon P. , Thongkrajai P. , Chongsomchai C. , Pakarasang M.
Published: February 2003

Objective: To assess how effective the pH test can detect infectious vaginitis. Methods: Ambulatory gynecological patients attending the gynecological out‐patient department of Srinagarind Hospital from May 1 to July 31, 1997 were assessed for vaginitis by history, overall physical examination and vaginal examination. Specimens were collected for microbiological examination and measurement of pH level. Results: Among 422 women recruited, a vaginal fluid pH level greater than 4.5 was found in 149 (35.3%) cases. The vaginal fluid pH as a screening test for infectious vaginitis showed a sensitivity of 49.7% (95% C.I.: 42.6–56.9). When using vaginal fluid pH combined with clinical symptoms and signs to screen for vaginitis the sensitivity was 67.5% (95% C.I.: 60.4–73.9). If a pH test was used to screen for BV, its sensitivity was 73.4% (95% C.I.; 60.7–83.3). Using a pH test in combination with clinical symptoms and signs of vaginitis to screen for BV, its sensitivity was 81.3% (95% C.I.: 69.2–89.5). Conclusion: Vaginal fluid pH combined with clinical symptoms and signs had a considerably high sensitivity to screen for BV.
Genetic analysis of familial and multiple malignancies of endometrial cancer
Authors: Kobayashi K. , Sagae S. , Takeda T. , Sugimura M. , Nishioka Y. , Kudo R.
Published: February 2003

The presence of the positive replication errors (RER) phenotype in familial and multiple primary malignancies of endometrial cancer, and its association with a poor prognosis was examined. We analyzed 40 endometrial cancers for RER. Eight endometrial cancers with the RER(+) phenotype at multiple microsatellite loci were detected. The presence of the RER(+) phenotype was higher than in non‐familial malignancies. None of the eight cases with the RER(+) phenotype involved multiple primary malignancies; however these patients had shorter survival times. In this study, we suggest that RER examination in endometrial cancer may be useful for establishing a diagnosis of a familial malignancy, and for predicting a poor prognosis.
The effects of A‐fiber pressure block on perception and neurophysiological correlates of brief non‐painful and painful CO2 laser stimuli in humans
Authors: Nahra Hicham , Plaghki Léon
Published: February 2003

This study examined the relative capacity of Aδ‐ and C‐fibers to encode non‐painful and painful brief CO2 laser stimuli by comparing the effects of Aδ/C‐fiber activation versus C‐fiber activation alone. In nine normal subjects, brief CO2 laser pulses of four different intensities (range 5.8–) were delivered at random on the first intermetacarpal zone of the dorsum of the hand. A‐fiber pressure block of the superficial radial nerve was performed to fully isolate the activity of C‐fibers. Quality and intensity (VAS) of percepts, reaction time (RT) and laser‐evoked potentials (LEPs) were examined in baseline and A‐fiber block conditions. During A‐fiber block, absolute detection threshold increased dramatically from 4.8±1.8 to , proportion of detected stimuli decreased from 87% to 47% and proportion of pain reports from 39% to 10%. The quality of sensations became mainly ‘light touch’ and the ‘pricking’ sensation almost vanished. The stimulus‐VAS curve shifted to the right and the slope was reduced. Signal Detection Theory analysis revealed that discrimination performance (P(A)) was significantly depressed and that response bias (B) evolved from a neutral towards a stoical attitude. Median RT increased from 492 to 1355 ms. The late LEPs, attributed to the activation of Aδ‐fibers, disappeared and ultra‐late LEPs were recorded at Cz with a positivity peaking around 800 ms. Collectively, these observations lead to the conclusion that Aδ‐fibers are the main peripheral mediators for the perception of brief CO2 laser stimuli and that they provide more sensory information than C‐fibers.
IKCa1 activity is required for cell shrinkage, phosphatidylserine translocation and death in T lymphocyte apoptosis
Authors: Elliott James I , Higgins Christopher F
Published: February 2003

Apoptotic cell volume decrease (AVD) and exposure of phosphatidylserine (PtdSer) at the cell surface are early events in apoptosis. However, the ion channels responsible for AVD, and their relationship to PtdSer translocation and cell death are poorly understood. Real‐time analysis of calcium‐induced apoptosis in lymphocytes and thymocytes showed that AVD occurs rapidly, and precedes PtdSer translocation. Blockers of the K+ channel IKCa1 completely inhibited AVD. Blockade of IKCa1, and hence AVD, also completely prevented PtdSer translocation and cell death. Thus, IKCa1‐mediated AVD is the earliest‐defined essential step in calcium‐induced apoptosis, required for both PtdSer translocation and cell death.
Stop‐transfer efficiency of marginally hydrophobic segments depends on the length of the carboxy‐terminal tail
Authors: Hessa Tara , Monné Magnus , von Heijne Gunnar
Published: February 2003

Hydrophobic stop‐transfer sequences generally serve to halt the translocation of polypeptide chains across the endoplasmic reticulum membrane and become integrated as transmembrane α‐helices. Using engineered glycosylation sites as topology reporters, we show that the length of the nascent chain between a hydrophobic segment and the carboxy terminus of the protein can affect stop‐transfer efficiency. We also show that glycosylation sites located close to a protein's C terminus are modified in two distinct kinetic phases, one fast and one slow. Our findings suggest that membrane integration of a hydrophobic segment is not simply a question of thermodynamic equilibrium, but can be influenced by details of the translocation mechanism.
Prion pathogenesis in the absence of Toll‐like receptor signalling
Authors: Prinz Marco , Heikenwalder Mathias , Schwarz Petra , Takeda Kiyoshi , Akira Shizuo , Aguzzi Adriano
Published: February 2003

To reach the brain from peripheral sites, prions must colonize various cell types within the lymphoreticular compartment. However, no prion entry receptors are yet known. Toll‐like receptors (TLRs) are pattern‐recognition receptors that bind a multitude of pathogens and are therefore candidates as effectors of prion entry. Moreover, injection of unmethylated CpG oligodinucleotides, which stimulate TLR9, has been reported to delay peripherally initiated scrapie. We therefore studied prion infection in MyD88−/− mice, which are defective in TLR signalling. Despite subtle defects in splenic microarchitecture, MyD88−/− mice challenged intraperitoneally or intracerebrally were fully susceptible to disease and died of scrapie after similar incubation times to those of wild‐type mice. Splenic infectivity titres rose to similar levels with the same kinetics, and brains showed similar histopathological changes. TLR signalling therefore does not have any major role in prion pathogenesis, and the protective effect of TLR stimulation is unlikely to result from direct interactions with prions.
Wnt1 and Wnt5a induce cyclin D1 expression through ErbB1 transactivation in HC11 mammary epithelial cells
Authors: Civenni Gianluca , Holbro Thomas , Hynes Nancy E
Published: February 2003

Constitutive expression of Wnt1 and Wnt5a in HC11 mammary cells led to elevated TCF transcriptional activity. Intriguingly, Wnt‐expressing cells also displayed activation of ErbB1 and mitogen‐activated protein kinase (MAPK), in contrast to control HC11 cells, which did not. Furthermore, conditioned media harvested from Wnt‐expressing cells stimulated ErbB1 and the MAPK cascade when added to control cells. This process was rapid and could be blocked by an ErbB1 antibody that interferes with ligand binding and by matrix metalloproteinase (MMP) inhibitors. These results suggest that in mammary cells Wnt binding to its receptor, Frizzled (Fz), transactivates ErbB1, probably by MMP‐mediated release of soluble ErbB1 ligands. Importantly, Wnt‐transactivated ErbB1 was responsible for MAPK activation and the increased levels of cyclin D1 present in the Wnt‐expressing HC11 cells. Our finding that Wnts transactivate ErbB1 in addition to stimulating the prototypic β‐catenin/TCF pathway may help to explain why wnt1 is a potent oncogene in the mammary gland.
Lumen Formation In Vivo Versus In Vitro Observations
Authors: EGGINTON STUART , GERRITSEN MARY
Published: February 2003

Lumen formation must accompany the de novo growth of blood vessels during embryological development, the production of new vessels (vasculogenesis), and the expansion or remodeling of the microcirculation in differentiated tissue (angiogenesis). The debate over lumen origin centers on whether this is an intracellular or intercellular phenomenon, entailing vesicle accretion or loss of endothelial cell (EC) contact, and whether this represents an intrinsic property of ECs or relies on extrinsic signals. In addition, recent in vivo data suggest that a third mechanism, that of longitudinal division, may be used to expand existing capillary networks. Importantly, more than one mechanism of lumen formation may be found in response to a given angiogenic signal. Tubule formation by ECs in a matrix is an increasingly popular form of in vitro angiogenesis assay, and it may offer insights into the mechanisms involved during growth in embryos or under pathological conditions in adults. Crucial to the validity of in vitro preparations is the extent to which tubule assembly and lumen formation mirrors that observed in vivo, although these data cannot elucidate the controls operative during adaptive remodeling of the vascular bed. Similar structures may be observed in vivo and in vitro, and may represent the situation found during angiogenesis and vasculogenesis, respectively. Lumen formation during angiogenesis, and tubule formation during EC culture, require the existence of cell polarity. As tubule formation is not a unique property of ECs, how this is developed is a key area where in vitro studies may extend our understanding of EC biology.
Application of partial observability for analysis and design of synchronized systems
Authors: Santoboni Giovanni , Pogromsky Alexander Yu. , Nijmeijer Henk
Published: February 2003

Synchronization in identical drive-response systems is a problem that can be cast in an observer design framework. In this paper we extend this approach by studying the analysis/design of partial synchronization by means of observer theory. In doing so, we introduce the concept of partial observer—an observer to reconstruct a part of the system state vector. It is also shown how the observability condition can be utilized to analyze the dynamics in an array of coupled identical systems.
A geometric theory of chaotic phase synchronization
Authors: Beck Margaret , Josić Krešimir
Published: February 2003

A rigorous mathematical treatment of chaotic phase synchronization is still lacking, although it has been observed in many numerical and experimental studies. In this article we address the extension of results on phase synchronization in periodic oscillators to systems with phase coherent chaotic attractors with small phase diffusion. As models of such systems we consider special flows over diffeomorphisms in which the neutral direction is periodically perturbed. A generalization of the Averaging Theorem for periodic systems is used to extend Kuramoto’s geometric theory of phase locking in periodically forced limit cycle oscillators to this class of systems. This approach results in reduced equations describing the dynamics of the phase difference between drive and response systems over long time intervals. The reduced equations are used to illustrate how the structure of a chaotic attractor is important in its response to a periodic perturbation, and to conclude that chaotic phase coherent systems may not always be treated as noisy periodic oscillators in this context. Although this approach is strictly justified for periodic perturbations affecting only the phase variable of a chaotic oscillator, we argue that these ideas are applicable much more generally.
Role of unstable periodic orbits in phase and lag synchronization between coupled chaotic oscillators
Authors: Pazó Diego , Zaks Michael A. , Kurths Jürgen
Published: February 2003

An increase of the coupling strength in the system of two coupled Rössler oscillators leads from a nonsynchronized state through phase synchronization to the regime of lag synchronization. The role of unstable periodic orbits in these transitions is investigated. Changes in the structure of attracting sets are discussed. We demonstrate that the onset of phase synchronization is related to phase-lockings on the surfaces of unstable tori, whereas transition from phase to lag synchronization is preceded by a decrease in the number of unstable periodic orbits.
Gauge theories of Yang–Mills vector fields coupled to antisymmetric tensor fields
Authors: Anco Stephen C.
Published: February 2003

A non-Abelian class of massless/massive nonlinear gauge theories of Yang–Mills vector potentials coupled to Freedman–Townsend antisymmetric tensor potentials is constructed in four space–time dimensions. These theories involve an extended Freedman–Townsend-type coupling between the vector and tensor fields, and a Chern–Simons mass term with the addition of a Higgs-type coupling of the tensor fields to the vector fields in the massive case. Geometrical, field theoretic, and algebraic aspects of the theories are discussed in detail. In particular, the geometrical structure mixes and unifies features of Yang–Mills theory and Freedman–Townsend theory formulated in terms of Lie algebra valued curvatures and connections associated to the fields and nonlinear field strengths. The theories arise from a general determination of all possible geometrical nonlinear deformations of linear Abelian gauge theory for one-form fields and two-form fields with an Abelian Chern–Simons mass term in four dimensions. For this type of deformation (with typical assumptions on the allowed form considered for terms in the gauge symmetries and field equations), an explicit classification of deformation terms at first-order is obtained, and uniqueness of deformation terms at all higher orders is proven. This leads to a uniqueness result for the non-Abelian class of theories constructed here.
Riccati solutions of discrete Painlevé equations with Weyl group symmetry of type E8(1)
Authors: Murata Mikio , Sakai Hidetaka , Yoneda Jin
Published: February 2003

We present special solutions of the discrete Painlevé equations associated with A0(1), A0(1)* and A0(1)**-surfaces. These solutions can be expressed by solutions of linear difference equations. Here the A0(1)-surface discrete Painlevé equation is the most generic difference equation, as all discrete Painlevé equations can be obtained by its degeneration limit. These special solutions exist when the parameters of the discrete Painlevé equation satisfy a particular constraint. We consider that these special functions belong to the hypergeometric family although they seem to go beyond the known discrete and q-discrete hypergeometric functions. We also discuss the degeneration scheme of these solutions.
Resolvent convergence of sphere interactions to point interactions
Authors: Shimada Shin-ichi
Published: February 2003

We consider the Hamiltonian H(a)=−Δ+a−1λ(a)q(x̂)δ(|x|−a) which describes a sphere interaction (x̂=x/|x|,λ(a)=1+αa+O(a2)). We study the convergence of H(a) when a↓0 in the norm resolvent sense. The existence of the zero resonance of −Δ+q(x̂)δ(|x|−1) affects the form of the limiting operator.
Topological degree theory and local analysis of area preserving maps
Authors: Polymilis C. , Servizi G. , Skokos Ch. , Turchetti G. , Vrahatis M. N.
Published: February 2003

We consider methods based on the topological degree theory to compute periodic orbits of area preserving maps. Numerical approximations to the Kronecker integral give the number of fixed points of the map provided that the integration step is “small enough.” Since in any neighborhood of a fixed point the map gets four different combinations of its algebraic signs we use points on a lattice to detect the candidate fixed points by selecting boxes whose corners show all combinations of signs. This method and the Kronecker integral can be applied to bounded continuous maps such as the beam–beam map. On the other hand, they cannot be applied to maps defined on the torus, such as the standard map which has discontinuity curves propagating by iteration. Although the use of the characteristic bisection method is, in some cases, unable to detect all fixed points up to a given order, their distribution gives us a clear picture of the dynamics of the map.
New summation technique for rapidly divergent perturbation series. Hydrogen atom in magnetic field
Authors: Čı́žek J. , Zamastil J. , Skála L.
Published: February 2003

The perturbation series for the ground state energy of the hydrogen atom in the external magnetic field is summed via the sequence transformations. The formula for the large-order behavior of the partial sums of the series is derived. From this formula a new general sequence transformation is suggested. This transformation contains free parameters that can be further optimized. It is shown that if the renormalization approach is used, the optimal choice of these parameters leads to the previously suggested Weniger transformation.
The partial averaging method
Authors: Predescu Cristian
Published: February 2003

The partial averaging technique is defined and used in conjunction with the random series implementation of the Feynman–Kaç formula. It enjoys certain properties such as good rates of convergence and convergence for potentials with coulombic singularities. In this work, I introduce the reader to the technique and I analyze the basic mathematical properties of the method. I show that the method is convergent for all Kato class potentials that have finite Gaussian transform.
Long time dynamics of Met-enkephalin: Tests of mode-coupling theory and implicit solvent models
Authors: Shen Min-yi , Freed Karl F.
Published: February 2003

We test a theory for the long time conformational dynamics of the penta-peptide Met-enkephalin by comparison with the explicit solvent molecular dynamics and implicit solvent Langevin dynamics simulations described earlier. Using the requisite equilibrium averages computed from these simulations and friction coefficients evaluated from shorter simulations obtained with the Pastor–Karplus scheme, the generalized Rouse and mode-coupling theory (MCT) generate a variety of time-correlation functions that probe both local and global dynamics. The comparison between different levels of MCT calculations demonstrates that the smallest eigenvalues (corresponding to the relaxation rates of the slowest modes) are insensitive to the choice of the high frequency coupled modes. Compared with the direct simulations, the MCT time correlation functions for the dynamics involving the motion of certain rigid groups, such as end-to-end, interphenyl vector or certain vectors between bonded backbone atoms, often exhibit a too rapid short time decay but an excellent representation of the long time relaxation rate. Thus, the MCT demonstrates its ability to predict the long time dynamics of solvated peptides using only atom friction coefficients and equilibrium averages, which are easier to simulate than the long time trajectories that are usually employed for probing dynamics with either explicit or implicit solvent descriptions.
Experimental observation on the effect of coupling on different synchronization phenomena in coupled nonidentical Chua’s oscillators
Authors: Roy Prodyot Kumar , Chakraborty Satyabrata , Dana Syamal Kumar
Published: February 2003

Experimental results are presented on the effect of coupling on synchronization of two coupled nonidentical Chua’s oscillators. Two oscillators are coupled in unidirectional drive response mode. The driver is always kept in chaotic (single scroll, double scroll) state while the response oscillator is kept in various dynamical states as point attractor, single scroll periodic, chaotic and double scroll. The strength of coupling plays a crucial role on synchronization between the coupled oscillators. With decreasing coupling strength, two routes of transitions, one route is through lag and intermittent lag synchronization and another one is through intermittency have been observed in single scroll cases. But the situations are slightly different when the driver is double scroll chaotic. Lag synchronization and intermittent lag synchronization regimes are present in double scroll situation, but an intermediate intermittency regime between ILS and PS has also been observed.
Phase transitions and tricriticality in the lattice restricted primitive model supplemented by short-range interactions
Authors: Diehl Alexandre , Panagiotopoulos Athanassios Z.
Published: February 2003

Monte Carlo simulations in the grand canonical ensemble have been performed to obtain the phase behavior of the lattice restricted primitive model with additional short-range attractive interactions. Multihistogram reweighting techniques were used to obtain the phase diagrams as a function of the parameter ε*, measuring the relative strength of the short-range (SR) to the Coulombic interactions. The results reveal a great variety of behaviors as ε* is varied. Specifically, for weak or vanishing SR interactions only order-disorder phase transitions and a tricritical point are found, while for strong SR interactions the high-density ordered phase becomes incommensurate with the lattice structure and only a gas-liquid coexistence and a critical point are observed. However, for a certain range of ε* between these two limits both the critical and the tricritical points can become stable.
An ab initio study of excited states of U and UF
Authors: Fedorov Dmitri G. , Nakajima Takahito , Hirao Kimihiko
Published: February 2003

By using the third-order Douglas-Kroll method and spin–orbit multiconfiguration quasidegenerate perturbation theory we have been able to predict the spectrum of odd parity states of uranium atom within at worst 1000–2000 cm−1 accuracy for the 48 states presented. For UF we have given Morse potential parameters for the lowest 18 Ω states. The ground state was found to be I9/24. The importance of dynamic correlation effects including core correlation treated on the same footing with spin–orbit coupling is elucidated.
Reaction pathway and energy disposal of the CaH product in the reaction of Ca(4s4p 1P1)+CH4→CaH(X 2∑+)+CH3
Authors: Chen Jye-Jong , Song Yu-Wen , Lin King-Chuen , Hung Yu-Ming
Published: February 2003

The reaction pathway for Ca(4s4p 1P1)+CH4→CaH(X 2∑+)+CH3 has been investigated by using the pump–probe technique in combination with potential energy surface (PES) calculations. The nascent product distributions of CaH have been found with a Boltzmann rotational temperature of 988±66 and 864±75 K for the v=0 and 1 levels, respectively, and a Boltzmann vibrational temperature of 1960±80 K. The rotational and vibrational energy partitions in CaH have been estimated to be 555±22 and 995±10 cm−1, respectively. According to the PES calculations, the pathway is found to favor an insertion mechanism. Ca(4 1P1) approaches CH4 in C2v or Cs symmetry and then the collision complex may undergo a series of surface transitions to the ground state surface with which the products correlate. The findings of low rotation and high vibration for CaH may be interpreted from two aspects. First, the Ca–C bond distance of the intermediate around the surface crossing region is 2.7–2.8 Å, close to the equilibrium bond distance 2.349 Å. The strong coupling of the moieties renders the energy transfer sufficient from CaH into the CH3 radical. Second, after the 2A′–1 A′ surface transition, the HCaCH3 intermediate with a small excess energy may be energetically stabilized. The long-lived collision complex may have enough time for energy randomization prior to flying apart.
N
-point deformation of algebraic K3 surfaces
Authors: Kim Hoil , Lee Chang-Yeong
Published: February 2003

We construct a set of noncommutative geometries by performing N-point deformation of algebraic K3 surfaces. First, we consider two-point deformation of algebraic K3 surfaces by performing algebraic deformation of a pair of commutative algebraic K3 surfaces. In this case, the moduli space of the noncommutative deformations is of dimension 19, the same as the moduli dimension of the complex deformations of commutative algebraic K3 surfaces. Then, we extend this method to the N-point case. In the N-point case, the dimension of deformation moduli space becomes 19N(N−1)/2.
Isotropic-nematic phase equilibria of polydisperse hard rods: The effect of fat tails in the length distribution
Authors: Speranza Alessandro , Sollich Peter
Published: February 2003

We study the phase behavior of hard rods with length polydispersity, within a simplified Onsager model. We focus on unusual effects occurring when the rod length distribution has a “fat” (e.g., log-normal) tail, up to some cutoff. The relatively large number of long rods in the system has strong effects: the isotropic cloud curve, which defines where a nematic phase first occurs as density is increased, exhibits a kink; the properties of the coexisting nematic shadow phase change discontinuously there. A narrow three-phase isotropic-nematic-nematic coexistence region exists near the kink in the cloud curve, even though the length distribution is unimodal. A theoretical derivation of the isotropic cloud curve and nematic shadow curve is sketched for the limit of large cutoff. The two curves are shown to collapse onto each other in the limit. The coexisting isotropic and nematic phases are essentially identical, the only difference being that the nematic contains a larger number of the longest rods; also, only long rods show significant nematic ordering.
Calculation of vapor pressure isotope effects in the rare gases and their mixtures using an integral equation theory
Authors: Canongia Lopes J. N. , Pádua A. A. H. , Rebelo L. P. N. , Bigeleisen J.
Published: February 2003

Vapor pressure isotope effects (VPIEs) in monatomic systems (neon to xenon, either between pure isotopes or in their binary mixtures) were evaluated using an integral equation theory for a Lennard-Jones fluid with the Duh–Haymet–Handerson closure. The most relevant quantity obtained in this way is the average of the Laplacian of the potential energy of the system, 〈∇2U〉, also known as the mean force constant. The results correctly predict the different rare-gas VPIEs which span over several orders of magnitude. Using a simple two-parameter corresponding states principle, the method is capable of predicting VPIEs simply from the knowledge of isotopically independent Lennard-Jones parameters of each rare gas and the masses of its isotopes. Each type of VPIE (in pure isotopes or mixtures) map onto two reduced variable equations in terms of ln(f1/fgo)* and ln(γ∞)*. The former quantity represents a reduced form of the reduced partition function ratio (a measure of the VPIE between pure isotopes) while the second is a reduced form of the liquid activity coefficient at infinite dilution (a measure of VPIEs in isotopic binary mixtures). Several issues related to the temperature and density dependence of 〈∇2U〉 are also addressed in this work.
Stochastic chemical kinetics and the quasi-steady-state assumption: Application to the Gillespie algorithm
Authors: Rao Christopher V. , Arkin Adam P.
Published: February 2003

Biochemical dynamics are often determined by series of single molecule events such as gene expression and reactions involving protein concentrations at nanomolar concentrations. Molecular fluctuations, consequently, may be of biological significance. For example, heterogeneity in clonal populations is believed to arise from molecular fluctuations in gene expression. A realistic description, therefore, requires a probabilistic description of the biochemical dynamics as deterministic descriptions cannot capture the inherent molecular fluctuations. The Gillespie algorithm [D. T. Gillespie, J. Phys. Chem. 81, 2350 (1977)] is a stochastic procedure for simulating chemical systems at low concentrations. A limitation of stochastic kinetic models is that they require detailed information about the chemical kinetics often unavailable in biological systems. Furthermore, the Gillespie algorithm is computationally intensive when there are many molecules and reaction events. In this article, we explore one approximation technique, well known in deterministic kinetics, for simplifying the stochastic model: the quasi-steady-state assumption (QSSA). We illustrate how the QSSA can be applied to the Gillespie algorithm. Using the QSSA, we derive stochastic Michaelis–Menten rate expressions for simple enzymatic reactions and illustrate how the QSSA is applied when modeling and simulating a simple genetic circuit.
Ab initio direct dynamics studies on the reactions of H atoms with CH3Cl and CH3Br
Authors: Sheng Li , Li Ze-Sheng , Liu Jing-Yao , Xiao Jing-Fa , Sun Chia-Chung
Published: February 2003

The multiple channel reactions (1) H+CH3Cl→products and (2) H+CH3Br→products have been studied by ab initio direct dynamics method. The potential-energy surface information is calculated at the BH&H-LYP/6-311G(d,p) level of theory. Energies along the minimum energy paths are further improved by single-point energy calculations at the PMP4(SDTQ)/6-311+G(3df,2p) level of theory. For the two reactions, each with two reaction channels, hydrogen atom abstraction and halogen atom abstraction have been identified. The rate constants for each reaction channel are calculated by using improved canonical variational transition state theory incorporating the small-curvature tunneling correction in the temperature range 200–3000 K. The theoretical total rate constants, which are calculated from the sum of the individual rate constants, are in good agreement with the experimental data. For reaction (1), H-abstraction reaction will be preferred in the whole temperature range. For reaction (2), Br-abstraction reaction is the major channel, while as the temperature increases, the contribution of the H-abstraction reaction channel should be taken into account.
On the dipole moment of the ground state X 3Δ of iron carbide, FeC
Authors: Tzeli Demeter , Mavridis Aristides
Published: February 2003

In the light of experimental results on the dipole moment of the FeC X 3Δ state, we have re-examined our recent theoretical numbers of this property, by increasing our basis set size and calculating also the dipole moment by the finite field method. Our best result is 1.94 D as compared to the experimental value of 2.36 D, signifying that care should be exercised in obtaining one-electron properties even from highly correlated wave functions.
Molecular integrals over the gauge-including atomic orbitals
Authors: Ishida Kazuhiro
Published: February 2003

Each general formula can be derived by the use of the solid harmonic gradient operator [K. Ishida, Recent Res. Dev. Quantum Chem. 2, 147 (2001)] for each of the ten kinds of molecular integral over the gauge-including atomic orbitals (GIAOs). Each is obtained with the accompanying coordinate expansion (ACE) formula. These ten kinds are the overlap, the kinetic energy, the nuclear attraction, the electron repulsion, the angular momentum, the quadrupole moment, the field, the first kind field gradient, the second kind field gradient, and the “dipole-field” integrals. Except for the overlap and angular momentum integrals, we derive the general formula of these eight molecular integrals at the first level. These ACE formulas will be useful, for example, for a calculation of a molecule in a uniform magnetic field, for a relativistic calculation, and so on, using GIAO as a basis function.
Effect of secondary structure on protein aggregation: A replica exchange simulation study
Authors: Bratko D. , Blanch H. W.
Published: February 2003

The ability to control or reverse protein aggregation is vital to the production and formulation of therapeutic proteins and may be the key to the prevention of a number of neurodegenerative diseases. In recent years, laboratory studies of the phenomenon have been accompanied by a growing number of computational treatments aimed at elucidating the molecular mechanisms of aggregation. The present article is a continuation of our simulation studies of coarse-grained model oligopeptides that mimic aggregating proteins. The potential function of a multichain system is expressed in terms of a generalized Go model for a set of sequences with varying contents of secondary-structural motifs akin to α-helices and β-sheets. Conformational evolution is considered by conventional Monte Carlo simulation, and by a variation of the Replica Monte Carlo technique that facilitates barrier-crossing in glasslike aggregated systems. The foldability and aggregation propensity are monitored as functions of the extent of different secondary structures and the length of the chains. Our results indicate that an increased proportion of sheetlike structures facilitates folding of isolated chains, but strongly favors the formation of misfolded aggregates in multichain systems, in agreement with experimental observations. This behavior is interpreted in terms of cooperativity effects associated with the formation of multiple residue–residue bonds involving adjacent monomers in interacting segments, which enhance both intramolecular binding and interprotein association.
Absolute charge transfer cross sections for the state-selected reactions O+(2D,2P)+O2
Authors: Li X. , Ng C. Y.
Published: February 2003

Absolute total cross sections for O2+ formed by state-selected charge transfer collisions of O+(2D,2P)+O2 have been measured in the center-of-mass kinetic energy range of ≈0.1–40 eV. The charge-transfer cross sections for O+(2P) are found to be significantly higher than those for O+(2D), which in turn are higher than those for O+(4S) in this kinetic energy range. This experiment indicates that the charge transfer reactions O+(2D,2P)+O2 are a major source of O2+ and must be taken into account in a reliable modeling of the ion chemistry in planetary ionospheres.