bluuebunny/crossref_metadata_2025 huggingface dataset:
“Illuminating” electron diffusion regions of collisionless magnetic reconnection using electron agyrotropy
Authors: Scudder Jack , Daughton William
Published: June 2008

Agyrotropy is a scalar measure of the departure of the pressure tensor from cylindrical symmetry about the local magnetic field direction. Ordinarily electrons are well modeled as gyrotropic with very small agyrotropy. Intensified layers of electron agyrotropy are demonstrated to highlight the thin electron gyroradius scale boundary regions adjoining separatrices, X and O lines of full particle simulations of collisionless magnetic reconnection. Examples are presented to show these effects in antiparallel and guide field geometries, pair plasmas, and simulations at a variety of mass ratios, including a hydrogen plasma. Agyrotropy has been determined from the PIC pressure tensor using a new, fast algorithm developed to correct discreteness contributions to the apparent agyrotropy. As a local scalar diagnostic, agyrotropy is shown to be potentially useful with single spacecraft data to identify the crossing or proximity of electron scale current layers, thus providing a kinetic level diagnosis of a given layer's ability to be a possible site of the collisionless reconnection process. Such kinetic tools are certainly complimentary to the other macroscopic signatures of reconnection. Because of the extreme circumstances required for electron agyrotropy, detection of these signatures with framing macroscopic signatures might prove useful for the discovery of new reconnection sites in nature and 3‐D codes of collisionless reconnection. The agyrotropy in the 2‐D PIC codes reflect long‐lived bulges on the distribution function that appear to be organized by the direction and size of slowly evolving perpendicular electric fields in these layers and are not consistent with gyrophase bunching.
Phospho‐dependent interactions between NBS1 and MDC1 mediate chromatin retention of the MRN complex at sites of DNA damage
Authors: Chapman J Ross , Jackson Stephen P
Published: June 2008

Mammalian cells respond to DNA double‐strand breaks (DSBs) by recruiting DNA repair and cell‐cycle checkpoint proteins to such sites. Central to these DNA damage response (DDR) events is the DNA damage mediator protein MDC1. MDC1 interacts with several DDR proteins, including the MRE11–RAD50–NBS1 (MRN) complex. Here, we show that MDC1 is phosphorylated on a cluster of conserved repeat motifs by casein kinase 2 (CK2). Moreover, we establish that this phosphorylation of MDC1 promotes direct, phosphorylation‐dependent interactions with NBS1 in a manner that requires the closely apposed FHA and twin BRCT domains in the amino terminus of NBS1. Finally, we show that these CK2‐targeted motifs in MDC1 are required to mediate NBS1 association with chromatin‐flanking sites of unrepaired DSBs. These findings provide a molecular explanation for the MDC1–MRN interaction and yield insights into how MDC1 coordinates the focal assembly and activation of several DDR factors in response to DNA damage.
Transcriptional regulation and function of the Neurospora clock gene white collar 2 and its isoforms
Authors: Neiss Andrea , Schafmeier Tobias , Brunner Michael
Published: June 2008

FREQUENCY (FRQ) and the White Collar Complex (WCC), consisting of WC1 and WC2 subunits, are crucial components of positive and negative feedback loops of the circadian clock of Neurospora. In the positive limb, FRQ supports the accumulation of WC1 on a post‐translational level and activates transcription of wc2. We analysed the transcriptional regulation of wc2. The WCC indirectly inhibits wc2 by controlling expression of a putative repressor. FRQ activates wc2 transcription by inhibiting WCC. A putative transcriptional activator binds to the wc2 promoter and antagonizes the repressor function. Furthermore, an internal promoter in the wc2 coding region drives expression of an amino‐terminally shortened isoform, sWC2. Full‐length WC2 and sWC2 are expressed in an antagonistic manner; thus, sWC2 expression seems to be a fail‐safe mechanism that maintains total WC2 levels above a threshold.
Hepatocyte growth factor activator inhibitor-1 has a complex subcellular itinerary
Authors: Godiksen Sine , Selzer-Plon Joanna , Pedersen Esben D. K. , Abell Kathrine , Rasmussen Hanne B. , Szabo Roman , Bugge Thomas H. , Vogel Lotte K.
Published: June 2008

HAI-1 [HGF (hepatocyte growth factor) activator inhibitor-1] is a Kunitz-type transmembrane serine protease inhibitor that forms inhibitor complexes with the trypsin-like serine protease, matriptase. HAI-1 is essential for mouse placental development and embryo survival and together with matriptase it is a key regulator of carcinogenesis. HAI-1 is expressed in polarized epithelial cells, which have the plasma membrane divided by tight junctions into an apical and a basolateral domain. In the present study we show that HAI-1 at steady-state is mainly located on the basolateral membrane of both Madin–Darby canine kidney cells and mammary gland epithelial cells. After biosynthesis, HAI-1 is exocytosed mainly to the basolateral plasma membrane from where 15% of the HAI-1 molecules are proteolytically cleaved and released into the basolateral medium. The remaining membrane-associated HAI-1 is endocytosed and then recycles between the basolateral plasma membrane and endosomes for hours until it is transcytosed to the apical plasma membrane. Minor amounts of HAI-1 present at the apical plasma membrane are proteolytically cleaved and released into the apical medium. Full-length membrane-bound HAI-1 has a half-life of 1.5 h and is eventually degraded in the lysosomes, whereas proteolytically released HAI-1 is more stable. HAI-1 is co-localized with its cognate protease, matriptase, at the basolateral plasma membrane. We suggest that HAI-1, in addition to its protease inhibitory function, plays a role in transporting matriptase as a matriptase–HAI-1 complex from the basolateral plama membrane to the apical plasma membrane, as matriptase is known to interact with prostasin, located at the apical plasma membrane.
The Hsp40 family chaperone protein DnaJB6 enhances Schlafen1 nuclear localization which is critical for promotion of cell-cycle arrest in T-cells
Authors: Zhang Yafeng , Yang Zhengmin , Cao Yonghao , Zhang Shijian , Li Hai , Huang Ying , Ding Yu-qiang , Liu Xiaolong
Published: June 2008

Tight control of cell-cycle progression is critical for T-lymphocytes to function properly. Slfn1 (Schlafen1) has been reported to play an important role in the establishment and maintenance of quiescence in T-lymphocytes. However, how Slfn1 accomplishes this critical function remains poorly understood. In the present study, we show that nuclear localization is a prerequisite for Slfn1 to induce cell-cycle arrest, with DnaJB6, identified as a new Slfn1-binding protein, playing a pivotal role in this process. DnaJB6, a chaperone protein of the DnaJ/Hsp (heat-shock protein) 40 family, stabilizes Slfn1 together with its partner Hsp70, and, more importantly, it enhances the nuclear import of Slfn1. Overexpression of DnaJB6 was found to increase Slfn1 nuclear accumulation and resulted in cell-cycle arrest, whereas, in DnaJB6 knock-down cells, Slfn1 was mainly sequestered in the cytoplasm and no cell-cycle arrest was observed. Furthermore, transgenic expression of DnaJB6 in T-lineage cells inhibited Slfn1's degradation, promoted its nuclear import and ultimately led to suppression of T-cell proliferation upon TCR (T-cell receptor) activation. In addition, DnaJB6 increased Slfn1's effect on its downstream target cyclin D1 in co-transfected cells. Altogether, our results demonstrate that DnaJB6 is necessary for translocation of Slfn1 into the nucleus, where Slfn1 down-regulates cyclin D1, induces cell-cycle arrest and programmes a quiescent state of T-cells.
Chaperone ligand-discrimination by the TPR-domain protein Tah1
Authors: Millson Stefan H. , Vaughan Cara K. , Zhai Chao , Ali Maruf M. U. , Panaretou Barry , Piper Peter W. , Pearl Laurence H. , Prodromou Chrisostomos
Published: June 2008

Tah1 [TPR (tetratricopeptide repeat)-containing protein associated with Hsp (heat-shock protein) 90] has been identified as a TPR-domain protein. TPR-domain proteins are involved in protein–protein interactions and a number have been characterized that interact either with Hsp70 or Hsp90, but a few can bind both chaperones. Independent studies suggest that Tah1 interacts with Hsp90, but whether it can also interact with Hsp70/Ssa1 has not been investigated. Amino-acid-sequence alignments suggest that Tah1 is most similar to the TPR2b domain of Hop (Hsp-organizing protein) which when mutated reduces binding to both Hsp90 and Hsp70. Our alignments suggest that there are three TPR-domain motifs in Tah1, which is consistent with the architecture of the TPR2b domain. In the present study we find that Tah1 is specific for Hsp90, and is able to bind tightly the yeast Hsp90, and the human Hsp90α and Hsp90β proteins, but not the yeast Hsp70 Ssa1 isoform. Tah1 acheives ligand discrimination by favourably binding the methionine residue in the conserved MEEVD motif (Hsp90) and positively discriminating against the first valine residue in the VEEVD motif (Ssa1). In the present study we also show that Tah1 can affect the ATPase activity of Hsp90, in common with some other TPR-domain proteins.
Conformation, catalytic site, and enzymatic mechanism of the PR10 allergen-related enzyme norcoclaurine synthase
Authors: Berkner Hanna , Schweimer Kristian , Matecko Irena , Rösch Paul
Published: June 2008

The enzyme NCS [(S)-norcoclaurine synthase; EC 4.2.1.78] found in the common meadow rue, Thalictrum flavum, and other plant species, is involved in the biosynthesis of BIAs (benzylisoquinoline alkaloids). This group of plant secondary metabolites comprises pharmacologically-active compounds such as morphine and codeine. NCS catalyses the condensation of 4-HPAA (4-hydroxyphenylacetaldehyde) and dopamine to (S)-norcoclaurine, the common precursor of all plant BIAs. Although enzymatic properties of NCS and mechanistic aspects of the reaction have been studied in detail, no structural information on NCS was available so far. The enzyme shows significant sequence homology to members of the PR10 proteins (class 10 of pathogenesis-related proteins) such as the major birch pollen allergen Bet v 1. Our CD and NMR spectroscopic data indicated high similarity of the NCS and the Bet v 1 fold and allowed us to model NCS using Bet v 1 as a template. Virtually complete backbone assignment of the NCS sequence was used to study substrate binding by NMR titration experiments. Although binding of 4-HPAA seems to induce side-chain rearrangements in an extensive part of the protein, the putative distinct interaction site for dopamine could be clearly identified. The oligomerization state of NCS that reportedly plays an important role in enzyme functionality was determined to be concentration-dependent by SEC (size-exclusion chromatography) as well as NMR relaxation measurements, and the enzyme was found to be predominantly a monomer at the low micromolar concentrations used for activity assays.
Crystal structures of the starch-binding domain from Rhizopus oryzae glucoamylase reveal a polysaccharide-binding path
Authors: Tung Jung-Yu , Chang Margaret Dah-Tsyr , Chou Wei-I , Liu Yen-Yi , Yeh Yi-Hung , Chang Fan-Yu , Lin Shu-Chuan , Qiu Zhen-Liang , Sun Yuh-Ju
Published: June 2008

GA (glucoamylase) hydrolyses starch and polysaccharides to β-D-glucose. RoGA (Rhizopus oryzae GA) consists of two functional domains, an N-terminal SBD (starch-binding domain) and a C-terminal catalytic domain, which are connected by an O-glycosylated linker. In the present study, the crystal structures of the SBD from RoGA (RoGACBM21) and the complexes with β-cyclodextrin (SBD–βCD) and maltoheptaose (SBD–G7) were determined. Two carbohydrate binding sites, I (Trp47) and II (Tyr32), were resolved and their binding was co-operative. Besides the hydrophobic interaction, two unique polyN loops comprising consecutive asparagine residues also participate in the sugar binding. A conformational change in Tyr32 was observed between unliganded and liganded SBDs. To elucidate the mechanism of polysaccharide binding, a number of mutants were constructed and characterized by a quantitative binding isotherm and Scatchard analysis. A possible binding path for long-chain polysaccharides in RoGACBM21 was proposed.
Structure and function of SirC from Bacillus megaterium: a metal-binding precorrin-2 dehydrogenase
Authors: Schubert Heidi L. , Rose Ruth S. , Leech Helen K. , Brindley Amanda A. , Hill Christopher P. , Rigby Stephen E. J. , Warren Martin J.
Published: June 2008

In Bacillus megaterium, the synthesis of vitamin B12 (cobalamin) and sirohaem diverges at sirohydrochlorin along the branched modified tetrapyrrole biosynthetic pathway. This key intermediate is made by the action of SirC, a precorrin-2 dehydrogenase that requires NAD+ as a cofactor. The structure of SirC has now been solved by X-ray crystallography to 2.8 Å (1 Å = 0.1 nm) resolution. The protein is shown to consist of three domains and has a similar topology to the multifunctional sirohaem synthases Met8p and the N-terminal region of CysG, both of which catalyse not only the dehydrogenation of precorrin-2 but also the ferrochelation of sirohydrochlorin to give sirohaem. Guided by the structure, in the present study a number of active-site residues within SirC were investigated by site-directed mutagenesis. No active-site general base was identified, although surprisingly some of the resulting protein variants were found to have significantly enhanced catalytic activity. Unexpectedly, SirC was found to bind metal ions such as cobalt and copper, and to bind them in an identical fashion with that observed in Met8p. It is suggested that SirC may have evolved from a Met8p-like protein by loss of its chelatase activity. It is proposed that the ability of SirC to act as a single monofunctional enzyme, in conjunction with an independent chelatase, may provide greater control over the intermediate at this branchpoint in the synthesis of sirohaem and cobalamin.
Metabolic pathways inAnopheles stephensimitochondria
Authors: Giulivi Cecilia , Ross-Inta Catherine , Horton Ashley A. , Luckhart Shirley
Published: June 2008

No studies have been performed on the mitochondria of malaria vector mosquitoes. This information would be valuable in understanding mosquito aging and detoxification of insecticides, two parameters that have a significant impact on malaria parasite transmission in endemic regions. In the present study, we report the analyses of respiration and oxidative phosphorylation in mitochondria of cultured cells [ASE (Anopheles stephensi Mos. 43) cell line] from A. stephensi, a major vector of malaria in India, South-East Asia and parts of the Middle East. ASE cell mitochondria share many features in common with mammalian muscle mitochondria, despite the fact that these cells are of larval origin. However, two major differences with mammalian mitochondria were apparent. One, the glycerol–phosphate shuttle plays as major a role in NADH oxidation in ASE cell mitochondria as it does in insect muscle mitochondria. In contrast, mammalian white muscle mitochondria depend primarily on lactate dehydrogenase, whereas red muscle mitochondria depend on the malate–oxaloacetate shuttle. Two, ASE mitochondria were able to oxidize proline at a rate comparable with that of α-glycerophosphate. However, the proline pathway appeared to differ from the currently accepted pathway, in that oxoglutarate could be catabolized completely by the tricarboxylic acid cycle or via transamination, depending on the ATP need.
Collective behavior of stabilized reaction-diffusion waves
Authors: Steele Aaron J. , Tinsley Mark , Showalter Kenneth
Published: June 2008

Stabilized wave segments in the photosensitive Belousov–Zhabotinsky reaction are directionally controlled with intensity gradients in the applied illumination. The constant-velocity waves behave like self-propelled particles, and multiple waves interact via an applied interaction potential. Alignment arises from the intrinsic properties of the interacting waves, leading to processional and rotational behavior.
Design and control of patterns in reaction-diffusion systems
Authors: Vanag Vladimir K. , Epstein Irving R.
Published: June 2008

We discuss the design of reaction-diffusion systems that display a variety of spatiotemporal patterns. We also consider how these patterns may be controlled by external perturbation, typically using photochemistry or temperature. Systems treated include the Belousov–Zhabotinsky (BZ) reaction, the chlorite-iodide-malonic acid and chlorine dioxide-malonic acid-iodine reactions, and the BZ–AOT system, i.e., the BZ reaction in a water-in-oil reverse microemulsion stabilized by the surfactant sodium bis(2-ethylhexyl) sulfosuccinate (AOT).
Shaping robust system through evolution
Authors: Kaneko Kunihiko
Published: June 2008

Biological functions are generated as a result of developmental dynamics that form phenotypes governed by genotypes. The dynamical system for development is shaped through genetic evolution following natural selection based on the fitness of the phenotype. Here we study how this dynamical system is robust to noise during development and to genetic change by mutation. We adopt a simplified transcription regulation network model to govern gene expression, which gives a fitness function. Through simulations of the network that undergoes mutation and selection, we show that a certain level of noise in gene expression is required for the network to acquire both types of robustness. The results reveal how the noise that cells encounter during development shapes any network’s robustness, not only to noise but also to mutations. We also establish a relationship between developmental and mutational robustness through phenotypic variances caused by genetic variation and epigenetic noise. A universal relationship between the two variances is derived, akin to the fluctuation-dissipation relationship known in physics.
Pattern formation in the ferrocyanide-iodate-sulfite reaction: The control of space scale separation
Authors: Szalai István , De Kepper Patrick
Published: June 2008

We revisit the conditions for the development of reaction-diffusion patterns in the ferrocyanide-iodate-sulfite bistable and oscillatory reaction. This hydrogen ion autoactivated reaction is the only example known to produce sustained stationary lamellar patterns and a wealth of other spatio-temporal phenomena including self-replication and localized oscillatory domain of spots, due to repulsive front interactions and to a parity-breaking front bifurcation (nonequilibrium Ising–Bloch bifurcation). We show experimentally that the space scale separation necessary for the observation of stationary patterns is mediated by the presence of low mobility weak acid functional groups. The presence of such groups was overlooked in the original observations made with hydrolyzable polyacrylamide gels. This missing information made the original observations difficult to reproduce and frustrated further experimental exploitation of the fantastic potentialities of this system. Using one-side-fed spatial reactors filled with agarose gel, we can reproduce all the previous pattern observations, in particular the stationary labyrinthine patterns, by introducing, above a critical concentration, well controlled amounts of polyacrylate chains in the gel network. We use two different geometries of spatial reactors (annular and disk shapes) to provide complementary information on the actual three-dimensional character of spatial patterns. We also reinvestigate the role of other feed parameters and show that the system exhibits both a domain of spatial bistability and of large-amplitude pH oscillations associated in a typical cross-shape diagram. The experimental method presented here can be adapted to produce patterns in the large number of oscillatory and bistable reactions, since the iodate-sulfite-ferrocynide reaction is a prototype of these systems.
Control of scroll wave turbulence in a three-dimensional reaction-diffusion system with gradient
Authors: Qiao Chun , Wu Yabi , Lu XiaoChuan , Wang ChunYan , Ouyang Qi , Wang Hongli
Published: June 2008

In this paper, we summarize our recent experimental and theoretical works on observation and control of scroll wave (SW) turbulence. The experiments were conducted in a three-dimensional Belousov–Zhabotinsky reaction-diffusion system with chemical concentration gradients in one dimension. A spatially homogeneous external forcing was used in the experiments as a control; it was realized by illuminating white light on the light sensitive reaction medium. We observed that, in the oscillatory regime of the system, SW can appear automatically in the gradient system, which will be led to spatiotemporal chaos under certain conditions. A suitable periodic forcing may stabilize inherent turbulence of SW. The mechanism of the transition to SW turbulence is due to the phase twist of SW in the presence of chemical gradients, while modulating the phase twist with a proper periodic forcing can delay this transition. Using the FitzHugh–Nagumo model with an external periodic forcing, we confirmed the control mechanism with numerical simulation. Moreover, we also show in the simulation that adding temporal external noise to the system may have the same control effect. During this process, we observed a new state called “intermittent turbulence,” which may undergo a transition into a new type of SW collapse when the noise intensity is further increased. The intermittent state and the collapse could be explained by a random process.
Adaptive synchronization of a switching system and its applications to secure communications
Authors: Xia Weiguo , Cao Jinde
Published: June 2008

This paper studies the adaptive synchronization of a switching system with unknown parameters which switches between the Rössler system and a unified chaotic system. Using the Lyapunov stability theory and adaptive control method, the receiver system will achieve synchronization with the drive system and the unknown parameters would be estimated by the receiver. Then the proposed switching system is used for secure communications based on the communication schemes including chaotic masking, chaotic modulation, and chaotic shift key strategies. Since the system switches between two chaotic systems and the parameters are almost unknown, it is more difficult for the intruder to extract the useful message from the transmission channel. In addition, two new schemes in which the chaotic signal used to mask (or modulate) the transmitted signal switches between two components of a chaotic system are also presented. Finally, some simulation results are given to show the effectiveness of the proposed communication schemes.
Fluid model for relativistic, magnetized plasmas
Authors: TenBarge J. M. , Hazeltine R. D. , Mahajan S. M.
Published: June 2008

Many astrophysical plasmas and some laboratory plasmas are relativistic: Either the thermal speed or the local bulk flow in some frame approaches the speed of light. Often, such plasmas are magnetized in the sense that the Larmor radius is smaller than any gradient scale length of interest. Conventionally, relativistic magnetohydrodynamics (MHD) is employed to treat relativistic, magnetized plasmas. However, MHD requires the collision time to be shorter than any other time scale in the system. Thus, MHD employs the thermodynamic equilibrium form of the stress tensor, neglecting pressure anisotropy and heat flow parallel to the magnetic field. Recent work has attempted to remedy these shortcomings. This paper re-examines the closure question and finds a more complete theory, which yields a more physical and self-consistent closure. Beginning with exact moments of the kinetic equation, we derive a closed set of Lorentz-covariant fluid equations for a magnetized plasma allowing for pressure and heat flow anisotropy. Basic predictions of the model, especially of the dispersion relation’s dependence upon relativistic temperature, are examined.
Nonlinear magnetohydrodynamics of pulsed parallel current drive in reversed-field pinches
Authors: Reynolds J. M. , Sovinec C. R. , Prager S. C.
Published: June 2008

Nonlinear simulation with a simple resistive magnetohydrodynamics model is used to investigate the stabilization of magnetic fluctuations in reversed-field pinch plasmas subject to pulsed-parallel current drive. Numerical results are diagnosed with computations of nonlinear power transfer and by evaluating sequences of profiles for linear stability. Results show that poloidal electric field pulsing promptly affects the exchange of energy between the mean profiles and both core-resonant m=1 fluctuations and high-axial-wavenumber fluctuations. Linear computations show that slight changes in edge profiles are sufficient to alter the stability of the marginal state. There is a slight delay in the response of energy exchanged among fluctuations, which reduces the m=0 fluctuations. Loss of dynamo effect as fluctuation amplitudes decrease leads to nonlocal pulse penetration that enhances pinching when toroidal drive is maintained. Reducing toroidal drive together with the application of poloidal electric field avoids pinching and maintains the stabilizing effect for a greater period of time.
Theoretical investigation on the linear and nonlinear susceptibilities of urea crystal
Authors: Olejniczak Małgorzata , Pecul Magdalena , Champagne Benoît , Botek Edith
Published: June 2008

The linear and second-order nonlinear susceptibilities of the urea crystal have been evaluated by applying the supermolecule approach. Calculations performed at the time-dependent Hartree–Fock (TDHF) level using the Austin model (AM1) semiempirical Hamiltonian have first demonstrated the almost additive character of the essential polarizability and first hyperpolarizability components. In fact, the only exception concerns the χcc(1) component when stacking urea molecules along the c axis, i.e., the axis of the hydrogen bonds. This behavior has been confirmed by ab initio calculations on small clusters. The macroscopic quantities have then been determined by adopting the multiplicative scheme and by correcting the TDHF/AM1 values for missing electron correlation by means of density functional theory and coupled cluster method. The reliability of the multiplicative scheme was demonstrated for clusters as large as 3a×3b×3c. While the electron correlation correction factors are similar for a single molecule and different small clusters, the global performance of the scheme differs for the linear and nonlinear responses. For the second-order nonlinear susceptibility, our predictions are in good agreement with experiment, while for the linear susceptibility and the associated refractive index, our predictions underestimate the experimental values. The limitations of our approach may be attributed to its inability to account for more subtle cooperative effects, like those associated with a network of hydrogen bonds. Together with other works, the supermolecule calculations confirm that the sign of χabc(2) is negative, contrary to an estimate from band structure calculation.
Comparative study of hydrogenated diamondlike carbon film and hard hydrogenated graphitelike carbon film
Authors: Wang Chengbing , Yang Shengrong , Wang Qi , Wang Zhou , Zhang Junyan
Published: June 2008

The structure, mechanical properties, and friction properties of hydrogenated graphitelike carbon film and typical hydrogenated diamondlike carbon film were investigated comparatively that the hydrogenated graphitelike carbon film has relatively high sp2 content and low bonded hydrogen content and possessed high hardness and elasticity. It was attributed to the curved graphene microstructure, which is able to form three-dimensional covalently bonded network. Furthermore, in comparison with the hydrogenated diamondlike carbon film, the hydrogenated graphitelike carbon film demonstrated excellent friction behavior probably due to the extraordinary structure of hydrogenated graphitelike carbon film.
The multiscale coarse-graining method. II. Numerical implementation for coarse-grained molecular models
Authors: Noid W. G. , Liu Pu , Wang Yanting , Chu Jhih-Wei , Ayton Gary S. , Izvekov Sergei , Andersen Hans C. , Voth Gregory A.
Published: June 2008

The multiscale coarse-graining (MS-CG) method [S. Izvekov and G. A. Voth, J. Phys. Chem. B 109, 2469 (2005); J. Chem. Phys. 123, 134105 (2005)] employs a variational principle to determine an interaction potential for a CG model from simulations of an atomically detailed model of the same system. The companion paper proved that, if no restrictions regarding the form of the CG interaction potential are introduced and if the equilibrium distribution of the atomistic model has been adequately sampled, then the MS-CG variational principle determines the exact many-body potential of mean force (PMF) governing the equilibrium distribution of CG sites generated by the atomistic model. In practice, though, CG force fields are not completely flexible, but only include particular types of interactions between CG sites, e.g., nonbonded forces between pairs of sites. If the CG force field depends linearly on the force field parameters, then the vector valued functions that relate the CG forces to these parameters determine a set of basis vectors that span a vector subspace of CG force fields. The companion paper introduced a distance metric for the vector space of CG force fields and proved that the MS-CG variational principle determines the CG force force field that is within that vector subspace and that is closest to the force field determined by the many-body PMF. The present paper applies the MS-CG variational principle for parametrizing molecular CG force fields and derives a linear least squares problem for the parameter set determining the optimal approximation to this many-body PMF. Linear systems of equations for these CG force field parameters are derived and analyzed in terms of equilibrium structural correlation functions. Numerical calculations for a one-site CG model of methanol and a molecular CG model of the EMIM+∕NO3− ionic liquid are provided to illustrate the method.
The multiscale coarse-graining method. I. A rigorous bridge between atomistic and coarse-grained models
Authors: Noid W. G. , Chu Jhih-Wei , Ayton Gary S. , Krishna Vinod , Izvekov Sergei , Voth Gregory A. , Das Avisek , Andersen Hans C.
Published: June 2008

Coarse-grained (CG) models provide a computationally efficient method for rapidly investigating the long time- and length-scale processes that play a critical role in many important biological and soft matter processes. Recently, Izvekov and Voth introduced a new multiscale coarse-graining (MS-CG) method [J. Phys. Chem. B 109, 2469 (2005); J. Chem. Phys. 123, 134105 (2005)] for determining the effective interactions between CG sites using information from simulations of atomically detailed models. The present work develops a formal statistical mechanical framework for the MS-CG method and demonstrates that the variational principle underlying the method may, in principle, be employed to determine the many-body potential of mean force (PMF) that governs the equilibrium distribution of positions of the CG sites for the MS-CG models. A CG model that employs such a PMF as a “potential energy function” will generate an equilibrium probability distribution of CG sites that is consistent with the atomically detailed model from which the PMF is derived. Consequently, the MS-CG method provides a formal multiscale bridge rigorously connecting the equilibrium ensembles generated with atomistic and CG models. The variational principle also suggests a class of practical algorithms for calculating approximations to this many-body PMF that are optimal. These algorithms use computer simulation data from the atomically detailed model. Finally, important generalizations of the MS-CG method are introduced for treating systems with rigid intramolecular constraints and for developing CG models whose equilibrium momentum distribution is consistent with that of an atomically detailed model.
The electronic spectrum of the C2P free radical and a Renner–Teller analysis of the Δ2 and X̃Π2 electronic states
Authors: Sunahori Fumie X. , Wei Jie , Clouthier Dennis J.
Published: June 2008

Subsequent to our spectroscopic detection of the C2X(X=P,As) free radicals [F. X. Sunahori et al., J. Am. Chem. Soc. 129, 9600 (2007)], we have studied the electronic spectrum of the Δi2-X̃Πr2 system of the jet-cooled C2P free radical in the 490–630nm region. The high-resolution laser-induced fluorescence spectrum of the two spin components of the 000 band of C212P has been recorded, and the rotational and spin-orbit coupling constants have been determined for both electronic states. The Renner–Teller effect has been observed in both the Π2 and the Δ2 states, and the vibrational structure has been assigned. For the ground state, all of the observed levels up to 3500cm−1 were fitted with a standard Renner–Teller model. The excited Δ2 state vibrational levels were successfully fitted using literature energy level expressions derived from perturbation theory, yielding vibrational and Renner–Teller parameters for both C212P and C213P. The molecular structure of C2P in the ground and excited states has also been estimated and compared to ab initio calculations and the geometries of similar molecules.
The effects of optical interference on exciton diffusion length measurements using photocurrent spectroscopy
Authors: Rim Seung-Bum , Peumans Peter
Published: June 2008

Wavelength-dependent measurements of photocurrent in single-layer devices are commonly used to determine the exciton diffusion length of organic thin films by comparing the Feng–Ghosh model for photocurrent response to experimental data. However, this model assumes that optical interference effects are negligible. For film thicknesses relevant to practical organic solar structures, optical interference effects cannot be avoided, leading to inaccurate estimates of the exciton diffusion length or apparent observation of two different types of excitons. This is illustrated for diindenoperylene and merocyanine thin films. The conditions under which a modified Feng–Ghosh model can be used are outlined.
Topological degree in analysis of chaotic behavior in singularly perturbed systems
Authors: Pokrovskii A. , Zhezherun A.
Published: June 2008

A scheme of applying topological degree theory to the analysis of chaotic behavior in singularly perturbed systems is suggested. The scheme combines one introduced by Zgliczyński [Topol. Methods Nonlinear Anal. 8, 169 (1996)] with the method of topological shadowing, but does not rely on computer based proofs. It is illustrated by a three-dimensional system with piecewise linear slow surface. This approach, when applicable, guarantees abundance of periodic orbits with arbitrarily large periods, each of which is a canard-type trajectory: at first it passes along, and close to, an attractive part of the slow surface of the singularly perturbed system and then continues for a while along the repulsive part of the slow surface. These periodic trajectories are robust in a topological sense with respect to small disturbances in the right-hand sides of the system under consideration, but typically not stable in the Lyapunov sense. Methods of localization of such periodic trajectories are briefly discussed, and numerical examples of localizations are given. The periodic trajectories that are useful from the applications point of view can be stabilized via an appropriate feedback control, for instance, the Pyragas control.
Numerical method based on the lattice Boltzmann model for the Fisher equation
Authors: Yan Guangwu , Zhang Jianying , Dong Yinfeng
Published: June 2008

In this paper, a lattice Boltzmann model for the Fisher equation is proposed. First, the Chapman–Enskog expansion and the multiscale time expansion are used to describe higher-order moment of equilibrium distribution functions and a series of partial differential equations in different time scales. Second, the modified partial differential equation of the Fisher equation with the higher-order truncation error is obtained. Third, comparison between numerical results of the lattice Boltzmann models and exact solution is given. The numerical results agree well with the classical ones.
Impulsive control of stochastic systems with applications in chaos control, chaos synchronization, and neural networks
Authors: Li Chunguang , Chen Luonan , Aihara Kazuyuki
Published: June 2008

Real systems are often subject to both noise perturbations and impulsive effects. In this paper, we study the stability and stabilization of systems with both noise perturbations and impulsive effects. In other words, we generalize the impulsive control theory from the deterministic case to the stochastic case. The method is based on extending the comparison method to the stochastic case. The method presented in this paper is general and easy to apply. Theoretical results on both stability in the pth mean and stability with disturbance attenuation are derived. To show the effectiveness of the basic theory, we apply it to the impulsive control and synchronization of chaotic systems with noise perturbations, and to the stability of impulsive stochastic neural networks. Several numerical examples are also presented to verify the theoretical results.
Femtosecond dynamics and laser control of charge transport in trans-polyacetylene
Authors: Franco Ignacio , Shapiro Moshe , Brumer Paul
Published: June 2008

The induction of dc electronic transport in rigid and flexible trans-polyacetylene oligomers according to the ω versus 2ω coherent control scenario is investigated using a quantum-classical mean field approximation. The approach involves running a large ensemble of mixed quantum-classical trajectories under the influence of ω+2ω laser fields and choosing the initial conditions by sampling the ground-state Wigner distribution function for the nuclei. The vibronic couplings are shown to change the mean single-particle spectrum, introduce ultrafast decoherence, and enhance intramolecular vibrational and electronic relaxation. Nevertheless, even in the presence of significant couplings, limited coherent control of the electronic dynamics is still viable, the most promising route involving the use of femtosecond pulses with a duration that is comparable to the electronic dephasing time. The simulations offer a realistic description of the behavior of a simple coherent control scenario in a complex system and provide a detailed account of the femtosecond photoinduced vibronic dynamics of a conjugated polymer.
Laser-induced currents along molecular wire junctions
Authors: Franco Ignacio , Shapiro Moshe , Brumer Paul
Published: June 2008

The treatment of the previous paper is extended to molecular wires. Specifically, the effect of electron-vibrational interactions on the electronic transport induced by femtosecond ω+2ω laser fields along unbiased molecular nanojunctions is investigated. For this, the photoinduced vibronic dynamics of trans-polyacetylene oligomers coupled to macroscopic metallic leads is followed in a mean-field mixed quantum-classical approximation. A reduced description of the dynamics is obtained by introducing projective lead-molecule couplings and deriving an effective Schrödinger equation satisfied by the orbitals in the molecular region. Two possible rectification mechanisms are identified and investigated. The first one relies on near-resonance photon-absorption and is shown to be fragile to the ultrafast electronic decoherence processes introduced by the wire’s vibrations. The second one employs the dynamic Stark effect and is demonstrated to be highly efficient and robust to electron-vibrational interactions.
Quantitative prediction of gas-phase F19 nuclear magnetic shielding constants
Authors: Harding Michael E. , Lenhart Michael , Auer Alexander A. , Gauss Jürgen
Published: June 2008

Benchmark calculations of F19 nuclear magnetic shielding constants are presented for a set of 28molecules. Near-quantitative accuracy (ca. 2ppm deviation from experiment) is achieved if (1) electron correlation is adequately treated by employing the coupled-cluster singles and doubles (CCSD) model augmented by a perturbative correction for triple excitations [CCSD(T)], (2) large (uncontracted) basis sets are used, (3) gauge-including atomic orbitals are used to ensure gauge-origin independence, (4) calculations are performed at accurate equilibrium geometries [obtained from CCSD(T)/cc-pVTZ calculations correlating all electrons], and (5) vibrational averaging and temperature corrections via second-order vibrational perturbation theory (VPT2) are included. For the CCSD(T)/13s9p4d3f calculations corrected for vibrational effects, mean and standard deviation from experiment are −1.9 and 1.6ppm, respectively. Less elaborate theoretical treatments result in larger errors. Consideration of relative shifts can reduce the mean deviation (through an appropriately chosen reference compound), but does not change the standard deviation. Density-functional theory calculations of absolute and relative F19 nuclear magnetic shielding constants are found to be, at best, as accurate as the corresponding Hartree–Fock self-consistent-field calculations and are not improved by consideration of vibrational effects. Molecular systems containing fluorine-oxygen, fluorine-nitrogen, and fluorine-fluorine bonds are found to be more challenging than the other investigated molecules for the considered theoretical methods.
Anomalous pulse interaction in dissipative media
Authors: Bordyugov Grigory , Engel Harald
Published: June 2008

We review a number of phenomena occurring in one-dimensional excitable media due to modified decay behind propagating pulses. Those phenomena can be grouped in two categories depending on whether the wake of a solitary pulse is oscillatory or not. Oscillatory decay leads to nonannihilative head-on collision of pulses and oscillatory dispersion relation of periodic pulse trains. Stronger wake oscillations can even result in a bistable dispersion relation. Those effects are illustrated with the help of the Oregonator and FitzHugh–Nagumo models for excitable media. For a monotonic wake, we show that it is possible to induce bound states of solitary pulses and anomalous dispersion of periodic pulse trains by introducing nonlocal spatial coupling to the excitable medium.
Self-motion of an oil droplet: A simple physicochemical model of active Brownian motion
Authors: Sumino Yutaka , Yoshikawa Kenichi
Published: June 2008

The self-motion of an oil droplet in an aqueous phase on a glass surface is reported. The aqueous phase contains a cationic surfactant, which tends to be adsorbed onto the glass surface. The oil droplet contains potassium iodide and iodine, which prefers to make an ion pair with the cationic surfactant. Since the ion pair is soluble in the oil droplet, dissolution of the surfactant into the oil droplet is promoted, i.e., the system is far from equilibrium with regard to surfactant concentration. The oil droplet is self-driven in a reactive manner by the spatial gradient of the glass surface tension. We discuss the intrinsic nature of this self-motion by developing a simple mathematical model that incorporates adsorption and desorption of the surfactant on the glass surface. Using this mathematical model we were able to construct an equation of motion that reproduces the observed self-motion of an oil droplet. This equation describes active Brownian motion. Theoretical considerations were used to predict the generation of the regular mode of oil-droplet motion, which was subsequently confirmed by experiments.
Local order around rare earth ions during the devitrification of oxyfluoride glasses
Authors: Silva Maurício A. P. , Dantelle Geraldine , Mortier Michel , Monteil André , Ribeiro Sidney J. L. , Messaddeq Younès , Briois Valérie , Poulain Marcel
Published: June 2008

Erbium L3-edge extended x-ray absorption fine structure (EXAFS) measurements were performed on rare earth doped fluorosilicate and fluoroborate glasses and glass ceramics. The well known nucleating effects of erbium ions for the crystallization of cubic lead fluoride (based on x-ray diffraction measurements) and the fact that the rare earth ions are present in the crystalline phase (as indicated by Er3+ emission spectra) seem in contradiction with the present EXAFS analysis, which indicates a lack of medium range structural ordering around the Er3+ ions and suggests that the lead fluoride crystallization does not occur in the nearest neighbor distance of the rare earth ion. Molecular dynamics simulations of the devitrification process of a lead fluoride glass doped with Er3+ ions were performed, and results indicate that Er3+ ions lower the devitrification temperature of PbF2, in good agreement with the experimental results. The genuine role of Er3+ ions in the devitrification process of PbF2 has been investigated. Although Er3+ ions could indeed act as seeds for crystallization, as experiments suggest, molecular dynamics simulation results corroborate the experimental EXAFS observation that the devitrification does not occur at its nearest neighbor distance.
Direct observation of local magnetic field generated by micromagnet
Authors: Watanabe Shinji , Sasaki Susumu , Sato Shinya , Isogai Naoki , Matsumoto Yoshinori
Published: June 2008

Using standard nuclear magnetic resonance (NMR) technique and a well-fabricated sample, we have succeeded in directly observing local magnetic field generated by a micromagnet Ni45Fe55 (with thickness of 400nm), which was sputtered on an Al layer of 20nm thickness. Improved sensitivity of our NMR technique enabled us to clearly observe Al-NMR signals, which are confirmed to come from Al nuclei in the 20nm layers. From the analysis of the Al-NMR spectra, the local magnetic field was found to be +0.17±0.02 (−0.20±0.01)T, the sign of which is consistent with the geometry that the external magnetic field was applied perpendicular (parallel) to the Al layer. The present study gives a potential key element toward realizing higher resolution in magnetic resonance imaging.
Binding energy and geometry of e+A (A=Li,Na) by the hyperspherical approach
Authors: Han Hui-li , Li Yong , Zhang Xian-zhou , Shi Ting-yun
Published: June 2008

We calculate the binding energy and geometry of the weakly bound e+Li and e+Na systems within the framework of hyperspherical coordinates. The Schrödinger equation in hyperangular coordinates is solved at a series of fixed hyper-radii using B-splines and the resulting coupled hyper-radial equation is solved using the slow variable discretization method developed by Tolstikhin et al. [J. Phys. B 29, L389 (1996)]. Great efforts are made in optimizing the distribution of B-splines to overcome the slow convergence of the binding energy and geometrical quantities. This approach allows us to obtain the results with improved convergence that are in good agreement with the best values reported to date. In addition, an analysis of the structure of the two systems is also made and the e+Na system is seen to exhibit quantum halo features.
Self-correcting networks: Function, robustness, and motif distributions in biological signal processing
Authors: Kaluza Pablo , Vingron Martin , Mikhailov Alexander S.
Published: June 2008

Statistical properties of large ensembles of networks, all designed to have the same functions of signal processing, but robust against different kinds of perturbations, are analyzed. We find that robustness against noise and random local damage plays a dominant role in determining motif distributions of networks and may underlie their classification into network superfamilies.