WorldWideScience

Sample records for body residual interaction

  1. Rotor/body aerodynamic interactions

    Science.gov (United States)

    Betzina, M. D.; Smith, C. A.; Shinoda, P.

    1985-01-01

    A wind tunnel investigation was conducted in which independent, steady state aerodynamic forces and moments were measured on a 2.24 m diam. two bladed helicopter rotor and on several different bodies. The mutual interaction effects for variations in velocity, thrust, tip-path-plane angle of attack, body angle of attack, rotor/body position, and body geometry were determined. The results show that the body longitudinal aerodynamic characteristics are significantly affected by the presence of a rotor and hub, and that the hub interference may be a major part of such interaction. The effects of the body on the rotor performance are presented.

  2. Interaction of disinfectant residues on cleanroom substrates.

    Science.gov (United States)

    Kaiser, H; Klein, D; Kopis, E; Leblanc, D; McDonnell, G; Tirey, J F

    1999-01-01

    This study will determine the levels of disinfectant residues on stainless steel surfaces after simulated manual cleaning activities. Additionally, this study will determine if chemical interactions between different chemical agents, representative of commonly used cleanroom disinfectant technologies, subsequently applied to the same surfaces exist, and to what degree these interactions impact sporicidal performance of an oxidizing biocide against Bacillus subtilis.

  3. HYDRODYNAMIC INTERACTIONS BETWEEN TWO BODIES

    Institute of Scientific and Technical Information of China (English)

    2007-01-01

    On the basis of model tests, potential flow theory, and viscous Computational Fluid Dynamics (CFD) method, the hydrodynamic interactions between two underwater bodies were investigated to determine the influencing factors, changing rule, interaction mechanism, and appropriate methods describing them. Some special phenomena were discovered in two series of near-wall interaction experiments. The mathematical model and predicting methods were presented for interacting forces near wall, and the calculation results agreed well with the experimental ones. From the comparisons among numerical results with respect to nonviscosity, numerical results with respect to viscosity, and measured results, data on the influence of viscosity on hydrodynamic interactions were obtained. For hydrodynamic interaction related to multi-body unsteady motions with six degrees of freedom that is difficult to simulate in tests, numerical predictions of unsteady interacting forces were given.

  4. Use of genotype × environment interaction model to accommodate genetic heterogeneity for residual feed intake, dry matter intake, net energy in milk, and metabolic body weight in dairy cattle.

    Science.gov (United States)

    Yao, C; de Los Campos, G; VandeHaar, M J; Spurlock, D M; Armentano, L E; Coffey, M; de Haas, Y; Veerkamp, R F; Staples, C R; Connor, E E; Wang, Z; Hanigan, M D; Tempelman, R J; Weigel, K A

    2017-03-01

    Feed efficiency in dairy cattle has gained much attention recently. Due to the cost-prohibitive measurement of individual feed intakes, combining data from multiple countries is often necessary to ensure an adequate reference population. It may then be essential to model genetic heterogeneity when making inferences about feed efficiency or selecting efficient cattle using genomic information. In this study, we constructed a marker × environment interaction model that decomposed marker effects into main effects and interaction components that were specific to each environment. We compared environment-specific variance component estimates and prediction accuracies from the interaction model analyses, an across-environment analyses ignoring population stratification, and a within-environment analyses using an international feed efficiency data set. Phenotypes included residual feed intake, dry matter intake, net energy in milk, and metabolic body weight from 3,656 cows measured in 3 broadly defined environments: North America (NAM), the Netherlands (NLD), and Scotland (SAC). Genotypic data included 57,574 single nucleotide polymorphisms per animal. The interaction model gave the highest prediction accuracy for metabolic body weight, which had the largest estimated heritabilities ranging from 0.37 to 0.55. The within-environment model performed the best when predicting residual feed intake, which had the lowest estimated heritabilities ranging from 0.13 to 0.41. For traits (dry matter intake and net energy in milk) with intermediate estimated heritabilities (0.21 to 0.50 and 0.17 to 0.53, respectively), performance of the 3 models was comparable. Genomic correlations between environments also were computed using variance component estimates from the interaction model. Averaged across all traits, genomic correlations were highest between NAM and NLD, and lowest between NAM and SAC. In conclusion, the interaction model provided a novel way to evaluate traits measured in

  5. Identification of NAD interacting residues in proteins

    Directory of Open Access Journals (Sweden)

    Raghava Gajendra PS

    2010-03-01

    Full Text Available Abstract Background Small molecular cofactors or ligands play a crucial role in the proper functioning of cells. Accurate annotation of their target proteins and binding sites is required for the complete understanding of reaction mechanisms. Nicotinamide adenine dinucleotide (NAD+ or NAD is one of the most commonly used organic cofactors in living cells, which plays a critical role in cellular metabolism, storage and regulatory processes. In the past, several NAD binding proteins (NADBP have been reported in the literature, which are responsible for a wide-range of activities in the cell. Attempts have been made to derive a rule for the binding of NAD+ to its target proteins. However, so far an efficient model could not be derived due to the time consuming process of structure determination, and limitations of similarity based approaches. Thus a sequence and non-similarity based method is needed to characterize the NAD binding sites to help in the annotation. In this study attempts have been made to predict NAD binding proteins and their interacting residues (NIRs from amino acid sequence using bioinformatics tools. Results We extracted 1556 proteins chains from 555 NAD binding proteins whose structure is available in Protein Data Bank. Then we removed all redundant protein chains and finally obtained 195 non-redundant NAD binding protein chains, where no two chains have more than 40% sequence identity. In this study all models were developed and evaluated using five-fold cross validation technique on the above dataset of 195 NAD binding proteins. While certain type of residues are preferred (e.g. Gly, Tyr, Thr, His in NAD interaction, residues like Ala, Glu, Leu, Lys are not preferred. A support vector machine (SVM based method has been developed using various window lengths of amino acid sequence for predicting NAD interacting residues and obtained maximum Matthew's correlation coefficient (MCC 0.47 with accuracy 74.13% at window length 17

  6. Five-body van der Waals interactions

    Science.gov (United States)

    Han, Jianing

    2017-06-01

    We report on the five-body repulsive and attractive van der Waals interactions between the strongly dipole-dipole coupled Rydberg states. Compared to four-body van der Waals interactions, five-body van der Waals interactions show more energy levels and more potential wells caused by avoided crossings. This research bridges the few-body physics and many-body physics. Other disciplines, such as chemistry, biology, and medical fields, will also benefit from better understanding van der Waals interactions.

  7. Identification of hot-spot residues in protein-protein interactions by computational docking

    Directory of Open Access Journals (Sweden)

    Fernández-Recio Juan

    2008-10-01

    Full Text Available Abstract Background The study of protein-protein interactions is becoming increasingly important for biotechnological and therapeutic reasons. We can define two major areas therein: the structural prediction of protein-protein binding mode, and the identification of the relevant residues for the interaction (so called 'hot-spots'. These hot-spot residues have high interest since they are considered one of the possible ways of disrupting a protein-protein interaction. Unfortunately, large-scale experimental measurement of residue contribution to the binding energy, based on alanine-scanning experiments, is costly and thus data is fairly limited. Recent computational approaches for hot-spot prediction have been reported, but they usually require the structure of the complex. Results We have applied here normalized interface propensity (NIP values derived from rigid-body docking with electrostatics and desolvation scoring for the prediction of interaction hot-spots. This parameter identifies hot-spot residues on interacting proteins with predictive rates that are comparable to other existing methods (up to 80% positive predictive value, and the advantage of not requiring any prior structural knowledge of the complex. Conclusion The NIP values derived from rigid-body docking can reliably identify a number of hot-spot residues whose contribution to the interaction arises from electrostatics and desolvation effects. Our method can propose residues to guide experiments in complexes of biological or therapeutic interest, even in cases with no available 3D structure of the complex.

  8. Novel feature for catalytic protein residues reflecting interactions with other residues.

    Directory of Open Access Journals (Sweden)

    Yizhou Li

    Full Text Available Owing to their potential for systematic analysis, complex networks have been widely used in proteomics. Representing a protein structure as a topology network provides novel insight into understanding protein folding mechanisms, stability and function. Here, we develop a new feature to reveal correlations between residues using a protein structure network. In an original attempt to quantify the effects of several key residues on catalytic residues, a power function was used to model interactions between residues. The results indicate that focusing on a few residues is a feasible approach to identifying catalytic residues. The spatial environment surrounding a catalytic residue was analyzed in a layered manner. We present evidence that correlation between residues is related to their distance apart most environmental parameters of the outer layer make a smaller contribution to prediction and ii catalytic residues tend to be located near key positions in enzyme folds. Feature analysis revealed satisfactory performance for our features, which were combined with several conventional features in a prediction model for catalytic residues using a comprehensive data set from the Catalytic Site Atlas. Values of 88.6 for sensitivity and 88.4 for specificity were obtained by 10-fold cross-validation. These results suggest that these features reveal the mutual dependence of residues and are promising for further study of structure-function relationship.

  9. Assessment of residual body weight gain and residual intake and body weight gain as feed efficiency traits in the turkey (Meleagris gallopavo)

    OpenAIRE

    Willems, Owen W; Miller, Stephen P.; Wood, Benjamin J

    2013-01-01

    Background Since feed represents 70% of the total cost in poultry production systems, an animal’s ability to convert feed is an important trait. In this study, residual feed intake (RFI) and residual body weight gain (RG), and their linear combination into residual feed intake and body weight gain (RIG) were studied to estimate their genetic parameters and analyze the potential differences in feed intake between the top ranked birds based on the criteria for each trait. Methods Phenotypic and...

  10. Assessment of residual body weight gain and residual intake and body weight gain as feed efficiency traits in the turkey (Meleagris gallopavo)

    OpenAIRE

    Willems, Owen W; Miller, Stephen P.; Wood, Benjamin J

    2013-01-01

    Background Since feed represents 70% of the total cost in poultry production systems, an animal’s ability to convert feed is an important trait. In this study, residual feed intake (RFI) and residual body weight gain (RG), and their linear combination into residual feed intake and body weight gain (RIG) were studied to estimate their genetic parameters and analyze the potential differences in feed intake between the top ranked birds based on the criteria for each trait. Methods Phenotypic and...

  11. Chaos in body-vortex interactions

    DEFF Research Database (Denmark)

    Pedersen, Johan Rønby; Aref, Hassan

    2010-01-01

    The model of body–vortex interactions, where the fluid flow is planar, ideal and unbounded, and the vortex is a point vortex, is studied. The body may have a constant circulation around it. The governing equations for the general case of a freely moving body of arbitrary shape and mass density...... of a circle is integrable. As the body is made slightly elliptic, a chaotic region grows from an unstable relative equilibrium of the circle-vortex case. The case of a cylindrical body of any shape moving in fluid otherwise at rest is also integrable. A second transition to chaos arises from the limit between...... and an arbitrary number of point vortices are presented. The case of a body and a single vortex is then investigated numerically in detail. In this paper, the body is a homogeneous, elliptical cylinder. For large body–vortex separations, the system behaves much like a vortex pair regardless of body shape. The case...

  12. Prediction of interface residue based on the features of residue interaction network.

    Science.gov (United States)

    Jiao, Xiong; Ranganathan, Shoba

    2017-11-07

    Protein-protein interaction plays a crucial role in the cellular biological processes. Interface prediction can improve our understanding of the molecular mechanisms of the related processes and functions. In this work, we propose a classification method to recognize the interface residue based on the features of a weighted residue interaction network. The random forest algorithm is used for the prediction and 16 network parameters and the B-factor are acting as the element of the input feature vector. Compared with other similar work, the method is feasible and effective. The relative importance of these features also be analyzed to identify the key feature for the prediction. Some biological meaning of the important feature is explained. The results of this work can be used for the related work about the structure-function relationship analysis via a residue interaction network model. Copyright © 2017 Elsevier Ltd. All rights reserved.

  13. Improved Interaction Potentials for Charged Residues in Proteins

    DEFF Research Database (Denmark)

    Kepp, Kasper Planeta

    2008-01-01

    Electrostatic interactions dominate the structure and free energy of biomolecules. To obtain accurate free energies involving charged groups from molecular simulations, OPLS-AA parameters have been reoptimized using Monte Carlo free energy perturbation. New parameters fit a self-consistent, exper...... directly in molecular simulations with no modification of neutral residues needed and are envisioned to be particular important in simulations where charged residues change environment....

  14. Whole body interaction with public displays

    CERN Document Server

    Walter, Robert

    2017-01-01

    This book develops valuable new approaches to digital out-of-home media and digital signage in urban environments. It offers solutions for communicating interactive features of digital signage to passers-by. Digital out-of-home media and digital signage screens are becoming increasingly interactive thanks to touch input technology and gesture recognition. To optimize their conversion rate, interactive public displays must 1) attract attention, 2) communicate to passers-by that they are interactive, 3) explain the interaction, and 4) provide a motivation for passers-by to interact. This book highlights solutions to problems 2 and 3 above. The focus is on whole-body interaction, where the positions and orientations of users and their individual body parts are captured by specialized sensors (e.g., depth cameras). The book presents revealing findings from a field study on communicating interactivity, a laboratory on analysing visual attention, a field study on mid-air gestures, and a field study on using mid-air...

  15. Investigation for interaction between residual gas and proton beam

    Energy Technology Data Exchange (ETDEWEB)

    Park, K. M.; Kim, H. S.; Yoon, S. P.; Kwon, H. J.; Cho, Y. S. [Korea Atomic Energy Research Institute, Daejeon (Korea, Republic of)

    2014-10-15

    The electromagnet, vacuum, and radio frequency (RF) are fundamental building blocks of accelerator. Most of the accelerators demands ultra-high vacuum except for linear accelerator in which particles travels to the target 1 time. The linear accelerators and normal vacuum devices are usually operated between 10{sup -7} and 10{sup -8} Torr. We have also tried to set up test stand for ion source generated in the pressure range from 10{sup -7} to 10{sup -8} Torr. As basic research for base pressure, we have examined the interactions between the accelerated particles and the residual gas in high vacuum based on the results of residual gas analysis (RGA). Based on RGA result, the interaction between residual gas and accelerated ion was examined. The residual gases were Ar, CO{sub 2}, H{sub 2}, H{sub 2}O, C{sub x}H{sub x}, N{sub 2}/CO, and O{sub 2} and most of residual gas was considered as H{sub 2}O. When number of collisions per second was considered, 1 neutron in 10{sup 11} had collision while traversing the target at 4 x 10{sup -8} Torr. Beam loss wasn't generated and energy loss and position distribution was calculated by using SRIM code.

  16. Computational learning on specificity-determining residue-nucleotide interactions

    KAUST Repository

    Wong, Ka-Chun

    2015-11-02

    The protein–DNA interactions between transcription factors and transcription factor binding sites are essential activities in gene regulation. To decipher the binding codes, it is a long-standing challenge to understand the binding mechanism across different transcription factor DNA binding families. Past computational learning studies usually focus on learning and predicting the DNA binding residues on protein side. Taking into account both sides (protein and DNA), we propose and describe a computational study for learning the specificity-determining residue-nucleotide interactions of different known DNA-binding domain families. The proposed learning models are compared to state-of-the-art models comprehensively, demonstrating its competitive learning performance. In addition, we describe and propose two applications which demonstrate how the learnt models can provide meaningful insights into protein–DNA interactions across different DNA binding families.

  17. The Nature of Intermolecular Interactions Between Aromatic Amino Acid Residues

    Energy Technology Data Exchange (ETDEWEB)

    Gervasio, Francesco; Chelli, Riccardo; Procacci, Piero; Schettino, Vincenzo

    2002-05-01

    The nature of intermolecular interactions between aromatic amino acid residues has been investigated by a combination of molecular dynamics and ab initio methods. The potential energy surface of various interacting pairs, including tryptophan, phenilalanine, and tyrosine, was scanned for determining all the relevant local minima by a combined molecular dynamics and conjugate gradient methodology with the AMBER force field. For each of these minima, single-point correlated ab initio calculations of the binding energy were performed. The agreement between empirical force field and ab initio binding energies of the minimum energy structures is excellent. Aromatic-aromatic interactions can be rationalized on the basis of electrostatic and van der Waals interactions, whereas charge transfer or polarization phenomena are small for all intermolecular complexes and, particularly, for stacked structures.

  18. Assessment of residual body weight gain and residual intake and body weight gain as feed efficiency traits in the turkey (Meleagris gallopavo).

    Science.gov (United States)

    Willems, Owen W; Miller, Stephen P; Wood, Benjamin J

    2013-07-16

    Since feed represents 70% of the total cost in poultry production systems, an animal's ability to convert feed is an important trait. In this study, residual feed intake (RFI) and residual body weight gain (RG), and their linear combination into residual feed intake and body weight gain (RIG) were studied to estimate their genetic parameters and analyze the potential differences in feed intake between the top ranked birds based on the criteria for each trait. Phenotypic and genetic analyses were completed on 8340 growing tom turkeys that were measured for feed intake and body weight gain over a four-week period from 16 to 20 weeks of age. The heritabilities of RG and RIG were 0.19 ± 0.03 and 0.23 ± 0.03, respectively. Residual body weight gain had moderate genetic correlations with feed intake (-0.41) and body weight gain (0.43). All three linear combinations to form the RIG traits had genetic correlations ranging from -0.62 to -0.52 with feed intake, and slightly weaker, 0.22 to 0.34, with body weight gain. Sorted into three equal groups (low, medium, high) based on RG, the most efficient group (high) gained 0.62 and 1.70 kg more (P feed intake for the high group was less (P feed intake (18.86 vs. 19.57 and 20.41 kg) and the highest (P feed intake between the top ranked birds based on different residual feed efficiency traits may be small when looking at the average individual, however, when extrapolated to the production level, the lower feed intake values could lead to significant savings in feed costs over time.

  19. Tissue factor residues that putatively interact with membrane phospholipids.

    Directory of Open Access Journals (Sweden)

    Ke Ke

    Full Text Available Blood clotting is initiated by the two-subunit enzyme consisting of the plasma protease, factor VIIa (the catalytic subunit, bound to the integral membrane protein, tissue factor (the regulatory subunit. Molecular dynamics simulations have predicted that certain residues in the tissue factor ectodomain interact with phosphatidylserine headgroups to ensure optimal positioning of the tissue factor/factor VIIa complex relative to its membrane-bound protein substrates, factors IX and X. In this study, we individually mutated to alanine all the putative phosphatidylserine-interactive residues in the tissue factor ectodomain and measured their effects on tissue factor cofactor function (activation of factors IX and X by tissue factor/factor VIIa, and clotting of plasma. Some tissue factor mutants exhibited decreased activity in all three assays, with the most profound defects observed from mutations in or near the flexible loop from Lys159 to Gly164. The decreased activity of all of these tissue factor mutants could be partially or completely overcome by increasing the phosphatidylserine content of tissue factor-liposomes. Additionally, yeast surface display was used to screen a random library of tissue factor mutants for enhanced factor VIIa binding. Surprisingly, mutations at a single amino acid (Lys165 predominated, with the Lys165→Glu mutant exhibiting a 3-fold enhancement in factor VIIa binding affinity. Our studies reveal the functional contributions of residues in the C-terminal half of the tissue factor ectodomain that are implicated in interacting with phosphatidylserine headgroups to enhance tissue factor cofactor activity, possibly by allosterically modulating the conformation of the adjacent substrate-binding exosite region of tissue factor.

  20. Improved Interaction Potentials for Charged Residues in Proteins

    DEFF Research Database (Denmark)

    Kepp, Kasper Planeta

    2008-01-01

    -consistent, experimental set of hydration free energies for acetate (Asp), propionate (Glu), 4-methylimidazolium (Hip), n-butylammonium (Lys), and n-propylguanidinium (Arg), all resembling charged residue side chains, including -carbons. It is shown that OPLS-AA free energies depend critically on the type of water model......, TIP4P or TIP3P; i.e., each water model requires specific water-charged molecule interaction potentials. New models (models 1 and 3) are thus described for both water models. Uncertainties in relative free energies of charged residues are ~2 kcal/mol with the new parameters, due to variations in system...... setup (MAEs of ca. 1 kcal/mol) and noise from simulations (ca. 1 kcal/mol). The latter error of ~1 kcal/mol contrasts MAEs from standard OPLS-AA of up to 13 kcal/mol for the entire series of charged residues or up to 5 kcal/mol for the cationic series Lys, Arg, and Hip. The new parameters can be used...

  1. Interpreting Interactions between Ozone and Residual Petroleum Hydrocarbons in Soil.

    Science.gov (United States)

    Chen, Tengfei; Delgado, Anca G; Yavuz, Burcu M; Maldonado, Juan; Zuo, Yi; Kamath, Roopa; Westerhoff, Paul; Krajmalnik-Brown, Rosa; Rittmann, Bruce E

    2017-01-03

    We evaluated how gas-phase O3 interacts with residual petroleum hydrocarbons in soil. Total petroleum hydrocarbons (TPH) were 18 ± 0.6 g/kg soil, and TPH carbon constituted ∼40% of the dichloromethane-extractable carbon (DeOC) in the soil. At the benchmark dose of 3.4 kg O3/kg initial TPH, TPH carbon was reduced by nearly 6 gC/kg soil (40%), which was accompanied by an increase of about 4 gC/kg soil in dissolved organic carbon (DOC) and a 4-fold increase in 5-day biochemical oxygen demand (BOD5). Disrupting gas channeling in the soil improved mass transport of O3 to TPH bound to soil and increased TPH removal. Ozonation resulted in two measurable alterations of the composition of the organic carbon. First, part of DeOC was converted to DOC (∼4.1 gC/kg soil), 75% of which was not extractable by dichloromethane. Second, the DeOC containing saturates, aromatics, resins, and asphaltenes (SARA), was partially oxidized, resulting in a decline in saturates and aromatics, but increases in resins and asphaltenes. Ozone attack on resins, asphaltenes, and soil organic matter led to the production of NO3(-), SO4(2-), and PO4(3-). The results illuminate the mechanisms by which ozone gas interacted with the weathered petroleum residuals in soil to generate soluble and biodegradable products.

  2. Exploring many body interactions with Raman spectroscopy

    Science.gov (United States)

    Tian, Yao

    Many-body interactions are cornerstones of contemporary solid state physics research. Especially, phonon related interactions such as phonon-phonon coupling, spin-phonon coupling and electron-phonon coupling constantly present new challenges. To study phonon related many-body interactions, temperature dependent Raman spectroscopy is employed. Firstly, a new design and construction of a Raman microscope aimed at high collection eciency, positional and thermal stability is discussed. The application of the home-built Raman microscope is shown in the context of two types of novel materials; Cr2Ge2Te6 (spin-phonon coupling) and Bi2Te3-xSex (phonon-phonon coupling). Cr2Ge2Te6 is one of the rare class of ferromagnetic semiconductors and recent thermal transport studies suggest the spin and lattice are strongly coupled in its cousin compound Cr2Si2Te6. In this work, the spin-phonon coupling in Cr2Ge2Te6 has been revealed in multiple ways: we observed a split of two phonon modes due to the breaking of time reversal symmetry; the anomalous hardening of an additional three modes; and a dramatic enhancement of the phonon lifetimes. It is well-known that the phonon-phonon interaction plays a signicant role in determining the thermal transport properties of thermoelectrics. A comprehensive study of the phonon dynamics of Bi2Te3-xSex has been performed. We found that the unusual temperature dependence of dierent phonon modes originates from both cubic and quartic anharmonicity. These results are consistent with the resonance bonding mechanism, suggesting that the resonance bonding may be a common feature for conventional thermoelectrics. In the Raman spectra of Bi2Te2Se, the origin of the extra Raman feature has been debated for decades. Through a temperature dependent Raman study, we were able to prove the feature is generated by a Te-Se antisite induced local mode. The anomalous linewidth of the local mode as well as the anharmonic behavior were explained through a statistical

  3. On gravitational interactions between two bodies

    CERN Document Server

    Szybka, Sebastian J

    2014-01-01

    Many physicists, following Einstein, believe that the ultimate aim of theoretical physics is to find a unified theory of all interactions which would not depend on any free dimensionless constant, i.e., a dimensionless constant that is only empirically determinable. We do not know if such a theory exists. Moreover, if it exists, there seems to be no reason for it to be comprehensible for the human mind. On the other hand, as pointed out in Wigner's famous paper, human mathematics is unbelievably successful in natural science. This seeming paradox may be mitigated by assuming that the mathematical structure of physical reality has many `layers'. As time goes by, physicists discover new theories that correspond to the physical reality on the deeper and deeper level. In this essay, I will take a narrow approach and discuss the mathematical structure behind a single physical phenomenon - gravitational interaction between two bodies. The main aim of this essay is to put some recent developments of this topic in a ...

  4. Detection of residual packets in cocaine body packers: low accuracy of abdominal radiography - a prospective study

    Energy Technology Data Exchange (ETDEWEB)

    Rousset, Pascal; Vadrot, Dominique; Revel, Marie-Pierre [Assistance Publique-Hopitaux de Paris, Paris (France); Hopital Hotel Dieu, Department of Radiology, Paris (France); Universite Paris-Descartes, Paris (France); Chaillot, Pierre-Fleury [Assistance Publique-Hopitaux de Paris, Paris (France); Hopital Hotel Dieu, Department of Radiology, Paris (France); Audureau, Etienne [Assistance Publique-Hopitaux de Paris, Paris (France); Hopital Hotel Dieu, Department of Biostatistics and Epidemiology, Paris (France); Universite Paris-Descartes, Paris (France); Rey-Salmon, Caroline; Becour, Bertrand [Assistance Publique-Hopitaux de Paris, Paris (France); Hopital Hotel Dieu, Department of Forensic, Paris (France); Fitton, Isabelle [Assistance Publique-Hopitaux de Paris, Paris (France); Hopital Europeen Georges Pompidou, Department of Radiology, Paris (France)

    2013-08-15

    To evaluate the accuracy of abdominal radiography (AXR) for the detection of residual cocaine packets by comparison with computed tomography (CT). Over a 1-year period unenhanced CT was systematically performed in addition to AXR for pre-discharge evaluation of cocaine body packers. AXR and CT were interpreted independently by two radiologists blinded to clinical outcome. Patient and packet characteristics were compared between the groups with residual portage and complete decontamination. Among 138 body packers studied, 14 (10 %) had one residual packet identified on pre-discharge CT. On AXR, at least one reader failed to detect the residual packet in 10 (70 %) of these 14 body packers. The sensitivity and specificity of AXR were 28.6 % (95 % CI: 8.4-58.1) and 100.0 % (95 % CI: 97.0-100.0) for reader 1 and 35.7 % (95 % CI: 12.8-64.9) and 97.6 % (95 % CI: 93.1-99.5) for reader 2. There were no significant patient or packet characteristics predictive of residual portage or AXR false negativity. All positive CT results were confirmed by delayed expulsion or surgical findings, while negative results were confirmed by further surveillance. Given the poor performance of AXR, CT should be systematically performed to ensure safe hospital discharge of cocaine body packers. (orig.)

  5. Body image and day-to-day social interaction.

    Science.gov (United States)

    Nezlek, J B

    1999-10-01

    Participants maintained a social interaction diary and completed a measure of body image. Body image was found to have three factors, body attractiveness, social attractiveness (how attractive people believed others found them to be), and general attractiveness. For both men and women, self-perceptions of body attractiveness and of social attractiveness were positively related to the intimacy they found in interaction. Self-perceptions of social attractiveness were positively related to women's confidence in social interaction and their perceived influence over interaction, whereas for men, confidence and influence were unrelated to social attractiveness. For both men and women, body image was unrelated to how enjoyable people found interactions to be and was weakly related to how responsive they felt others were to them. For both men and women, body image was also unrelated to how socially active people were and to the relative distribution of same- and opposite-sex interactions.

  6. Prediction of residue-residue contact matrix for protein-protein interaction with Fisher score features and deep learning.

    Science.gov (United States)

    Du, Tianchuan; Liao, Li; Wu, Cathy H; Sun, Bilin

    2016-11-01

    Protein-protein interactions play essential roles in many biological processes. Acquiring knowledge of the residue-residue contact information of two interacting proteins is not only helpful in annotating functions for proteins, but also critical for structure-based drug design. The prediction of the protein residue-residue contact matrix of the interfacial regions is challenging. In this work, we introduced deep learning techniques (specifically, stacked autoencoders) to build deep neural network models to tackled the residue-residue contact prediction problem. In tandem with interaction profile Hidden Markov Models, which was used first to extract Fisher score features from protein sequences, stacked autoencoders were deployed to extract and learn hidden abstract features. The deep learning model showed significant improvement over the traditional machine learning model, Support Vector Machines (SVM), with the overall accuracy increased by 15% from 65.40% to 80.82%. We showed that the stacked autoencoders could extract novel features, which can be utilized by deep neural networks and other classifiers to enhance learning, out of the Fisher score features. It is further shown that deep neural networks have significant advantages over SVM in making use of the newly extracted features.

  7. Instability domain of Bose–Einstein condensates with quantum fluctuations and three-body interactions

    Energy Technology Data Exchange (ETDEWEB)

    Wamba, Etienne, E-mail: wambaetienne@yahoo.fr [Laboratory of Mechanics, Department of Physics, Faculty of Science, University of Yaoundé I, P.O. Box 812, Yaoundé (Cameroon); Department of Physics, Pondicherry University, Puducherry 605014 (India); Porsezian, K., E-mail: ponz.phy@pondiuni.edu.in [Department of Physics, Pondicherry University, Puducherry 605014 (India); Mohamadou, Alidou, E-mail: mohdoufr@yahoo.fr [The Abdus Salam International Centre for Theoretical Physics, P.O. Box 586, Strada Costiera 11, I-34014, Trieste (Italy); Condensed Matter Laboratory, Department of Physics, Faculty of Science, University of Douala, P.O. Box 24157, Douala (Cameroon); Kofané, Timoléon C. [Laboratory of Mechanics, Department of Physics, Faculty of Science, University of Yaoundé I, P.O. Box 812, Yaoundé (Cameroon)

    2013-01-03

    Through a Gross–Pitaevskii equation comprising cubic, quartic, residual, and quintic nonlinearities, we examine the modulational instability (MI) of Bose–Einstein condensates at higher densities in the presence of quantum fluctuations. We obtain an explicit time-dependent criteria for the MI and the instability domains of the condensates. Solitons are generated by suitably exciting the MI, and their stability is analyzed. We find that quantum fluctuations can completely change the instability of condensates by reversing the nature of the effective two-body interactions. The interplay between three-body interactions and quantum fluctuations is shown. Numerical simulations performed agree with analytical predictions.

  8. Many-body fits of phase-equivalent effective interactions

    CERN Document Server

    Johnson, Calvin W

    2010-01-01

    In many-body theory it is often useful to renormalize short-distance, high-momentum components of an interaction via unitary transformations. Such transformations preserve the on-shell physical observables of the two-body system (mostly phase-shifts, hence unitarily-connected effective interactions are often called phase-equivalent), while modifying off-shell T-matrix elements influential in many-body systems. In this paper I lay out a general and systematic approach for controlling the off-shell behavior of an effective interaction, which can be adjusted to many-body properties, and present an application to trapped fermions at the unitary

  9. Reconstruction of the residual stresses in a hyperelastic body using ultrasound techniques

    KAUST Repository

    Joshi, Sunnie

    2013-09-01

    This paper focuses on a novel approach for characterizing the residual stress field in soft tissue using ultrasound interrogation. A nonlinear inverse spectral technique is developed that makes fundamental use of the finite strain nonlinear response of the material to a quasi-static loading. The soft tissue is modeled as a nonlinear, prestressed and residually stressed, isotropic, slightly compressible elastic body with a rectangular geometry. A boundary value problem is formulated for the residually stressed and prestressed soft tissue, the boundary of which is subjected to a quasi-static pressure, and then an idealized model for the ultrasound interrogation is constructed by superimposing small amplitude time harmonic infinitesimal vibrations on static finite deformation via an asymptotic construction. The model is studied, through a semi-inverse approach, for a specific class of deformations that leads to a system of second order differential equations with homogeneous boundary conditions of Sturm-Liouville type. By making use of the classical theory of inverse Sturm-Liouville problems, and root finding and optimization techniques, several inverse spectral algorithms are developed to approximate the residual stress distribution in the body, given the first few eigenfrequencies of several induced static pressures. © 2013 Elsevier Ltd. All rights reserved.

  10. Electron Microscope Characterization of Carbohydrate Residues on the Body Wall of Xiphinema index.

    Science.gov (United States)

    Spiegal, Y; Robertson, W M; Himmelhoch, S; Zuckerman, B M

    1983-10-01

    The location of carbohydrate moieties on the outer cuticle of Xiphinema index was examined by electron microcopy using several different reagents: a) The periodic acid-thiosemicarbazide-silver proteinate reaction was used as a general stain for carbohydrates. In sectioned material it stained the canal system and deeper layers of the cuticle as well as the outer surface, b) Cationized ferritin at pH 2.5, which identifies carboxyl and sulfate groups, was used to identify sialic acid residues and also labelled parts of the canal system, c) Ferritin-goat anti rabbit IgG coupled to a DNP ligand was used to label either sialyl or galactosyl/N-acetyl-D-galactosaminyl residues, d) Ferritin hydrazide, a new reagent, was used for the ultrastructural localization of glyco-conjugates. Reagents c) (with appropriate antisera) and d) were applied only to the outer surfaces of the cuticle; they showed that sialic acid residues were concentrated mainly on the outer body wall of the head, the lips, oral opening, amphid apertures, and outer surface of protruded odontostyles. Ferritin distribution was not altered by pretreatment with neurantinidase. Galactose oxidase treatments revealed galactose/N-acetyl-D-galactosamine residues along the entire body wall. These results confirmed earlier findings obtained by fluorescence microscopy.

  11. Extending the Body for Interaction with Reality

    DEFF Research Database (Denmark)

    Feuchtner, Tiare; Müller, Jörg

    2017-01-01

    In this paper, we explore how users can control remote devices with a virtual long arm, while preserving the perception that the artificial arm is actually part of their own body. Instead of using pointing, speech, or a remote control, the users’ arm is extended in augmented reality, allowing...

  12. Extending the Body for Interaction with Reality

    DEFF Research Database (Denmark)

    Feuchtner, Tiare; Müller, Jörg

    2017-01-01

    In this paper, we explore how users can control remote devices with a virtual long arm, while preserving the perception that the artificial arm is actually part of their own body. Instead of using pointing, speech, or a remote control, the users’ arm is extended in augmented reality, allowing...

  13. Three-Body Interactions in Many-Body Effective Field Theory

    CERN Document Server

    Furnstahl, R J

    2003-01-01

    This contribution is an advertisement for applying effective field theory (EFT) to many-body problems, including nuclei and cold atomic gases. Examples involving three-body interactions are used to illustrate how EFT's quantify and systematically eliminate model dependence, and how they make many-body calculations simpler and more powerful.

  14. Interactions between coilin and PIASy partially link Cajal bodies to PML bodies.

    Science.gov (United States)

    Sun, Jun; Xu, Hongzhi; Subramony, S H; Hebert, Michael D

    2005-11-01

    The eukaryotic nucleus contains a variety of dynamic structures, yet studies into the functional relationship of one type of subnuclear domain to another have been limited. For example, PML bodies and Cajal bodies associate, but the functional consequence of this association and the mediating factors are unknown. Here we report that an associated PML body/Cajal body can co-localize to an snRNA gene locus, with the Cajal body invariably situated between the PML body and the snRNA locus. Binding studies demonstrate that coilin (a Cajal body protein) directly interacts with PIASy (a PML body protein). Cell biological experiments using coilin and PIASy knockout cell lines demonstrate that interactions between coilin and PIASy account in part for the observed association of Cajal bodies with PML bodies. When the PIASy interaction region on coilin is deleted, the frequency of the association between Cajal bodies and PML bodies is reduced. These studies provide another example of coilin's role in the functional organization of the nucleus.

  15. Few-body interactions in frozen Rydberg gases

    Science.gov (United States)

    Faoro, Riccardo; Pelle, Bruno; Zuliani, Alexandre

    2016-12-01

    The strong dipole-dipole coupling and the Stark tunability make Förster resonances an attractive tool for the implementation of quantum gates. In this direction a generalization to a N-body process would be a powerful instrument to implement multi-qubit gate and it will also path the way to the understanding of many-body physics. In this review, we give a general introduction on Förster resonances, also known as two-body FRET, giving an overview of the different application in quantum engineering and quantum simulation. Then we will describe an analogous process, the quasi-forbidden FRET, which is related to the Stark mixing due to the presence of an external electric field. We will then focus on its use in a peculiar four-body FRET. The second part of this review is focused on our study of few-body interactions in a cold gas of Cs Rydberg atoms. After a detailed description of a series of quasi-forbidden resonances detected in the proximity of an allowed two-body FRET we will show our most promising result: the observation of a three-body FRET. This process corresponds to a generalization of the usual two-body FRET, where a third atom serves as a relay for the energy transport. This relay also compensates for the energy mismatch which prevents a direct two-body FRET between the donor and the acceptor, but on the other side allowed a three-body process; for this reason, the three-body FRET observed is a "Borromean" process. It can be generalized for any quantum system displaying two-body FRET from quasi-degenerate levels. We also predict N-body FRET, based on the same interaction scheme. Three-body FRET thus promises important applications in the formation of macro-trimers, implementation of few-body quantum gates, few-body entanglement or heralded entanglement.

  16. Sensitivity analysis of random two-body interactions

    CERN Document Server

    Johnson, Calvin W

    2010-01-01

    The input to the configuration-interaction shell model includes many dozens or hundreds of independent two-body matrix elements. Previous studies have shown that when fitting to experimental low-lying spectra, the greatest sensitivity is to only a few linear combinations of matrix elements. Here we consider interactions drawn from the two-body random ensemble, or TBRE, and find that the low-lying spectra are also most sensitive to only a few linear combinations of two-body matrix elements, in a fashion nearly indistinguishable from an interaction empirically fit to data. We find in particular the spectra for both the random and empirical interactions are sensitive to similar matrix elements, which we analyze using monopole and contact interactions.

  17. Pattern Formation Around Interacting Bodies in Rotating Fluids

    Institute of Scientific and Technical Information of China (English)

    Karl B(U)HLER

    2006-01-01

    The interaction of bodies like spheres and disks in rotating fluids leads to novel flow structures. The primary swirling flow in circumferential direction is superimposed by a secondary motion in the meridional plane. The flow is visualized by introducing ink through a hole in the center of the axes and distributed radially in the central plane between the interacting bodies. The flow structure depends on the shape of the bodies, their geometrical arrangement and the Reynolds number given by the rotational speed. The observed flow structures gave rise to further investigations with PIV-measurements and numerical simulations.

  18. Many-body localization due to random interactions

    Science.gov (United States)

    Sierant, Piotr; Delande, Dominique; Zakrzewski, Jakub

    2017-02-01

    The possibility of observing many-body localization of ultracold atoms in a one-dimensional optical lattice is discussed for random interactions. In the noninteracting limit, such a system reduces to single-particle physics in the absence of disorder, i.e., to extended states. In effect, the observed localization is inherently due to interactions and is thus a genuine many-body effect. In the system studied, many-body localization manifests itself in a lack of thermalization visible in temporal propagation of a specially prepared initial state, in transport properties, in the logarithmic growth of entanglement entropy, and in statistical properties of energy levels.

  19. Three-Body Interacting Bosons in Free Space

    Science.gov (United States)

    Petrov, D. S.

    2014-03-01

    We propose a method of controlling two- and three-body interactions in an ultracold Bose gas in any dimension. The method requires us to have two coupled internal single-particle states split in energy such that the upper state is occupied virtually but amply during collisions. By varying system parameters, one can switch off the two-body interaction while maintaining a strong three-body one. The mechanism can be implemented for dipolar bosons in the bilayer configuration with tunneling or in an atomic system by using radio-frequency fields to couple two hyperfine states. One can then aim to observe a purely three-body interacting gas, dilute self-trapped droplets, the paired superfluid phase, Pfaffian state, and other exotic phenomena.

  20. Brownian dynamics simulations with hard-body interactions: Spherical particles

    CERN Document Server

    Behringer, Hans; 10.1063/1.4761827

    2012-01-01

    A novel approach to account for hard-body interactions in (overdamped) Brownian dynamics simulations is proposed for systems with non-vanishing force fields. The scheme exploits the analytically known transition probability for a Brownian particle on a one-dimensional half-line. The motion of a Brownian particle is decomposed into a component that is affected by hard-body interactions and into components that are unaffected. The hard-body interactions are incorporated by replacing the affected component of motion by the evolution on a half-line. It is discussed under which circumstances this approach is justified. In particular, the algorithm is developed and formulated for systems with space-fixed obstacles and for systems comprising spherical particles. The validity and justification of the algorithm is investigated numerically by looking at exemplary model systems of soft matter, namely at colloids in flow fields and at protein interactions. Furthermore, a thorough discussion of properties of other heurist...

  1. Time-dependent lethal body residues for the toxicity of pentachlorobenzene to Hyalella azteca

    Science.gov (United States)

    Landrum, Peter F.; Steevens, Jeffery A.; Gossiaux, Duane C.; McElroy, Michael; Robinson, Sander; Begnoche, Linda; Chernyak, Sergei; Hickey, James

    2004-01-01

    The study examined the temporal response of Hyalella azteca to pentachlorobenzene (PCBZ) in water-only exposures. Toxicity was evaluated by calculating the body residue of PCBZ associated with survival. The concentration of PCBZ in the tissues of H. azteca associated with 50% mortality decreased from 3 to 0.5 μmol/g over the temporal range of 1 to 28 d, respectively. No significant difference was observed in the body residue calculated for 50% mortality when the value was determined using live or dead organisms. Metabolism of PCBZ was not responsible for the temporal response because no detectable PCBZ biotransformation occurred over an exposure period of 10 d. A damage assessment model was used to evaluate the impact and repair of damage by PCBZ on H. azteca. The toxicokinetics were determined so that the temporal toxicity data could be fit to a damage assessment model. The half-life calculated for the elimination of PCBZ averaged approximately 49 h, while the value determined for the half-life of damage repair from the damage assessment model was 33 h.

  2. Heritability of gross feed efficiency and associations with yield, intake, residual intake, body weight, and body condition score in 11 commercial Pennsylvania tie stalls.

    Science.gov (United States)

    Vallimont, J E; Dechow, C D; Daubert, J M; Dekleva, M W; Blum, J W; Barlieb, C M; Liu, W; Varga, G A; Heinrichs, A J; Baumrucker, C R

    2011-04-01

    The objectives of this study were to calculate the heritability of feed efficiency and residual feed intake, and examine the relationships between feed efficiency and other traits of productive and economic importance. Intake and body measurement data were collected monthly on 970 cows in 11 tie-stall herds for 6 consecutive mo. Measures of efficiency for this study were: dry matter intake efficiency (DMIE), defined as 305-d fat-corrected milk (FCM)/305-d DMI, net energy for lactation efficiency (NELE), defined as 305-d FCM/05-d NEL intake, and crude protein efficiency (CPE), defined as 305-d true protein yield/305-d CP intake. Residual feed intake (RFI) was calculated by regressing daily DMI on daily milk, fat, and protein yields, body weight (BW), daily body condition score (BCS) gain or loss, the interaction between BW and BCS gain or loss, and days in milk (DIM). Data were analyzed with 3- and 4-trait animal models and included 305-d FCM or protein yield, DM, NEL, or CP intake, BW, BCS, BCS change between DIM 1 and 60, milk urea nitrogen, somatic cell score, RFI, or an alternative efficiency measure. Data were analyzed with and without significant covariates for BCS and BCS change between DIM 1 and 60. The average DMIE, NELE, and CPE were 1.61, 0.98, and 0.32, respectively. Heritability of gross feed efficiency was 0.14 for DMIE, 0.18 for NELE, and 0.21 for CPE, and heritability of RFI was 0.01. Body weight and BCS had high and negative correlations with the efficiency traits (-0.64 to -0.70), indicating that larger and fatter cows were less feed efficient than smaller and thinner cows. When BCS covariates were included in the model, cows identified as being highly efficient produced 2.3 kg/d less FCM in early lactation due to less early lactation loss of BCS. Results from this study suggest that selection for higher yield and lower BW will increase feed efficiency, and that body tissue mobilization should be considered. Copyright © 2011 American Dairy Science

  3. Novel simulation model for many-body multipole dispersion interactions

    Science.gov (United States)

    van der Hoef Paul, Martin A.; Madden, A.

    We present a novel simulation technique, within the framework of a molecular dynamics simulation, which accounts for both two- and three-body dispersion interactions, up to the triple-quadrupole interaction. This technique involves a unification of molecular dynamics and quantum-mechanical variational methods, in the spirit of the Car-Parrinello method. The advantage of this new method compared to existing techniques for simulating three-body dispersion forces, is that it allows for a consistent treatment of both dispersion damping and periodic boundary conditions at the pair and three-body level. The latter means that it would be possible, for the first time, to include many-body dispersion effects in the simulation of bulk properties of materials, without making use of effective pair potentials.

  4. Multinucleon Ejection Model for Two Body Current Neutrino Interactions

    Energy Technology Data Exchange (ETDEWEB)

    Sobczyk, Jan T.; /Fermilab

    2012-06-01

    A model is proposed to describe nucleons ejected from a nucleus as a result of two-body-current neutrino interactions. The model can be easily implemented in Monte Carlo neutrino event generators. Various possibilities to measure the two-body-current contribution are discussed. The model can help identify genuine charge current quasielastic events and allow for a better determination of the systematic error on neutrino energy reconstruction in neutrino oscillation experiments.

  5. Allometric functional response model: body masses constrain interaction strengths.

    Science.gov (United States)

    Vucic-Pestic, Olivera; Rall, Björn C; Kalinkat, Gregor; Brose, Ulrich

    2010-01-01

    1. Functional responses quantify the per capita consumption rates of predators depending on prey density. The parameters of these nonlinear interaction strength models were recently used as successful proxies for predicting population dynamics, food-web topology and stability. 2. This study addressed systematic effects of predator and prey body masses on the functional response parameters handling time, instantaneous search coefficient (attack coefficient) and a scaling exponent converting type II into type III functional responses. To fully explore the possible combinations of predator and prey body masses, we studied the functional responses of 13 predator species (ground beetles and wolf spiders) on one small and one large prey resulting in 26 functional responses. 3. We found (i) a power-law decrease of handling time with predator mass with an exponent of -0.94; (ii) an increase of handling time with prey mass (power-law with an exponent of 0.83, but only three prey sizes were included); (iii) a hump-shaped relationship between instantaneous search coefficients and predator-prey body-mass ratios; and (iv) low scaling exponents for low predator-prey body mass ratios in contrast to high scaling exponents for high predator-prey body-mass ratios. 4. These scaling relationships suggest that nonlinear interaction strengths can be predicted by knowledge of predator and prey body masses. Our results imply that predators of intermediate size impose stronger per capita top-down interaction strengths on a prey than smaller or larger predators. Moreover, the stability of population and food-web dynamics should increase with increasing body-mass ratios in consequence of increases in the scaling exponents. 5. Integrating these scaling relationships into population models will allow predicting energy fluxes, food-web structures and the distribution of interaction strengths across food web links based on knowledge of the species' body masses.

  6. Molecular interactions and residues involved in force generation in the T4 viral DNA packaging motor.

    Science.gov (United States)

    Migliori, Amy D; Smith, Douglas E; Arya, Gaurav

    2014-12-12

    Many viruses utilize molecular motors to package their genomes into preformed capsids. A striking feature of these motors is their ability to generate large forces to drive DNA translocation against entropic, electrostatic, and bending forces resisting DNA confinement. A model based on recently resolved structures of the bacteriophage T4 motor protein gp17 suggests that this motor generates large forces by undergoing a conformational change from an extended to a compact state. This transition is proposed to be driven by electrostatic interactions between complementarily charged residues across the interface between the N- and C-terminal domains of gp17. Here we use atomistic molecular dynamics simulations to investigate in detail the molecular interactions and residues involved in such a compaction transition of gp17. We find that although electrostatic interactions between charged residues contribute significantly to the overall free energy change of compaction, interactions mediated by the uncharged residues are equally if not more important. We identify five charged residues and six uncharged residues at the interface that play a dominant role in the compaction transition and also reveal salt bridging, van der Waals, and solvent hydrogen-bonding interactions mediated by these residues in stabilizing the compact form of gp17. The formation of a salt bridge between Glu309 and Arg494 is found to be particularly crucial, consistent with experiments showing complete abrogation in packaging upon Glu309Lys mutation. The computed contributions of several other residues are also found to correlate well with single-molecule measurements of impairments in DNA translocation activity caused by site-directed mutations.

  7. Nuclear structure with unitarily transformed two-body plus phenomenological three-body interactions

    Energy Technology Data Exchange (ETDEWEB)

    Guenther, Anneke

    2011-02-02

    The importance of three-nucleon forces for a variety of nuclear structure phenomena is apparent in various investigations. This thesis provides a first step towards the inclusion of realistic three-nucleon forces by studying simple phenomenological threebody interactions. The Unitary Correlation Operator Method (UCOM) and the Similarity Renormalization Group (SRG) provide two different approaches to derive soft phase-shift equivalent nucleon-nucleon (NN) interactions via unitary transformations. Although their motivations are quite different the NN interactions obtained with the two methods exhibit some similarities. The application of the UCOM- or SRG-transformed Argonne V18 potential in the Hartree-Fock (HF) approximation and including the second-order energy corrections emerging from many-body perturbation theory (MBPT) reveals that the systematics of experimental ground-state energies can be reproduced by some of the interactions considering a series of closed-shell nuclei across the whole nuclear chart. However, charge radii are systematically underestimated, especially for intermediate and heavy nuclei. This discrepancy to experimental data is expected to result from neglected three-nucleon interactions. As first ansatz for a three-nucleon force, we consider a finite-range three-body interaction of Gaussian shape. Its influence on ground-state energies and charge radii is discussed in detail on the basis of HF plus MBPT calculations and shows a significant improvement in the description of experimental data. As the handling of the Gaussian three-body interaction is time-extensive, we show that it can be replaced by a regularized three-body contact interaction exhibiting a very similar behavior. An extensive study characterizes its properties in detail and confirms the improvements with respect to nuclear properties. To take into account information of an exact numerical solution of the nuclear eigenvalue problem, the No-Core Shell Model is applied to

  8. Estimation of human body concentrations of DDT from indoor residual spraying for malaria control.

    Science.gov (United States)

    Gyalpo, Tenzing; Fritsche, Lukas; Bouwman, Henk; Bornman, Riana; Scheringer, Martin; Hungerbühler, Konrad

    2012-10-01

    Inhabitants of dwellings treated with DDT for indoor residual spraying show high DDT levels in blood and breast milk. This is of concern since mothers transfer lipid-soluble contaminants such as DDT via breastfeeding to their children. Focusing on DDT use in South Africa, we employ a pharmacokinetic model to estimate DDT levels in human lipid tissue over the lifetime of an individual to determine the amount of DDT transferred to children during breastfeeding, and to identify the dominant DDT uptake routes. In particular, the effects of breastfeeding duration, parity, and mother's age on DDT concentrations of mother and infant are investigated. Model results show that primiparous mothers have greater DDT concentrations than multiparous mothers, which causes higher DDT exposure of first-born children. DDT in the body mainly originates from diet. Generally, our modeled DDT levels reproduce levels found in South African biomonitoring data within a factor of 3.

  9. Universal few-body physics in resonantly interacting spinor condensates

    Science.gov (United States)

    Colussi, V. E.; Greene, Chris H.; D'Incao, J. P.

    2016-03-01

    Optical trapping techniques allow for the formation of bosonic condensates with internal degrees of freedom, so-called spinor condensates. Mean-field models of spinor condensates highlight the sensitivity of the quantum phases of the system to the relative strength of the two-body interaction in the different spin-channels. Such a description captures the regime where these interactions are weak. In the opposite and largely unexplored regime of strongly correlated spinor condensates, three-body interactions can play an important role through the Efimov effect, producing possible novel phases. Here, we study the three-body spinor problem using the hyperspherical adiabatic representation for spin-1, -2 and -3 condensates in the strongly-correlated regime. We characterize the Efimov physics for such systems and the relevant three-body mean-field parameters. We find that the Efimov effect can strongly affect the spin dynamics and three-body mean-field contributions to the possible quantum phases of the condensate through universal contributions to scattering observables.

  10. Device and method for measuring the dynamic interaction between bodies

    NARCIS (Netherlands)

    Veltink, Petrus H.

    2008-01-01

    The invention relates to a device for measuring the dynamic interaction, in particular power transfer and work performed, between a first and a second body, in particular during relatively random movements. The device comprises a housing in which at least one kinematic sensor and at least one

  11. Numerical Simulation of Shock(Blast)Wave Interaction with Bodies

    Institute of Scientific and Technical Information of China (English)

    JialingLE

    1999-01-01

    Some typical results of computation on the shock(blast)wave interaction (2-D and 3-D) with bodies and its experimental validation in shock tube are summarized,suggestions for improving the numerical method(Difference scheme and grid systems).developing 3-D optical quantitative visualization technology and further studying the unsteady turbulent flow are put forward.

  12. Regularities of many-body systems interacting by a two-body random ensemble

    Energy Technology Data Exchange (ETDEWEB)

    Zhao, Y.M. [Department of Physics, Shanghai Jiao-Tong University, Shanghai 200030 (China) and Cyclotron Center, Institute of Physical and Chemical Research - RIKEN, Hirosawa 2-1, Wako-shi, Saitama 351-0198 (Japan) and Department of Physics, Southeast University, Nanjing 210018 (China)]. E-mail: ymzhao@riken.jp; Arima, A. [Science Museum, Japan Science Foundation, 2-1 Kitanomaru-Koen, Chiyodaku, Tokyo 102-0091 (Japan); Yoshinaga, N. [Department of Physics, Saitama University, Saitama 338-0625 (Japan)

    2004-10-01

    The ground states of all even-even nuclei have angular momentum, I, equal to zero, I=0, and positive parity, {pi}=+. This feature was believed to be a consequence of the attractive short-range interaction between nucleons. However, in the presence of two-body random interactions, the predominance of I{pi}=0+ ground states (0 g.s.) was found to be robust both for bosons and for an even number of fermions. For simple systems, such as d bosons, sp bosons, sd bosons, and a few fermions in single-j shells for small j, there are a few approaches to predict and/or explain spin I ground state (I g.s.) probabilities. An empirical approach to predict I g.s. probabilities is available for general cases, such as fermions in a single-j (j>72) or many-j shells and various boson systems, but a more fundamental understanding of the robustness of 0 g.s. dominance is still out of reach. Further interesting results are also reviewed concerning other robust phenomena of many-body systems in the presence of random two-body interactions, such as the odd-even staggering of binding energies, generic collectivity, the behavior of average energies, correlations, and regularities of many-body systems interacting by a displaced two-body random ensemble.

  13. Mind-Body Interactions in Anxiety and Somatic Symptoms.

    Science.gov (United States)

    Mallorquí-Bagué, Núria; Bulbena, Antonio; Pailhez, Guillem; Garfinkel, Sarah N; Critchley, Hugo D

    2016-01-01

    Anxiety and somatic symptoms have a high prevalence in the general population. A mechanistic understanding of how different factors contribute to the development and maintenance of these symptoms, which are highly associated with anxiety disorders, is crucial to optimize treatments. In this article, we review recent literature on this topic and present a redefined model of mind-body interaction in anxiety and somatic symptoms, with an emphasis on both bottom-up and top-down processes. Consideration is given to the role played in this interaction by predisposing physiological and psychological traits (e.g., interoception, anxiety sensitivity, and trait anxiety) and to the levels at which mindfulness approaches may exert a therapeutic benefit. The proposed model of mind-body interaction in anxiety and somatic symptoms is appraised in the context of joint hypermobility syndrome, a constitutional variant associated with autonomic abnormalities and vulnerability to anxiety disorders.

  14. Many-body interactions in quasi-freestanding graphene

    Science.gov (United States)

    Siegel, David A.; Park, Cheol-Hwan; Hwang, Choongyu; Deslippe, Jack; Fedorov, Alexei V.; Louie, Steven G.; Lanzara, Alessandra

    2011-01-01

    The Landau–Fermi liquid picture for quasiparticles assumes that charge carriers are dressed by many-body interactions, forming one of the fundamental theories of solids. Whether this picture still holds for a semimetal such as graphene at the neutrality point, i.e., when the chemical potential coincides with the Dirac point energy, is one of the long-standing puzzles in this field. Here we present such a study in quasi-freestanding graphene by using high-resolution angle-resolved photoemission spectroscopy. We see the electron–electron and electron–phonon interactions go through substantial changes when the semimetallic regime is approached, including renormalizations due to strong electron–electron interactions with similarities to marginal Fermi liquid behavior. These findings set a new benchmark in our understanding of many-body physics in graphene and a variety of novel materials with Dirac fermions. PMID:21709258

  15. Many-body diffusion algorithm for interacting harmonic fermions

    Science.gov (United States)

    Luczak, F.; Brosens, F.; Devreese, J. T.; Lemmens, L. F.

    1999-09-01

    A new quantum Monte Carlo algorithm is presented to numerically implement the recently developed many-body diffusion approach for identical particles. For fermions, the procedure avoids the sign problem by defining a set of independent stochastic diffusion processes. Based on a symmetry analysis of both the free density matrix and the potential, the total random process is restricted to a well-defined state space with absorbing or reflecting boundary conditions. The absorption rate of the walkers at absorbing boundaries contributes substantially to the ground-state energy. The feasibility of the many-body diffusion algorithm is illustrated by its application to interacting harmonic fermions.

  16. Hamiltonian dynamics of several rigid bodies interacting with point vortices

    CERN Document Server

    Weissmann, Steffen

    2013-01-01

    We introduce a Hamiltonian description for the dynamics of several rigid bodies interacting with point vortices in an inviscid, incompressible fluid. We adopt the idea of Vankerschaver et al. (2009) to derive the Hamiltonian formulation via symplectic reduction of a canonical Hamiltonian system on a principle fibre bundle. On the reduced phase space we determine the magnetic symplectic form directly, without resorting to the machinery of mechanical connections on principle fibre bundles. We derive the equations of motion for the general case, and also for the special Lie-Poisson case of a single rigid body and zero total vorticity. Finally we give a partly degenerate Lagrangian formulation for the system.

  17. Identification of protein-RNA interaction sites using the information of spatial adjacent residues

    Directory of Open Access Journals (Sweden)

    Cheng Yong-Mei

    2011-10-01

    Full Text Available Abstract Background Protein-RNA interactions play an important role in numbers of fundamental cellular processes such as RNA splicing, transport and translation, protein synthesis and certain RNA-mediated enzymatic processes. The more knowledge of Protein-RNA recognition can not only help to understand the regulatory mechanism, the site-directed mutagenesis and regulation of RNA–protein complexes in biological systems, but also have a vitally effecting for rational drug design. Results Based on the information of spatial adjacent residues, novel feature extraction methods were proposed to predict protein-RNA interaction sites with SVM-KNN classifier. The total accuracies of spatial adjacent residue profile feature and spatial adjacent residues weighted accessibility solvent area feature are 78%, 67.07% respectively in 5-fold cross-validation test, which are 1.4%, 3.79% higher than that of sequence neighbour residue profile feature and sequence neighbour residue accessibility solvent area feature. Conclusions The results indicate that the performance of feature extraction method using the spatial adjacent information is superior to the sequence neighbour information approach. The performance of SVM-KNN classifier is little better than that of SVM. The feature extraction method of spatial adjacent information with SVM-KNN is very effective for identifying protein-RNA interaction sites and may at least play a complimentary role to the existing methods.

  18. Interaction of ethanol and mercury body burden in the mouse

    Energy Technology Data Exchange (ETDEWEB)

    Dunn, J.D.

    1978-01-01

    The interaction of ethanol with mercury in the body resulting in increased exhalation of the metal was studied in the mouse. A persistent elimination of the metal in the breath was demonstrated after single, sublethal (<1 mgHg/Kg body weight) exposures to mercury vapor (Hg/sup 0/) or mercury II chloride (HgCl/sub 2/). The amount of mercury exhaled per unit time was enhanced by oral or parenteral administration of ethanol solutions. These modifications were investigated in dose-response studies in which the drug was administered in doses ranging from 0.2g to 5.5g/Kg to mice pretreated with mercury. The EC/sub 50/ for blood ethanol with respect to mercury exhalation was determined to be approximately 200 mg/dl corresponding to an output rate of approximately 0.1% of the simultaneous body burden in 30 min several days after mercury. A hypothesis that mercury expired by these animals was proportional to the body burden after mercury administration was addressed in experiments whereby mice given one of several doses of mercuric chloride (0.16 to 500 ..mu..g/Kg) were monitored for pulmonary mercury elimination for a fifteen day period. The high correlation obtained between the amount of mercury exhaled in a standard time period and the body burden by group indicated that breath sampling could be applied as an indicator of the mercury body burden which may not be limited to the mouse.

  19. An Open Platform for Full Body Interactive Sonification Exergames

    Directory of Open Access Journals (Sweden)

    Simone Ghisio

    2015-08-01

    Full Text Available This paper addresses the use of a remote interactive platform to support home-based rehabilitation for children with motor and cognitive impairment. The interaction between user and platform is achieved on customizable full-body interactive serious games (exergames. These exergames perform real-time analysis of multimodal signals to quantify movement qualities and postural attitudes. Interactive sonification of movement is then applied for providing a real-time feedback based on “aesthetic resonance” and engagement of the children. The games also provide log file recordings therapists can use to assess the performance of the children and the effectiveness of the games. The platform allows the customization of the games to address the children’s needs. The platform is based on the EyesWeb XMI software, and the games are designed for home usage, based on Kinect for Xbox One and simple sensors including 3-axis accelerometers available in low-cost Android smartphones.

  20. Prediction of vitamin interacting residues in a vitamin binding protein using evolutionary information

    Directory of Open Access Journals (Sweden)

    Panwar Bharat

    2013-02-01

    Full Text Available Abstract Background The vitamins are important cofactors in various enzymatic-reactions. In past, many inhibitors have been designed against vitamin binding pockets in order to inhibit vitamin-protein interactions. Thus, it is important to identify vitamin interacting residues in a protein. It is possible to detect vitamin-binding pockets on a protein, if its tertiary structure is known. Unfortunately tertiary structures of limited proteins are available. Therefore, it is important to develop in-silico models for predicting vitamin interacting residues in protein from its primary structure. Results In this study, first we compared protein-interacting residues of vitamins with other ligands using Two Sample Logo (TSL. It was observed that ATP, GTP, NAD, FAD and mannose preferred {G,R,K,S,H}, {G,K,T,S,D,N}, {T,G,Y}, {G,Y,W} and {Y,D,W,N,E} residues respectively, whereas vitamins preferred {Y,F,S,W,T,G,H} residues for the interaction with proteins. Furthermore, compositional information of preferred and non-preferred residues along with patterns-specificity was also observed within different vitamin-classes. Vitamins A, B and B6 preferred {F,I,W,Y,L,V}, {S,Y,G,T,H,W,N,E} and {S,T,G,H,Y,N} interacting residues respectively. It suggested that protein-binding patterns of vitamins are different from other ligands, and motivated us to develop separate predictor for vitamins and their sub-classes. The four different prediction modules, (i vitamin interacting residues (VIRs, (ii vitamin-A interacting residues (VAIRs, (iii vitamin-B interacting residues (VBIRs and (iv pyridoxal-5-phosphate (vitamin B6 interacting residues (PLPIRs have been developed. We applied various classifiers of SVM, BayesNet, NaiveBayes, ComplementNaiveBayes, NaiveBayesMultinomial, RandomForest and IBk etc., as machine learning techniques, using binary and Position-Specific Scoring Matrix (PSSM features of protein sequences. Finally, we selected best performing SVM modules and

  1. Device and method for measuring the dynamic interaction between bodies

    OpenAIRE

    Veltink, Petrus H.

    2008-01-01

    The invention relates to a device for measuring the dynamic interaction, in particular power transfer and work performed, between a first and a second body, in particular during relatively random movements. The device comprises a housing in which at least one kinematic sensor and at least one kinetic sensor is arranged, in addition to processing means for processing the signals from the sensors, and communication means for data exchange with the outside world. The invention also relates to a ...

  2. Residue Specific and Chirality Dependent Interactions between Carbon Nanotubes and Flagellin.

    Science.gov (United States)

    Macwan, Isaac G; Zhao, Zihe; Sobh, Omar T; Mukerji, Ishita; Dharmadhikari, Bhushan; Patra, Prabir K

    2016-01-01

    Flagellum is a lash-like cellular appendage found in many single-celled living organisms. The flagellin protofilaments contain 11-helix dual turn structure in a single flagellum. Each flagellin consists of four sub-domains - two inner domains (D0, D1) and two outer domains (D2, D3). While inner domains predominantly consist of α-helices, the outer domains are primarily beta sheets with D3. In flagellum, the outermost sub-domain is the only one that is exposed to the native environment. This study focuses on the interactions of the residues of D3 of an R-type flagellin with 5nm long chiral (5,15) and arm-chair (12,12) single-walled carbon nanotubes (SWNT) using molecular dynamics simulation. It presents the interactive forces between the SWNT and the residues of D3 from the perspectives of size and chirality of the SWNT. It is found that the metallic (arm-chair) SWNT interacts the most with glycine and threonine residues through van der Waals and hydrophobic interactions, whereas the semiconducting (chiral) SWNT interacts largely with the area of protein devoid of glycine by van der Waals, hydrophobic interactions, and hydrogen bonding. This indicates a crucial role that glycine plays in distinguishing metallic from semiconducting SWNTs.

  3. Spin Structure of Many-Body Systems with Two-Body Random Interactions

    CERN Document Server

    Kaplan, L; Johnson, C W; Kaplan, Lev; Papenbrock, Thomas; Johnson, Calvin W.

    2001-01-01

    We investigate the spin structure of many-fermion systems with a spin-conserving two-body random interaction. We find a strong dominance of spin-0 ground states and considerable correlations between energies and wave functions of low-lying states with different spin, but no indication of pairing. The spectral densities exhibit spin-dependent shapes and widths, and depend on the relative strengths of the spin-0 and spin-1 couplings in the two-body random matrix. The spin structure of low-lying states can largely be explained analytically.

  4. Determination of the critical residues responsible for cardiac myosin binding protein C's interactions.

    Science.gov (United States)

    Bhuiyan, Md Shenuarin; Gulick, James; Osinska, Hanna; Gupta, Manish; Robbins, Jeffrey

    2012-12-01

    Despite early demonstrations of myosin binding protein C's (MyBP-C) interaction with actin, different investigators have reached different conclusions regarding the relevant and necessary domains mediating this binding. Establishing the detailed structure-function relationships is needed to fully understand cMyBP-C's ability to impact on myofilament contraction as mutations in different domains are causative for familial hypertrophic cardiomyopathy. We defined cMyBP-C's N-terminal structural domains that are necessary or sufficient to mediate interactions with actin and/or the head region of the myosin heavy chain (S2-MyHC). Using a combination of genetics and functional assays, we defined the actin binding site(s) present in cMyBP-C. We confirmed that cMyBP-C's C1 and m domains productively interact with actin, while S2-MyHC interactions are restricted to the m domain. Using residue-specific mutagenesis, we identified the critical actin binding residues and distinguished them from the residues that were critical for S2-MyHC binding. To validate the structural and functional significance of these residues, we silenced the endogenous cMyBP-C in neonatal rat cardiomyocytes (NRC) using cMyBP-C siRNA, and replaced the endogenous cMyBP-C with normal or actin binding-ablated cMyBP-C. Replacement with actin binding-ablated cMyBP-C showed that the mutated protein did not incorporate into the sarcomere normally. Residues responsible for actin and S2-MyHC binding are partially present in overlapping domains but are unique. Expression of an actin binding-deficient cMyBP-C resulted in abnormal cytosolic distribution of the protein, indicating that interaction with actin is essential for the formation and/or maintenance of normal cMyBP-C sarcomeric distribution.

  5. Determination of whole-body rotenone residues in the brown tree snake (Boiga irregularis).

    Science.gov (United States)

    Mauldin, R E; Furcolow, C A; Johnston, J J; Kimball, B A

    2000-06-01

    The brown tree snake (Boiga irregularis) is an introduced pest in Guam, responsible for extensive agricultural damage, the extinction of several bird species, and severe and frequent electrical power outages. Rotenone, a naturally occurring pesticide, has been investigated as a possible chemical control agent. An analytical method was developed to assess whole body rotenone residues ranging in concentration from 0.035 to 250 microg g(-)(1) in snakes. The method employed ethyl acetate extraction of 2 g samples of cryogenically frozen, pulverized snakes, followed by silica and Florisil solid-phase extraction cleanup. Extract analysis was performed using a high-performance liquid chromatography system employing a cyanopropyl analytical column. Tissues fortified to concentrations of 0.035, 4.82, and 250 microg g(-)(1) yielded analyte recoveries of 85.1, 85.6, and 83.5%, respectively. The linear response of rotenone standard solutions was assessed from 0. 025 to 0.25 microg mL(-)(1) (r(2) = 0.9968) and from 0.250 to 125 microg mL(-)(1) (r(2) = 0.9999). The method was simple, rugged, and reliable.

  6. Tryptophan probes reveal residue-specific phospholipid interactions of apolipoprotein C-III.

    Science.gov (United States)

    Pfefferkorn, Candace M; Walker, Robert L; He, Yi; Gruschus, James M; Lee, Jennifer C

    2015-11-01

    Apolipoproteins are essential human proteins for lipid metabolism. Together with phospholipids, they constitute lipoproteins, nm to μm sized particles responsible for transporting cholesterol and triglycerides throughout the body. To investigate specific protein-lipid interactions, we produced and characterized three single-Trp containing apolipoprotein C-III (ApoCIII) variants (W42 (W54F/W65F), W54 (W42F/W65F), W65 (W42F/W54F)). Upon binding to phospholipid vesicles, wild-type ApoCIII adopts an α-helical conformation (50% helicity) as determined by circular dichroism spectroscopy with an approximate apparent partition constant of 3×10(4) M(-1). Steady-state and time-resolved fluorescence measurements reveal distinct residue-specific behaviors with W54 experiencing the most hydrophobic environment followed by W42 and W65. Interestingly, time-resolved anisotropy measurements show a converse trend for relative Trp mobility with position 54 being the least immobile. To determine the relative insertion depths of W42, W54, and W65 in the bilayer, fluorescence quenching experiments were performed using three different brominated lipids. W65 had a clear preference for residing near the headgroup while W54 and W42 sample the range of depths ~8-11 Å from the bilayer center. On average, W54 is slightly more embedded than W42. Based on Trp spectral differences between ApoCIII binding to phospholipid vesicles and sodium dodecyl sulfate micelles, we suggest that ApoCIII adopts an alternate helical conformation on the bilayer which could have functional implications.

  7. Revised scaling variables in systems with many-body interactions

    Science.gov (United States)

    Goldstein, Raymond E.; Parola, Alberto

    1987-06-01

    Thermodynamic perturbation theory and the Kirkwood-Salsburg correlation function identities are used to study nearest-neighbor lattice gases with certain weak symmetry-breaking many-body interactions. It is shown that such systems may be mapped onto symmetric models by the introduction of suitable effective interactions and a shifted chemical potential, both of which depend explicitly on the temperature and fugacity of the original model. In the critical region, such a thermodynamic-state dependence implies the existence of a thermal scaling field which depends on the bare chemical potential, and this ``field mixing'' leads to a breakdown in the classical law of the rectilinear diameter. These results give a microscopic interpretation to a field-theoretic renormalization-group analysis which derives such a diameter singularity from the presence of terms cubic and higher in the order parameter and its gradients in an asymmetric Landau-Ginzburg-Wilson Hamiltonian. For a primarily repulsive three-body potential like the Axilrod-Teller interaction in classical insulating fluids, and in comparison with recent experiments, the analysis correctly describes the observed trends in the critical and near-critical behavior of the diameters with increasing particle polarizability.

  8. Identifying body residues of HCBP associated with 10-d mortality and partial life cycle effects in the midge, Chironomus riparius.

    Science.gov (United States)

    Hwang, H; Fisher, S W; Landrum, P F

    2001-05-01

    The relationship between the body residue of 2,2',4,4',5,5'-hexachlorobiphenyl (HCBP) and its effects, including 10-d mortality and chronic sublethal effects on the midge, Chironomus riparius, are examined in a partial life cycle assessment. The alga, Chlorella vulgaris, was loaded with 14C-labeled HCBP and fed to midges as the method for delivery of the toxicant. In a 10-d bioassay, median lethal body residue (LR50) was 0.57 (95% CI: 0.49-0.66) mmol/kg. In the partial life cycle test, midges were fed a mixture of 12C- and 14C-HCBP-laden algae and exposed in four separate tests to assess the different developmental stages representing 2nd to 3rd instar, 2nd to 4th, 2nd to pupa, and 2nd to adult stages. A variety of sublethal endpoints were monitored, including developmental time within a stadium, body concentration at the end of each stadium, body weight, and fecundity (the number of ova) for the female pupae and adults. Overall, midge body concentrations of HCBP increased with increasing exposure concentration. Body weight was not significantly affected by HCBP except during the 4th instar. Body residue also increased with each successive stadium. Developmental time increased significantly with increasing body concentration in 2nd to 4th, 2nd to pupa, and 2nd to adult tests, while there was no statistical significance in developmental time for the 2nd to 3rd instar test. The number of ova decreased significantly in adults with increasing body concentration of HCBP, with an average of 345 ova in controls, 289 ova at 0.028 mmol/kg of HCBP, and 258 ova at 0.250 mmol/kg. These data, which relate chronic endpoints to body residues, suggest that sublethal endpoints in invertebrates are useful for defining sublethal hazards of PCBs. These data also suggest that ecological consequences may result from relatively low body burdens of PCBs.

  9. Few-body quantum physics with strongly interacting Rydberg polaritons

    Science.gov (United States)

    Bienias, Przemyslaw

    2016-12-01

    We present an extension of our recent paper [Bienias et al., Phys. Rev. A 90, 053804 (2014)] in which we demonstrated the scattering properties and bound-state structure of two Rydberg polaritons, as well as the derivation of the effective low-energy many-body Hamiltonian. Here, we derive a microscopic Hamiltonian describing the propagation of Rydberg slow light polaritons in one dimension. We describe possible decoherence processes within a Master equation approach, and derive equations of motion in a Schroedinger picture by using an effective non-Hermitian Hamiltonian. We illustrate diagrammatic methods on two examples: First, we show the solution for a single polariton in an external potential by exact summation of Feynman diagrams. Secondly, we solve the two body problem in a weakly interacting regime exactly.

  10. Inverse problem for multi-body interaction of nonlinear waves

    CERN Document Server

    Marruzzo, Alessia; Antenucci, Fabrizio; Pagnani, Andrea; Leuzzi, Luca

    2016-01-01

    The inverse problem is studied in multi-body systems with nonlinear dynamics representing, e.g., phase-locked wave systems, standard multimode and random lasers. Using a general model for four-body interacting complex-valued variables we test two methods based on pseudolikelihood, respectively with regularization and with decimation, to determine the coupling constants from sets of measured configurations. We test statistical inference predictions for increasing number of sampled configurations and for an externally tunable {\\em temperature}-like parameter mimicing real data noise and helping minimization procedures. Analyzed models with phasors and rotors are generalizations of problems of real-valued spherical problems (e.g., density fluctuations), discrete spins (Ising and vectorial Potts) or finite number of states (standard Potts): inference methods presented here can, then, be straightforward applied to a large class of inverse problems.

  11. Few-body quantum physics with strongly interacting Rydberg polaritons

    CERN Document Server

    Bienias, Przemyslaw

    2016-01-01

    We present an extension of our recent paper [Bienias et al., Phys. Rev. A 90, 053804 (2014)] in which we demonstrated the scattering properties and bound-state structure of two Rydberg polaritons, as well as the derivation of the effective low-energy many-body Hamiltonian. Here, we derive a microscopic Hamiltonian describing the propagation of Rydberg slow light polaritons in one dimension. We describe possible decoherence processes within a Master equation approach, and derive equations of motion in a Schroedinger picture by using an effective non-Hermitian Hamiltonian. We illustrate diagrammatic methods on two examples: First, we show the solution for a single polariton in an external potential by exact summation of Feynman diagrams. Secondly, we solve the two body problem in a weakly interacting regime exactly.

  12. Sulphur Atoms from Methionines Interacting with Aromatic Residues Are Less Prone to Oxidation

    Science.gov (United States)

    Aledo, Juan C.; Cantón, Francisco R.; Veredas, Francisco J.

    2015-01-01

    Methionine residues exhibit different degrees of susceptibility to oxidation. Although solvent accessibility is a relevant factor, oxidation at particular sites cannot be unequivocally explained by accessibility alone. To explore other possible structural determinants, we assembled different sets of oxidation-sensitive and oxidation-resistant methionines contained in human proteins. Comparisons of the proteins containing oxidized methionines with all proteins in the human proteome led to the conclusion that the former exhibit a significantly higher mean value of methionine content than the latter. Within a given protein, an examination of the sequence surrounding the non-oxidized methionine revealed a preference for neighbouring tyrosine and tryptophan residues, but not for phenylalanine residues. However, because the interaction between sulphur atoms and aromatic residues has been reported to be important for the stabilization of protein structure, we carried out an analysis of the spatial interatomic distances between methionines and aromatic residues, including phenylalanine. The results of these analyses uncovered a new determinant for methionine oxidation: the S-aromatic motif, which decreases the reactivity of the involved sulphur towards oxidants. PMID:26597773

  13. Sulphur Atoms from Methionines Interacting with Aromatic Residues Are Less Prone to Oxidation

    Science.gov (United States)

    Aledo, Juan C.; Cantón, Francisco R.; Veredas, Francisco J.

    2015-11-01

    Methionine residues exhibit different degrees of susceptibility to oxidation. Although solvent accessibility is a relevant factor, oxidation at particular sites cannot be unequivocally explained by accessibility alone. To explore other possible structural determinants, we assembled different sets of oxidation-sensitive and oxidation-resistant methionines contained in human proteins. Comparisons of the proteins containing oxidized methionines with all proteins in the human proteome led to the conclusion that the former exhibit a significantly higher mean value of methionine content than the latter. Within a given protein, an examination of the sequence surrounding the non-oxidized methionine revealed a preference for neighbouring tyrosine and tryptophan residues, but not for phenylalanine residues. However, because the interaction between sulphur atoms and aromatic residues has been reported to be important for the stabilization of protein structure, we carried out an analysis of the spatial interatomic distances between methionines and aromatic residues, including phenylalanine. The results of these analyses uncovered a new determinant for methionine oxidation: the S-aromatic motif, which decreases the reactivity of the involved sulphur towards oxidants.

  14. Inverse problem for multi-body interaction of nonlinear waves.

    Science.gov (United States)

    Marruzzo, Alessia; Tyagi, Payal; Antenucci, Fabrizio; Pagnani, Andrea; Leuzzi, Luca

    2017-06-14

    The inverse problem is studied in multi-body systems with nonlinear dynamics representing, e.g., phase-locked wave systems, standard multimode and random lasers. Using a general model for four-body interacting complex-valued variables we test two methods based on pseudolikelihood, respectively with regularization and with decimation, to determine the coupling constants from sets of measured configurations. We test statistical inference predictions for increasing number of sampled configurations and for an externally tunable temperature-like parameter mimicing real data noise and helping minimization procedures. Analyzed models with phasors and rotors are generalizations of problems of real-valued spherical problems (e.g., density fluctuations), discrete spins (Ising and vectorial Potts) or finite number of states (standard Potts): inference methods presented here can, then, be straightforward applied to a large class of inverse problems. The high versatility of the exposed techniques also concerns the number of expected interactions: results are presented for different graph topologies, ranging from sparse to dense graphs.

  15. A method for computing the inter-residue interaction potentials for reduced amino acid alphabet

    Indian Academy of Sciences (India)

    Abhinav Luthra; Anupam Nath Jha; G K Ananthasuresh; Saraswathi Vishveswara

    2007-08-01

    Inter-residue potentials are extensively used in the design and evaluation of protein structures. However, dealing with all (20×20) interactions becomes computationally difficult in extensive investigations. Hence, it is desirable to reduce the alphabet of 20 amino acids to a smaller number. Currently, several methods of reducing the residue types exist; however a critical assessment of these methods is not available. Towards this goal, here we review and evaluate different methods by comparing with the complete (20×20) matrix of Miyazawa-Jernigan potential, including a method of grouping adopted by us, based on multi dimensional scaling (MDS). The second goal of this paper is the computation of inter-residue interaction energies for the reduced amino acid alphabet, which has not been explicitly addressed in the literature until now. By using a least squares technique, we present a systematic method of obtaining the interaction energy values for any type of grouping scheme that reduces the amino acid alphabet. This can be valuable in designing the protein structures.

  16. PAIRpred: partner-specific prediction of interacting residues from sequence and structure.

    Science.gov (United States)

    Minhas, Fayyaz ul Amir Afsar; Geiss, Brian J; Ben-Hur, Asa

    2014-07-01

    We present a novel partner-specific protein-protein interaction site prediction method called PAIRpred. Unlike most existing machine learning binding site prediction methods, PAIRpred uses information from both proteins in a protein complex to predict pairs of interacting residues from the two proteins. PAIRpred captures sequence and structure information about residue pairs through pairwise kernels that are used for training a support vector machine classifier. As a result, PAIRpred presents a more detailed model of protein binding, and offers state of the art accuracy in predicting binding sites at the protein level as well as inter-protein residue contacts at the complex level. We demonstrate PAIRpred's performance on Docking Benchmark 4.0 and recent CAPRI targets. We present a detailed performance analysis outlining the contribution of different sequence and structure features, together with a comparison to a variety of existing interface prediction techniques. We have also studied the impact of binding-associated conformational change on prediction accuracy and found PAIRpred to be more robust to such structural changes than existing schemes. As an illustration of the potential applications of PAIRpred, we provide a case study in which PAIRpred is used to analyze the nature and specificity of the interface in the interaction of human ISG15 protein with NS1 protein from influenza A virus. Python code for PAIRpred is available at http://combi.cs.colostate.edu/supplements/pairpred/. © 2013 Wiley Periodicals, Inc.

  17. Regularities in Many-body Systems Interacting by a Two-body Random Ensemble

    CERN Document Server

    Zhao, Y M; Yoshinaga, N

    2003-01-01

    The even-even nuclei always have zero ground state angular momenta $I$ and positive parities $\\pi$. This feature was believed to be just a consequence of the attractive short-range interactions between nucleons. However, in the presence of two-body random interactions, the predominance of $I^{\\pi}=0^+$ ground states (0 g.s.) was found to be robust both for bosons and for an even number of fermions. For simple systems, such as $d$ bosons, $sp$ bosons, $sd$ bosons, and a few fermions in single-$j$ shells for small $j$, there are a few approaches to predict and/or explain the distribution of angular momentum $I$ ground state probabilities. An empirical recipe to predict the $I$ g.s. probabilities is available for general cases, but a more fundamental understanding of the robustness of 0 g.s. dominance is still out of reach. Other interesting results are also reviewed concerning other robust phenomena of many-body systems in the presence of random interactions, such as odd-even staggering of binding energies, gen...

  18. The RING 2.0 web server for high quality residue interaction networks.

    Science.gov (United States)

    Piovesan, Damiano; Minervini, Giovanni; Tosatto, Silvio C E

    2016-07-08

    Residue interaction networks (RINs) are an alternative way of representing protein structures where nodes are residues and arcs physico-chemical interactions. RINs have been extensively and successfully used for analysing mutation effects, protein folding, domain-domain communication and catalytic activity. Here we present RING 2.0, a new version of the RING software for the identification of covalent and non-covalent bonds in protein structures, including π-π stacking and π-cation interactions. RING 2.0 is extremely fast and generates both intra and inter-chain interactions including solvent and ligand atoms. The generated networks are very accurate and reliable thanks to a complex empirical re-parameterization of distance thresholds performed on the entire Protein Data Bank. By default, RING output is generated with optimal parameters but the web server provides an exhaustive interface to customize the calculation. The network can be visualized directly in the browser or in Cytoscape. Alternatively, the RING-Viz script for Pymol allows visualizing the interactions at atomic level in the structure. The web server and RING-Viz, together with an extensive help and tutorial, are available from URL: http://protein.bio.unipd.it/ring.

  19. Automated detection and quantification of residual brain tumor using an interactive computer-aided detection scheme

    Science.gov (United States)

    Gaffney, Kevin P.; Aghaei, Faranak; Battiste, James; Zheng, Bin

    2017-03-01

    Detection of residual brain tumor is important to evaluate efficacy of brain cancer surgery, determine optimal strategy of further radiation therapy if needed, and assess ultimate prognosis of the patients. Brain MR is a commonly used imaging modality for this task. In order to distinguish between residual tumor and surgery induced scar tissues, two sets of MRI scans are conducted pre- and post-gadolinium contrast injection. The residual tumors are only enhanced in the post-contrast injection images. However, subjective reading and quantifying this type of brain MR images faces difficulty in detecting real residual tumor regions and measuring total volume of the residual tumor. In order to help solve this clinical difficulty, we developed and tested a new interactive computer-aided detection scheme, which consists of three consecutive image processing steps namely, 1) segmentation of the intracranial region, 2) image registration and subtraction, 3) tumor segmentation and refinement. The scheme also includes a specially designed and implemented graphical user interface (GUI) platform. When using this scheme, two sets of pre- and post-contrast injection images are first automatically processed to detect and quantify residual tumor volume. Then, a user can visually examine segmentation results and conveniently guide the scheme to correct any detection or segmentation errors if needed. The scheme has been repeatedly tested using five cases. Due to the observed high performance and robustness of the testing results, the scheme is currently ready for conducting clinical studies and helping clinicians investigate the association between this quantitative image marker and outcome of patients.

  20. A critical assessment of two-body and three-body interactions in water

    CERN Document Server

    Medders, Gregory R; Paesani, Francesco

    2012-01-01

    The microscopic behavior of water under different conditions and in different environments remains the subject of intense debate. A great number of the controversies arise due to the contradictory predictions obtained within different theoretical models. Relative to conclusions derived from force fields or density functional theory, there is comparably less room to dispute highly-correlated electronic structure calculations. Unfortunately, such ab initio calculations are severely limited by system size. In this study, a detailed analysis of the two- and three-body water interactions evaluated at the CCSD(T) level is carried out to quantitatively assess the accuracy of several force fields, density functional theory, and ab initio-based interaction potentials that are commonly used in molecular simulations. Based on this analysis, a new model, HBB2-pol, is introduced which is capable of accurately mapping CCSD(T) results for water dimers and trimers into an efficient analytical function. The accuracy of HBB2-p...

  1. Three-body interacting dipolar bosons and the fate of lattice supersolidity

    Science.gov (United States)

    Singh, Manpreet; Mishra, Tapan

    2016-12-01

    We investigate a system of dipolar bosons in an optical lattice with local two- and three-body interactions. Using the mean-field-theory approach, we obtain the ground-state phase diagram of the extended Bose-Hubbard model with both repulsive and attractive three-body interactions. We show that the additional three-body on-site interaction has strong effects on the phase diagram, especially on the supersolid phase. Positive values of the three-body interaction lead to the enhancement of the gapped phases at densities larger than unity by reducing the supersolid region. However, a small attractive three-body interaction enhances the supersolid phase.

  2. Predicting important residues and interaction pathways in proteins using Gaussian Network Model: binding and stability of HLA proteins.

    Directory of Open Access Journals (Sweden)

    Turkan Haliloglu

    Full Text Available A statistical thermodynamics approach is proposed to determine structurally and functionally important residues in native proteins that are involved in energy exchange with a ligand and other residues along an interaction pathway. The structure-function relationships, ligand binding and allosteric activities of ten structures of HLA Class I proteins of the immune system are studied by the Gaussian Network Model. Five of these models are associated with inflammatory rheumatic disease and the remaining five are properly functioning. In the Gaussian Network Model, the protein structures are modeled as an elastic network where the inter-residue interactions are harmonic. Important residues and the interaction pathways in the proteins are identified by focusing on the largest eigenvalue of the residue interaction matrix. Predicted important residues match those known from previous experimental and clinical work. Graph perturbation is used to determine the response of the important residues along the interaction pathway. Differences in response patterns of the two sets of proteins are identified and their relations to disease are discussed.

  3. [An interactive three-dimensional model of the human body].

    Science.gov (United States)

    Liem, S L

    2009-01-01

    Driven by advanced computer technology, it is now possible to show the human anatomy on a computer. On the internet, the Visible Body programme makes it possible to navigate in all directions through the anatomical structures of the human body, using mouse and keyboard. Visible Body is a wonderful tool to give insight in the human structures, body functions and organs.

  4. Analytic, group-theoretic wave functions for confined, correlated N-body systems with general two-body interactions

    Science.gov (United States)

    Dunn, M.; Watson, D. K.; Loeser, J. G.

    2006-08-01

    In this paper, we develop an analytic N-body wave function for identical particles under quantum confinement with a general two-body interaction. A systematic approach to correlation is developed by combining three theoretical methods: dimensional perturbation theory, the FG method of Wilson et. al., and the group theory of the symmetric group. Analytic results are achieved for a completely general interaction potential. Unlike conventional perturbation methods which are applicable only for weakly interacting systems, this analytic approach is applicable to both weakly and strongly interacting systems. This method directly accounts for each two-body interaction, rather than an average interaction so even lowest-order results include beyond-mean-field effects. One major advantage is that N appears as a parameter in the analytical expressions for the energy so results for different N are easy to obtain.

  5. Defining HIV-1 Vif residues that interact with CBFβ by site-directed mutagenesis.

    Science.gov (United States)

    Matsui, Yusuke; Shindo, Keisuke; Nagata, Kayoko; Io, Katsuhiro; Tada, Kohei; Iwai, Fumie; Kobayashi, Masayuki; Kadowaki, Norimitsu; Harris, Reuben S; Takaori-Kondo, Akifumi

    2014-01-20

    Vif is essential for HIV-1 replication in T cells and macrophages. Vif recruits a host ubiquitin ligase complex to promote proteasomal degradation of the APOBEC3 restriction factors by poly-ubiquitination. The cellular transcription cofactor CBFβ is required for Vif function by stabilizing the Vif protein and promoting recruitment of a cellular Cullin5-RING ubiquitin ligase complex. Interaction between Vif and CBFβ is a promising therapeutic target, but little is known about the interfacial residues. We now demonstrate that Vif conserved residues E88/W89 are crucial for CBFβ binding. Substitution of E88/W89 to alanines impaired binding to CBFβ, degradation of APOBEC3, and virus infectivity in the presence of APOBEC3 in single-cycle infection. In spreading infection, NL4-3 with Vif E88A/W89A mutation replicated comparably to wild-type virus in permissive CEM-SS cells, but not in multiple APOBEC3 expressing non-permissive CEM cells. These results support a model in which HIV-1 Vif residues E88/W89 may participate in binding CBFβ.

  6. On the Interaction between a Nanoparticulate System and the Human Body in Body Area Nanonetworks

    Directory of Open Access Journals (Sweden)

    Valeria Loscrí

    2015-08-01

    Full Text Available In this work, we investigate the interaction of a nanoparticulate system for nanomedicine applications with the biological environment, i.e., the human body. Following the molecular communication paradigm, we assess how our nanoparticulate system model is suitable for coexistence in a biological environment. Specifically, we assume the presence of the human immune system that can affect the optimal behavior of nanoparticles, aiming to locally deliver drug inside the human body. When a flow of nanoparticles is injected into the blood, the interference due to the immune system can provide a strong decrease of the nanoparticle concentration, by means of “humoral immunity”, the phagocytosis process, etc. As a consequence, the correct drug delivery will occur with a lower probability. Since the mechanism behind the biological immune system is very complicated, in this paper, we start from a simplistic nanoparticulate model, where the nanoparticles and the cells of the immune system are subject to the diffusion laws. Finally, we derive the end-to-end physical model of our nanoparticulate nanomedicine system with the presence of the human immune system cells. The error analysis is then investigated in terms of how these errors can affect the performance of the system, i.e., nanoparticle survival probability.

  7. Simulation of general three-body interactions in a nuclear magnetic resonance ensemble quantum computer

    Institute of Scientific and Technical Information of China (English)

    2008-01-01

    Three-body interaction plays an important role in many-body physics,and quantum computer is efficient in simulating many-body interactions. We have experimentally demonstrated the general three-body interactions in a three-qubit nuclear magnetic resonance ensemble quantum computer. Using a nuclear magnetic resonance computer we implemented general forms of three-body interactions including σ 1x σ z2 σ x3 and σ 1x σ z2 σ y3 . The results show good agreement between theory and experiment. We have also given a concise and practical formula for a general n-body interaction in terms of one-and two-body interactions.

  8. Appearance-related residual injury, posttraumatic stress, and body image: Associations within a sample of female victims of intimate partner violence.

    Science.gov (United States)

    Weaver, Terri L; Resnick, Heidi S; Kokoska, Mimi S; Etzel, Julie C

    2007-12-01

    One third of women who experience intimate partner violence (IPV) receive some form of injury. After acute injuries have healed, a victim's physical appearance may be altered with residual changes including marks or scars. This study included 56 female victims of IPV (31 with appearance-related residual injury and a comparison group of 25 with no appearance-related residual injury) and examined the associations between violence-related experiences, body image distress, and symptoms of posttraumatic stress disorder (PTSD). Appearance-related residual injury status moderated the relationship between body image distress and symptoms of PTSD. In addition, within the appearance-related residual injury group, body image distress emerged a unique predictor of PTSD explaining incremental variance beyond that explained by severity of psychological maltreatment.

  9. Intragenic suppressor of Osiaa23 revealed a conserved tryptophan residue crucial for protein-protein interactions.

    Directory of Open Access Journals (Sweden)

    Jun Ni

    Full Text Available The Auxin/Indole-3-Acetic Acid (Aux/IAA and Auxin Response Factor (ARF are two important families that play key roles in auxin signal transduction. Both of the families contain a similar carboxyl-terminal domain (Domain III/IV that facilitates interactions between these two families. In spite of the importance of protein-protein interactions among these transcription factors, the mechanisms involved in these interactions are largely unknown. In this study, we isolated six intragenic suppressors of an auxin insensitive mutant, Osiaa23. Among these suppressors, Osiaa23-R5 successfully rescued all the defects of the mutant. Sequence analysis revealed that an amino acid substitution occurred in the Tryptophan (W residue in Domain IV of Osiaa23. Yeast two-hybrid experiments showed that the mutation in Domain IV prevents the protein-protein interactions between Osiaa23 and OsARFs. Phylogenetic analysis revealed that the W residue is conserved in both OsIAAs and OsARFs. Next, we performed site-specific amino acid substitutions within Domain IV of OsARFs, and the conserved W in Domain IV was exchanged by Serine (S. The mutated OsARF(WSs can be released from the inhibition of Osiaa23 and maintain the transcriptional activities. Expression of OsARF(WSs in Osiaa23 mutant rescued different defects of the mutant. Our results suggest a previously unknown importance of Domain IV in both families and provide an indirect way to investigate functions of OsARFs.

  10. Interaction of 18-residue peptides derived from amphipathic helical segments of globular proteins with model membranes

    Indian Academy of Sciences (India)

    Chandrasekaran Sivakamasundari; Ramakrishnan Nagaraj

    2009-06-01

    We investigated the interaction of six 18-residue peptides derived from amphipathic helical segments of globular proteins with model membranes. The net charge of the peptides at neutral pH varies from –1 to +6. Circular dichroism spectra indicate that peptides with a high net positive charge tend to fold into a helical conformation in the presence of negatively charged lipid vesicles. In helical conformation, their average hydrophobic moment and hydrophobicity would render them surface-active. The composition of amino acids on the polar face of the helix in the peptides is considerably different. The peptides show variations in their ability to permeabilise zwitterionic and anionic lipid vesicles. Whereas increased net positive charge favours greater permeabilisation, the distribution of charged residues in the polar face also plays a role in determining membrane activity. The distribution of amino acids in the polar face of the helix in the peptides that were investigated do not fall into the canonical classes described. Amphipathic helices, which are part of proteins, with a pattern of amino acid distribution different from those observed in class L, A and others, could help in providing newer insights into peptide–membrane interactions.

  11. Efficient quantum transport in disordered interacting many-body networks

    Science.gov (United States)

    Ortega, Adrian; Stegmann, Thomas; Benet, Luis

    2016-10-01

    The coherent transport of n fermions in disordered networks of l single-particle states connected by k -body interactions is studied. These networks are modeled by embedded Gaussian random matrix ensemble (EGE). The conductance bandwidth and the ensemble-averaged total current attain their maximal values if the system is highly filled n ˜l -1 and k ˜n /2 . For the cases k =1 and k =n the bandwidth is minimal. We show that for all parameters the transport is enhanced significantly whenever centrosymmetric embedded Gaussian ensemble (csEGE) are considered. In this case the transmission shows numerous resonances of perfect transport. Analyzing the transmission by spectral decomposition, we find that centrosymmetry induces strong correlations and enhances the extrema of the distributions. This suppresses destructive interference effects in the system and thus causes backscattering-free transmission resonances that enhance the overall transport. The distribution of the total current for the csEGE has a very large dominating peak for n =l -1 , close to the highest observed currents.

  12. Human body micro-environment: The benefits of controlling airflow interaction

    DEFF Research Database (Denmark)

    Melikov, Arsen Krikor

    2015-01-01

    This paper focuses on the micro-environment around a human body, and especially on its interaction with the surrounding environment. Research on the free convection flow generated by a human body (including the convective boundary layer around the body and the thermal plume above the body), its...

  13. Determining high-quality critical body residues for multiple species and chemicals by applying improved experimental design and data interpretation concepts

    NARCIS (Netherlands)

    van der Heijden, Stephan A; Hermens, Joop L M; Sinnige, Theo L; Mayer, Philipp; Gilbert, Dorothea; Jonker, Michiel T O

    2015-01-01

    Ecotoxicological effect data are generally expressed as effective concentrations in the external exposure medium and do thus not account for differences in chemical uptake, bioavailability, and metabolism, which can introduce substantial data variation. The Critical Body Residue (CBR) concept provid

  14. Determining high-quality critical body residues for multiple species and chemicals by applying improved experimental design and data interpretation concepts

    NARCIS (Netherlands)

    van der Heijden, Stephan A; Hermens, Joop L M; Sinnige, Theo L; Mayer, Philipp; Gilbert, Dorothea; Jonker, Michiel T O

    2015-01-01

    Ecotoxicological effect data are generally expressed as effective concentrations in the external exposure medium and do thus not account for differences in chemical uptake, bioavailability, and metabolism, which can introduce substantial data variation. The Critical Body Residue (CBR) concept

  15. Integrability and chaos in body-vortex interactions

    DEFF Research Database (Denmark)

    Pedersen, Johan Rønby; Aref, Hassan

    2009-01-01

    have fixed strengths and are intended to model vortices that have been shed by the body or elsewhere in the flow field. The flow at any given time and position is determined by the instantaneous vortex and body positions together with the instantaneous linear and angular velocity of the body...

  16. Three-body bound states with zero-range interaction in the Bethe-Salpeter approach

    Science.gov (United States)

    Ydrefors, E.; Alvarenga Nogueira, J. H.; Gigante, V.; Frederico, T.; Karmanov, V. A.

    2017-07-01

    The Bethe-Salpeter equation for three bosons with zero-range interaction is solved for the first time. For comparison the light-front equation is also solved. The input is the two-body scattering length and the outputs are the three-body binding energies, Bethe-Salpeter amplitudes and light-front wave functions. Three different regimes are analyzed: (i) For weak enough two-body interaction the three-body system is unbound. (ii) For stronger two-body interaction a three-body bound state appears. It provides an interesting example of a deeply bound Borromean system. (iii) For even stronger two-body interaction this state becomes unphysical with a negative mass squared. However, another physical (excited) state appears, found previously in light-front calculations. The Bethe-Salpeter approach implicitly incorporates three-body forces of relativistic origin, which are attractive and increase the binding energy.

  17. Residues in Conserved Loops of Intramembrane Metalloprotease SpoIVFB Interact with Residues near the Cleavage Site in Pro-σK

    Science.gov (United States)

    Zhang, Yang; Luethy, Paul M.

    2013-01-01

    Intramembrane metalloproteases (IMMPs) control critical biological processes by cleaving membrane-associated proteins within a transmembrane segment or at a site near the membrane surface. Phylogenetic analysis divides IMMPs into four groups. SpoIVFB is a group III IMMP that regulates Bacillus subtilis endospore formation by cleaving Pro-σK and releasing the active sigma factor from a membrane. To elucidate the enzyme-substrate interaction, single-cysteine versions of catalytically inactive SpoIVFB and C-terminally truncated Pro-σK(1-126) (which can be cleaved by active SpoIVFB) were coexpressed in Escherichia coli, and proximity was tested by disulfide cross-linking in vivo. As expected, the results provided evidence that catalytic residue Glu-44 of SpoIVFB is near the cleavage site in the substrate. Also near the cleavage site were two residues of SpoIVFB in predicted conserved loops; Pro-135 in a short loop and Val-70 in a longer loop. Pro-135 corresponds to Pro-399 of RseP, a group I IMMP, and Pro-399 was reported previously to interact with substrate near the cleavage site, suggesting a conserved interaction across IMMP subfamilies. Val-70 follows a newly recognized conserved motif, PXGG (X is a large hydrophobic residue), which is in a hydrophobic region predicted to be a membrane reentrant loop. Following the hydrophobic region is a negatively charged region that is conserved in IMMPs of groups I and III. At least two residues with a negatively charged side chain are required in this region for activity of SpoIVFB. The region exhibits other features in IMMPs of groups II and IV. Its possible roles, as well as that of the short loop, are discussed. New insights into IMMP-substrate interaction build toward understanding how IMMPs function and may facilitate manipulation of their activity. PMID:23995631

  18. Protein kinase D interacts with neuronal nitric oxide synthase and phosphorylates the activatory residue serine 1412.

    Directory of Open Access Journals (Sweden)

    Lucía Sánchez-Ruiloba

    Full Text Available Neuronal Nitric Oxide Synthase (nNOS is the biosynthetic enzyme responsible for nitric oxide (·NO production in muscles and in the nervous system. This constitutive enzyme, unlike its endothelial and inducible counterparts, presents an N-terminal PDZ domain known to display a preference for PDZ-binding motifs bearing acidic residues at -2 position. In a previous work, we discovered that the C-terminal end of two members of protein kinase D family (PKD1 and PKD2 constitutes a PDZ-ligand. PKD1 has been shown to regulate multiple cellular processes and, when activated, becomes autophosphorylated at Ser 916, a residue located at -2 position of its PDZ-binding motif. Since nNOS and PKD are spatially enriched in postsynaptic densities and dendrites, the main objective of our study was to determine whether PKD1 activation could result in a direct interaction with nNOS through their respective PDZ-ligand and PDZ domain, and to analyze the functional consequences of this interaction. Herein we demonstrate that PKD1 associates with nNOS in neurons and in transfected cells, and that kinase activation enhances PKD1-nNOS co-immunoprecipitation and subcellular colocalization. However, transfection of mammalian cells with PKD1 mutants and yeast two hybrid assays showed that the association of these two enzymes does not depend on PKD1 PDZ-ligand but its pleckstrin homology domain. Furthermore, this domain was able to pull-down nNOS from brain extracts and bind to purified nNOS, indicating that it mediates a direct PKD1-nNOS interaction. In addition, using mass spectrometry we demonstrate that PKD1 specifically phosphorylates nNOS in the activatory residue Ser 1412, and that this phosphorylation increases nNOS activity and ·NO production in living cells. In conclusion, these novel findings reveal a crucial role of PKD1 in the regulation of nNOS activation and synthesis of ·NO, a mediator involved in physiological neuronal signaling or neurotoxicity under

  19. Protein Kinase D Interacts with Neuronal Nitric Oxide Synthase and Phosphorylates the Activatory Residue Serine1412

    Science.gov (United States)

    García-Guerra, Lucía; Pose-Utrilla, Julia; Rodríguez-Crespo, Ignacio; Iglesias, Teresa

    2014-01-01

    Neuronal Nitric Oxide Synthase (nNOS) is the biosynthetic enzyme responsible for nitric oxide (·NO) production in muscles and in the nervous system. This constitutive enzyme, unlike its endothelial and inducible counterparts, presents an N-terminal PDZ domain known to display a preference for PDZ-binding motifs bearing acidic residues at -2 position. In a previous work, we discovered that the C-terminal end of two members of protein kinase D family (PKD1 and PKD2) constitutes a PDZ-ligand. PKD1 has been shown to regulate multiple cellular processes and, when activated, becomes autophosphorylated at Ser916, a residue located at -2 position of its PDZ-binding motif. Since nNOS and PKD are spatially enriched in postsynaptic densities and dendrites, the main objective of our study was to determine whether PKD1 activation could result in a direct interaction with nNOS through their respective PDZ-ligand and PDZ domain, and to analyze the functional consequences of this interaction. Herein we demonstrate that PKD1 associates with nNOS in neurons and in transfected cells, and that kinase activation enhances PKD1-nNOS co-immunoprecipitation and subcellular colocalization. However, transfection of mammalian cells with PKD1 mutants and yeast two hybrid assays showed that the association of these two enzymes does not depend on PKD1 PDZ-ligand but its pleckstrin homology domain. Furthermore, this domain was able to pull-down nNOS from brain extracts and bind to purified nNOS, indicating that it mediates a direct PKD1-nNOS interaction. In addition, using mass spectrometry we demonstrate that PKD1 specifically phosphorylates nNOS in the activatory residue Ser1412, and that this phosphorylation increases nNOS activity and ·NO production in living cells. In conclusion, these novel findings reveal a crucial role of PKD1 in the regulation of nNOS activation and synthesis of ·NO, a mediator involved in physiological neuronal signaling or neurotoxicity under pathological conditions

  20. Correlated responses in sow appetite, residual feed intake, body composition, and reproduction after divergent selection for residual feed intake in the growing pig.

    Science.gov (United States)

    Gilbert, H; Bidanel, J-P; Billon, Y; Lagant, H; Guillouet, P; Sellier, P; Noblet, J; Hermesch, S

    2012-04-01

    Residual feed intake (RFI) has been explored as an alternative selection criterion to feed conversion ratio to capture the fraction of feed intake not explained by expected production and maintenance requirements. Selection experiments have found that low RFI in the growing pig is genetically correlated with reduced fatness and feed intake. Selection for feed conversion ratio also reduces sow appetite and fatness, which, together with increased prolificacy, has been seen as a hindrance for sow lifetime performance. The aims of our study were to derive equations for sow RFI during lactation (SRFI) and to evaluate the effect of selection for RFI during growth on sow traits during lactation. Data were obtained on 2 divergent lines selected for 7 generations for low and high RFI during growth in purebred Large Whites. The RFI was measured on candidates for selection (1,065 pigs), and sow performance data were available for 480 sows having from 1 to 3 parities (1,071 parities). Traits measured were sow daily feed intake (SDFI); sow BW and body composition before farrowing and at weaning (28.4 ± 1.7d); number of piglets born total, born alive, and surviving at weaning; and litter weight, average piglet BW, and within-litter SD of piglet BW at birth, 21 d of age (when creep feeding was available), and weaning. Sow RFI was defined as the difference between observed SDFI and SDFI predicted for sow maintenance and production. Daily production requirements were quantified by litter size and daily litter BW gain as well as daily changes in sow body reserves. The SRFI represented 24% of the phenotypic variability of SDFI. Heritability estimates for RFI and SRFI were both 0.14. The genetic correlation between RFI and SRFI was 0.29 ± 0.23. Genetic correlations of RFI with sow traits were low to moderate, consistent with responses to selection; selection for low RFI during growth reduced SDFI and increased number of piglets and litter growth, but also increased mobilization of

  1. Connections among residual strong interaction, the EMC effect and short range correlations

    CERN Document Server

    Wang, Rong

    2015-01-01

    A linear correlation is shown quantitatively between the magnitude of the EMC effect measured in electron deep inelastic scattering (DIS) and the nuclear residual strong interaction energy (RSIE) obtained from the nuclear binding energy subtracting the Coulomb energy part. The observed correlation supports the recent speculation that the nuclear dependence of quark distributions depend on the local nuclear density. This phenomenological relationship can be used to extract the size of in-medium correction (IMC) effect on deuteron. Most importantly, the EMC slopes $dR_{EMC}/dx$ of nuclei can be predicted with the nuclear binding energy data. The relationship between nucleon-nucleon (N-N) short range correlation (SRC) and RSIE is also presented.

  2. Relationship between Functional Residual Capacity to Various Body Measurements in Normal Sheep

    Science.gov (United States)

    1992-12-01

    and maximum breathing capacity. Thorax 9:313-320.were conducted using the plethysmographic technique, the 9. Hutchison, A. A., K . L. Brigham, and J...Immunol. 79:339-344. icant correlations between FRC and several external body 11. Ahmed, T., P. Eyre, A. J. Januszkiewicz , et al. 1980. Role of...16. Wheeler, A. P., G. Jesmok, and K . L. Brigham. 1990 Tu1mor icb in conscious sheep. response to methiacholine. J. Appi. necrosis factor’s effects

  3. Exploration of CH···π mediated stacking interactions in saccharide: aromatic residue complexes through conformational sampling.

    Science.gov (United States)

    Kumari, Manju; Sunoj, Raghavan B; Balaji, Petety V

    2012-11-01

    Saccharides interact with aromatic residues mostly through CH···π mediated stacking interactions. The energetics of such interactions depends upon the mutual position-orientations (POs) of the two moieties. The POs found in the crystal structures are only a subset of the various possible ways of interaction. Hence, potential energy surfaces of saccharide-aromatic residue complexes have been explored by mixed Monte Carlo multiple minimum/low mode sampling. The saccharides considered in this study are α/β-D-glucose, β-D-galactose, α-D-mannose, and α/β-L-fucose. p-Hydroxytoluene, toluene, and 3-methylindole were used as analogs of tyrosine, phenylalanine, and tryptophan, respectively. The saccharides interact from either above or below the π-cloud of an aromatic ring but not along the edges. The POs preferred by different saccharides, both in the preferred chair and skew-boat forms, for interacting with different aromatic amino acid residue analogs have been identified. Aromatic residues can interact with the same -CH group in many POs but not so with the -OH groups. Changes in the configurations of pyranose ring carbon atoms cause remarkable changes in stacking preferences. β-D-Galactose and β-L-fructose interact only through their b- and a-faces, respectively. Saccharides use a wide variety of apolar patches for stacking against aromatic residues and these have been analyzed in detail. As many as four -CH groups can simultaneously participate in CH···π interactions, especially with 3-methylindole owing to its larger surface area.

  4. C-H…pi interactions in proteins: prevalence, pattern of occurrence, residue propensities, location, and contribution to protein stability.

    Science.gov (United States)

    Kumar, Manjeet; Balaji, Petety V

    2014-02-01

    C-H…pi interactions are a class of non-covalent interactions found in different molecular systems including organic crystals, proteins and nucleic acids. High-resolution protein structures have been analyzed in the present study to delineate various aspects of C-H…pi interactions. Additionally, to determine the extent to which redundancy of a database biases the outcome, two datasets differing from each other in the level of redundancy have been analyzed. On average, only one out of six {with C-H(Aro) group} or eight {with C-H(Ali) group} residues in a protein participate as C-H group donors. Neither the frequency of occurrence in proteins nor the number of C-H groups present in it is correlated to the propensity of an amino acid to participate in C-H…pi interactions. Most of the residues that participate in C-H…pi interactions are solvent-shielded. Solvent shielded nature of most of the C-H…pi interactions and prevalence of intra- as well as inter-secondary structural element C-H…pi interactions suggest that the contribution of these interactions to the enthalpy of folded form will be significant. The separation in the primary structure between donor and acceptor residues is found to be correlated to secondary structure type. Other insights obtained from this study include the presence of networks of C-H…pi interactions spanning multiple secondary structural elements. To our knowledge this has not been reported so far. A substantial number of residues involved in C-H…pi interactions are found in catalytic and ligand binding sites suggesting their possible role in maintaining active site geometry. No significant differences of C-H…pi interactions in the two datasets are found for any of the parameters/features analyzed.

  5. The Benefits of Sensorimotor Knowledge: Body-Object Interaction Facilitates Semantic Processing

    Science.gov (United States)

    Siakaluk, Paul D.; Pexman, Penny M.; Sears, Christopher R.; Wilson, Kim; Locheed, Keri; Owen, William J.

    2008-01-01

    This article examined the effects of body-object interaction (BOI) on semantic processing. BOI measures perceptions of the ease with which a human body can physically interact with a word's referent. In Experiment 1, BOI effects were examined in 2 semantic categorization tasks (SCT) in which participants decided if words are easily imageable.…

  6. A DLM/FD method for fluid/flexible-body interactions

    NARCIS (Netherlands)

    Yu, Zhaosheng

    2005-01-01

    In this study, we extended the distributed-Lagrange-multiplier/fictitious-domain (DLM/FD) formulation of Glowinski et al. [Int. J. Multiphase Flow 25 (1999) 755] for the fluid/rigid-body interactions to deal with the fluid/flexible-body interactions by replacing Newton’s equations of motion for the

  7. Simulation of the four-body interaction in a nuclear magnetic resonance quantum information processor

    Institute of Scientific and Technical Information of China (English)

    LIU WenZhang; ZHANG JingFu; LONG GuiLu

    2009-01-01

    The four-body interaction plays an important role in many-body systems,and it can exhibit interesting phase transition behaviors.In this letter,we report the experimental demonstration of a four-body interaction in a four-qubit nuclear magnetic resonance quantum information processor.The strongly modulating pulse is used to implement spin selective excitation.The results show a good agreement between theory and experiment.

  8. Interactions Between Body and Social Awareness in Yoga.

    Science.gov (United States)

    Fiori, Francesca; Aglioti, Salvatore M; David, Nicole

    2017-03-01

    Bodily processes have been intimately linked to social-cognitive and affective functions, such as compassion and empathy. Yet, little is known about how awareness of bodily processes influences social awareness and vice versa, especially in nonobservational but experiential investigations. This study investigated the relationship between psychometrically reported body and social awareness (including altruism, empathy, perspective-taking, and compassion) in 90 yoga and yoga-/mediation-naive control participants. In modern postural yoga, advanced practitioners claim both increased compassion and inner focus. Multiple regression analyses were conducted to predict (1) the level of yoga practice from body awareness and social awareness skills in the yoga group and (2) body awareness from social skills in both groups. Body awareness and compassion were significant positive and independent predictors of yoga expertise. This finding supports practitioners' anecdotal claims but also implies that both functions tap into different aspects of yoga expertise. When body awareness was predicted, altruism emerged as a significant negative predictor in the yoga group (but not control group) as a function of yoga practice. These results might compellingly suggest that, despite high compassion, heightened bodily self-awareness might increase a self-centred perspective and limit altruistic acts in advanced yoga practitioners.

  9. Mood contagion of robot body language in human robot interaction

    NARCIS (Netherlands)

    Xu, J.; Broekens, J.; Hindriks, K.; Neerincx, M.A.

    2015-01-01

    The aim of our work is to design bodily mood expressions of humanoid robots for interactive settings that can be recognized by users and have (positive) effects on people who interact with the robots. To this end, we develop a parameterized behavior model for humanoid robots to express mood through

  10. Mood contagion of robot body language in human robot interaction

    NARCIS (Netherlands)

    Xu, J.; Broekens, D.J.; Hindriks, K.V.; Neerincx, M.A.

    2015-01-01

    The aim of our work is to design bodily mood expressions of humanoid robots for interactive settings that can be recognized by users and have (positive) effects on people who interact with the robots. To this end, we develop a parameterized behavior model for humanoid robots to express mood through

  11. INTERACTIVITY BETWEEN BODIES AND MILIEUS WITHIN TECHNO-AESTHETIC ART OBJECTS

    Directory of Open Access Journals (Sweden)

    Andreia Machado Oliveira

    Full Text Available Abstract Relations consist of processual interactivity between bodies and milieus which do not differentiate between the natural and the artificial, human and non-human. Our paper seeks to problematize the experience of the encounter with an artwork seen as a techno-aesthetic object constitutive of interactivity and addresses the idea of degrees of interactivity as produced with and within an artwork as an associated milieu. In this sense, we posit various degrees of interactivity in a relational experience: mixtures, attractions, embodiments and perceptions. Thus, interactive processes are driven by an ethics of the potential of bodies to act by what a body can do in its intensity, in the dynamics of degrees of interactivity in the experience. These ideas emerge from the philosophical writings of Baruch Spinoza, Gilbert Simondon and Gilles Deleuze and are applied to the field of art in order to allow an understanding of the relations between bodies and associated milieus.

  12. Tidal interactions - crude body model in dynamical investigations

    CERN Document Server

    Gabryszewski, Ryszard

    2011-01-01

    The paper presents results of investigations of small bodies dynamics in a vicinity of giant planets. We used the most simple body model: gravitationally bounded, rotating contact binary affected by the tidal force acting from a planet. Spin variations of such binaries were extensively studied during planetary close encounters. Two main types of dynamical behaviour were observed: (i) huge but interim fluctuations of the angular velocity and (ii) permanent changes of a rotation during a close approach. The first type is observed mainly for fast rotators, while the second one was encountered in a population of slowly spinning objects with periods longer than 12 hours. Conclusions on usability of such crude physical body models in dynamical investigations and a comparison to previous results were attached. The results allow us to formulate a thesis explaining the phenomenon of creation of the extremely slow rotators and an observational excess of such type of objects.

  13. Brain, mind, and body: interactions with art in renaissance Italy.

    Science.gov (United States)

    Ginn, Sheryl R; Lorusso, Lorenzo

    2008-01-01

    The Renaissance saw the first systematic anatomical and physiological studies of the brain and human body because scientists, for the first time in centuries, were allowed to dissect human bodies for study. Renaissance artists were frequently found at dissections and their attention to detail can be observed in their products. Scientists themselves were increasingly artistic, and they created astonishing anatomical models and illustrations that can still be studied. The cross-fertilization of art and science in the Renaissance resulted in more scientific analyses of neuroanatomy as well as more creative ways in which such analyses could be depicted. Both art and science benefited from the reciprocal ways in which the two influenced each other even as they provided new ways of explaining the mysteries of the human body and mind.

  14. Chaos and Integrability in Ideal Body-Fluid Interactions

    DEFF Research Database (Denmark)

    Pedersen, Johan Rønby

    2011-01-01

    of additional conserved quantities is discussed. A survey of the integrable motions of the system is given. Integrability is demonstrated explicitly by exploiting conservation laws to devise reduced phase space coordinates in which the orbits of the system are the contours of an energy landscape. The existence...... of relative equilibria, their stability, and the qualitatively dierent kinds of motion is studied analytically and numerically. We then perform small parametric perturbations destroying the symmetry or conservation law that makes the system integrable. The emergence of chaos in the system is diagnosed......, no assumptions are made on the body shape or on its internal mass distribution. There may also be an arbitrary and constant circulation around the body. The governing equations reduce to an autonomous set of coupled ODEs for the vortex positions and the body position and orientation. The form of these equations...

  15. the application of body language in interactive english teaching

    Institute of Scientific and Technical Information of China (English)

    党风琴

    2011-01-01

    with the limitation of students' vocabulary,teachers have to simplify their teaching language with the help of facial expressions and body movements.so body language has been widely used in communication in and out of class.it can be vocal language' s vital complement by intensifying the language information retention and leaving the students deeper impression.it helps the students to improve listening,speaking,reading and writing level and help the teachers achieve a higher teaching goal and further mutual understanding.

  16. Beam, vacuum and walls, a 3-body interaction; Faisceau et vide, un melodrame a trois

    Energy Technology Data Exchange (ETDEWEB)

    Arianer, J

    2002-11-01

    The interactions between beams of accelerated particles, residual gas and walls involve complex physical processes. In most cases these interactions affect the quality of the vacuum and the value of the pressure. This course reviews all these interactions in a pedagogical and practical way that may be useful for any user of devices involving beams of particles. This document is made up of 6 chapters: 1) basic notions (Maxwell-Boltzmann distribution, kinematics of charged particles, collisions, excitation and ionization), 2) properties of beams (emittance, local effects, and synchrotron radiation), 3) interactions between residual gas and particle beams (Bremsstrahlung radiation, energy loss due to ionization, charge shift of ion beams, photo-absorption and photo-ionization, and slowing-down in a plasma), 4) surface properties (crystal structure, and interaction between surface and the residual gas), 5) interaction between the beam and walls (reflection and diffraction of electrons, secondary emission of electrons, desorption induced by electron and ion impacts, photon production, ion-wall interaction, sputtering, ion penetration, surface ionization and thermal-ionization), and 6) radiation-wall interaction (diffusion, damping, photo-electric effect, desorption induced by photons, pair production and laser-surface interaction). (A.C.)

  17. Hubbard model for ultracold bosonic atoms interacting via zero-point-energy-induced three-body interactions

    Science.gov (United States)

    Paul, Saurabh; Johnson, P. R.; Tiesinga, Eite

    2016-04-01

    We show that, for ultracold neutral bosonic atoms held in a three-dimensional periodic potential or optical lattice, a Hubbard model with dominant, attractive three-body interactions can be generated. In fact, we derive that the effect of pairwise interactions can be made small or zero starting from the realization that collisions occur at the zero-point energy of an optical lattice site and the strength of the interactions is energy dependent from effective-range contributions. We determine the strength of the two- and three-body interactions for scattering from van der Waals potentials and near Fano-Feshbach resonances. For van der Waals potentials, which for example describe scattering of alkaline-earth atoms, we find that the pairwise interaction can only be turned off for species with a small negative scattering length, leaving the 88Sr isotope a possible candidate. Interestingly, for collisional magnetic Feshbach resonances this restriction does not apply and there often exist magnetic fields where the two-body interaction is small. We illustrate this result for several known narrow resonances between alkali-metal atoms as well as chromium atoms. Finally, we compare the size of the three-body interaction with hopping rates and describe limits due to three-body recombination.

  18. Organization of circadian functions: interaction with the body.

    NARCIS (Netherlands)

    Buijs, R.M.; Scheer, F.A.; Kreier, F.; Yi, C.; Bos, N.; Goncharuk, V.D.; Kalsbeek, A

    2006-01-01

    The hypothalamus integrates information from the brain and the body; this activity is essential for survival of the individual (adaptation to the environment) and the species (reproduction). As a result, countless functions are regulated by neuroendocrine and autonomic hypothalamic processes in conc

  19. Many Body Diffusion and Interacting Electrons in a Harmonic Confinement

    Science.gov (United States)

    Luczak, F.; Brosens, F.; Devreese, J. T.; Lemmens, L. F.

    2001-06-01

    We present numerically exact energy estimates for two-dimensional electrons in a parabolic confinement. By application of an extension of the recently introduced many-body diffusion algorithm, the ground-state energies are simulated very efficiently. The new algorithm relies on partial antisymmetrization under permutation of particle coordinates. A comparison is made with earlier theoretical results for that system.

  20. Molecular Interactions with Many-Body Perturbation Theory.

    Science.gov (United States)

    1981-09-11

    Medcine , Ne. York, York, June 4, 1979. R. J. Bartlett, "Many-Body Perturbation Thery", Aarhus University, Aarhus, Denmark, June 18, 1979. R. J. Bartlett...editor can be accepted for speedy publication. Permission is granted to authors of scientific articles and books to quote from this journal provided

  1. Organization of circadian functions: interaction with the body.

    NARCIS (Netherlands)

    Buijs, R.M.; Scheer, F.A.; Kreier, F.; Yi, C.; Bos, N.; Goncharuk, V.D.; Kalsbeek, A

    2006-01-01

    The hypothalamus integrates information from the brain and the body; this activity is essential for survival of the individual (adaptation to the environment) and the species (reproduction). As a result, countless functions are regulated by neuroendocrine and autonomic hypothalamic processes in

  2. Body sway during quiet standing: is it the residual chattering of an intermittent stabilization process?

    Science.gov (United States)

    Bottaro, Alessandra; Casadio, Maura; Morasso, Pietro G; Sanguineti, Vittorio

    2005-08-01

    This paper reviews different approaches for explaining body sway while quiet standing that directly address the instability of the human inverted pendulum. We argue that both stiffness control [Winter, D. A., Patla, A. E., Riedtyk, S., & Ishac, M. (2001). Ankle muscle stiffness in the control of balance during quiet standing. Journal of Neurophysiology, 85, 2630-2633] and continuous feedback control by means of a PID (Proportional, Integral, Derivative) mechanism [Peterka, R. J. (2000). Postural control model interpretation of stabilogram diffusion analysis. Biological Cybernetics, 83, 335-343.] can guarantee asymptotic stability of controlled posture at the expense of unrealistic assumptions: the level of intrinsic muscle stiffness in the former case, and the level of background noise in the latter, which also determines an unrealistic level of jerkiness in the sway. We show that the decomposition of the control action into a slow and a fast component (rambling and trembling, respectively, as proposed by [Zatsiorsky, V. M., & Duarte, M. (1999). Instant equilibrium point and its migration in standing tasks: Rambling and trembling components of the stabilogram. Motor Control, 4, 185-200; Zatsiorsky, V. M., & Duarte, M. (2000). Rambling and trembling in quiet standing. Motor Control, 4, 185-200.]) is useful but must be modified in order to take into account that rambling is not a stable equilibrium trajectory. We address the possibility of a form of stability weaker than asymptotic stability in light of the intermittent stabilization mechanism outlined by [Loram, I. D., & Lakie, M. (2002a). Human balancing of an inverted pendulum: position control by small, ballistic-like, throw and catch movements. Journal of Physiology, 540, 1111-1124.], and propose an indicator of intermittent stabilization that is related to the phase portrait of the human inverted pendulum. This indicator provides a further argument against the plausibility of PID-like control mechanisms

  3. Association of residual feed intake with growth and slaughtering performance, blood metabolism, and body composition in growing lambs.

    Science.gov (United States)

    Zhang, Xiaoxue; Wang, Weimin; Mo, Futao; La, Yongfu; Li, Chong; Li, Fadi

    2017-10-04

    The aim of this study was to determine the association of residual feed intake (RFI) with growth performance, blood metabolic parameters, and body composition factors in growing lambs. Individual body weight (BW) and dry matter intake (DMI) were determined in 137 male Hu lambs that were given a pellet feed four times a day for 50 d. RFI did not show a correlation with metabolic BW (MBW) or average daily gain (ADG), but it showed a positive correlation with DMI and feed conversation ratio (FCR). Organ weight and intestine length had a large influence on RFI in lambs. The low-RFI lambs have smaller rumen and longer duodenum indicating the less feed intake and more sufficient absorption rate of low-RFI lambs. The smaller organs like liver, lung and kidney in low-RFI lambs may be related to lower energy consumption and slower metabolic rate. The observed bigger testis was in low-RFI lambs was another cause of the improved feed efficiency. Finally, the plasma concentrations of thyroxine (T4) and adrenocorticotropic hormone (ACTH) were lower in the ELow-RFI group than in the EHigh-RFI group. This study provides new insight into the biological processes underlying variations in feed efficiency in growing lambs.

  4. A cation-pi interaction in the binding site of the glycine receptor is mediated by a phenylalanine residue

    DEFF Research Database (Denmark)

    Pless, Stephan Alexander; Millen, Kat S; Hanek, Ariele P;

    2008-01-01

    Cys-loop receptor binding sites characteristically contain many aromatic amino acids. In nicotinic ACh and 5-HT3 receptors, a Trp residue forms a cation-pi interaction with the agonist, whereas in GABA(A) receptors, a Tyr performs this role. The glycine receptor binding site, however, contains pr...

  5. Wettability and interfacial interactions in bioceramic-body-liquid systems.

    Science.gov (United States)

    Agathopoulos, S; Nikolopoulos, P

    1995-04-01

    Wetting experiments, by the sessile drop technique, were carried out at 37 degrees C in air to determine the surface and interfacial interactions that take place in various solid bioceramics based on Al2O3, ZrO2(YPZ), SiO2, and TiO2 in contact with water, Ringer solution, artificial synovial fluid, calf serum, human plasma, and whole blood (+ EDTA). The surface energy of the liquids was measured by the ring method. The calculated values of the energy of interaction (work of adhesion) reveal that intermolecular forces act across the solid-liquid interfaces. The contribution of the dispersion and polar interactions to the surface energy of the polar liquids and the pure or mixed oxides was determined assuming that in the system of Mn-steel-liquids only dispersion forces act at the interface. It was found that the contribution of the polar interactions to the energy of interaction at the solid-liquid interface increases with the glassy phase content of the oxide that causes reduction of the measured contact angle.

  6. Application of information theory to a three-body coarse-grained representation of proteins in the PDB: insights into the structural and evolutionary roles of residues in protein structure.

    Science.gov (United States)

    Thompson, Jared J; Tabatabaei Ghomi, Hamed; Lill, Markus A

    2014-12-01

    Knowledge-based methods for analyzing protein structures, such as statistical potentials, primarily consider the distances between pairs of bodies (atoms or groups of atoms). Considerations of several bodies simultaneously are generally used to characterize bonded structural elements or those in close contact with each other, but historically do not consider atoms that are not in direct contact with each other. In this report, we introduce an information-theoretic method for detecting and quantifying distance-dependent through-space multibody relationships between the sidechains of three residues. The technique introduced is capable of producing convergent and consistent results when applied to a sufficiently large database of randomly chosen, experimentally solved protein structures. The results of our study can be shown to reproduce established physico-chemical properties of residues as well as more recently discovered properties and interactions. These results offer insight into the numerous roles that residues play in protein structure, as well as relationships between residue function, protein structure, and evolution. The techniques and insights presented in this work should be useful in the future development of novel knowledge-based tools for the evaluation of protein structure. © 2014 Wiley Periodicals, Inc.

  7. Scars of Invariant Manifolds in Interacting Few-Body Systems

    CERN Document Server

    Papenbrock, T; Weidenmüller, H A

    1997-01-01

    We present a novel extension of the concept of scars for the wave functions of classically chaotic few--body systems of identical particles with rotation and permutation symmetry. Generically there exist manifolds in classical phase space which are invariant under the action of a common subgroup of these two symmetries. Such manifolds are associated with highly symmetric configurations and, if sufficiently stable, support quantum resonances. Although not directly associated to individual periodic orbits, the resonances nevertheless cause scars which signify collective motion on the quantum level and which should be experimentally observable.

  8. Many-body Systems Interacting via a Two-body Random Ensemble; 1, Angular Momentum distribution in the ground states

    CERN Document Server

    Zhao, Y M; Yoshinaga, N

    2002-01-01

    In this paper, we discuss the angular momentum distribution in the ground states of many-body systems interacting via a two-body random ensemble. Beginning with a few simple examples, a simple approach to predict P(I)'s, angular momenta I ground state (g.s.) probabilities, of a few solvable cases, such as fermions in a small single-j shell and d boson systems, is given. This method is generalized to predict P(I)'s of more complicated cases, such as even or odd number of fermions in a large single-j shell or a many-j shell, d-boson, sd-boson or sdg-boson systems, etc. By this method we are able to tell which interactions are essential to produce a sizable P(I) in a many-body system. The g.s. probability of maximum angular momentum $I_{max}$ is discussed. An argument on the microscopic foundation of our approach, and certain matrix elements which are useful to understand the observed regularities, are also given or addressed in detail. The low seniority chain of 0 g.s. by using the same set of two-body interact...

  9. Vortex/Body Interaction and Sound Generation in Low-Speed Flow

    Science.gov (United States)

    Kao, Hsiao C.

    1998-01-01

    The problem of sound generation by vortices interacting with an arbitrary body in a low-speed flow has been investigated by the method of matched asymptotic expansions. For the purpose of this report, it is convenient to divide the problem into three parts. In the first part the mechanism of the vortex/body interaction, which is essentially the inner solution in the inner region, is examined. The trajectories for a system of vortices rotating about their centroid are found to undergo enormous changes after interaction; from this, some interesting properties emerged. In the second part, the problem is formulated, the outer solution is found, matching is implemented, and solutions for acoustic pressure are obtained. In the third part, Fourier integrals are evaluated and predicated results presented. An examination of these results reveals the following: (a) the background noise can be either augmented or attenuated by a body after interaction, (b) sound generated by vortex/body interaction obeys a scaling factor, (C) sound intensity can be reduced substantially by positioning the vortex system in the "favorable" side of the body instead of the "unfavorable" side, and (d) acoustic radiation from vortex/bluff-body interaction is less than that from vortex/airfoil interaction under most circumstances.

  10. Hamiltonian Dynamics of Several Rigid Bodies Interacting with Point Vortices

    Science.gov (United States)

    Weißmann, Steffen

    2014-04-01

    We derive the dynamics of several rigid bodies of arbitrary shape in a two-dimensional inviscid and incompressible fluid, whose vorticity is given by point vortices. We adopt the idea of Vankerschaver et al. (J. Geom. Mech. 1(2): 223-226, 2009) to derive the Hamiltonian formulation via symplectic reduction from a canonical Hamiltonian system. The reduced system is described by a noncanonical symplectic form, which has previously been derived for a single circular disk using heavy differential-geometric machinery in an infinite-dimensional setting. In contrast, our derivation makes use of the fact that the dynamics of the fluid, and thus the point vortex dynamics, is determined from first principles. Using this knowledge we can directly determine the dynamics on the reduced, finite-dimensional phase space, using only classical mechanics. Furthermore, our approach easily handles several bodies of arbitrary shape. From the Hamiltonian description we derive a Lagrangian formulation, which enables the system for variational time integrators. We briefly describe how to implement such a numerical scheme and simulate different configurations for validation.

  11. Interaction between soil mineralogy and the application of crop residues on aggregate stability and hydraulic conductivity of the soil

    Science.gov (United States)

    Lado, M.; Kiptoon, R.; Bar-Tal, A.; Wakindiki, I. I. C.; Ben-Hur, M.

    2012-04-01

    One of the main goals of modern agriculture is to achieve sustainability by maintaining crop productivity while avoiding soil degradation. Intensive cultivation could lead to a reduction in soil organic matter that could affect the structure stability and hydraulic conductivity of the soil. Moreover, crops extract nutrients from the soil that are taken away from the field when harvested, and as a consequence, the addition of fertilizers to the soil is necessary to maintain crop productivity. One way to deal with these problems is to incorporate crop residues into the soil after harvest. Crop residues are a source of organic matter that could improve soil physical properties, such as aggregate stability and soil hydraulic conductivity. However, this effect could vary according to other soil properties, such as clay content, clay mineralogy, and the presence of other cementing materials in the soil (mainly carbonates and aluminum and iron oxides). In the present work, the interaction between the addition of chickpea crop residues to the soil and clay mineralogy on aggregate stability and saturated hydraulic conductivity were studied. Chickpea plant residues were added at a rate of 0.5% (w/w) to smectitic, kaolinitic, illitic and non-phyllosilicate soils from different regions. The soils without (control) and with chickpea residues were incubated for 0, 3, 7 and 30 days, and the saturated hydraulic conductivity of the soils was measured in columns after each incubation time. The response of hydraulic conductivity to the addition of residues and incubation time was different in the soils with various mineralogies, although in general, the addition of chickpea residues increased the saturated hydraulic conductivity as compared with the control soils. This positive effect of crop residues on hydraulic conductivity was mainly a result of improved aggregate stability and resistance to slaking during wetting.

  12. Reducible chiral four-body interactions in nuclear matter

    CERN Document Server

    Kaiser, N

    2015-01-01

    The method of unitary transformations generates five classes of leading-order reducible chiral four-nucleon interactions which involve pion-exchanges and a spin-spin contact-term. Their first-order contributions to the energy per particle of isospin-symmetric nuclear matter and pure neutron matter are evaluated in detail. For most of the closed four-loop diagrams the occurring integrals over four Fermi-spheres can be reduced to easily manageable one- or two-parameter integrals. One observes substantial cancelations among the different contributions arising from 2-ring and 1-ring diagrams. Altogether, the net attraction generated by the chiral four-nucleon interaction does not exceed values of $-1.3$\\,MeV for densities $\\rho<2\\rho_0$.

  13. Reducible chiral four-body interactions in nuclear matter

    Energy Technology Data Exchange (ETDEWEB)

    Kaiser, N.; Milkus, R. [Technische Universitaet Muenchen, Physik-Department T39, Garching (Germany)

    2016-01-15

    The method of unitary transformations generates five classes of leading-order reducible chiral four-nucleon interactions which involve pion exchanges and a spin-spin contact term. Their first-order contributions to the energy per particle of isospin-symmetric nuclear matter and pure neutron matter are evaluated in detail. For most of the closed four-loop diagrams the occurring integrals over four Fermi spheres can be reduced to easily manageable one- or two-parameter integrals. One finds substantial compensations among the different contributions arising from 2-ring and 1-ring diagrams. Altogether, the net attraction generated by the chiral four-nucleon interaction does not exceed values of -1.3 MeV for densities ρ < 2ρ{sub 0}. (orig.)

  14. Effective three-body interactions of neutral bosons in optical lattices

    Energy Technology Data Exchange (ETDEWEB)

    Johnson, P R [Department of Physics, American University, Washington, DC 20016 (United States); Tiesinga, E; Porto, J V; Williams, C J [Joint Quantum Institute, National Institute of Standards and Technology and University of Maryland, Gaithersburg, MD 20899 (United States)], E-mail: pjohnson@american.edu

    2009-09-15

    We show that there are effective three- and higher-body interactions generated by the two-body collisions of atoms confined in the lowest vibrational states of a three-dimensional (3D) optical lattice. The collapse and revival dynamics of approximate coherent states loaded into a lattice are a particularly sensitive probe of these higher-body interactions; the visibility of interference fringes depend on both two-, three- and higher-body energy scales, and these produce an initial dephasing that can help explain the surprisingly rapid decay of revivals seen in experiments. If inhomogeneities in the lattice system are sufficiently reduced, longer timescale partial and nearly full revivals will be visible. Using Feshbach resonances or control of the lattice potential it is possible to tune the effective higher-body interactions and simulate effective field theories in optical lattices.

  15. Continuous Choreographies as Limiting Solutions of N-body Type Problems with Weak Interaction

    Science.gov (United States)

    Castaneira, Reynaldo; Padilla, Pablo; Sánchez-Morgado, Héctor

    2016-10-01

    We consider the limit Nto +∞ of N-body type problems with weak interaction, equal masses and -σ-homogeneous potential, 0absolute minimizer of the action functional among zero mean (travelling wave) loops of class H^1.

  16. Ambulatory Sensing of the Dynamic interaction between the human body and the environment

    NARCIS (Netherlands)

    Veltink, Petrus H.; Schepers, H. Martin; Cooper, R.A.

    2010-01-01

    This paper presents a method to estimate power transfer between the human body and the environment during short interactions and relatively arbitrary movements with net displacement and varying loads (mass and spring), and appeared to be accurate within 4%.

  17. Effects of three-body interaction on collective excitation and stability of Bose-Einstein condensate

    Institute of Scientific and Technical Information of China (English)

    Peng Ping; Li Guan-Qiang

    2009-01-01

    This paper investigates the collective excitation and stability of low-dimensional Bose-Einstein condensates with two-and three-body interactions by the variational analysis of the time-dependent Gross-Pitaevskii-Ginzburg equation.The spectrum of the low-energy excitation and the effective potential for the width of the condensate are obtained.The results show that:(i) the repulsive two-body interaction among atoms makes the frequency red-shifted for the internal excitation and the repulsive or attractive three-body interaction always makes it blue-shifted; (ii) the region for the existence of the stable bound states is obtained by identifying the critical value of the two-and three-body interactions.

  18. Functional interactions between residues in the S1, S4, and S5 domains of Kv2.1.

    Science.gov (United States)

    Bocksteins, E; Ottschytsch, N; Timmermans, J-P; Labro, A J; Snyders, D J

    2011-06-01

    The voltage-gated potassium channel subunit Kv2.1 forms heterotetrameric channels with the silent subunit Kv6.4. Chimeric Kv2.1 channels containing a single transmembrane segment from Kv6.4 have been shown to be functional. However, a Kv2.1 chimera containing both S1 and S5 from Kv6.4 was not functional. Back mutation of individual residues in this chimera (to the Kv2.1 counterpart) identified four positions that were critical for functionality: A200V and A203T in S1, and T343M and P347S in S5. To test for possible interactions in Kv2.1, we used substitutions with charged residues and tryptophan for the outermost pair 203/347. Combinations of substitutions with opposite charges at both T203 and S347 were tolerated but resulted in channels with altered gating kinetics, as did the combination of negatively charged aspartate substitutions. Double mutant cycle analysis with these mutants indicated that both residues are energetically coupled. In contrast, replacing both residues with a positively charged lysine together (T203K + S347K) was not tolerated and resulted in a folding or trafficking deficiency. The nonfunctionality of the T203K + S347K mutation could be restored by introducing the R300E mutation in the S4 segment of the voltage sensor. These results indicate that these specific S1, S4, and S5 residues are in close proximity and interact with each other in the functional channel, but are also important determinants for Kv2.1 channel maturation. These data support the view of an anchoring interaction between S1 and S5, but indicate that this interaction surface is more extensive than previously proposed.

  19. Calculation of local pressure tensors in systems with many-body interactions.

    Science.gov (United States)

    Heinz, Hendrik; Paul, Wolfgang; Binder, Kurt

    2005-12-01

    Local pressures are important in the calculation of interface tensions and in analyzing micromechanical behavior. The calculation of local pressures in computer simulations has been limited to systems with pairwise interactions between the particles, which is not sufficient for chemically detailed systems with many-body potentials such as angles and torsions. We introduce a method to calculate local pressures in systems with n-body interactions (n=2,3,4,) based on a micromechanical definition of the pressure tensor. The local pressure consists of a kinetic contribution from the linear momentum of the particles and an internal contribution from dissected many-body interactions by infinitesimal areas. To define dissection by a small area, respective n-body interactions are divided into two geometric centers, effectively reducing them to two-body interactions. Consistency with hydrodynamics-derived formulas for systems with two-body interactions [J. H. Irving and J. G. Kirkwood, J. Chem. Phys. 18, 817 (1950)], for average cross-sectional pressures [B. D. Todd, D. J. Evans, and P. J. Daivis, Phys. Rev. E 52, 1627 (1995)], and for volume averaged pressures (virial formula) is shown. As a simple numerical example, we discuss liquid propane in a cubic box. Local, cross-sectional, and volume-averaged pressures as well as relative contributions from two-body and three-body forces are analyzed with the proposed method, showing full numerical equivalence with the existing approaches. The method allows computing local pressures in the presence of many-body interactions in atomistic simulations of complex materials and biological systems.

  20. Wearable wireless tactile display for virtual interactions with soft bodies

    Directory of Open Access Journals (Sweden)

    Gabriele eFrediani

    2014-09-01

    Full Text Available We describe here a wearable, wireless, compact and lightweight tactile display, able to mechanically stimulate the fingertip of users, so as to simulate contact with soft bodies in virtual environments. The device was based on dielectric elastomer actuators, as high-performance electromechanically active polymers. The actuator was arranged at the user’s fingertip, integrated within a plastic case, which also hosted a compact high-voltage circuitry. A custom-made wireless control unit was arranged on the forearm and connected to the display via low-voltage leads. We present the structure of the device and a characterization of it, in terms of electromechanical response and stress relaxation. Furthermore, we present results of a psychophysical test aimed at assessing the ability of the system to generate different levels of force that can be perceived by users.

  1. Mechanisms underlying rhythmic locomotion: body-fluid interaction in undulatory swimming.

    Science.gov (United States)

    Chen, J; Friesen, W O; Iwasaki, T

    2011-02-15

    Swimming of fish and other animals results from interactions of rhythmic body movements with the surrounding fluid. This paper develops a model for the body-fluid interaction in undulatory swimming of leeches, where the body is represented by a chain of rigid links and the hydrodynamic force model is based on resistive and reactive force theories. The drag and added-mass coefficients for the fluid force model were determined from experimental data of kinematic variables during intact swimming, measured through video recording and image processing. Parameter optimizations to minimize errors in simulated model behaviors revealed that the resistive force is dominant, and a simple static function of relative velocity captures the essence of hydrodynamic forces acting on the body. The model thus developed, together with the experimental kinematic data, allows us to investigate temporal and spatial (along the body) distributions of muscle actuation, body curvature, hydrodynamic thrust and drag, muscle power supply and energy dissipation into the fluid. We have found that: (1) thrust is generated continuously along the body with increasing magnitude toward the tail, (2) drag is nearly constant along the body, (3) muscle actuation waves travel two or three times faster than the body curvature waves and (4) energy for swimming is supplied primarily by the mid-body muscles, transmitted through the body in the form of elastic energy, and dissipated into the water near the tail.

  2. Contact point generation for convex polytopes in interactive rigid body dynamics

    DEFF Research Database (Denmark)

    Silcowitz-Hansen, Morten; Abel, Sarah Maria Niebe; Erleben, Kenny

    When computing contact forces in rigid body dynamics systems, most state-of-the-art solutions use iterative methods such as the projected Gauss–Seidel (PGS) method. Methods such as the PGS method are preferred for their robustness. However, the time-critical nature of interactive applications...... for convex polytopes. A novel contact point generation method is presented, which is based on growth distances and Gauss maps. We demonstrate improvements when using our method in the context of interactive rigid body simulation...

  3. Ionic interaction of positive amino acid residues of fungal hydrophobin RolA with acidic amino acid residues of cutinase CutL1.

    Science.gov (United States)

    Takahashi, Toru; Tanaka, Takumi; Tsushima, Yusei; Muragaki, Kimihide; Uehara, Kenji; Takeuchi, Shunsuke; Maeda, Hiroshi; Yamagata, Youhei; Nakayama, Mayumi; Yoshimi, Akira; Abe, Keietsu

    2015-04-01

    Hydrophobins are amphipathic proteins secreted by filamentous fungi. When the industrial fungus Aspergillus oryzae is grown in a liquid medium containing the polyester polybutylene succinate co-adipate (PBSA), it produces RolA, a hydrophobin, and CutL1, a PBSA-degrading cutinase. Secreted RolA attaches to the surface of the PBSA particles and recruits CutL1, which then condenses on the particles and stimulates the hydrolysis of PBSA. Here, we identified amino acid residues that are required for the RolA-CutL1 interaction by using site-directed mutagenesis. We quantitatively analyzed kinetic profiles of the interactions between RolA variants and CutL1 variants by using a quartz crystal microbalance (QCM). The QCM analyses revealed that Asp142, Asp171 and Glu31, located on the hydrophilic molecular surface of CutL1, and His32 and Lys34, located in the N-terminus of RolA, play crucial roles in the RolA-CutL1 interaction via ionic interactions. RolA immobilized on a QCM electrode strongly interacted with CutL1 (K(D)  = 6.5 nM); however, RolA with CutL1 variants, or RolA variants with CutL1, showed markedly larger KD values, particularly in the interaction between the double variant RolA-H32S/K34S and the triple variant CutL1-E31S/D142S/D171S (K(D)  = 78.0 nM). We discuss a molecular prototype model of hydrophobin-based enzyme recruitment at the solid-water interface.

  4. Projected Gauss-Seidel subspace minimization method for interactive rigid body dynamics

    DEFF Research Database (Denmark)

    Silcowitz-Hansen, Morten; Abel, Sarah Maria Niebe; Erleben, Kenny

    2010-01-01

    In interactive physical simulation, contact forces are applied to prevent rigid bodies from penetrating and to control slipping between bodies. Accurate contact force determination is a computationally hard problem. Thus, in practice one trades accuracy for performance. This results in visual...

  5. Fading characterization for context aware body area networks (CABAN) in interactive smart environments

    NARCIS (Netherlands)

    Heaney, S.F.; Scanlon, W.G.; Garcia-Palacios, E.; Cotton, S.L.

    2010-01-01

    Body Area Networks are unique in that the large-scale mobility of users allows the network itself to travel across a diverse range of operating domains. This presents the possibility of creating interactive smart environments where Context Aware Body Area Networks can sense and co-operate with nearb

  6. Aging dynamics in interacting many-body systems

    CERN Document Server

    Sanders, Lloyd P; Lizana, Ludvig; Fogelmark, Karl; Metzler, Ralf; Ambjörnsson, Tobias

    2013-01-01

    Low-dimensional, complex systems are often characterized by logarithmically slow dynamics. We study the generic motion of a labeled particle in an ensemble of identical diffusing particles with hardcore interactions in a strongly disordered, one-dimensional environment. Each particle in this single file is trapped for a random waiting time $\\tau$ with power law distribution $\\psi(\\tau)\\simeq\\tau^{-1- \\alpha}$, such that the $\\tau$ values are independent, local quantities for all particles. From scaling arguments and simulations, we find that for the scale-free waiting time case $02$ we recover Harris law $\\simeq t^{1/2}$.

  7. Interactive effects of rice residue and water stress on growth and metabolism of wheat seedlings

    Directory of Open Access Journals (Sweden)

    Nimisha Amist

    2014-08-01

    Full Text Available In the present study effects of rice residue with and without water stress were studied on Triticum aestivum L. cv. Shatabadi. The mixture of residue and garden soil in 1:1 ratio was considered as 50% (R1 and only decomposed residue as 100% (R2. Garden soil was taken as control. Twenty five seeds were sown in each experimental trays filled with soil mixture according to the treatments. Trays were arranged in two groups. After 15 days one set was subjected to water stress (WS by withholding water supply for 3 days. Morphological and biochemical parameters of 18 days old seedlings were recorded. Seedling height decreased in all treatments. A gradual decrease in relative water content, pigment and protein contents of wheat seedlings were observed. Sugar and proline contents increased in treatments. An increase in malondialdehyde (MDA content and antioxidative enzyme activities was recorded. Elevation in catalase activity was observed in all treatments except in plants with water deficit. Ascorbate peroxidase (APX and guaiacol peroxidase (GPX activities increased when residue mixed with soil but decreased in seedlings under the combined influence of the residue and water stress. Higher amount of MDA and lower activities of APX and GPX reflected the oxidative damage in seedlings under combined treatments. Rice residue inhibited growth of wheat seedlings. Water stress intensified the effects of residue.

  8. Dependence of the frequency spectrum of small amplitude vibrations superimposed on finite deformations of a nonlinear, cylindrical elastic body on residual stress

    KAUST Repository

    Gorb, Yuliya

    2010-11-01

    We model and analyze the response of nonlinear, residually stressed elastic bodies subjected to small amplitude vibrations superimposed upon large deformations. The problem derives from modeling the use of intravascular ultrasound (IVUS) imaging to interrogate atherosclerotic plaques in vivo in large arteries. The goal of this investigation is twofold: (i) introduce a modeling framework for residual stress that unlike traditional Fung type classical opening angle models may be used for a diseased artery, and (ii) investigate the sensitivity of the spectra of small amplitude high frequency time harmonic vibrations superimposed on a large deformation to the details of the residual stress stored in arteries through a numerical simulation using physiologic parameter values under both low and high blood pressure loadings. The modeling framework also points the way towards an inverse problem using IVUS techniques to estimate residual stress in healthy and diseased arteries. © 2010 Elsevier Ltd. All rights reserved.

  9. Robot Acting on Moving Bodies (RAMBO): Interaction with tumbling objects

    Science.gov (United States)

    Davis, Larry S.; Dementhon, Daniel; Bestul, Thor; Ziavras, Sotirios; Srinivasan, H. V.; Siddalingaiah, Madhu; Harwood, David

    1989-01-01

    Interaction with tumbling objects will become more common as human activities in space expand. Attempting to interact with a large complex object translating and rotating in space, a human operator using only his visual and mental capacities may not be able to estimate the object motion, plan actions or control those actions. A robot system (RAMBO) equipped with a camera, which, given a sequence of simple tasks, can perform these tasks on a tumbling object, is being developed. RAMBO is given a complete geometric model of the object. A low level vision module extracts and groups characteristic features in images of the object. The positions of the object are determined in a sequence of images, and a motion estimate of the object is obtained. This motion estimate is used to plan trajectories of the robot tool to relative locations rearby the object sufficient for achieving the tasks. More specifically, low level vision uses parallel algorithms for image enhancement by symmetric nearest neighbor filtering, edge detection by local gradient operators, and corner extraction by sector filtering. The object pose estimation is a Hough transform method accumulating position hypotheses obtained by matching triples of image features (corners) to triples of model features. To maximize computing speed, the estimate of the position in space of a triple of features is obtained by decomposing its perspective view into a product of rotations and a scaled orthographic projection. This allows use of 2-D lookup tables at each stage of the decomposition. The position hypotheses for each possible match of model feature triples and image feature triples are calculated in parallel. Trajectory planning combines heuristic and dynamic programming techniques. Then trajectories are created using dynamic interpolations between initial and goal trajectories. All the parallel algorithms run on a Connection Machine CM-2 with 16K processors.

  10. A Statistical Analysis of Protein-Protein Interaction with Knowledge-Based Potential at Residue Level

    Institute of Scientific and Technical Information of China (English)

    林巍; 孙飞; 饶子和

    2003-01-01

    Protein-protein recognition is an important step in biological processes, which still largely remains elusive.The inter-residue contact potential, CPij, describes the propensity of contact between two types of residue.In this study, several different CPij variants were examined with the objective of discriminating the binding potential of surface pairs.Using solvent mediated inter-molecule contact potential (SM-IMCPij), an evaluation model was deduced and tested.Using the evaluation model it was found that the SM-IMCPij gives a better performance than either residue mediated IMCPij(RM-IMCPij) or folding-residue contact potential (FCPij).The results suggest that the evaluation model provides a fast, effective, and discriminative method for the evaluation of proposed binding interfaces.

  11. On the interaction of sublimating gas with cometary bodies

    Science.gov (United States)

    Steckloff, Jordan K.

    Sublimation of volatiles is a defining process of comet nuclei, and profoundly affects their dynamics, structure, and appearance. Central to understanding the processes by which comets formed and subsequently evolved is a careful computation of this sublimation pressure as a function of heliocentric distance. Unlike previous efforts, I develop a thermodynamic method to numerically compute the sublimation pressure of any species from limited knowledge of its physical properties. I then describe a novel cometary disruption mechanism in which this sublimation pressure induces differential stresses within the body of the nucleus that exceed its material strength, resulting in structural failure and breakup of the nucleus. I show that this mechanism is consistent with the behavior of Comet ISON (C/2012 S1), and use it to estimate the cohesive strength of ISON's nucleus, a first for a Long-Period Comet. Sublimating volatiles can also generate sublimative torques that alter the rotation state of the nucleus. However, computing these torques requires high-resolution information on the shape and activity of the nucleus, which is available only for the few nuclei visited by spacecraft. To remedy this, I develop a novel framework based on the YORP Effect (the torques asteroids experience by emitting thermal photons from their asymmetric shapes) to study the effects of sublimative torques on populations of cometary bodies. I take advantage of the similar manner in which surfaces emit both thermal photons and sublimating molecules to derive numerical relationships that describe sublimative torques by appropriately scaling the YORP torque equations. I then use this framework to explain the formation of dust striae (long linear features in the tails of Long-Period Comets that align with the Sun), which has remained an enigma for more than a century. I show that the observed ˜10-100 m chunks ejected from comet nuclei experience sublimative torques that spin them up to the point

  12. Learning of Abstract Concepts through Full-Body Interaction: A Systematic Review

    Science.gov (United States)

    Malinverni, Laura; Pares, Narcis

    2014-01-01

    Over the past ten years several learning environments based on novel interaction modalities have been developed. Within this field, Full-body Interaction Learning Environments open promising possibilities given their capacity to involve the users at different levels, such as sensorimotor experience, cognitive aspects and affective factors.…

  13. The self-consistent field model for Fermi systems with account of three-body interactions

    Directory of Open Access Journals (Sweden)

    Yu.M. Poluektov

    2015-12-01

    Full Text Available On the basis of a microscopic model of self-consistent field, the thermodynamics of the many-particle Fermi system at finite temperatures with account of three-body interactions is built and the quasiparticle equations of motion are obtained. It is shown that the delta-like three-body interaction gives no contribution into the self-consistent field, and the description of three-body forces requires their nonlocality to be taken into account. The spatially uniform system is considered in detail, and on the basis of the developed microscopic approach general formulas are derived for the fermion's effective mass and the system's equation of state with account of contribution from three-body forces. The effective mass and pressure are numerically calculated for the potential of "semi-transparent sphere" type at zero temperature. Expansions of the effective mass and pressure in powers of density are obtained. It is shown that, with account of only pair forces, the interaction of repulsive character reduces the quasiparticle effective mass relative to the mass of a free particle, and the attractive interaction raises the effective mass. The question of thermodynamic stability of the Fermi system is considered and the three-body repulsive interaction is shown to extend the region of stability of the system with the interparticle pair attraction. The quasiparticle energy spectrum is calculated with account of three-body forces.

  14. Faraday Waves in Cold-Atom Systems with Two- and Three-Body Interactions

    Science.gov (United States)

    Tomio, Lauro; Gammal, A.; Abdullaev, F. K.

    2017-03-01

    We report an investigation on Bose-Einstein condensates with two-body (cubic) and three-body (quintic) interactions in the corresponding nonlinear Schrödinger equation, considering s-wave two-body scattering length a_s periodically varying in time. For the quintic interacting term, the dependence on a_s was considered within two models, being quadratic or quartic. It was shown that parametric instabilities can lead to th e generation of Faraday wave resonances in this system, with wavelengths depending on the background scattering length, as well as on the corresponding modulation parameters. A few sample results are shown here for repulsive a_s, in case of quadratic and quartic three-body interactions. The effect of dissipation is also verified on the amplitude of the resonances. Analytical predictions for the resonance positions are confirmed by our numerical simulations.

  15. Correlated responses in sow appetite, residual feed intake, body composition, and reproduction after divergent selection for residual feed intake in the growing pig

    OpenAIRE

    Bidanel, Jean Pierre; Billon, Yvon; Lagant, Herve; Guillouet, Philippe; Sellier, Pierre; NOBLET, Jean; Hermesch,

    2012-01-01

    Residual feed intake (RFI) has been explored as an alternative selection criterion to feed conversion ratio to capture the fraction of feed intake not explained by expected production and maintenance requirements. Selection experiments have found that low RFI in the growing pig is genetically correlated with reduced fatness and feed intake. Selection for feed conversion ratio also reduces sow appetite and fatness, which, together with increased prolificacy, has been seen as a hindrance for so...

  16. Energy and structural properties of N -boson clusters attached to three-body Efimov states: Two-body zero-range interactions and the role of the three-body regulator

    Science.gov (United States)

    Yan, Yangqian; Blume, D.

    2015-09-01

    The low-energy spectrum of N -boson clusters with pairwise zero-range interactions is believed to be governed by a three-body parameter. We study the ground state of N -boson clusters with infinite two-body s -wave scattering length by performing ab initio Monte Carlo simulations. To prevent Thomas collapse, different finite-range three-body regulators are used. The energy and structural properties for the three-body Hamiltonian with two-body zero-range interactions and three-body regulator are in much better agreement with the "ideal zero-range Efimov theory" results than those for Hamiltonian with two-body finite-range interactions. For larger clusters we find that the ground-state energy and structural properties of the Hamiltonian with two-body zero-range interactions and finite-range three-body regulators are not universally determined by the three-body parameter, i.e., dependencies on the specific form of the three-body regulator are observed. For comparison, we consider Hamiltonian with two-body van der Waals interactions and no three-body regulator. For the interactions considered, the ground-state energy of the N -body clusters is—if scaled by the three-body ground-state energy—fairly universal, i.e., the dependence on the short-range details of the two-body van der Waals potentials is small. Our results are compared with those in the literature.

  17. Interaction Design for and with the Lived Body: Some Implications of Merleau-Ponty’s Phenomenology

    DEFF Research Database (Denmark)

    Svanæs, Dag

    2013-01-01

    In 2001, Paul Dourish proposed the term embodied interaction to describe a new paradigm for interaction design that focuses on the physical, bodily, and social aspects of our interaction with digital technology. Dourish used Merleau-Ponty’s phenomenology of perception as the theoretical basis...... for his discussion of the bodily nature of embodied interaction. This article extends Dourish’s work to introduce the human-computer interaction community to ideas related to Merleau-Ponty’s concept of the lived body. It also provides a detailed analysis of two related topics: (1) embodied perception...

  18. Interactions between internal forces, body stiffness, and fluid environment in a neuromechanical model of lamprey swimming.

    Science.gov (United States)

    Tytell, Eric D; Hsu, Chia-Yu; Williams, Thelma L; Cohen, Avis H; Fauci, Lisa J

    2010-11-16

    Animal movements result from a complex balance of many different forces. Muscles produce force to move the body; the body has inertial, elastic, and damping properties that may aid or oppose the muscle force; and the environment produces reaction forces back on the body. The actual motion is an emergent property of these interactions. To examine the roles of body stiffness, muscle activation, and fluid environment for swimming animals, a computational model of a lamprey was developed. The model uses an immersed boundary framework that fully couples the Navier-Stokes equations of fluid dynamics with an actuated, elastic body model. This is the first model at a Reynolds number appropriate for a swimming fish that captures the complete fluid-structure interaction, in which the body deforms according to both internal muscular forces and external fluid forces. Results indicate that identical muscle activation patterns can produce different kinematics depending on body stiffness, and the optimal value of stiffness for maximum acceleration is different from that for maximum steady swimming speed. Additionally, negative muscle work, observed in many fishes, emerges at higher tail beat frequencies without sensory input and may contribute to energy efficiency. Swimming fishes that can tune their body stiffness by appropriately timed muscle contractions may therefore be able to optimize the passive dynamics of their bodies to maximize peak acceleration or swimming speed.

  19. Interaction between the cytoplasmic domains of HIV-1 Vpu and CD4: role of Vpu residues involved in CD4 interaction and in vitro CD4 degradation.

    Science.gov (United States)

    Margottin, F; Benichou, S; Durand, H; Richard, V; Liu, L X; Gomas, E; Benarous, R

    1996-09-15

    The Vpu and CD4 cytoplasmic domains were found, by using a two-hybrid assay in yeast, to interact in the absence of their membrane anchor domains. Studies on several deletion and point mutants revealed that the overall structure of the Vpu cytoplasmic domain is required for this interaction. The Vpu amino acid residues involved in the interaction with CD4 were identified. Deletion of the C-terminal residues of Vpu, required for CD4 degradation, as well as the double mutation on the casein kinase II phosphorylation sites S52N-S56N, also involved in CD4 degradation, resulted in the loss of interaction with CD4 and in the inability to induce CD4 degradation. These results suggest that the ability of Vpu to mediate the degradation of CD4 is linked to its capacity to physically interact with CD4. However, additional mutagenesis on the S52 site revealed that the interaction between the cytoplasmic domains of Vpu and CD4 is not sufficient for in vitro Vpu-mediated CD4 degradation.

  20. Universal three-body recombination via resonant d-wave interactions

    CERN Document Server

    Wang, Jia; Wang, Yujun; Greene, Chris H

    2012-01-01

    For a system of three identical bosons interacting via short-range forces, when two of the atoms are about to form a two-body s-wave dimer, there exists an infinite number of three-body bound states. This effect is the well-known Efimov effect. These three-body states (Efimov states) are found to be universal for ultracold atomic gases and the lowest Efimov state crosses the three-body break-up threshold when the s-wave two-body scattering length is $a \\approx -9.73 r_{\\rm vdW}$, $r_{\\rm vdW}$ being the van der Waals length. This article focuses on a generalized version of this Efimov scenario, where two of the atoms are about to form a two-body d-wave dimer, which leads to strong d-wave interactions. In a recent paper [B. Gao, Phys. Rev. A. {\\bf 62}, 050702(R) (2000)], Bo Gao has predicted that for broad resonances the d-wave dimer is always formed near $a \\approx 0.956 r_{\\rm vdW}$. Here we find that a single universal three-body state associated with the d-wave dimer is also formed near the three-body brea...

  1. A Database of Transition-Metal-Coordinated Peptide Cross-Sections: Selective Interaction with Specific Amino Acid Residues

    Science.gov (United States)

    Dilger, Jonathan M.; Glover, Matthew S.; Clemmer, David E.

    2017-07-01

    Ion mobility mass spectrometry (IMS-MS) techniques were used to generate a database of 2288 collision cross sections of transition-metal-coordinated tryptic peptide ions. This database consists of cross sections for 1253 [Pep + X]2+ and 1035 [Pep + X + H]3+, where X2+ corresponds to Mn2+, Co2+, Ni2+, Cu2+, or Zn2+. This number of measurements enables the extraction of structural trends for transition-metal-coordinated peptide ions. The range of structures and changes in collision cross sections for X2+-coordinated species (compared with protonated species of the same charge state) is similar to Mg2+-coordinated species. This suggests that the structures are largely determined by similarities in cation size with differences among the cross section distributions presumably caused by X2+ interactions with specific functional groups offered by the residue R-groups or the peptide backbone. Cross section contributions for individual residues upon X2+ solvation are assessed with the derivation of intrinsic size parameters (ISPs). The comparison of the [Pep + X]2+ ISPs with those previously reported for [Pep + Mg]2+ ions displays a lower contribution to the cross section for His, carboxyamidomethylated Cys, and Met, and is consistent with specific metal-residue interactions identified within protein X-ray crystallography databases.

  2. Effect of Interaction of Non-residual Fractions on Adsorption of Atrazine onto Surficial Sediments and Natural Surface Coating Samples

    Institute of Scientific and Technical Information of China (English)

    LI Yu; LI Shan-shan; GAO Qian; WANG Ao

    2011-01-01

    To quantify the effect of the interaction of non-residual fractions[Fe oxides(Fe), Mn oxide(Mn), organic materials(OMs)] in the surficial sediments and the natural surface coating samples on the adsorption of atrazine(AT),an AT multiple regression adsorption modeI(AT-MRAM) was developed. The AT-MRAM improves upon the previous AT additional adsorption modeI(AT-AAM) with superior goodness-of-fit test(adjusted R2=ca.l.000), F-test and t-test(P<0.01), and reveals the effect of the interaction among the components in the surficial sediments(SSs) and natural surface coatings samples(NSCSs) on the adsorption of AT, which was neglected by the AT-AAM. Meanwhile, the AT-MRAM was also verified through adsorption experiments of AT and the relative deviation between predicted maximum adsorption of AT and the experimental one is less than 15%. The resulted information shows that Mn is prone to interact with other non-residual components, the total maximum adsorption of AT is inversly proportional to the level of Mn, and Fe and OMs facilitate the adsorption of AT. The results also indicate that the adsorption of AT is not only dominated by Fe, OMs, Fe/OMs, but also restrained by Fe/Mn, Fe/Mn/OMs, with lesser roles attributed to Mn, and the estimated AT distributions among the components do not agree with that previously predicted by the AT-AAM, especially with the relative contribution of Mn to the adsorption of AT, revealing significant contribution of the interactions among non-residual components in controlling the behavior of AT in aquatic environments.

  3. De novo design of protein-protein interactions through modification of inter-molecular helix-helix interface residues.

    Science.gov (United States)

    Yagi, Sota; Akanuma, Satoshi; Yamagishi, Manami; Uchida, Tatsuya; Yamagishi, Akihiko

    2016-05-01

    For de novo design of protein-protein interactions (PPIs), information on the shape and chemical complementarity of their interfaces is generally required. Recent advances in computational PPI design have allowed for de novo design of protein complexes, and several successful examples have been reported. In addition, a simple and easy-to-use approach has also been reported that arranges leucines on a solvent-accessible region of an α-helix and places charged residues around the leucine patch to induce interactions between the two helical peptides. For this study, we adopted this approach to de novo design a new PPI between the helical bundle proteins sulerythrin and LARFH. A non-polar patch was created on an α-helix of LARFH around which arginine residues were introduced to retain its solubility. The strongest interaction found was for the LARFH variant cysLARFH-IV-3L3R and the sulerythrin mutant 6L6D (KD=0.16 μM). This artificial protein complex is maintained by hydrophobic and ionic interactions formed by the inter-molecular helical bundle structure. Therefore, by the simple and easy-to-use approach to create de novo interfaces on the α-helices, we successfully generated an artificial PPI. We also created a second LARFH variant with the non-polar patch surrounded by positively charged residues at each end. Upon mixing this LARFH variant with 6L6D, mesh-like fibrous nanostructures were observed by atomic force microscopy. Our method may, therefore, also be applicable to the de novo design of protein nanostructures. Copyright © 2016 Elsevier B.V. All rights reserved.

  4. Sequence specificity between interacting and non-interacting homologs identifies interface residues - a homodimer and monomer use case

    NARCIS (Netherlands)

    Hou, Qingzhen; Dutilh, Bas E; Huynen, Martijn A; Heringa, Jaap; Feenstra, K Anton

    2015-01-01

    BACKGROUND: Protein families participating in protein-protein interactions may contain sub-families that have different binding characteristics, ranging from right binding to showing no interaction at all. Composition differences at the sequence level in these sub-families are often decisive to thei

  5. Stability and Chaos of Two Coupled Bose-Einstein Condensates with Three-Body Interaction

    Institute of Scientific and Technical Information of China (English)

    2005-01-01

    We study the dynamics of two Bose-Einstein condensates (BECs) tunnel-coupled by a double-well potential.A real three-body interaction term is considered and a two-mode approximation is used to derive two coupled equations,which describe the relative population and relative phase. By solving the equations and analyzing the stability of the system, we find the stable stationary solutions for a constant atomic scattering length. When a periodically time-varying scattering length is applied, Melnikov analysis and numerical calculation demonstrate the existence of chaotic behavior and the dependence of chaos on the three-body interaction parameters.

  6. IRBIT Interacts with the Catalytic Core of Phosphatidylinositol Phosphate Kinase Type Iα and IIα through Conserved Catalytic Aspartate Residues.

    Directory of Open Access Journals (Sweden)

    Hideaki Ando

    Full Text Available Phosphatidylinositol phosphate kinases (PIPKs are lipid kinases that generate phosphatidylinositol 4,5-bisphosphate (PI(4,5P2, a critical lipid signaling molecule that regulates diverse cellular functions, including the activities of membrane channels and transporters. IRBIT (IP3R-binding protein released with inositol 1,4,5-trisphosphate is a multifunctional protein that regulates diverse target proteins. Here, we report that IRBIT forms signaling complexes with members of the PIPK family. IRBIT bound to all PIPK isoforms in heterologous expression systems and specifically interacted with PIPK type Iα (PIPKIα and type IIα (PIPKIIα in mouse cerebellum. Site-directed mutagenesis revealed that two conserved catalytic aspartate residues of PIPKIα and PIPKIIα are involved in the interaction with IRBIT. Furthermore, phosphatidylinositol 4-phosphate, Mg2+, and/or ATP interfered with the interaction, suggesting that IRBIT interacts with catalytic cores of PIPKs. Mutations of phosphorylation sites in the serine-rich region of IRBIT affected the selectivity of its interaction with PIPKIα and PIPKIIα. The structural flexibility of the serine-rich region, located in the intrinsically disordered protein region, is assumed to underlie the mechanism of this interaction. Furthermore, in vitro binding experiments and immunocytochemistry suggest that IRBIT and PIPKIα interact with the Na+/HCO3- cotransporter NBCe1-B. These results suggest that IRBIT forms signaling complexes with PIPKIα and NBCe1-B, whose activity is regulated by PI(4,5P2.

  7. Many-body dispersion interactions from the exchange-hole dipole moment model.

    Science.gov (United States)

    Otero-de-la-Roza, A; Johnson, Erin R

    2013-02-07

    In this article, we present the extension of the exchange-hole dipole moment model (XDM) of dispersion interactions to the calculation of two-body and three-body dispersion energy terms to any order, 2(l)-pole oscillator strengths, and polarizabilities. By using the newly-formulated coefficients, we study the relative importance of the higher-order two-body and the leading non-additive three-body (triple-dipole) interactions in gas-phase as well as in condensed systems. We show that the two-body terms up to R(-10), but not the terms of higher-order, are essential in the correct description of the dispersion energy, while there are a number of difficulties related to the choice of the damping function, which precludes the use three-body triple-dipole contributions in XDM. We conclude that further study is required before the three-body term can be used in production XDM density-functional calculations and point out the salient problems regarding its use.

  8. Molecular Determinants Underlying Binding Specificities of the ABL Kinase Inhibitors: Combining Alanine Scanning of Binding Hot Spots with Network Analysis of Residue Interactions and Coevolution.

    Directory of Open Access Journals (Sweden)

    Amanda Tse

    Full Text Available Quantifying binding specificity and drug resistance of protein kinase inhibitors is of fundamental importance and remains highly challenging due to complex interplay of structural and thermodynamic factors. In this work, molecular simulations and computational alanine scanning are combined with the network-based approaches to characterize molecular determinants underlying binding specificities of the ABL kinase inhibitors. The proposed theoretical framework unveiled a relationship between ligand binding and inhibitor-mediated changes in the residue interaction networks. By using topological parameters, we have described the organization of the residue interaction networks and networks of coevolving residues in the ABL kinase structures. This analysis has shown that functionally critical regulatory residues can simultaneously embody strong coevolutionary signal and high network centrality with a propensity to be energetic hot spots for drug binding. We have found that selective (Nilotinib and promiscuous (Bosutinib, Dasatinib kinase inhibitors can use their energetic hot spots to differentially modulate stability of the residue interaction networks, thus inhibiting or promoting conformational equilibrium between inactive and active states. According to our results, Nilotinib binding may induce a significant network-bridging effect and enhance centrality of the hot spot residues that stabilize structural environment favored by the specific kinase form. In contrast, Bosutinib and Dasatinib can incur modest changes in the residue interaction network in which ligand binding is primarily coupled only with the identity of the gate-keeper residue. These factors may promote structural adaptability of the active kinase states in binding with these promiscuous inhibitors. Our results have related ligand-induced changes in the residue interaction networks with drug resistance effects, showing that network robustness may be compromised by targeted mutations

  9. Molecular dynamics of protein A and a WW domain with a united-residue model including hydrodynamic interaction

    Science.gov (United States)

    Lipska, Agnieszka G.; Seidman, Steven R.; Sieradzan, Adam K.; Giełdoń, Artur; Liwo, Adam; Scheraga, Harold A.

    2016-05-01

    The folding of the N-terminal part of the B-domain of staphylococcal protein A (PDB ID: 1BDD, a 46-residue three-α-helix bundle) and the formin-binding protein 28 WW domain (PDB ID: 1E0L, a 37-residue three-stranded anti-parallel β protein) was studied by means of Langevin dynamics with the coarse-grained UNRES force field to assess the influence of hydrodynamic interactions on protein-folding pathways and kinetics. The unfolded, intermediate, and native-like structures were identified by cluster analysis, and multi-exponential functions were fitted to the time dependence of the fractions of native and intermediate structures, respectively, to determine bulk kinetics. It was found that introducing hydrodynamic interactions slows down both the formation of an intermediate state and the transition from the collapsed structures to the final native-like structures by creating multiple kinetic traps. Therefore, introducing hydrodynamic interactions considerably slows the folding, as opposed to the results obtained from earlier studies with the use of Gō-like models.

  10. Feasibility of Using Electrocochleography for Objective Estimation of Electro-Acoustic Interactions in Cochlear Implant Recipients with Residual Hearing

    Directory of Open Access Journals (Sweden)

    Kanthaiah Koka

    2017-06-01

    Full Text Available Although cochlear implants (CI traditionally have been used to treat individuals with bilateral profound sensorineural hearing loss, a recent trend is to implant individuals with residual low-frequency hearing. Patients who retain some residual acoustic hearing after surgery often can benefit from electro-acoustic stimulation (EAS technologies, which combine conventional acoustic amplification with electrical stimulation. However, interactions between acoustic and electrical stimulation may affect outcomes adversely and are time-consuming and difficult to assess behaviorally. This study demonstrated the feasibility of using the Advanced Bionics HiRes90K Advantage implant electronics and HiFocus Mid Scala/1j electrode to measure electrocochleography (ECochG responses in the presence of electrical stimulation to provide an objective estimate of peripheral physiologic EAS interactions. In general, electrical stimulation reduced ECochG response amplitudes to acoustic stimulation. The degree of peripheral EAS interaction varied as a function of acoustic pure tone frequency and the intra-cochlear location of the electrically stimulated electrode. Further development of this technique may serve to guide and optimize clinical EAS system fittings in the future.

  11. Intra-residue interactions in proteins: interplay between serine or cysteine side chains and backbone conformations, revealed by laser spectroscopy of isolated model peptides.

    Science.gov (United States)

    Alauddin, Mohammad; Biswal, Himansu S; Gloaguen, Eric; Mons, Michel

    2015-01-21

    Intra-residue interactions play an important role in proteins by influencing local folding of the backbone. Taking advantage of the capability of gas phase experiments to provide relevant information on the intrinsic H-bonding pattern of isolated peptide chains, the intra-residue interactions of serine and cysteine residues, i.e., OH/SH···OC(i) C6 and NH(i···)O/S C5 interactions in Ser/Cys residues, are probed by laser spectroscopy of isolated peptides. The strength of these local side chain-main chain interactions, elegantly documented from their IR spectral features for well-defined conformations of the main chain, demonstrates that a subtle competition exists between the two types of intra-residue bond: the C6 H-bond is the major interaction with Ser, in contrast to Cys where C5 interaction takes over. The restricted number of conformers observed in the gas phase experiment with Ser compared to Cys (where both extended and folded forms are observed) also suggests a significant mediation role of these intra-residue interactions on the competition between the several main chain folding patterns.

  12. Drosophila sperm surface alpha-L-fucosidase interacts with the egg coats through its core fucose residues.

    Science.gov (United States)

    Intra, Jari; Concetta, Veltri; Daniela, De Caro; Perotti, Maria Elisa; Pasini, Maria Enrica

    2015-08-01

    Sperm-oocyte interaction during fertilization is multiphasic, with multicomponent events, taking place between egg's glycoproteins and sperm surface receptors. Protein-carbohydrate complementarities in gamete recognition have observed in cases throughout the whole evolutionary scale. Sperm-associated α-L-fucosidases have been identified in various organisms. Their wide distribution and known properties reflect the hypothesis that fucose and α-L-fucosidases have fundamental function(s) during gamete interactions. An α-L-fucosidase has been detected as transmembrane protein on the surface of spermatozoa of eleven species across the genus Drosophila. Immunofluorescence labeling showed that the protein is localized in the sperm plasma membrane over the acrosome and the tail, in Drosophila melanogaster. In the present study, efforts were made to analyze with solid phase assays the oligosaccharide recognition ability of fruit fly sperm α-L-fucosidase with defined carbohydrate chains that can functionally mimic egg glycoconjugates. Our results showed that α-L-fucosidase bound to fucose residue and in particular it prefers N-glycans carrying core α1,6-linked fucose and core α1,3-linked fucose in N-glycans carrying only a terminal mannose residue. The ability of sperm α-L-fucosidase to bind to the micropylar chorion and to the vitelline envelope was examined in in vitro assays in presence of α-L-fucosidase, either alone or in combination with molecules containing fucose residues. No binding was detected when α-L-fucosidase was pre-incubated with fucoidan, a polymer of α-L-fucose and the monosaccharide fucose. Furthermore, egg labeling with anti-horseradish peroxidase, that recognized only core α1,3-linked fucose, correlates with α-L-fucosidase micropylar binding. Collectively, these data support the hypothesis of the potential role of this glycosidase in sperm-egg interactions in Drosophila.

  13. Scaling and universality in two dimensions: three-body bound states with short-ranged interactions

    Energy Technology Data Exchange (ETDEWEB)

    Bellotti, F F; Frederico, T [Instituto Tecnologico de Aeronautica, DCTA, 12.228-900 Sao Jose dos Campos, SP (Brazil); Yamashita, M T [Instituto de Fisica Teorica, UNESP-Univ Estadual Paulista, CP 70532-2, CEP 01156-970, Sao Paulo, SP (Brazil); Fedorov, D V; Jensen, A S; Zinner, N T, E-mail: zinner@phys.au.dk [Department of Physics and Astronomy-Aarhus University, Ny Munkegade, bygn. 1520, DK-8000 Arhus C (Denmark)

    2011-10-28

    The momentum space zero-range model is used to investigate universal properties of three interacting particles confined to two dimensions. The pertinent equations are first formulated for a system of two identical and one distinct particle and the two different two-body subsystems are characterized by two-body energies and masses. The three-body energy in units of one of the two-body energies is a universal function of the other two-body energy and the mass ratio. We derive convenient analytical formulae for calculations of the three-body energy as a function of these two independent parameters and exhibit the results as universal curves. In particular, we show that the three-body system can have any number of stable bound states. When the mass ratio of the distinct to identical particles is greater than 0.22, we find that at most two stable bound states exist, while for two heavy and one light mass an increasing number of bound states is possible. The specific number of stable bound states depends on the ratio of two-body bound state energies and on the mass ratio, and we map out an energy-mass phase diagram of the number of stable bound states. Realizable systems of both fermions and bosons are discussed in this framework.

  14. Fin-Body Interaction and its Hydrodynamic Benefits in Fish's Steady Swimming

    Science.gov (United States)

    Liu, Geng; Ren, Yan; Dong, Haibo; Lauder, George

    2016-11-01

    In many past studies on fish swimming, the hydrodynamics of fish caudal fins were investigated separately. However, fish body inevitably interacts with the caudal fin since the fin flaps in the wake of the body during swimming. In this work, an integrated experimental and computational approach has been used to investigate hydrodynamic performance improvement and the vortex dynamics associated with the fin-body interactions of a jack fish in steady swimming. Realistic 3D jack fish geometry and the undulatory kinematics are reconstructed based on the output of a high-speed photogrammetry system. Hydrodynamic performance and wake structures are simulated by an in-house immersed-boundary-method flow solver. It is found that the body-fin interactions enhance the thrust production of the caudal fin by more than 30% compared to that produced by an isolated caudal fin. Further analysis on the vortex dynamics has shown that the vortices shed from the posterior part of the fish body are captured by the leading edge portion of the caudal fin. This further enhances the strength of the leading-edge vortex attaching to the caudal fin and results in larger thrust production. This work reveals a potential performance enhancement mechanism in fish's steady swimming. This work was supported by NSF CBET-1313217 and ONR MURI N00014-14-1-0533.

  15. Advanced human body modelling to support designing products for physical interaction

    NARCIS (Netherlands)

    Moes, C.C.M.

    2004-01-01

    We are using many designed artefacts in our daily life. These artefacts are typically in physical interaction with the human body, and cause stresses and deformations inside the tissues. When these stresses exceed a given level, the proper physiological functioning of the tissues is limited, and erg

  16. Advanced human body modelling to support designing products for physical interaction

    NARCIS (Netherlands)

    Moes, C.C.M.

    2004-01-01

    We are using many designed artefacts in our daily life. These artefacts are typically in physical interaction with the human body, and cause stresses and deformations inside the tissues. When these stresses exceed a given level, the proper physiological functioning of the tissues is limited, and

  17. Many-body localization in Ising models with random long-range interactions

    Science.gov (United States)

    Li, Haoyuan; Wang, Jia; Liu, Xia-Ji; Hu, Hui

    2016-12-01

    We theoretically investigate the many-body localization phase transition in a one-dimensional Ising spin chain with random long-range spin-spin interactions, Vi j∝|i-j |-α , where the exponent of the interaction range α can be tuned from zero to infinitely large. By using exact diagonalization, we calculate the half-chain entanglement entropy and the energy spectral statistics and use them to characterize the phase transition towards the many-body localization phase at infinite temperature and at sufficiently large disorder strength. We perform finite-size scaling to extract the critical disorder strength and the critical exponent of the divergent localization length. With increasing α , the critical exponent experiences a sharp increase at about αc≃1.2 and then gradually decreases to a value found earlier in a disordered short-ranged interacting spin chain. For α localized and the increase in the disorder strength may drive a transition between two many-body localized phases. In contrast, for α >αc , the transition is from a thermalized phase to the many-body localization phase. Our predictions could be experimentally tested with an ion-trap quantum emulator with programmable random long-range interactions, or with randomly distributed Rydberg atoms or polar molecules in lattices.

  18. Genotype x diet interactions in mice predisposed to mammary cancer. I. Body weight and fat

    DEFF Research Database (Denmark)

    Gordon, Ryan R; Hunter, Kent W; Sørensen, Peter;

    2008-01-01

    of the F(2) population (n = 615) which resulted from a cross between the polygenic obesity model M16i and FVB/NJ-TgN (MMTV-PyMT)(634Mul), effects of diet on growth and body composition, and QTL and QTL x diet and/or gender interaction effects for growth and obesity-related phenotypes. We identified 38 QTL...

  19. Traveller: An Interactive Cultural Training System Controlled by User-Defined Body Gestures

    NARCIS (Netherlands)

    Kistler, F.; André, E.; Mascarenhas, S.; Silva, A.; Paiva, A.; Degens, D.M.; Hofstede, G.J.; Krumhuber, E.; Kappas, A.; Aylett, R.

    2013-01-01

    In this paper, we describe a cultural training system based on an interactive storytelling approach and a culturally-adaptive agent architecture, for which a user-defined gesture set was created. 251 full body gestures by 22 users were analyzed to find intuitive gestures for the in-game actions in

  20. Three-body interactions and the Landau levels using Nikiforov–Uvarov method

    Indian Academy of Sciences (India)

    P K Bera

    2013-08-01

    In this article, the eigenvalues for the three-body interactions on the line and the Landau levels in the presence of topological defects have been regenerated by the Nikiforov–Uvarov (NU) method. Two exhaustive lists of such exactly solvable potentials are given.

  1. A transmon quantum annealer: decomposing many-body Ising constraints into pair interactions

    Science.gov (United States)

    Leib, Martin; Zoller, Peter; Lechner, Wolfgang

    2016-12-01

    Adiabatic quantum computing is an analogue quantum computing scheme with various applications in solving optimisation problems. In the parity picture of quantum optimization, the problem is encoded in local fields that act on qubits that are connected via local four-body terms We present an implementation of a parity annealer with Transmon qubits with a specifically tailored Ising interaction from Josephson ring modulators.

  2. Interactions between dietary vitamin E intake and SIRT1 genetic variation influence body mass index

    NARCIS (Netherlands)

    M.C. Zillikens (Carola); J.B.J. van Meurs (Joyce); F. Rivadeneira Ramirez (Fernando); A. Hofman (Albert); B.A. Oostra (Ben); E.J.G. Sijbrands (Eric); J.C.M. Witteman (Jacqueline); H.A.P. Pols (Huib); P. Tikka-Kleemola (Päivi); A.G. Uitterlinden (André)

    2010-01-01

    textabstractBackground: Genetic variation in SIRT1 has been associated with body mass index (BMI) and risk of obesity. SIRT1 may be influenced by diet. Objective: We studied the gene-diet interaction on BMI at the SIRT1 locus. Design: In 4575 elderly men and women in the population-based Rotterdam S

  3. ENA imaging near Planetary Bodies: Interaction between Plasma, Exosphere and Surface

    CERN Document Server

    Futaana, Yoshifumi

    2013-01-01

    Energetic Neutral Atom (ENA) imaging has been noticed as a powerful tool for remote sensing the plasma-neutral interaction in space. Particularly, the technique is used for investigation of space plasma near planetary bodies. Hear we provide a short review of recent low-energy ENA observations (up to ~1 keV) near Mars, Venus and the Moon.

  4. Interactions between dietary vitamin E intake and SIRT1 genetic variation influence body mass index

    NARCIS (Netherlands)

    M.C. Zillikens (Carola); J.B.J. van Meurs (Joyce); F. Rivadeneira Ramirez (Fernando); A. Hofman (Albert); B.A. Oostra (Ben); E.J.G. Sijbrands (Eric); J.C.M. Witteman (Jacqueline); H.A.P. Pols (Huib); P. Tikka-Kleemola (Päivi); A.G. Uitterlinden (André)

    2010-01-01

    textabstractBackground: Genetic variation in SIRT1 has been associated with body mass index (BMI) and risk of obesity. SIRT1 may be influenced by diet. Objective: We studied the gene-diet interaction on BMI at the SIRT1 locus. Design: In 4575 elderly men and women in the population-based Rotterdam

  5. Aerodynamic Interactions Between Wing and Body of a Model Insect in Forward Flight and Maneuvers

    Institute of Scientific and Technical Information of China (English)

    Bin Liang; Mao Sun

    2013-01-01

    The aerodynamic interactions between the body and the wings of a model insect in forward flight and maneuvers are studied using the method of numerically solving the Navier-Stokes equations over moving overset grids.Three cases are considered,including a complete insect,wing pair only and body only.By comparing the results of these cases,the interaction effect between the body and the wing pair can be identified.The changes in the force and moment coefficients of the wing pair due to the presence of the body are less than 4.5% of the mean vertical force coefficient of the model insect; the changes in the aerodynamic force coefficients of the body due to the presence of the wings are less than 5.0% of the mean vertical force coefficient of the model insect.The results of this paper indicate that in studying the aerodynamics and flight dynamics of a flapping insect in forward flight or maneuver,separately computing (or measuring) the aerodynamic forces and moments on the wing pair and on the body could be a good approximation.

  6. Interaction of wave with a body floating on a wide polynya

    Science.gov (United States)

    Li, Z. F.; Shi, Y. Y.; Wu, G. X.

    2017-09-01

    A method based on wide spacing approximation is proposed for the interaction of water wave with a body floating on a polynya. The ice sheet is modelled as an elastic plate and fluid flow is described by the velocity potential theory. The solution procedure is constructed based on the assumption that when the distance between two disturbances to the free surface is sufficiently large, the interactions between them involve only the travelling waves caused by the disturbances and the effect of the evanescent waves is ignored. The solution for the problem can then be obtained from those for a floating body without an ice sheet and for an ice sheet/free surface without a floating body. Both latter solutions have already been found previously and therefore there will be no additional effort in solution once the wide spacing approximation formulation is derived. Extensive numerical results are provided to show that the method is very accurate compared with the exact solution. The obtained formulations are then used to provide some insightful explanations for the physics of flow behaviour, as well as the mechanism for the highly oscillatory features of the hydrodynamic force and body motion. Some explicit equations are derived to show zero reflection by the polynya and peaks and troughs of the force and excited body motion. It is revealed that some of the peaks of the body motion are due to resonance while others are due to the wave characters in the polynya.

  7. Nematode succession and microfauna-microorganism interactions during root residue decomposition

    DEFF Research Database (Denmark)

    Georgieva, Slavka; Christensen, Søren; Andersen, Karen Stevnbak

    2005-01-01

    The quality of plant material affects the vigor of the decomposition process and composition of the decomposer biota. Root residues from hairy vetch (Vicia villosa Roth), rye (Secale cereale L.) and vetch+rye, packed in litterbags were placed in pots of soil at 15 C and the content of the bags...... in rye. At week 12 no species dominated the nematode assemblages that were similar between the resources. The differences between nematode assemblages among plant resources at 2 week were similar to the results of a field study sampled after 6 weeks with the same soil and plant resources. This lends...

  8. A generalized variational principle and theoretical model for magnetoelastic interaction of ferromagnetic bodies

    Institute of Scientific and Technical Information of China (English)

    周又和; 郑晓静

    1999-01-01

    The quantitative analysis shows that no theoretical model for 3-d magnetoelastic bodies, in literatures to date, can commonly simulate two kinds of distinct experimental phenomena on magnetoelastic interaction of ferromagnetic structures. This makes it difficult to effectively discribe the magnetoelastic mechanical behavior of structures with complex geometry, such as shells. Therefore, it is a key step for simulating magnetoelastic mechanical characteristics of structures with complex geometry to establish a 3-d model which also can commonly characterize the two distinct experimental phenomena. A theoretical model for three dimension magnetizable elastic bodies, which is commonly suitable for the two kinds of experimental phenomena on magnetoelastic interaction of ferromagnetic plates, is presented by the variational principle for the total energy functional of the coupling system of the 3-d ferromagnetic bodies. It is found that for the case of linear isotropic magnetic materials, the magnetic forces

  9. CCHCR1 interacts with EDC4, suggesting its localization in P-bodies

    Energy Technology Data Exchange (ETDEWEB)

    Ling, Y.H.; Wong, C.C. [School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong (China); Li, K.W. [Department of Molecular and Cellular Neurobiology, Center for Neurogenomics and Cognitive Research, Neuroscience Campus Amsterdam, VU University, 1081 HV Amsterdam (Netherlands); Chan, K.M. [School of Life Sciences, Faculty of Science, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong (China); Boukamp, P. [Division of Genetics of Skin Carcinogenesis, A110 German Cancer Research Center, Im Neuenheimer Feld 280, D-69120 Heidelberg (Germany); Liu, W.K., E-mail: ken-liu@cuhk.edu.hk [School of Biomedical Sciences, Faculty of Medicine, The Chinese University of Hong Kong, Shatin, N.T., Hong Kong (China)

    2014-09-10

    Coiled‐coil alpha‐helical rod protein 1 (CCHCR1) is suggested as a candidate biomarker for psoriasis for more than a decade but its function remains poorly understood because of the inconsistent findings in the literature. CCHCR1 protein is suggested to be localized in the cytoplasm, nucleus, mitochondria, or centrosome and to regulate various cellular functions, including steroidogenesis, proliferation, differentiation, and cytoskeleton organization. In this study, we attempted to find a consensus between these findings by identifying the interaction partners of CCHCR1 using co-immunoprecipiation with a stable cell line expressing EGFP-tagged CCHCR1. Out of more than 100 co-immunoprecipitants identified by liquid chromatography-tandem mass spectrometry (LC-MS/MS), the enhancer of mRNA-decapping protein 4 (EDC4), which is a processing body (P-body) component, was particularly found to be the major interacting partner of CCHCR1. Confocal imaging confirmed the localization of CCHCR1 in P-bodies and its N-terminus is required for this subcellular localization, suggesting that CCHCR1 is a novel P-body component. As P-bodies are the site for mRNA metabolism, our findings provide a molecular basis for the function of CCHCR1, any disruption of which may affect the transcriptome of the cell, and causing abnormal cell functions. - Highlights: • We identified CCHCR1 as a novel P-body component. • We identified EDC4 as the major interacting partner of CCHCR1. • N-terminus of CCHCR1 protein is required for its P-bodies localization.

  10. Two hydrophobic residues can determine the specificity of mitogen-activated protein kinase docking interactions.

    Science.gov (United States)

    Bardwell, A Jane; Bardwell, Lee

    2015-10-30

    MAPKs bind to many of their upstream regulators and downstream substrates via a short docking motif (the D-site) on their binding partner. MAPKs that are in different families (e.g. ERK, JNK, and p38) can bind selectively to D-sites in their authentic substrates and regulators while discriminating against D-sites in other pathways. Here we demonstrate that the short hydrophobic region at the distal end of the D-site plays a critical role in determining the high selectivity of JNK MAPKs for docking sites in their cognate MAPK kinases. Changing just 1 or 2 key hydrophobic residues in this submotif is sufficient to turn a weak JNK-binding D-site into a strong one, or vice versa. These specificity-determining differences are also found in the D-sites of the ETS family transcription factors Elk-1 and Net. Moreover, swapping two hydrophobic residues between these D-sites switches the relative efficiency of Elk-1 and Net as substrates for ERK versus JNK, as predicted. These results provide new insights into docking specificity and suggest that this specificity can evolve rapidly by changes to just 1 or 2 amino acids.

  11. JSPAM: A restricted three-body code for simulating interacting galaxies

    Science.gov (United States)

    Wallin, J. F.; Holincheck, A. J.; Harvey, A.

    2016-07-01

    Restricted three-body codes have a proven ability to recreate much of the disturbed morphology of actual interacting galaxies. As more sophisticated n-body models were developed and computer speed increased, restricted three-body codes fell out of favor. However, their supporting role for performing wide searches of parameter space when fitting orbits to real systems demonstrates a continuing need for their use. Here we present the model and algorithm used in the JSPAM code. A precursor of this code was originally described in 1990, and was called SPAM. We have recently updated the software with an alternate potential and a treatment of dynamical friction to more closely mimic the results from n-body tree codes. The code is released publicly for use under the terms of the Academic Free License ("AFL") v. 3.0 and has been added to the Astrophysics Source Code Library.

  12. JSPAM: A restricted three-body code for simulating interacting galaxies

    CERN Document Server

    Wallin, John; Harvey, Allen

    2015-01-01

    Restricted three-body codes have a proven ability to recreate much of the disturbed morphology of actual interacting galaxies. As more sophisticated n-body models were developed and computer speed increased, restricted three-body codes fell out of favor. However, their supporting role for performing wide searches of parameter space when fitting orbits to real systems demonstrates a continuing need for their use. Here we present the model and algorithm used in the JSPAM code. A precursor of this code was originally described in 1990, and was called SPAM. We have recently updated the software with an alternate potential and a treatment of dynamical friction to more closely mimic the results from n-body tree codes. The code is released publicly for use under the terms of the Academic Free License (AFL) v.3.0 and has been added to the Astrophysics Source Code Library.

  13. The interactive effect of fungicide residues and yeast assimilable nitrogen on fermentation kinetics and hydrogen sulfide production during cider fermentation.

    Science.gov (United States)

    Boudreau, Thomas F; Peck, Gregory M; O'Keefe, Sean F; Stewart, Amanda C

    2017-01-01

    Fungicide residues on fruit may adversely affect yeast during cider fermentation, leading to sluggish or stuck fermentation or the production of hydrogen sulfide (H2 S), which is an undesirable aroma compound. This phenomenon has been studied in grape fermentation but not in apple fermentation. Low nitrogen availability, which is characteristic of apples, may further exacerbate the effects of fungicides on yeast during fermentation. The present study explored the effects of three fungicides: elemental sulfur (S(0) ) (known to result in increased H2 S in wine); fenbuconazole (used in orchards but not vineyards); and fludioxonil (used in post-harvest storage of apples). Only S(0) led to increased H2 S production. Fenbuconazole (≥0.2 mg L(-1) ) resulted in a decreased fermentation rate and increased residual sugar. An interactive effect of yeast assimilable nitrogen (YAN) concentration and fenbuconazole was observed such that increasing the YAN concentration alleviated the negative effects of fenbuconazole on fermentation kinetics. Cidermakers should be aware that residual fenbuconazole (as low as 0.2 mg L(-1) ) in apple juice may lead to stuck fermentation, especially when the YAN concentration is below 250 mg L(-1) . These results indicate that fermentation problems attributed to low YAN may be caused or exacerbated by additional factors such as fungicide residues, which have a greater impact on fermentation performance under low YAN conditions. © 2016 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry. © 2016 The Authors. Journal of The Science of Food and Agriculture published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

  14. Vestibular-somatosensory interactions: effects of passive whole-body rotation on somatosensory detection.

    Directory of Open Access Journals (Sweden)

    Elisa Raffaella Ferrè

    Full Text Available Vestibular signals are strongly integrated with information from several other sensory modalities. For example, vestibular stimulation was reported to improve tactile detection. However, this improvement could reflect either a multimodal interaction or an indirect interaction driven by vestibular effects on spatial attention and orienting. Here we investigate whether natural vestibular activation induced by passive whole-body rotation influences tactile detection. In particular, we assessed the ability to detect faint tactile stimuli to the fingertips of the left and right hand during spatially congruent or incongruent rotations. We found that passive whole-body rotations significantly enhanced sensitivity to faint shocks, without affecting response bias. Critically, this enhancement of somatosensory sensitivity did not depend on the spatial congruency between the direction of rotation and the hand stimulated. Thus, our results support a multimodal interaction, likely in brain areas receiving both vestibular and somatosensory signals.

  15. An approximate many-body calculation for trapped bosons with attractive interaction

    Energy Technology Data Exchange (ETDEWEB)

    Kundu, Anasuya [Department of Physics, University of Calcutta, 92 A P C Road, Calcutta-700 009 (India); Chakrabarti, Barnali [Department of Physics, Lady Brabourne College, P1/2 Surawardi Avenue, Calcutta-700 017 (India); Das, Tapan Kumar [Department of Physics, University of Calcutta, 92 A P C Road, Calcutta-700 009 (India); Canut, Sylvio [Instituto de Fisica, Universidade de Sao Paulo, CP 66318, 05315-970, Sao Paulo, SP (Brazil)

    2007-06-28

    The stability of trapped interacting bosons with attractive interactions is studied using an approximate many-body calculation. Instead of using the traditional hyperspherical harmonics expansion method we prescribe a potential harmonics expansion method (PHEM). The justification of the use of PHEM in connection with dilute condensates is presented. The choice of a correlation function is justified as it correctly reproduces the short-range two-body correlation in the wavefunction as also the correct value of the s-wave scattering length (a{sub s}). Applications to {sup 7}Li and {sup 85}Rb condensates with the realistic van der Waals interaction give good agreement with the Rice and JILA experiments, respectively. The JILA experiment used controlled collapse of the {sup 85}Rb condensate for different values of a{sub s}. Our calculations agree with the experimental results within the experimental error bars.

  16. Many-body effects of Coulomb interaction on Landau levels in graphene

    Science.gov (United States)

    Sokolik, A. A.; Zabolotskiy, A. D.; Lozovik, Yu. E.

    2017-03-01

    In strong magnetic fields, massless electrons in graphene populate relativistic Landau levels with the square-root dependence of each level energy on its number and magnetic field. Interaction-induced deviations from this single-particle picture were observed in recent experiments on cyclotron resonance and magneto-Raman scattering. Previous attempts to calculate such deviations theoretically using the unscreened Coulomb interaction resulted in overestimated many-body effects. This work presents many-body calculations of cyclotron and magneto-Raman transitions in single-layer graphene in the presence of Coulomb interaction, which is statically screened in the random-phase approximation. We take into account self-energy and excitonic effects as well as Landau level mixing, and achieve good agreement of our results with the experimental data for graphene on different substrates. The important role of a self-consistent treatment of the screening is found.

  17. Functions of key residues in the ligand-binding pocket of vitamin D receptor: Fragment molecular orbital interfragment interaction energy analysis

    Science.gov (United States)

    Yamagishi, Kenji; Yamamoto, Keiko; Yamada, Sachiko; Tokiwa, Hiroaki

    2006-03-01

    Fragment molecular orbital-interfragment interaction energy calculations of the vitamin D receptor (VDR)/1α,25-dihydroxyvitamin D 3 complex were utilized to assign functions of key residues of the VDR. Only one residue forms a significant interaction with the corresponding hydroxy group of the ligand, although two residues are located around each hydroxy group. The degradation of binding affinity for derivatives upon removal of a hydroxy group is closely related to the trend in the strength of the hydrogen bonds. Type II hereditary rickets due to an Arg274 point mutation is caused by the lack of the strongest hydrogen bond.

  18. FTO Genotype Interacts with Improvement in Aerobic Fitness on Body Weight Loss During Lifestyle Intervention

    Directory of Open Access Journals (Sweden)

    Corinna Sailer

    2016-06-01

    Full Text Available Objective: Not every participant responds with a comparable body weight loss to lifestyle intervention, despite the same compliance. Genetic factors may explain parts of this difference. Variation in fat mass and obesity-associated gene (FTO is the strongest common genetic determinant of body weight. The aim of the present study was to evaluate the impact of FTO genotype differences in the link between improvement of fitness and reduction of body weight during a lifestyle intervention. Methods: We genotyped 292 healthy subjects for FTO rs8050136. Participants underwent a 9-month lifestyle intervention. Before and after intervention, aerobic fitness was tested by bicycle (VO2max and treadmill spiroergometry (individual anaerobic threshold (IAT, subgroup of N = 192. Results: Participants lost body weight (p FTO genotype (p = 0.5. There was a significant correlation between improvement in VO2max and decrease in body weight (p FTO genotype interacted with this relationship (p = 0.0042 for VO2max, p = 0.0049 for IAT. When stratifying the cohort according to their improvement in VO2max, FTO obesity-risk A-allele carriers in the higher quartiles of improvement in fitness lost significantly less body weight. Conclusions: Our data reveal that genetic variation in FTO impacts on body weight reduction during lifestyle intervention only in subjects with marked improvement in aerobic fitness.

  19. Influences of heterogeneous native contact energy and many-body interactions on the prediction of protein folding mechanisms.

    Science.gov (United States)

    Zhang, Zhuqing; Ouyang, Yanhua; Chen, Tao

    2016-11-16

    Since single-point mutant perturbation has been used to probe protein folding mechanisms in experiments, the ϕ-value has become a critical parameter to infer the transition state (TS) for two-state proteins. Experimentally, large scale analysis has shown a nearly single uniform ϕ-value with normally distributed error from 24 different proteins; moreover, in zero stability conditions, the intrinsic variable ϕ(0) is around 0.36. To explore how and to what extent theoretical models can capture experimental phenomena, we here use structure-based explicit chain coarse-grained models to investigate the influence of single-point mutant perturbation on protein folding for single domain two-state proteins. Our results indicate that uniform, additive contact energetic interactions cannot predict experimental Brønsted plots well. Those points deviate largely from the main data sets in Brønsted plots, are mostly hydrophobic, and are located in N- and C-terminal contacting regions. Heterogenous contact energy, which is dependent on sequence separation, can narrow the point dispersion in a Brønsted plot. Moreover, we demonstrate that combining many-body interactions with heterogeneous native contact energy can present mean ϕ-values consistent with experimental findings, with a comparable distributed error. This indicates that for more accurate elucidation of protein folding mechanisms by residue-level structure-based models, these elements should be considered.

  20. The F13 residue is critical for interaction among the coat protein subunits of papaya mosaic virus.

    Science.gov (United States)

    Laliberté Gagné, M E; Lecours, K; Gagné, S; Leclerc, D

    2008-04-01

    Papaya mosaic virus (PapMV) coat protein (CP) in Escherichia coli was previously showed to self-assemble in nucleocapsid-like particles (NLPs) that were similar in shape and appearance to the native virus. We have also shown that a truncated CP missing the N-terminal 26 amino acids is monomeric and loses its ability to bind RNA. It is likely that the N-terminus of the CP is important for the interaction between the subunits in self-assembly into NLPs. In this work, through deletion and mutation analysis, we have shown that the deletion of 13 amino acids is sufficient to generate the monomeric form of the CP. Furthermore, we have shown that residue F13 is critical for self-assembly of the CP subunits into NLPs. The replacement of F13 with hydrophobic residues (L or Y) generated mutated forms of the CP that were able to self-assemble into NLPs. However, the replacement of F13 by A, G, R, E or S was detrimental to the self-assembly of the protein into NLPs. We concluded that a hydrophobic interaction at the N-terminus is important to ensure self-assembly of the protein into NLPs. We also discuss the importance of F13 for assembly of other members of the potexvirus family.

  1. Interaction with specific HSP90 residues as a scoring function: validation in the D3R Grand Challenge 2015

    Science.gov (United States)

    Santos-Martins, Diogo

    2016-09-01

    Here is reported the development of a novel scoring function that performs remarkably well at identifying the native binding pose of a subset of HSP90 inhibitors containing aminopyrimidine or resorcinol based scaffolds. This scoring function is called PocketScore, and consists of the interaction energy between a ligand and three residues in the binding pocket: Asp93, Thr184 and a water molecule. We integrated PocketScore into a molecular docking workflow, and used it to participate in the Drug Design Data Resource (D3R) Grand Challenge 2015 (GC2015). PocketScore was able to rank 180 molecules of the GC2015 according to their binding affinity with satisfactory performance. These results indicate that the specific residues considered by PocketScore are determinant to properly model the interaction between HSP90 and its subset of inhibitors containing aminopyrimidine or resorcinol based scaffolds. Moreover, the development of PocketScore aimed at improving docking power while neglecting the prediction of binding affinities, suggesting that accurate identification of native binding poses is a determinant factor for the performance of virtual screens.

  2. Many-body Systems Interacting via a Two-body Random Ensemble average energy of each angular momentum

    CERN Document Server

    Zhao, Y M; Yoshinaga, N

    2002-01-01

    In this paper, we discuss the regularities of energy of each angular momentum $I$ averaged over all the states for a fixed angular momentum (denoted as $\\bar{E}_I$'s) in many-body systems interacting via a two-body random ensemble. It is found that $\\bar{E}_I$'s with $I \\sim I_{min}$ (minimum of $I$) or $I_{max}$ have large probabilities (denoted as ${\\cal P}(I)$) to be the lowest, and that ${\\cal P}(I)$ is close to zero elsewhere. A simple argument based on the randomness of the two-particle cfp's is given. A compact trajectory of the energy $\\bar{E}_I$ vs. $I(I+1)$ is found to be robust. Regular fluctuations of the $P(I)$ (the probability of finding $I$ to be the ground state) and ${\\cal P}(I)$ of even fermions in a single-$j$ shell and boson systems are found to be reverse, and argued by the dimension fluctuation of the model space. Other regularities, such as why there are 2 or 3 sizable ${\\cal P}(I)$'s with $I\\sim I_{min}$ and ${\\cal P}(I) \\ll {\\cal P}(I_{max})$'s with $I\\sim I_{max}$, why the coefficien...

  3. Structural Characterization and Antioxidative Activity of Low-Molecular-Weights Beta-1,3-Glucan from the Residue of Extracted Ganoderma lucidum Fruiting Bodies

    Directory of Open Access Journals (Sweden)

    Pai-Feng Kao

    2012-01-01

    Full Text Available The major cell wall constituent of Ganoderma lucidum (G. lucidum is β-1,3-glucan. This study examined the polysaccharide from the residues of alkaline-extracted fruiting bodies using high-performance anion-exchange chromatography (HPAEC, and it employed nuclear magnetic resonance (NMR and mass spectrometry (MS to confirm the structures. We have successfully isolated low-molecular-weight β-1,3-glucan (LMG, in high yields, from the waste residue of extracted fruiting bodies of G. lucidum. The 3-(4,5-dimethylthiazol-2-yl-2,5-diphenyl tetrazolium bromide (MTT assay evaluated the capability of LMG to suppress H2O2-induced cell death in RAW264.7 cells, identifying that LMG protected cells from H2O2-induced damage. LMG treatment decreased H2O2-induced intracellular reactive oxygen species (ROS production. LMG also influenced sphingomyelinase (SMase activity, stimulated by cell death to induce ceramide formation, and then increase cell ROS production. Estimation of the activities of neutral and acid SMases in vitro showed that LMG suppressed the activities of both neutral and acid SMases in a concentration-dependent manner. These results suggest that LMG, a water-soluble β-1,3-glucan recycled from extracted residue of G. lucidum, possesses antioxidant capability against H2O2-induced cell death by attenuating intracellular ROS and inhibiting SMase activity.

  4. Sucrose Production Mediated by Lipid Metabolism Suppresses the Physical Interaction of Peroxisomes and Oil Bodies during Germination of Arabidopsis thaliana.

    Science.gov (United States)

    Cui, Songkui; Hayashi, Yasuko; Otomo, Masayoshi; Mano, Shoji; Oikawa, Kazusato; Hayashi, Makoto; Nishimura, Mikio

    2016-09-16

    Physical interaction between organelles is a flexible event and essential for cells to adapt rapidly to environmental stimuli. Germinating plants utilize oil bodies and peroxisomes to mobilize storage lipids for the generation of sucrose as the main energy source. Although membrane interaction between oil bodies and peroxisomes has been widely observed, its underlying molecular mechanism is largely unknown. Here we present genetic evidence for control of the physical interaction between oil bodies and peroxisomes. We identified alleles of the sdp1 mutant altered in oil body morphology. This mutant accumulates bigger and more oil body aggregates compared with the wild type and showed defects in lipid mobilization during germination. SUGAR DEPENDENT 1 (SDP1) encodes major triacylglycerol lipase in Arabidopsis Interestingly, sdp1 seedlings show enhanced physical interaction between oil bodies and peroxisomes compared with the wild type, whereas exogenous sucrose supplementation greatly suppresses the interaction. The same phenomenon occurs in the peroxisomal defective 1 (ped1) mutant, defective in lipid mobilization because of impaired peroxisomal β-oxidation, indicating that sucrose production is a key factor for oil body-peroxisomal dissociation. Peroxisomal dissociation and subsequent release from oil bodies is dependent on actin filaments. We also show that a peroxisomal ATP binding cassette transporter, PED3, is the potential anchor protein to the membranes of these organelles. Our results provide novel components linking lipid metabolism and oil body-peroxisome interaction whereby sucrose may act as a negative signal for the interaction of oil bodies and peroxisomes to fine-tune lipolysis.

  5. Fujiwhara interaction of tropical cyclone scale vortices using a weighted residual collocation method

    CERN Document Server

    Walsh, Raymond P

    2016-01-01

    The fundamental interaction between tropical cyclones was investigated through a series of water tank experiements by Fujiwhara [20, 21, 22]. However, a complete understanding of tropical cyclones remains an open research challenge although there have been numerous investigations through measurments with aircrafts/satellites, as well as with numerical simulations. This article presents a computational model for simulating the interaction between cyclones. The proposed numerical method is presented briefly, where the time integration is performed by projecting the discrete system onto a Krylov subspace. The method filters the large scale fluid dynamics using a multiresolution approximation, and the unresolved dynamics is modeled with a Smagorinsky type subgrid scale parameterization scheme. Numerical experiments with Fujiwhara interactions are considered to verify modeling accuracy. An excellent agreement between the present simulation and a reference simulation at Re = 5000 has been demonstrated. At Re = 3744...

  6. Multi-level learning: improving the prediction of protein, domain and residue interactions by allowing information flow between levels

    Directory of Open Access Journals (Sweden)

    McDermott Drew

    2009-08-01

    Full Text Available Abstract Background Proteins interact through specific binding interfaces that contain many residues in domains. Protein interactions thus occur on three different levels of a concept hierarchy: whole-proteins, domains, and residues. Each level offers a distinct and complementary set of features for computationally predicting interactions, including functional genomic features of whole proteins, evolutionary features of domain families and physical-chemical features of individual residues. The predictions at each level could benefit from using the features at all three levels. However, it is not trivial as the features are provided at different granularity. Results To link up the predictions at the three levels, we propose a multi-level machine-learning framework that allows for explicit information flow between the levels. We demonstrate, using representative yeast interaction networks, that our algorithm is able to utilize complementary feature sets to make more accurate predictions at the three levels than when the three problems are approached independently. To facilitate application of our multi-level learning framework, we discuss three key aspects of multi-level learning and the corresponding design choices that we have made in the implementation of a concrete learning algorithm. 1 Architecture of information flow: we show the greater flexibility of bidirectional flow over independent levels and unidirectional flow; 2 Coupling mechanism of the different levels: We show how this can be accomplished via augmenting the training sets at each level, and discuss the prevention of error propagation between different levels by means of soft coupling; 3 Sparseness of data: We show that the multi-level framework compounds data sparsity issues, and discuss how this can be dealt with by building local models in information-rich parts of the data. Our proof-of-concept learning algorithm demonstrates the advantage of combining levels, and opens up

  7. Effects of residual feed intake and dam body weight on replacement heifer intake, efficiency, performance, and metabolic response.

    Science.gov (United States)

    Walker, R S; Martin, R M; Buttrey, B

    2015-07-01

    Thirty-eight Angus-based, crossbred, nulliparous beef heifers (BW = 280 ± 26.3 kg) sired by 2 Angus sires were used to determine if dam BW affected heifer performance, DMI, residual feed intake (RFI), and endocrine markers. Heifers were housed in individual pens (2.2 by 9.1 m) equipped with 2.2 m of bunk space and fed a diet (90.4% DM, 13.7% CP, 67.2% NDF, and 56.2% TDN) consisting of 87.2% bermudagrass hay and 12.8% liquid protein supplement for a 14-d adaption period and a 70-d feeding period. Individual daily feed intake was used to calculate RFI for each heifer, and heifer was the experimental unit. Two-day beginning and end BW were recorded and hip height was used to calculate frame score (FS). Heifer dams were assigned to a light (LIT; 544 ± 21.3 kg) or heavy (HEV; 621 ± 34.8 kg) BW group on the basis of mean BW at the beginning of their lactation period the previous year to determine differences in heifer offspring DMI and RFI. Based on heifer RFI ranking, heifers were classified as positive (POS; 0.34) or negative (NEG; –0.31) RFI and low (LOW; –0.45), medium (MED; 0.00), or high (HI; 0.49) RFI for analysis of BW, FS, BW gain, and DMI. There were no dam BW group × sire interactions (P > 0.10) for all independent variables. Beginning and end BW was greater (P 0.10) for heifers out of HEV compared with LIT BW dams; however, a sire effect existed (P 0.10) whereas DMI was greater (P = 0.03) among heifers in the POS compared with the NEG RFI group and greater (P = 0.01) among heifers in the MED and HI compared with LOW RFI group, respectively. Plasma insulin levels were greater (P = 0.03) in the NEG compared with the POS RFI heifers, and thyroxine (T4) levels were greater (P = 0.02) in the POS compared with the NEG RFI heifers. A positive relationship existed (P ≤ 0.05) between dam BW and heifer DMI (r = 0.42), beginning and end BW (r = 0.45 and 54), and FS (r = 0.58) and between RFI and d 70 triiodothyronine (r = 0.34), d 70 T4 (r = 0.35), and d 0 and

  8. Wall effect on fluid-structure interactions of a tethered bluff body

    Science.gov (United States)

    Sharma, Sumant; Raghav, Vrishank; Komerath, Narayanan; Smith, Marilyn

    2013-11-01

    Wind tunnel experiments have shown an unexplained amplification of the free motion of a tethered bluff body in a small wind tunnel relative to that in a large wind tunnel. The influence of wall proximity on fluid-structure interaction is explored using a compound pendulum motion in the plane orthogonal to a steady freestream with a doublet model for aerodynamic forces. Wall proximity amplifies a purely symmetric single degree of freedom oscillation with the addition of an out-of-phase force. The success of this simple level of simulation enables progress to develop metrics for unsteady wall interference in dynamic testing of tethered bluff bodies.

  9. Phonon-magnon interactions in body centered cubic iron: A combined molecular and spin dynamics study

    Energy Technology Data Exchange (ETDEWEB)

    Perera, Dilina, E-mail: dilinanp@physast.uga.edu; Landau, David P. [Center for Simulational Physics, The University of Georgia, Georgia 30602 (United States); Nicholson, Don M.; Malcolm Stocks, G.; Eisenbach, Markus; Yin, Junqi [Oak Ridge National Laboratory, Oak Ridge, Tennessee 37831 (United States); Brown, Gregory [Florida State University, Tallahassee, Florida 32306 (United States)

    2014-05-07

    Combining an atomistic many-body potential with a classical spin Hamiltonian parameterized by first principles calculations, molecular-spin dynamics computer simulations were performed to investigate phonon-magnon interactions in body centered cubic iron. Results obtained for spin-spin and density-density dynamic structure factors show that noticeable softening and damping of magnon modes occur due to the presence of lattice vibrations. Furthermore, as a result of the phonon-magnon coupling, additional longitudinal spin wave excitations are observed, with the same frequencies as the longitudinal phonon modes.

  10. Validation of a Wave-Body Interaction Model by Experimental Tests

    DEFF Research Database (Denmark)

    Ferri, Francesco; Kramer, Morten; Pecher, Arthur

    2013-01-01

    Within the wave energy field, numerical simulation has recently acquired a worldwide consent as being a useful tool, besides physical model testing. The main goal of this work is the validation of a numerical model by experimental results. The numerical model is based on a linear wave-body intera......-body interaction theory, applied for a point absorber wave energy converter. The results show that the ratio floater size/wave amplitude is a key parameter for the validity of the applied theory....

  11. A Pipeline for Constructing Optimized N-Body Models of Interacting Galaxies

    Science.gov (United States)

    Harvey, Allen S., Jr.

    Galaxies form the building blocks of our understanding of a hierarchical evolution of the universe. Galaxies interact with other galaxies by impacting each other's gravitational fields, exchanging mass, spurring star formation, and even by merging. As sky surveys continue to capture images of interacting galaxies as they were in a snapshot of time so long ago, simulations of their evolution are needed to understand how they have arrived at their observed state. Restricted three-body simulations have advanced to produce realistic gravitational potentials to rapidly model interacting galaxies. Much research has been conducted to advance the creation and convergence of these models to obtain good matches to observed galaxies. Unfortunately, these models lack the physics for rich and realistic tidal features, gas dynamics, stellar black holes, and star formation, among others, that necessitate the use of higher fidelity models, such as N-Body gravity methods. The parameters describing the interacting galaxies from a restricted three-body simulation can be backwards integrated to estimate reasonable initial parameters for the galaxies well before their observed state. However, the backwards and forward integration in time of these simulations must be tuned by carefully choosing a tuning scalar to capture the dynamical friction of the interacting galaxies. This dissertation presents a prototype pipeline to link computationally efficient restricted three-body simulations of galaxy interactions to full, high resolution N-Body simulations. The software iterates between both classes of simulations to converge on the best match to an observed galaxy merger state. The system begins with a state vector from a merger at its peri-center as determined by the restricted three-body simulation code, SPAM, with an uncertain value for a dynamical friction scalar. The pipeline uses this vector to backwards integrate another SPAMmodel that systematically varies a scalar for dynamical

  12. PTPRT regulates the interaction of Syntaxin-binding protein 1 with Syntaxin 1 through dephosphorylation of specific tyrosine residue

    Energy Technology Data Exchange (ETDEWEB)

    Lim, So-Hee; Moon, Jeonghee [Biomedical Proteomics Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305-806 (Korea, Republic of); Lee, Myungkyu [Bionanotechnology Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305-806 (Korea, Republic of); Lee, Jae-Ran, E-mail: leejr@kribb.re.kr [Biomedical Proteomics Research Center, Korea Research Institute of Bioscience and Biotechnology, Daejeon 305-806 (Korea, Republic of)

    2013-09-13

    Highlights: •PTPRT is a brain-specific, expressed, protein tyrosine phosphatase. •PTPRT regulated the interaction of Syntaxin-binding protein 1 with Syntaxin 1. •PTPRT dephosphorylated the specific tyrosine residue of Syntaxin-binding protein 1. •Dephosphorylation of Syntaxin-binding protein 1 enhanced the interaction with Syntaxin 1. •PTPRT appears to regulate the fusion of synaptic vesicle through dephosphorylation. -- Abstract: PTPRT (protein tyrosine phosphatase receptor T), a brain-specific tyrosine phosphatase, has been found to regulate synaptic formation and development of hippocampal neurons, but its regulation mechanism is not yet fully understood. Here, Syntaxin-binding protein 1, a key component of synaptic vesicle fusion machinery, was identified as a possible interaction partner and an endogenous substrate of PTPRT. PTPRT interacted with Syntaxin-binding protein 1 in rat synaptosome, and co-localized with Syntaxin-binding protein 1 in cultured hippocampal neurons. PTPRT dephosphorylated tyrosine 145 located around the linker between domain 1 and 2 of Syntaxin-binding protein 1. Syntaxin-binding protein 1 directly binds to Syntaxin 1, a t-SNARE (soluble N-ethylmaleimide-sensitive factor attachment protein receptor) protein, and plays a role as catalysts of SNARE complex formation. Syntaxin-binding protein 1 mutant mimicking non-phosphorylation (Y145F) enhanced the interaction with Syntaxin 1 compared to wild type, and therefore, dephosphorylation of Syntaxin-binding protein 1 appeared to be important for SNARE-complex formation. In conclusion, PTPRT could regulate the interaction of Syntaxin-binding protein 1 with Syntaxin 1, and as a result, the synaptic vesicle fusion appeared to be controlled through dephosphorylation of Syntaxin-binding protein 1.

  13. Consistent description of 12C and 16O using finite range three-body interaction

    CERN Document Server

    Itagaki, N

    2016-01-01

    Consistent description of 12C and 16O has been a long standing problem of microscopic alpha cluster models, where the wave function is fully antisymmetrized and the effective interaction is applied not between alpha clusters but between nucleons. When the effective interaction is designed to reproduce the binding energy of 16O (four alpha), the binding energy of 12C (three alpha) becomes underbound by about 10 MeV. In the present study, by taking into account the coupling with the jj-coupling shell model components and utilizing Tohsaki interaction, which is phenomenological but has finite-range three-body interaction terms, we show that consistent understanding of these nuclei can be achieved. The original Tohsaki interaction gives small overbound of about 3 MeV for 16O, and this is improved by slightly modifying three-body Majorana exchange parameter. Also, the coupling with the jj-coupling shell model wave function strongly contributes to the increase of the binding energy of 12C. So far the application of...

  14. Role of interactions in a dissipative many-body localized system

    Science.gov (United States)

    Everest, Benjamin; Lesanovsky, Igor; Garrahan, Juan P.; Levi, Emanuele

    2017-01-01

    Recent experimental and theoretical efforts have focused on the effect of dissipation on quantum many-body systems in their many-body localized (MBL) phase. While in the presence of dephasing noise such systems reach a unique ergodic state, their dynamics is characterized by slow relaxation manifested in nonexponential decay of self-correlations. Here we shed light on a currently much debated issue, namely, the role of interactions for this relaxation dynamics. We focus on the experimentally relevant situation of the evolution from an initial charge density wave in the presence of strong dephasing noise. We find a crossover from a regime dominated by disorder to a regime dominated by interactions, with an accompanying change of time correlators from stretched exponential to compressed exponential form. The strongly interacting regime can be explained in terms of nucleation and growth dynamics of relaxing regions—reminiscent of the kinetics of crystallization in soft matter systems—and should be observable experimentally. This interaction-driven crossover suggests that the competition between interactions and noise gives rise to a much richer structure of the MBL phase than anticipated so far.

  15. One spatial dimensional finite volume three-body interaction for a short-range potential

    CERN Document Server

    Guo, Peng

    2016-01-01

    In this work, we use McGuire's model to describe scattering of three spinless identical particles in one spatial dimension, we first present analytic solutions of Faddeev's equation for scattering of three spinless particles in free space. The three particles interaction in finite volume is derived subsequently, and the quantization conditions by matching wave functions in free space and finite volume are presented in terms of two-body scattering phase shifts. The quantization conditions obtained in this work for short range interaction are L\\"uscher's formula like and consistent with Yang's results in \\cite{Yang:1967bm}.

  16. Strain Control of Fermiology and Many-Body Interactions in Two-Dimensional Ruthenates

    Science.gov (United States)

    Burganov, B.; Adamo, C.; Mulder, A.; Uchida, M.; King, P. D. C.; Harter, J. W.; Shai, D. E.; Gibbs, A. S.; Mackenzie, A. P.; Uecker, R.; Bruetzam, M.; Beasley, M. R.; Fennie, C. J.; Schlom, D. G.; Shen, K. M.

    2016-05-01

    Here we demonstrate how the Fermi surface topology and quantum many-body interactions can be manipulated via epitaxial strain in the spin-triplet superconductor Sr2RuO4 and its isoelectronic counterpart Ba2RuO4 using oxide molecular beam epitaxy, in situ angle-resolved photoemission spectroscopy, and transport measurements. Near the topological transition of the γ Fermi surface sheet, we observe clear signatures of critical fluctuations, while the quasiparticle mass enhancement is found to increase rapidly and monotonically with increasing Ru-O bond distance. Our work demonstrates the possibilities for using epitaxial strain as a disorder-free means of manipulating emergent properties, many-body interactions, and potentially the superconductivity in correlated materials.

  17. Hyperchaos of two coupled Bose-Einstein condensates with a three-body interaction

    Institute of Scientific and Technical Information of China (English)

    Wang Zhi-Xia; Zhang Xi-He; Shen Ke

    2008-01-01

    We investigate the dynamics of two tunnel-coupled Boee-Einstein condensates(BECs)in a double-well potential.The effects of the three-body recombination loss and the feeding of the condensates from the thermal cloud are studied in the case of attractive interatomic interaction.An imaginary three-body interaction term is considered and a two-mode approximation is used to derive three coupled equations which describe the total atomic numbers of the two condensates,the relative population and relative phase respectively.Theoretical analyses and numerical calculations demonstrate the existence of chaotic and hyperchaotic behaviour by using a periodically time-varying scattering length.

  18. Many-body localization transition in random quantum spin chains with long-range interactions

    Science.gov (United States)

    Moure, N.; Haas, S.; Kettemann, S.

    2015-07-01

    While there are well-established methods to study delocalization transitions of single particles in random systems, it remains a challenging problem how to characterize many-body delocalization transitions. Here, we use a generalized real-space renormalization group technique to study the anisotropic Heisenberg model with long-range interactions, decaying with a power α, which are generated by placing spins at random positions along the chain. This method permits a large-scale finite-size scaling analysis. We examine the full distribution function of the excitation energy gap from the ground state and observe a crossover with decreasing α. At αc the full distribution coincides with a critical function. Thereby, we find strong evidence for the existence of a many-body localization transition in disordered antiferromagnetic spin chains with long-range interactions.

  19. Coulomb-Sturmian separable expansion approach three-body Faddeev calculations for Coulomb-like interactions

    CERN Document Server

    Papp, Z

    1996-01-01

    We demonstrate the feasibility and efficiency of the Coulomb-Sturmian separable expansion method for generating accurate solutions of the Faddeev equations. Results obtained with this method are reported for several benchmark cases of bosonic and fermionic three-body systems. Correct bound-state results in agreement with the ones established in the literature are achieved for short-range interactions. We outline the formalism for the treatment of three-body Coulomb systems and present a bound-state calculation for a three-boson system interacting via Coulomb plus short-range forces. The corresponding result is in good agreement with the answer from a recent stochastic-variational-method calculation.

  20. Few-body Cs Rydberg Atom Interactions in a 1064 nm Dipole Trap

    Science.gov (United States)

    Booth, Donald; Tallant, Jonathan; Marangoni, Bruno; Marcassa, Luis; Shaffer, James

    2011-05-01

    In studying few-body physics, the number density of atoms is an important parameter in achieving a good signal to noise ratio. We have recently improved our apparatus by implementing a crossed 1064 nm far off-resonance trap (FORT), which enables us to trap atoms at three orders of magnitude greater density than our MOT. Future directions for the apparatus, which include the study of anisotropic interactions among Rydberg atoms in the dipole trap, three-body recombination, ``trilobite-like'' molecules, and the detection of ultra-long range Rydberg macrodimers in Cs, will be described. Our presentation will focus on data on three-body recombination and long-range Rydberg ``trilobite-like'' molecules. We acknowledge funding from ARO (W911NF-08-1-0257), NSF (PHY-0855324) and NSF (OISE-0756321).

  1. Comparison of electromagnetically induced transparency schemes in semiconductor quantum dot structures: Impact of many-body interactions

    DEFF Research Database (Denmark)

    Houmark-Nielsen, Jakob; Nielsen, Torben Roland; Mørk, Jesper;

    2009-01-01

    We investigate the impact of many-body interactions on group-velocity slowdown achieved via electromagnetically induced transparency in quantum dots using three different coupling-probe schemes (ladder, V, and Lambda, respectively). We find that for all schemes many-body interactions have...

  2. Evidence for the Activation of Sensorimotor Information during Visual Word Recognition: The Body-Object Interaction Effect

    Science.gov (United States)

    Siakaluk, Paul D.; Pexman, Penny M.; Aguilera, Laura; Owen, William J.; Sears, Christopher R.

    2008-01-01

    We examined the effects of sensorimotor experience in two visual word recognition tasks. Body-object interaction (BOI) ratings were collected for a large set of words. These ratings assess perceptions of the ease with which a human body can physically interact with a word's referent. A set of high BOI words (e.g., "mask") and a set of low BOI…

  3. Partial dynamical symmetry as a selection criterion for many-body interactions

    CERN Document Server

    Leviatan, A; Van Isacker, P

    2013-01-01

    We propose the use of partial dynamical symmetry (PDS) as a selection criterion for higher-order terms in situations when a prescribed symmetry is obeyed by some states and is strongly broken in others. The procedure is demonstrated in a first systematic classification of many-body interactions with SU(3) PDS that can improve the description of deformed nuclei. As an example, the triaxial features of the nucleus 156Gd are analyzed.

  4. Ground state spin 0$^+$ dominance of many-body systems with random interactions and related topics

    CERN Document Server

    Arima, A; Zhao, Y M

    2003-01-01

    In this talk we shall show our recent results in understanding the spin$^{\\rm parity}$ 0$^+$ ground state (0 g.s.) dominance of many-body systems. We propose a simple approach to predict the spin $I$ g.s. probabilities which does not require the diagonalization of a Hamiltonian with random interactions. Some findings related to the 0 g.s. dominance will also be discussed.

  5. Accurate method for the Brownian dynamics simulation of spherical particles with hard-body interactions

    Science.gov (United States)

    Barenbrug, Theo M. A. O. M.; Peters, E. A. J. F. (Frank); Schieber, Jay D.

    2002-11-01

    In Brownian Dynamics simulations, the diffusive motion of the particles is simulated by adding random displacements, proportional to the square root of the chosen time step. When computing average quantities, these Brownian contributions usually average out, and the overall simulation error becomes proportional to the time step. A special situation arises if the particles undergo hard-body interactions that instantaneously change their properties, as in absorption or association processes, chemical reactions, etc. The common "naı̈ve simulation method" accounts for these interactions by checking for hard-body overlaps after every time step. Due to the simplification of the diffusive motion, a substantial part of the actual hard-body interactions is not detected by this method, resulting in an overall simulation error proportional to the square root of the time step. In this paper we take the hard-body interactions during the time step interval into account, using the relative positions of the particles at the beginning and at the end of the time step, as provided by the naı̈ve method, and the analytical solution for the diffusion of a point particle around an absorbing sphere. Öttinger used a similar approach for the one-dimensional case [Stochastic Processes in Polymeric Fluids (Springer, Berlin, 1996), p. 270]. We applied the "corrected simulation method" to the case of a simple, second-order chemical reaction. The results agree with recent theoretical predictions [K. Hyojoon and Joe S. Kook, Phys. Rev. E 61, 3426 (2000)]. The obtained simulation error is proportional to the time step, instead of its square root. The new method needs substantially less simulation time to obtain the same accuracy. Finally, we briefly discuss a straightforward way to extend the method for simulations of systems with additional (deterministic) forces.

  6. Parameters of social existence and social functioning of lesbians: Lesbian body in processes of social interactions

    OpenAIRE

    Mršević Zorica Ž.

    2004-01-01

    Analysis of characteristics of a lesbian body in processes of social interaction is a method of analysis social relations of lesbians, their relationships with the heterosexual world and revealing specific lesbian practices, outlooks, habits and customs, behavior and general characteristics of lesbian sub culture. Making somebody different than a "normal human", meaning less human, is the main way of making the whole group target of justified discrimination, violence and hate crime. Therefore...

  7. Interactive Structure (EUCLID) For Static And Dynamic Representation Of Human Body

    Science.gov (United States)

    Renaud, Ch.; Steck, R.

    1983-07-01

    A specific software (EUCLID) for static and dynamic representation of human models is described. The data processing system is connected with ERGODATA and used in interactive mode by intrinsic or specific functions. More or less complex representations in 3-D view of models of the human body are developed. Biostereometric and conventional anthropometric raw data from the data bank are processed for different applications in ergonomy.

  8. Growth performance, feed digestibility, body composition, and feeding behavior of high- and low-residual feed intake fat-tailed lambs under moderate feed restriction.

    Science.gov (United States)

    Rajaei Sharifabadi, H; Naserian, A A; Valizadeh, R; Nassiry, M R; Bottje, W G; Redden, R R

    2016-08-01

    Two experiments were conducted to evaluate the effect of moderate feed restriction on productivity of lambs classified on the basis of phenotypic expression of residual feed intake (RFI). In Exp. 1, 58 fat-tailed Kurdi ram lambs (32.1 ± 4.2 kg BW) were individually fed, ad libitum, a pelleted diet (35% alfalfa hay and 65% concentrate). Feed intake and ADG were determined for a 6-wk period and 3 feed efficiency measures including RFI, G:F, and partial efficiency of maintenance (PEM) were calculated. The lambs were sorted based on RFI and the 16 highest RFI (RFI ≥ mean + 0.5 SD) and 16 lowest RFI (RFI ≤ mean - 0.5 SD) lambs were subjected to body composition (BC) and DM digestibility (DMD) analysis. Feeding behavior traits (FB) were also evaluated for 24 h using a regular 5-min interval observation method. The high- and low-RFI lambs (14 lambs/RFI group) so classified in Exp. 1 were used in Exp. 2. Half of the lambs in each RFI group were randomly selected to be fed ad libitum or 85% of ad libitum (restricted feeding), which resulted in 4 experimental groups: 1) ad libitum high-RFI, 2) feed restricted high-RFI, 3) ad libitum low-RFI, and 4) feed restricted low-RFI. The lambs were fed the same diet as Exp. 1, and growth efficiency during a 6-wk test period as well as BC, DMD, and FB were also determined in Exp. 2. In Exp. 1, the low-RFI lambs consumed 14% ( feed than high-RFI lambs. Differences were also observed between high- and low-RFI groups for G:F ( = 0.01), RFI ( 0.72), and FB ( > 0.24). In Exp.2, the restriction feeding regime negatively affected ADG ( feed restriction condition. No effects of feed restriction on DMD ( = 0.87) and BC ( > 0.05) were observed. The lambs fed at the restricted level of intake presented a greater time ( feeding events were decreased ( feed restriction, no interaction ( > 0.05) was detected between RFI phenotype and feeding regime for FB. In summary, feeding high-RFI lambs at 85% of ad libitum level improved G:F with no effect

  9. An interactive VR system based on full-body tracking and gesture recognition

    Science.gov (United States)

    Zeng, Xia; Sang, Xinzhu; Chen, Duo; Wang, Peng; Guo, Nan; Yan, Binbin; Wang, Kuiru

    2016-10-01

    Most current virtual reality (VR) interactions are realized with the hand-held input device which leads to a low degree of presence. There is other solutions using sensors like Leap Motion to recognize the gestures of users in order to interact in a more natural way, but the navigation in these systems is still a problem, because they fail to map the actual walking to virtual walking only with a partial body of the user represented in the synthetic environment. Therefore, we propose a system in which users can walk around in the virtual environment as a humanoid model, selecting menu items and manipulating with the virtual objects using natural hand gestures. With a Kinect depth camera, the system tracks the joints of the user, mapping them to a full virtual body which follows the move of the tracked user. The movements of the feet can be detected to determine whether the user is in walking state, so that the walking of model in the virtual world can be activated and stopped by means of animation control in Unity engine. This method frees the hands of users comparing to traditional navigation way using hand-held device. We use the point cloud data getting from Kinect depth camera to recognize the gestures of users, such as swiping, pressing and manipulating virtual objects. Combining the full body tracking and gestures recognition using Kinect, we achieve our interactive VR system in Unity engine with a high degree of presence.

  10. Fluid-structure interaction of complex bodies in two-phase flows on locally refined grids

    Science.gov (United States)

    Angelidis, Dionysios; Shen, Lian; Sotiropoulos, Fotis

    2016-11-01

    Many real-life flow problems in engineering applications involve fluid-structure interaction (FSI) of arbitrarily complex geometries interacting with free surface flows. Despite the recent significant computational advances, conventional numerical methods are inefficient to resolve the prevailing complex dynamics due to the inherent large disparity of spatial and temporal scales that emerge in the air/water phases of the flow and around rigid bodies. To this end, the new generation 3D, unsteady, unstructured Cartesian incompressible flow solver, developed at the Saint Anthony Falls Laboratory (SAFL), is integrated with a FSI immersed boundary method and is coupled with the level-set formulation. The predictive capabilities of our method to simulate non-linear free surface phenomena, with low computational cost, are significantly improved by locally refining the computational grid in the vicinity of solid boundaries and around the free surface interface. We simulate three-dimensional complex flows involving complex rigid bodies interacting with a free surface both with prescribed body motion and coupled FSI and we investigate breaking wave events. In all the cases, very good agreement with benchmark data is found. This material is based upon work supported by the National Science Foundation (CBET-1509071).

  11. The First Residue of the PWWP Motif Modulates HATH Domain Binding, Stability, and Protein-Protein Interaction.

    Science.gov (United States)

    Hung, Yi-Lin; Lee, Hsia-Ju; Jiang, Ingjye; Lin, Shang-Chi; Lo, Wei-Cheng; Lin, Yi-Jan; Sue, Shih-Che

    2015-07-01

    Hepatoma-derived growth factor (hHDGF) and HDGF-related proteins (HRPs) contain conserved N-terminal HATH domains with a characteristic structural motif, namely the PWWP motif. The HATH domain has attracted attention because of its ability to bind with heparin/heparan sulfate, DNA, and methylated histone peptide. Depending on the sequence of the PWWP motif, HRP HATHs are classified into P-type (Pro-His-Trp-Pro) and A-type (Ala-His-Trp-Pro) forms. A-type HATH is highly unstable and tends to precipitate in solution. We replaced the Pro residue in P-type HATHHDGF with Ala and evaluated the influence on structure, dynamics, and ligand binding. Nuclear magnetic resonance (NMR) hydrogen/deuterium exchange and circular dichroism (CD) measurements revealed reduced stability. Analysis of NMR backbone (15)N relaxations (R1, R2, and nuclear Overhauser effect) revealed additional backbone dynamics in the interface between the β-barrel and the C-terminal helix bundle. The β1-β2 loop, where the AHWP sequence is located, has great structural flexibility, which aids HATH-HATH interaction through the loop. A-type HATH, therefore, shows a stronger tendency to aggregate when binding with heparin and DNA oligomers. This study defines the role of the first residue of the PWWP motif in modulating HATH domain stability and oligomer formation in binding.

  12. Fast and accurate multivariate Gaussian modeling of protein families: predicting residue contacts and protein-interaction partners.

    Directory of Open Access Journals (Sweden)

    Carlo Baldassi

    Full Text Available In the course of evolution, proteins show a remarkable conservation of their three-dimensional structure and their biological function, leading to strong evolutionary constraints on the sequence variability between homologous proteins. Our method aims at extracting such constraints from rapidly accumulating sequence data, and thereby at inferring protein structure and function from sequence information alone. Recently, global statistical inference methods (e.g. direct-coupling analysis, sparse inverse covariance estimation have achieved a breakthrough towards this aim, and their predictions have been successfully implemented into tertiary and quaternary protein structure prediction methods. However, due to the discrete nature of the underlying variable (amino-acids, exact inference requires exponential time in the protein length, and efficient approximations are needed for practical applicability. Here we propose a very efficient multivariate Gaussian modeling approach as a variant of direct-coupling analysis: the discrete amino-acid variables are replaced by continuous Gaussian random variables. The resulting statistical inference problem is efficiently and exactly solvable. We show that the quality of inference is comparable or superior to the one achieved by mean-field approximations to inference with discrete variables, as done by direct-coupling analysis. This is true for (i the prediction of residue-residue contacts in proteins, and (ii the identification of protein-protein interaction partner in bacterial signal transduction. An implementation of our multivariate Gaussian approach is available at the website http://areeweb.polito.it/ricerca/cmp/code.

  13. Residues of the UL25 protein of herpes simplex virus that are required for its stable interaction with capsids.

    Science.gov (United States)

    Cockrell, Shelley K; Huffman, Jamie B; Toropova, Katerina; Conway, James F; Homa, Fred L

    2011-05-01

    The herpes simplex virus 1 (HSV-1) UL25 gene product is a minor capsid component that is required for encapsidation, but not cleavage, of replicated viral DNA. UL25 is located on the capsid surface in a proposed heterodimer with UL17, where five copies of the heterodimer are found at each of the capsid vertices. Previously, we demonstrated that amino acids 1 to 50 of UL25 are essential for its stable interaction with capsids. To further define the UL25 capsid binding domain, we generated recombinant viruses with either small truncations or amino acid substitutions in the UL25 N terminus. Studies of these mutants demonstrated that there are two important regions within the capsid binding domain. The first 27 amino acids are essential for capsid binding of UL25, while residues 26 to 39, which are highly conserved in the UL25 homologues of other alphaherpesviruses, were found to be critical for stable capsid binding. Cryo-electron microscopy reconstructions of capsids containing either a small tag on the N terminus of UL25 or the green fluorescent protein (GFP) fused between amino acids 50 and 51 of UL25 demonstrate that residues 1 to 27 of UL25 contact the hexon adjacent to the penton. A second region, most likely centered on amino acids 26 to 39, contacts the triplex that is one removed from the penton. Importantly, both of these UL25 capsid binding regions are essential for the stable packaging of full-length viral genomes.

  14. Residues of the UL25 Protein of Herpes Simplex Virus That Are Required for Its Stable Interaction with Capsids ▿

    Science.gov (United States)

    Cockrell, Shelley K.; Huffman, Jamie B.; Toropova, Katerina; Conway, James F.; Homa, Fred L.

    2011-01-01

    The herpes simplex virus 1 (HSV-1) UL25 gene product is a minor capsid component that is required for encapsidation, but not cleavage, of replicated viral DNA. UL25 is located on the capsid surface in a proposed heterodimer with UL17, where five copies of the heterodimer are found at each of the capsid vertices. Previously, we demonstrated that amino acids 1 to 50 of UL25 are essential for its stable interaction with capsids. To further define the UL25 capsid binding domain, we generated recombinant viruses with either small truncations or amino acid substitutions in the UL25 N terminus. Studies of these mutants demonstrated that there are two important regions within the capsid binding domain. The first 27 amino acids are essential for capsid binding of UL25, while residues 26 to 39, which are highly conserved in the UL25 homologues of other alphaherpesviruses, were found to be critical for stable capsid binding. Cryo-electron microscopy reconstructions of capsids containing either a small tag on the N terminus of UL25 or the green fluorescent protein (GFP) fused between amino acids 50 and 51 of UL25 demonstrate that residues 1 to 27 of UL25 contact the hexon adjacent to the penton. A second region, most likely centered on amino acids 26 to 39, contacts the triplex that is one removed from the penton. Importantly, both of these UL25 capsid binding regions are essential for the stable packaging of full-length viral genomes. PMID:21411517

  15. Interaction of residue tetracycline hydrochloride in milk with β-galactosidase protein by multi-spectrum methods and molecular docking

    Science.gov (United States)

    Gao, Xin; Bi, Hongna; Zuo, Huijun; Jia, Jingjing; Tang, Lin

    2017-08-01

    The purpose of this study was to explore the effect of residue tetracycline hydrochloride (TCH) in milk on molecular structure and activity of β-Gal. Inhibition kinetics assay showed the TCH inhibited β-Gal activity reversibly in a competitive manner. In addition, differences in the activity of β-Gal in the absence and presence of TCH as a function of pH and temperature were found although the optimum pH and temperature of β-Gal remained similar. Fluorescence experiment results showed that TCH effectively quenched the intrinsic fluorescence of β-Gal via static quenching. Thermodynamic parameters delineated the major roles of electrostatic forces played between β-Gal and TCH. Additionally, synchronous fluorescence and circular dichroism spectra (CD spectra) results indicated the secondary structure of β-Gal was changed due to the formation of β-Gal-TCH complexes. The molecular docking further revealed that TCH interacted with some amino acid residues of β-Gal, affecting the active site of the enzyme and thus leading to change in enzyme activity. These alterations in conformation and activity of β-Gal should be taken into consideration while using β-Gal for producing oligosaccharide prebiotics on dairy industries.

  16. Transient interaction model of electromagnetic field generated by lightning current pulses and human body

    Science.gov (United States)

    Iváncsy, T.; Kiss, I.; Szücs, L.; Tamus, Z. Á.

    2015-10-01

    The lightning current generates time-varying magnetic field near the down- conductor and the down-conductors are mounted on the wall of the buildings where residential places might be situated. It is well known that the rapidly changing magnetic fields can generate dangerous eddy currents in the human body.The higher duration and gradient of the magnetic field can cause potentially life threatening cardiac stimulation. The coupling mechanism between the electromagnetic field and the human body is based on a well-known physical phenomena (e.g. Faradays law of induction). However, the calculation of the induced current is very complicated because the shape of the organs is complex and the determination of the material properties of living tissues is difficult, as well. Our previous study revealed that the cardiac stimulation is independent of the rising time of the lightning current and only the peak of the current counts. In this study, the authors introduce an improved model of the interaction of electromagnetic fields of lighting current near down-conductor and human body. Our previous models are based on the quasi stationer field calculations, the new improved model is a transient model. This is because the magnetic field around the down-conductor and in the human body can be determined more precisely, therefore the dangerous currents in the body can be estimated.

  17. Genotype by Energy Expenditure Interaction and Body Composition Traits: The Portuguese Healthy Family Study

    Directory of Open Access Journals (Sweden)

    D. M. Santos

    2014-01-01

    Full Text Available Background and Aims. Energy expenditure has been negatively correlated with fat accumulation. However, this association is highly variable. In the present study we applied a genotype by environment interaction method to examine the presence of Genotype x by Total Daily Energy Expenditure and Genotype x by Daily Energy Expenditure interactions in the expression of different body composition traits. Methods and Results. A total of 958 subjects from 294 families of The Portuguese Healthy Family Study were included in the analysis. TDEE and DEE were assessed using a physical activity recall. Body fat percentages were measured with a bioelectrical impedance scale. GxTDEE and GxDEE examinations were performed using SOLAR 4.0 software. All BC traits were significantly heritable, with heritabilities ranging from 21% to 34%. The GxTDEE and GxDEE interaction models fitted the data better than the polygenic model for all traits. For all traits, a significant GxTDEE and GxDEE interaction was due to variance heterogeneity among distinct levels of TDEE and DEE. For WC, GxTDEE was also significant due to the genetic correlation function. Conclusions. TDEE and DEE are environmental constraints associated with the expression of individuals’ BC genotypes, leading to variability in the phenotypic expression of BC traits.

  18. Human UBL5 protein interacts with coilin and meets the Cajal bodies

    Energy Technology Data Exchange (ETDEWEB)

    Švéda, Martin; Častorálová, Markéta; Lipov, Jan; Ruml, Tomáš; Knejzlík, Zdeněk, E-mail: knejzliz@vscht.cz

    2013-06-28

    Highlights: •Localization of the UBL5 protein in Hela cells was determined by fluorescence microscopy and biochemical fractionation. •Colocalization of UBL5 with Cajal bodies was observed. •Interaction of UBL5 with coilin was proven by pull-down. -- Abstract: UBL5 protein, a structural homologue of ubiquitin, was shown to be involved in pre-mRNA splicing and transcription regulation in yeast and Caenorhabditis elegans, respectively. However, role of the UBL5 human orthologue is still elusive. In our study, we observed that endogenous human UBL5 that was localized in the nucleus, partially associates with Cajal bodies (CBs), nuclear domains where spliceosomal components are assembled. Simultaneous expression of exogenous UBL5 and coilin resulted in their nuclear colocalization in HeLa cells. The ability of UBL5 to interact with coilin was proved by GST pull-down assay using coilin that was either in vitro translated or extracted from HEK293T cells. Further, our results showed that the UBL5–coilin interaction was not influenced by coilin phosphorylation. These results suggest that UBL5 could be targeted to CBs via its interaction with coilin. Relation between human UBL5 protein and CBs is in the agreement with current observations about yeast orthologue Hub1 playing important role in alternative splicing.

  19. Sensitivity of P-glycoprotein tryptophan residues to benzodiazepines and ATP interaction.

    Science.gov (United States)

    Lima, Sofia A C; Cordeiro-da-Silva, Anabela; de Castro, Baltazar; Gameiro, Paula

    2007-01-01

    Plasma membrane P-glycoprotein is a member of the ATP-binding cassette family of membrane transporters. In the present study tryptophan intrinsic fluorescence was used to understand the P-glycoprotein response to three benzodiazepines (bromazepam, chlordiazepoxide and flurazepam) in the presence and absence of ATP. Fluorescence emission spectra showed a red shift on the maximal emission wavelength upon interaction of P-glycoprotein with all benzodiazepines. Benzodiazepine association with nucleotide-bound P-glycoprotein also showed this trend and the quenching profile was attributed to a sphere-of-action model, for static fluorescence. Furthermore, quenching data of benzodiazepine-bound P-glycoprotein with ATP were concentration dependent and saturable, indicating that nucleotide binds to P-glycoprotein whether drug is present or not. These results seems in agreement with the proposal of the ATP-switch model by Higgins and Linton, where substrate binding to the transporters initiates the transport cycle by increasing the ATP binding affinity.

  20. Computational Analysis of Residue Interaction Networks and Coevolutionary Relationships in the Hsp70 Chaperones: A Community-Hopping Model of Allosteric Regulation and Communication.

    Directory of Open Access Journals (Sweden)

    Gabrielle Stetz

    2017-01-01

    Full Text Available Allosteric interactions in the Hsp70 proteins are linked with their regulatory mechanisms and cellular functions. Despite significant progress in structural and functional characterization of the Hsp70 proteins fundamental questions concerning modularity of the allosteric interaction networks and hierarchy of signaling pathways in the Hsp70 chaperones remained largely unexplored and poorly understood. In this work, we proposed an integrated computational strategy that combined atomistic and coarse-grained simulations with coevolutionary analysis and network modeling of the residue interactions. A novel aspect of this work is the incorporation of dynamic residue correlations and coevolutionary residue dependencies in the construction of allosteric interaction networks and signaling pathways. We found that functional sites involved in allosteric regulation of Hsp70 may be characterized by structural stability, proximity to global hinge centers and local structural environment that is enriched by highly coevolving flexible residues. These specific characteristics may be necessary for regulation of allosteric structural transitions and could distinguish regulatory sites from nonfunctional conserved residues. The observed confluence of dynamics correlations and coevolutionary residue couplings with global networking features may determine modular organization of allosteric interactions and dictate localization of key mediating sites. Community analysis of the residue interaction networks revealed that concerted rearrangements of local interacting modules at the inter-domain interface may be responsible for global structural changes and a population shift in the DnaK chaperone. The inter-domain communities in the Hsp70 structures harbor the majority of regulatory residues involved in allosteric signaling, suggesting that these sites could be integral to the network organization and coordination of structural changes. Using a network-based formalism of

  1. Interaction-Induced Characteristic Length in Strongly Many-Body Localized Systems

    CERN Document Server

    He, Rong-Qiang

    2016-01-01

    We propose a numerical method for explicitly constructing a complete set of local integrals of motion (LIOM) and definitely show the existence of LIOM for strongly many-body localized systems. The method starts with a complete set of maximally localized guessed LIOM, gradually deforms it into a complete set of true LIOM. By using this method we find that for strongly disordered and weakly interacting systems, there are two characteristic lengths in the LIOM. The first one is governed by disorder and is of Anderson-localization nature. The second one is induced by interaction but independent of the strength of interaction, showing a nonperturbative nature. We prove that the entanglement and correlation in any eigenstate extend not longer than twice the second length.

  2. Many-body effects in the van der Waals-Casimir interaction between graphene layers

    Science.gov (United States)

    Sarabadani, Jalal; Naji, Ali; Asgari, Reza; Podgornik, Rudolf

    2011-10-01

    Van der Waals-Casimir dispersion interactions between two apposed graphene layers, a graphene layer and a substrate, and in a multilamellar graphene system are analyzed within the framework of the Lifshitz theory. This formulation hinges on a known form of the dielectric response function of an undoped or doped graphene sheet, assumed to be of a random-phase-approximation form. In the geometry of two apposed layers, the separation dependence of the van der Waals-Casimir interaction for both types of graphene sheets is determined and critically compared with some well-known limiting cases. In a multilamellar array, the many-body effects are quantified and shown to increase the magnitude of the van der Waals-Casimir interactions.

  3. Accessing Rydberg-dressed interactions using many-body Ramsey dynamics

    Science.gov (United States)

    Mukherjee, Rick; Killian, Thomas C.; Hazzard, Kaden R. A.

    2016-11-01

    We demonstrate that Ramsey spectroscopy can be used to observe Rydberg-dressed interactions in a many-body system well within experimentally measured lifetimes, in contrast to previous research, which either focused on interactions near Förster resonances or on few-atom systems. We build a spin-1/2 from one level that is Rydberg-dressed and another that is not. These levels may be hyperfine or long-lived electronic states. An Ising spin model governs the Ramsey dynamics, which we demonstrate can be used to characterize the Rydberg-dressed interactions. Furthermore, the dynamics can differ significantly from that observed in other spin systems. As one example, spin echo can increase the rate at which coherence decays. The results also apply to bare (undressed) Rydberg states as a special case, for which we quantitatively reproduce recent ultrafast experiments without fitting.

  4. Risk evaluation of the Arctic environmental POP exposure based on critical body residue and critical daily dose using captive Greenland sledge dogs (Canis familiaris) as surrogate species.

    Science.gov (United States)

    Sonne, Christian; Gustavson, Kim; Eulaers, Igor; Desforges, Jean-Pierre; Letcher, Robert J; Rigét, Frank F; Styrishave, Bjarne; Dietz, Rune

    2016-03-01

    The risk from POP (persistent organic pollutant) exposure and subsequent reproductive, immunotoxic and liver histopathological effects was evaluated in a classical parallel trial on Greenland sledge dogs (Canis familiaris) fed contaminated minke whale (Balaenoptera acutorostrata) blubber. First the critical body residues (CBRs) were estimated using the physiologically-based pharmacokinetic (PBPK) model for seven POP compounds based on rat critical daily doses (CDDs). These were then compared with the actual daily oral POP doses (DD) and body residues (BR) in the sledge dogs by calculating risk quotients (RQDD: DD/CDD; RQBR: BR/CBR; ≥1 indicates risk). The results showed that risk quotients for reproductive, immunotoxic and liver histopathological effects were significantly lowest in the control group (pPOP exposure negatively impacts steroid hormones, various immune parameters, as well as liver histopathology in sledge dogs. It is also clear that RQBR is the best reflector of health effects from POP exposure and that it is especially accurate in predicting immune and reproductive effects. We recommend that PBPK modelled (CBR) and RQBR should be used in the assessment of POP exposure and health effects in Arctic top predators. Copyright © 2015 Elsevier Ltd. All rights reserved.

  5. Interactions of bluff-body obstacles with turbulent airflows affecting evaporative fluxes from porous surfaces

    Science.gov (United States)

    Haghighi, Erfan; Or, Dani

    2015-11-01

    Bluff-body obstacles interacting with turbulent airflows are common in many natural and engineering applications (from desert pavement and shrubs over natural surfaces to cylindrical elements in compact heat exchangers). Even with obstacles of simple geometry, their interactions within turbulent airflows result in a complex and unsteady flow field that affects surface drag partitioning and transport of scalars from adjacent evaporating surfaces. Observations of spatio-temporal thermal patterns on evaporating porous surfaces adjacent to bluff-body obstacles depict well-defined and persistent zonation of evaporation rates that were used to construct a simple mechanistic model for surface-turbulence interactions. Results from evaporative drying of sand surfaces with isolated cylindrical elements (bluff bodies) subjected to constant turbulent airflows were in good agreement with model predictions for localized exchange rates. Experimental and theoretical results show persistent enhancement of evaporative fluxes from bluff-rough surfaces relative to smooth flat surfaces under similar conditions. The enhancement is attributed to formation of vortices that induce a thinner boundary layer over part of the interacting surface footprint. For a practical range of air velocities (0.5-4.0 m/s), low-aspect ratio cylindrical bluff elements placed on evaporating sand surfaces enhanced evaporative mass losses (relative to a flat surface) by up to 300% for high density of elements and high wind velocity, similar to observations reported in the literature. Concepts from drag partitioning were used to generalize the model and upscale predictions to evaporation from surfaces with multiple obstacles for potential applications to natural bluff-rough surfaces.

  6. Stereotactic Body Radiation Therapy Can Be Used Safely to Boost Residual Disease in Locally Advanced Non-Small Cell Lung Cancer: A Prospective Study

    Energy Technology Data Exchange (ETDEWEB)

    Feddock, Jonathan, E-mail: jmfedd0@uky.edu [Department of Radiation Medicine, University of Kentucky, Lexington, Kentucky (United States); Arnold, Susanne M. [Department of Radiation Medicine, University of Kentucky, Lexington, Kentucky (United States); Department of Medical Oncology, University of Kentucky, Lexington, Kentucky (United States); Shelton, Brent J. [Department of Biostatistics, University of Kentucky, Lexington, Kentucky (United States); Sinha, Partha; Conrad, Gary [Department of Radiology, University of Kentucky, Lexington, Kentucky (United States); Chen, Li [Department of Biostatistics, University of Kentucky, Lexington, Kentucky (United States); Rinehart, John [Department of Medical Oncology, University of Kentucky, Lexington, Kentucky (United States); McGarry, Ronald C. [Department of Radiation Medicine, University of Kentucky, Lexington, Kentucky (United States)

    2013-04-01

    Purpose: To report the results of a prospective, single-institution study evaluating the feasibility of conventional chemoradiation (CRT) followed by stereotactic body radiation therapy (SBRT) as a means of dose escalation for patients with stage II-III non-small cell lung cancer (NSCLC) with residual disease. Methods and Materials: Patients without metastatic disease and with radiologic evidence of limited residual disease (≤5 cm) within the site of the primary tumor and good or complete nodal responses after standard CRT to a target dose of 60 Gy were considered eligible. The SBRT boost was done to achieve a total combined dose biological equivalent dose >100 Gy to the residual primary tumor, consisting of 10 Gy × 2 fractions (20 Gy total) for peripheral tumors, and 6.5 Gy × 3 fractions (19.5 Gy total) for medial tumors using the Radiation Therapy Oncology Group protocol 0813 definitions. The primary endpoint was the development of grade ≥3 radiation pneumonitis (RP). Results: After a median follow-up of 13 months, 4 patients developed acute grade 3 RP, and 1 (2.9%) developed late and persistent grade 3 RP. No patients developed grade 4 or 5 RP. Mean lung dose, V2.5, V5, V10, and V20 values were calculated for the SBRT boost, and none were found to significantly predict for RP. Only advancing age (P=.0147), previous smoking status (P=.0505), and high CRT mean lung dose (P=.0295) were significantly associated with RP development. At the time of analysis, the actuarial local control rate at the primary tumor site was 82.9%, with only 6 patients demonstrating recurrence. Conclusions: Linear accelerator-based SBRT for dose escalation of limited residual NSCLC after definitive CRT was feasible and did not increase the risk for toxicity above that for standard radiation therapy.

  7. NUMERICAL METHOD FOR MULTI-BODY FLUID INTERACTION BASED ON IMMERSED BOUNDARY METHOD

    Institute of Scientific and Technical Information of China (English)

    MING Ping-jian; ZHANG Wen-ping

    2011-01-01

    A Cartesian grid based on Immersed Boundary Method(IBM),proposed by the present authors,is extended to unstructured grids.The advantages of IBM and Body Fitted Grid(BFG)are taken to enhance the computation efficiency of the fluid structure interaction in a complex domain.There are many methods to generate the BFG,among which the unstructured grid method is the most popular.The concept of Volume Of Solid(VOS)is used to deal with the multi rigid body and fluid interaction.Each body surface is represented by a set of points which can be traced in an anti-clockwise order with the solid area on the left side of surface.An efficient Lagrange point tracking algorithm on the fixed grid is applied to search the moving boundary grid points.This method is verified by low Reynolds number flows in the range from Re =100 to 1 000 in the cavity with a moving lid.The results are in a good agreement with experimental data in literature.Finally,the flow past two moving cylinders is simulated to test the capability of the method.

  8. 铝废渣制备青花日用陶瓷坯体的研究%Preparation of Porcelain Body with Waste Aluminum Residue

    Institute of Scientific and Technical Information of China (English)

    黄智明; 王慧; 曾令可

    2016-01-01

    The rapid development has produced a lot of industrial waste. Recycling and reusing such waste in the ceramic industry are of great signiifcance to the environmental protection, the effective using of resources and energy, and the sustainable development of ceramic industry. First, this paper introduced the generation of waste aluminum residue and its recycling. Then the physical and chemical properties of this low-quality raw material were tested and analyzed by XRD and SEM. It’s proved that adding the right amount of waste aluminum residue did not cause adverse effects on body composition, the use of aluminum oxide impurities in the waste can improve the appearance quality of the porcelain body and lower its ifring temperature. The body phase composition and microstructure were obtained by XRD and SEM, and adding waste aluminum residue had little effect on body whiteness. The highest adding amount in the experiment was 25%. When the adding amount was 15%, the water absorption was the lowest and the strength was the highest.%工业的迅速发展产生了大量的工业废料,在陶瓷工业中回收利用这些废料无论是对环境保护、资源能源的有效利用,还是对陶瓷行业的可持续发展都具有重要意义。本文首先介绍了铝型材工业废渣(简称铝废渣)产生和回收利用现状,然后通过X射线衍射(XRD)、扫描电子显微镜(SEM)对这种低品位原料的理化性能进行了测试分析。结果表明:铝废渣的适量加入不会对青花陶瓷坯体的组成造成不良影响,利用铝废渣中的杂质氧化物可提高瓷坯的外观品质、降低烧成温度。通过XRD和SEM得到坯体的物相组成和显微结构,铝废渣的掺入对青花陶瓷坯体的白度影响较小。实验中最大的掺入量达25%,当掺入量为15%时,坯体的吸水率最低,强度最高。

  9. Tyr-199 and charged residues of pharaonis Phoborhodopsin are important for the interaction with its transducer.

    Science.gov (United States)

    Sudo, Yuki; Iwamoto, Masayuki; Shimono, Kazumi; Kamo, Naoki

    2002-01-01

    pharaonis Phoborhodopsin (ppR; also pharaonis sensory rhodopsin II, psRII) is a retinal protein in Natronobacterium pharaonis and is a receptor of negative phototaxis. It forms a complex with its transducer, pHtrII, in membranes and transmits light signals by protein-protein interaction. Tyr-199 is conserved completely in phoborhodopsins among a variety of archaea, but it is replaced by Val (for bacteriorhodopsin) and Phe (for sensory rhodopsin I). Previously, we (Sudo, Y., M. Iwamoto, K. Shimono, and N. Kamo, submitted for publication) showed that analysis of flash-photolysis data of a complex between D75N and the truncated pHtrII (t-Htr) give a good estimate of the dissociation constant K(D) in the dark. To investigate the importance of Tyr-199, K(D) of double mutants of D75N/Y199F or D75N/Y199V with t-Htr was estimated by flash-photolysis and was approximately 10-fold larger than that of D75N, showing the significant contribution of Tyr-199 to binding. The K(D) of the D75N/t-Htr complex increased with decreasing pH, and the data fitted well with the Henderson-Hasselbach equation with a single pK(a) of 3.86 +/- 0.02. This suggests that certain deprotonated carboxyls at the surface of the transducer (possibly Asp-102, Asp-104, and Asp-106) are needed for the binding. PMID:12080131

  10. Apolipoprotein A2 polymorphism interacts with intakes of dairy foods to influence body weight in 2 U.S. populations

    Science.gov (United States)

    The interaction between a functional apolipoprotein A2 gene (APOA2) variant and saturated fatty acids (SFAs) for the outcome of body mass index (BMI) is among the most widely replicated gene-nutrient interactions. Whether this interaction can be extrapolated to food-based sources of SFAs, specifical...

  11. Body fat estimations by electrical impedance and infra-red interactance.

    Science.gov (United States)

    Brodie, D A; Eston, R G

    1992-05-01

    The purpose of this study was to examine body fat estimation using three methods of electrical impedance (the BIA-103 Body Composition Analyser--RJL Systems, Detroit; the BMR 2000 Body Composition Analyzer--Berkeley Medical Research, San Leandro; the BC300 Body Composition Analyzer--Spacelabs, Dallas) and an infra-red interactance method (Futrex 5000 Analyzer--Futrex Inc. Gaithersburg) as an alternative to hydrodensitometry. Five different groups were examined using at least one of the electrical systems and in all cases utilising hydrodensitometry as the criterion method. The results produced highly significant correlations between all methods, but caution is recommended due to the limited common variance in some cases. The individual electrical methods differed from hydrodensitometry by a maximum of 1.1% in obese women, by 21.6% in athletic adults, by 6.2% in the slightly obese group, by 8.1% in normal women and by 56.0% in normal children. Significant mean differences between one of the impedance methods and hydrodensitometry were only noted in two of the groups tested. This suggests, allowing for the limitations of hydrodensitometry itself, that the other three electrical methods appear to be reasonably valid alternatives to underwater weighing, especially for field work of an epidemiological nature.

  12. Patterning of mutually interacting bacterial bodies: close contacts and airborne signals

    Directory of Open Access Journals (Sweden)

    Markoš Anton

    2010-05-01

    Full Text Available Abstract Background Bacterial bodies (colonies can develop complex patterns of color and structure. These patterns may arise as a result of both colony-autonomous developmental and regulatory processes (self-patterning and environmental influences, including those generated by neighbor bodies. We have studied the interplay of intra-colony signaling (self-patterning and inter-colony influences in related clones of Serratia rubidaea grown on rich media. Results Colonies are shaped by both autonomous patterning and by signals generated by co-habitants of the morphogenetic space, mediating both internal shaping of the body, and communication between bodies sharing the same living space. The result of development is affected by the overall distribution of neighbors in the dish. The neighbors' presence is communicated via at least two putative signals, while additional signals may be involved in generating some unusual patterns observed upon encounters of different clones. A formal model accounting for some aspects of colony morphogenesis and inter-colony interactions is proposed. Conclusions The complex patterns of color and texture observed in Serratia rubidaea colonies may be based on at least two signals produced by cells, one of them diffusing through the substrate (agar and the other carried by a volatile compound and absorbed into the substrate. Differences between clones with regard to the interpretation of signals may result from different sensitivity to signal threshold(s.

  13. Long-range interacting many-body systems with alkaline-earth-metal atoms

    CERN Document Server

    Olmos, B; Singh, Y; Schreck, F; Bongs, K; Lesanovsky, I

    2012-01-01

    Alkaline-earth-metal atoms exhibit long-range dipolar interactions, which are generated via the coherent exchange of photons on the 3P_0-3D_1-transition of the triplet manifold. In case of bosonic strontium, which we discuss here, this transition has a wavelength of 2.7 \\mu m and a dipole moment of 2.46 Debye, and there exists a magic wavelength permitting the creation of optical lattices that are identical for the states 3P_0 and 3D_1. This interaction enables the realization and study of mixtures of hard-core lattice bosons featuring long-range hopping, with tuneable disorder and anisotropy. We derive the many-body Master equation, investigate the dynamics of excitation transport and analyze spectroscopic signatures stemming from coherent long-range interactions and collective dissipation. Our results show that lattice gases of alkaline-earth-metal atoms permit the creation of long-lived collective atomic states and constitute a simple and versatile platform for the exploration of many-body systems with lon...

  14. Does seeing ice really feel cold? Visual-thermal interaction under an illusory body-ownership.

    Directory of Open Access Journals (Sweden)

    Shoko Kanaya

    Full Text Available Although visual information seems to affect thermal perception (e.g. red color is associated with heat, previous studies have failed to demonstrate the interaction between visual and thermal senses. However, it has been reported that humans feel an illusory thermal sensation in conjunction with an apparently-thermal visual stimulus placed on a prosthetic hand in the rubber hand illusion (RHI wherein an individual feels that a prosthetic (rubber hand belongs to him/her. This study tests the possibility that the ownership of the body surface on which a visual stimulus is placed enhances the likelihood of a visual-thermal interaction. We orthogonally manipulated three variables: induced hand-ownership, visually-presented thermal information, and tactically-presented physical thermal information. Results indicated that the sight of an apparently-thermal object on a rubber hand that is illusorily perceived as one's own hand affects thermal judgments about the object physically touching this hand. This effect was not observed without the RHI. The importance of ownership of a body part that is touched by the visual object on the visual-thermal interaction is discussed.

  15. Relationships between postweaning residual feed intake in heifers and forage use, body composition, feeding behavior, physical activity, and heart rate of pregnant beef females.

    Science.gov (United States)

    Hafla, A N; Carstens, G E; Forbes, T D A; Tedeschi, L O; Bailey, J C; Walter, J T; Johnson, J R

    2013-11-01

    The objectives of this study were to determine if residual feed intake (RFI) classification of beef heifers affected efficiency of forage utilization, body composition, feeding behavior, heart rate, and physical activity of pregnant females. Residual feed intake was measured in growing Bonsmara heifers for 2 yr (n=62 and 53/yr), and heifers with the lowest (n=12/yr) and highest (n=12/yr) RFI were retained for breeding. Of the 48 heifers identified as having divergent RFI, 19 second-parity and 23 first-parity females were used in the subsequent pregnant-female trial. Pregnant females were fed a chopped hay diet (ME=2.11 Mcal kg(-1) DM) in separate pens equipped with GrowSafe bunks to measure individual intake and feeding behavior. Body weights were measured at 7-d intervals and BCS and ultrasound measurements of 12th-rib fat depth, rump fat depth, and LM area obtained on d 0 and 77. Heart rate and physical activity were measured for 7 consecutive d. First-parity females had lower (PResidual feed intake classification did not affect bunk visit frequency, but low-RFI females spent 26% less time (Presidual gain were positively correlated with forage intake (r=0.38) and RFI (r=0.42) of pregnant females. Results indicate that heifers identified as having low postweaning RFI have greater efficiency of forage utilization as pregnant females, with minimal impacts on growth, body composition, calving date, and calf birth BW, compared to their high-RFI counterparts.

  16. Spring Chinook Salmon Interactions Indices and Residual/Precocial Monitoring in the Upper Yakima Basin, 1998 Annual Report.

    Energy Technology Data Exchange (ETDEWEB)

    James, Brenda B.; Pearsons, Todd N.; McMichael, Geoffrey A. (Washington Department of Fish and Wildlife, Olympia, WA)

    1999-12-01

    Select ecological interactions and spring chinook salmon residual/precocial abundance were monitored in 1998 as part of the Yakima/Klickitat Fisheries Project's supplementation monitoring program. Monitoring these variables is part of an effort to help evaluate the factors that contribute to, or limit supplementation success. The ecological interactions that were monitored were prey consumption, competition for food, and competition for space. The abundance of spring chinook salmon life-history forms that have the potential to be influenced by supplementation and that have important ecological and genetic roles were monitored (residuals and precocials). Residual spring chinook salmon do not migrate to the ocean during the normal emigration period and continue to rear in freshwater. Precocials are those salmon that precocially mature in freshwater. The purpose of sampling during 1998 was to collect baseline data one year prior to the release of hatchery spring chinook salmon which occurred during the spring of 1999. All sampling that the authors report on here was conducted in upper Yakima River during summer and fall 1998. The stomach fullness of juvenile spring chinook salmon during the summer and fall averaged 12%. The food competition index suggested that mountain whitefish (0.59), rainbow trout (0.55), and redside shiner (0.55) were competing for food with spring chinook salmon. The space competition index suggested that rainbow trout (0.31) and redside shiner (0.39) were competing for space with spring chinook salmon but mountain whitefish (0.05) were not. Age-0 spring chinook salmon selected a fairly narrow range of microhabitat parameters in the summer and fall relative to what was available. Mean focal depths and velocities for age 0 spring chinook salmon during the summer were 0.5 m {+-} 0.2 m and 0.26 m/s {+-} 0.19 m/s, and during the fall 0.5 m {+-} 0.2 m and 0.24 m/s {+-} 0.18 m/s. Among potential competitors, age 1+ rainbow trout exhibited the

  17. Energy Centroids of Spin $I$ States by Random Two-body Interactions

    CERN Document Server

    Zhao, Y M; Ogawa, K

    2005-01-01

    In this paper we study the behavior of energy centroids (denoted as $\\bar{E_I}$) of spin $I$ states in the presence of random two-body interactions, for systems ranging from very simple systems (e.g. single-$j$ shell for very small $j$) to very complicated systems (e.g., many-$j$ shells with different parities and with isospin degree of freedom). Regularities of $\\bar{E_I}$'s discussed in terms of the so-called geometric chaoticity (or quasi-randomness of two-body coefficients of fractional parentage) in earlier works are found to hold even for very simple systems in which one cannot assume the geometric chaoticity. It is shown that the inclusion of isospin and parity does not "break" the regularities of $\\bar{E_I}$'s.

  18. Simulating open quantum systems: from many-body interactions to stabilizer pumping

    CERN Document Server

    Mueller, M; Zhou, Y L; Roos, C F; Zoller, P

    2011-01-01

    In a recent experiment, Barreiro et al. demonstrated the fundamental building blocks of an open-system quantum simulator with trapped ions [Nature 470, 486 (2011)]. Using up to five ions, single- and multi-qubit entangling gate operations were combined with optical pumping in stroboscopic sequences. This enabled the implementation of both coherent many-body dynamics as well as dissipative processes by controlling the coupling of the system to an artificial, suitably tailored environment. This engineering was illustrated by the dissipative preparation of entangled two- and four-qubit states, the simulation of coherent four-body spin interactions and the quantum non-demolition measurement of a multi-qubit stabilizer operator. In the present paper, we present the theoretical framework of this gate-based ("digital") simulation approach for open-system dynamics with trapped ions. In addition, we discuss how within this simulation approach minimal instances of spin models of interest in the context of topological q...

  19. Complex-Dynamical Solution to Many-Body Interaction Problem and Its Applications in Fundamental Physics

    CERN Document Server

    Kirilyuk, Andrei P

    2012-01-01

    We review the recently proposed unreduced, complex-dynamical solution to many-body problem with arbitrary interaction and its application to unified solution of fundamental problems, including foundations of causally complete quantum mechanics, relativity, particle properties and cosmology. We first analyse the universal properties of many-body problem solution without any perturbative reduction and show that the emerging new quality of fundamental dynamic multivaluedness (or redundance) of resulting system configuration leads to universal concept of dynamic complexity, chaoticity and fractality of any real system behaviour. We then consider unified features of this complex dynamics. Applications of that universal description to systems at various complexity levels have been performed and in this paper we review those at the lowest, fundamental complexity levels leading to causal understanding of unified origins of quantum mechanics, relativity (special and general), elementary particles, their intrinsic prop...

  20. Investigations of the structure and electromagnetic interactions of few-body systems

    Energy Technology Data Exchange (ETDEWEB)

    Lehman, D.R.; Haberzettl, H.; Maximon, L.C.; Parke, W.C.

    1992-07-01

    In order to make it easy for the reader to see the specific research carried out and the progress made, the following report of progress is done by topic. Each item has a format layout of Topic, Investigators, Objective, Significance, and Description of Progress, followed at the end by the relevant references. As is clear from the topics listed, the emphasis of the George Washington University (GWU) theory group has been on the structure and electromagnetic interactions of few-body nuclei. Both low- and intermediate-energy electromagnetic disintegration of these nuclei is considered. When the excitation energy of the target nucleus is low, the aim has been to handle the continuum part of the theoretical work numerically with no approximations, that is, by means of full three- or four-body dynamics. When structure questions axe the issue, numerically accurate calculations axe always carried through, limited only by the underlying two-body or three-body interactions used as input. Implicit in our work is the question of how far one can go within the traditional nuclear physics framework, i.e., nucleons and mesons in a nonrelativistic setting. Our central goal is to carry through state-of-the-art fewbody calculations that wig serve as a means of determining at what point standard nuclear physics requires quark degrees of freedom in order to understand the phenomena in question. So far, in the problems considered, there has been no evidence of the necessity to go beyond the traditional approach, though we always keep in mind that possibility. As our work is involved with questions in the intermediate-energy realm, moving from a nonrelativistic framework to a relativistic one is always a consideration. Currently, for the problems that have been pursued in this domain of energy, the issues concern far more the mechanisms of the reactions and structural questions than the need to move to relativistic dynamics.

  1. Electromagnetic field interactions with the human body: Observed effects and theories

    Science.gov (United States)

    Raines, J. K.

    1981-01-01

    The effects of nonionizing electromagnetic (EM) field interactions with the human body were reported and human related studies were collected. Nonionizing EM fields are linked to cancer in humans in three different ways: cause, means of detection, and effective treatment. Bad and benign effects are expected from nonionizing EM fields and much more knowledge is necessary to properly categorize and qualify EM field characteristics. It is concluded that knowledge of the boundary between categories, largely dependent on field intensity, is vital to proper future use of EM radiation for any purpose and the protection of the individual from hazard.

  2. On the change of density of states in two-body interactions

    CERN Document Server

    Gao, Bo

    2016-01-01

    We derive a general relation in two-body scattering theory that more directly relates the change of density of states (DDOS) due to interaction to the shape of the potential. The relation allows us to infer certain global properties of the DDOS from the global properties of the potential. In particular, we show that DDOS is negative at all energies and for all partial waves, for potentials that are more repulsive than $+1/r^2$ everywhere. This behavior represents a different class of global properties of DDOS from that described by the Levinson's theorem.

  3. Atomistic formulas for local properties in systems with many-body interactions

    Science.gov (United States)

    Hardy, Robert J.

    2016-11-01

    Atomistic formulas are derived for the local densities and fluxes used in the continuum description of energy and momentum transport. Two general methods for the distribution of potential energy among a system's constituent particles are presented and analyzed. The resulting formulas for the heat flux and stress tensor and the equations for energy and momentum transport are exact consequences of the definitions of the densities and the equations of classical mechanics. The formulas and equations obtained are valid for systems with very general types of many-body interactions.

  4. Characterizing the interaction among bullet, body armor, and human and surrogate targets.

    Science.gov (United States)

    Shen, Weixin; Niu, Yuqing; Bykanova, Lucy; Laurence, Peter; Link, Norman

    2010-12-01

    This study used a combined experimental and modeling approach to characterize and quantify the interaction among bullet, body armor, and human surrogate targets during the 10-1000 μs range that is crucial to evaluating the protective effectiveness of body armor against blunt injuries. Ballistic tests incorporating high-speed flash X-ray measurements were performed to acquire the deformations of bullets and body armor samples placed against ballistic clay and gelatin targets with images taken between 10 μs and 1 ms of the initial impact. Finite element models (FEMs) of bullet, armor, and gelatin and clay targets were developed with material parameters selected to best fit model calculations to the test measurements. FEMs of bullet and armor interactions were then assembled with a FEM of a human torso and FEMs of clay and gelatin blocks in the shape of a human torso to examine the effects of target material and geometry on the interaction. Test and simulation results revealed three distinct loading phases during the interaction. In the first phase, the bullet was significantly slowed in about 60 μs as it transferred a major portion of its energy into the body armor. In the second phase, fibers inside the armor were pulled toward the point of impact and kept on absorbing energy until about 100 μs after the initial impact when energy absorption reached its peak. In the third phase, the deformation on the armor's back face continued to grow and energies inside both armor and targets redistributed through wave propagation. The results indicated that armor deformation and energy absorption in the second and third phases were significantly affected by the material properties (density and stiffness) and geometrical characteristics (curvature and gap at the armor-target interface) of the targets. Valid surrogate targets for testing the ballistic resistance of the armor need to account for these factors and produce the same armor deformation and energy absorption as on a

  5. Parameters of social existence and social functioning of lesbians: Lesbian body in processes of social interactions

    Directory of Open Access Journals (Sweden)

    Mršević Zorica Ž.

    2004-01-01

    Full Text Available Analysis of characteristics of a lesbian body in processes of social interaction is a method of analysis social relations of lesbians, their relationships with the heterosexual world and revealing specific lesbian practices, outlooks, habits and customs, behavior and general characteristics of lesbian sub culture. Making somebody different than a "normal human", meaning less human, is the main way of making the whole group target of justified discrimination, violence and hate crime. Therefore, providing understanding of differences provides a ground for personal, political and legal sensitivity, understanding and tolerance towards both the "otherness" and the "others".

  6. Quantum simulation of a three-body interaction Hamiltonian on an NMR quantum computer

    CERN Document Server

    Tseng, C H; Sharf, Y; Knill, E H; Laflamme, R; Havel, T F; Cory, D G

    2000-01-01

    Extensions of average Hamiltonian theory to quantum computation permit the design of arbitrary Hamiltonians, allowing rotations throughout a large Hilbert space. In this way, the kinematics and dynamics of any quantum system may be simulated by a quantum computer. A basis mapping between the systems dictates the average Hamiltonian in the quantum computer needed to implement the desired Hamiltonian in the simulated system. The flexibility of the procedure is illustrated with NMR on 13-C labelled Alanine by creating the non-physical Hamiltonian ZZZ corresponding to a three body interaction.

  7. Quantum simulation of a three-body-interaction Hamiltonian on an NMR quantum computer

    Energy Technology Data Exchange (ETDEWEB)

    Tseng, C. H. [Department of Nuclear Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139 (United States); Somaroo, S. [Department of Nuclear Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139 (United States); Sharf, Y. [Department of Nuclear Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139 (United States); Knill, E. [Theoretical Physics Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87455 (United States); Laflamme, R. [Theoretical Physics Division, Los Alamos National Laboratory, Los Alamos, New Mexico 87455 (United States); Havel, T. F. [BCMP Harvard Medical School, 240 Longwood Avenue, Boston Massachusetts 02115 (United States); Cory, D. G. [Department of Nuclear Engineering, Massachusetts Institute of Technology, Cambridge, Massachusetts 02139 (United States)

    2000-01-01

    Extensions of average Hamiltonian theory to quantum computation permit the design of arbitrary Hamiltonians, allowing rotations throughout a large Hilbert space. In this way, the kinematics and dynamics of any quantum system may be simulated by a quantum computer. A basis mapping between the systems dictates the average Hamiltonian in the quantum computer needed to implement the desired Hamiltonian in the simulated system. The flexibility of the procedure is illustrated with NMR on {sup 13}C labeled alanine by creating the nonphysical Hamiltonian {sigma}{sub z}{sigma}{sub z}{sigma}{sub z} corresponding to a three-body interaction. (c) 1999 The American Physical Society.

  8. A New Application of Multi- Body System Dynamics in Vehicle- Road Interaction Simulation

    Institute of Scientific and Technical Information of China (English)

    Ren Wei-qun; Zhang Yun-qing; Jin Guo-dong

    2003-01-01

    In vehicle-road interaction simulation, multi-body system (MBS) dynamics as well as the corresponding software ADAMS has been employed to model the nonlinear vehicle in more detail. The simulation method has been vali-dated by the test data, and been compared to the former sim-ple models. This method can be used for estimating the effects of dynamic tire forces and other vehicle features on road damage so that the "road- friend liness" can be assessed in vehicle design process.

  9. The immune-body cytokine network defines a social architecture of cell interactions

    Directory of Open Access Journals (Sweden)

    Alon Uri

    2006-10-01

    Full Text Available Abstract Background Three networks of intercellular communication can be associated with cytokine secretion; one limited to cells of the immune system (immune cells, one limited to parenchymal cells of organs and tissues (body cells, and one involving interactions between immune and body cells (immune-body interface. These cytokine connections determine the inflammatory response to injury and subsequent healing as well as the biologic consequences of the adaptive immune response to antigens. We informatically probed the cytokine database to uncover the underlying network architecture of the three networks. Results We now report that the three cytokine networks are among the densest of complex networks yet studied, and each features a characteristic profile of specific three-cell motifs. Some legitimate cytokine connections are shunned (anti-motifs. Certain immune cells can be paired by their input-output positions in a cytokine architecture tree of five tiers: macrophages (MΦ and B cells (BC comprise the first tier; the second tier is formed by T helper 1 (Th1 and T helper 2 (Th2 cells; the third tier includes dendritic cells (DC, mast cells (MAST, Natural Killer T cells (NK-T and others; the fourth tier is formed by neutrophils (NEUT and Natural Killer cells (NK; and the Cytotoxic T cell (CTL stand alone as a fifth tier. The three-cell cytokine motif architecture of immune system cells places the immune system in a super-family that includes social networks and the World Wide Web. Body cells are less clearly stratified, although cells involved in wound healing and angiogenesis are most highly interconnected with immune cells. Conclusion Cytokine network architecture creates an innate cell-communication platform that organizes the biologic outcome of antigen recognition and inflammation. Informatics sheds new light on immune-body systems organization. Reviewers This article was reviewed by Neil Greenspan, Matthias von Herrath and Anne Cooke.

  10. Development of a body motion interactive system with a weight voting mechanism and computer vision technology

    Science.gov (United States)

    Lin, Chern-Sheng; Chen, Chia-Tse; Shei, Hung-Jung; Lay, Yun-Long; Chiu, Chuang-Chien

    2012-09-01

    This study develops a body motion interactive system with computer vision technology. This application combines interactive games, art performing, and exercise training system. Multiple image processing and computer vision technologies are used in this study. The system can calculate the characteristics of an object color, and then perform color segmentation. When there is a wrong action judgment, the system will avoid the error with a weight voting mechanism, which can set the condition score and weight value for the action judgment, and choose the best action judgment from the weight voting mechanism. Finally, this study estimated the reliability of the system in order to make improvements. The results showed that, this method has good effect on accuracy and stability during operations of the human-machine interface of the sports training system.

  11. Analytical nuclear gradients for the range-separated many-body dispersion model of noncovalent interactions

    CERN Document Server

    Blood-Forsythe, Martin A; DiStasio, Robert A; Car, Roberto; Aspuru-Guzik, Alán

    2015-01-01

    Accurate treatment of the long-range electron correlation energy, including van der Waals (vdW) or dispersion interactions, is essential for describing the structure, dynamics, and function of a wide variety of systems. Among the most accurate models for including dispersion into density functional theory (DFT) is the range-separated many-body dispersion (MBD) method [A. Ambrossetti et al., J. Chem. Phys. 140, 18A508 (2014)], in which the correlation energy is modeled at short-range by a semi-local density functional and at long-range by a model system of coupled quantum harmonic oscillators. In this work, we develop analytical gradients of the MBD energy with respect to nuclear coordinates, including all implicit coordinate dependencies arising from the partitioning of the charge density into Hirshfeld effective volumes. To demonstrate the efficiency and accuracy of these MBD gradients for geometry optimizations of systems with intermolecular and intramolecular interactions, we optimized conformers of the be...

  12. Many-Body Coarse-Grained Interactions using Gaussian Approximation Potentials

    CERN Document Server

    John, S T

    2016-01-01

    This thesis introduces a framework that is able to describe general many-body coarse-grained interactions. We make use of this to describe the free energy surface as a cluster expansion in terms of monomer, dimer, and trimer terms. The contributions to the free energy due to these terms are inferred from MD results of the underlying all-atom model using Gaussian Approximation Potentials, a type of machine-learning potential based on Gaussian process regression. This provides CG interactions that are much more accurate than is possible with site-based pair potentials. While slower than these, it can still be faster than all-atom simulations for solvent-free CG models of systems with a large amount of solvent, as is common in biomolecular simulations.

  13. Many-body correlations in Semiclassical Molecular Dynamics and Skyrme interaction

    CERN Document Server

    Papa, Massimo

    2012-01-01

    Constraint Molecular dynamics CoMD calculations have been performed for asymmetric nuclear matter (NM) by using a simple effective interactions of the Skyrme type. The set of parameter values reproducing common accepted saturation properties of nuclear matter have been obtained for different degree of stiffness characterizing the iso-vectorial potential density dependence. A comparison with results obtained in the limit of the Semi-Classical Mean Field approximation using the same kind of interaction put in evidence the role played by the many-body correlations in to explain the noticeable differences obtained in the parameter values in the two cases. Even if from a numerical point of view the obtained results are strictly valid for the CoMD model, some rather general feature of the discussed correlations can give a wider meaning to the obtained differences being strongly related to the spacial correlations generated in the semiclassical wave packets dynamics.

  14. A Fully Immersive Set-Up for Remote Interaction and Neurorehabilitation Based on Virtual Body Ownership

    Science.gov (United States)

    Perez-Marcos, Daniel; Solazzi, Massimiliano; Steptoe, William; Oyekoya, Oyewole; Frisoli, Antonio; Weyrich, Tim; Steed, Anthony; Tecchia, Franco; Slater, Mel; Sanchez-Vives, Maria V.

    2012-01-01

    Although telerehabilitation systems represent one of the most technologically appealing clinical solutions for the immediate future, they still present limitations that prevent their standardization. Here we propose an integrated approach that includes three key and novel factors: (a) fully immersive virtual environments, including virtual body representation and ownership; (b) multimodal interaction with remote people and virtual objects including haptic interaction; and (c) a physical representation of the patient at the hospital through embodiment agents (e.g., as a physical robot). The importance of secure and rapid communication between the nodes is also stressed and an example implemented solution is described. Finally, we discuss the proposed approach with reference to the existing literature and systems. PMID:22787454

  15. Accessing Rydberg-dressed interactions using many-body Ramsey dynamics

    Science.gov (United States)

    Mukherjee, Rick; Killian, Thomas; Hazzard, Kaden

    2016-05-01

    We demonstrate that Ramsey spectroscopy can be used to observe Rydberg-dressed interactions in a many-body system. Our scheme operates comfortably within experimentally measured lifetimes, and accesses a regime where quantum superpositions are crucial. We build a spin-1/2 from one level that is Rydberg-dressed and another that is not. These levels may be hyperfine or long-lived electronic states. An Ising spin model governs the Ramsey dynamics, for which we derive an exact solution. Due to the structure of Rydberg interactions, the dynamics differs significantly from that in other spin systems. As one example, spin echo can increase the rate at which coherence decays. The results are relevant for the current ongoing experiments, including those at Rice University.

  16. One dimensional scattering of a two body interacting system by an infinite wall

    CERN Document Server

    Moro, A M; Gomez-Camacho, J

    2010-01-01

    The one-dimensional scattering of a two body interacting system by an infinite wall is studied in a quantum-mechanical framework. This problem contains some of the dynamical features present in the collision of atomic, molecular and nuclear systems. The scattering problem is solved exactly, for the case of a harmonic interaction between the fragments. The exact result is used to assess the validity of two different approximations to the scattering process. The adiabatic approximation, which considers that the relative co-ordinate is frozen during the scattering process, is found to be inadequate for this problem. The uncorrelated scattering approximation, which neglects the correlation between the fragments, gives results in accordance with the exact calculations when the scattering energy is high compared to the oscillator parameter.

  17. Conformational mapping and energetics of saccharide-aromatic residue interactions: implications for the discrimination of anomers and epimers and in protein engineering.

    Science.gov (United States)

    Kumari, Manju; Sunoj, Raghavan B; Balaji, Petety V

    2012-06-07

    Aromatic residues play a key role in saccharide-binding sites. Experimental studies have given an estimate of the energetics of saccharide-aromatic residue interactions. In this study, dependence of the energetics on the mutual position-orientation (PO) of saccharide and aromatic residue has been investigated by geometry optimization of a very large number (164) of complexes at MP2/6-31G(d,p) level of theory. The complexes are of Tyr and Phe analogs with α/β-D-Glc, β-D-Gal, α-D-Man and α/β-L-Fuc. A number of iso-energy POs are found for the complexes of all six saccharides. Stacking and non-stacking modes of binding are found to be of comparable strengths. In general, complexes of p-OHTol are stronger than those of Tol, and those dominated by OH···O interactions are more stable than ones dominated by CH···π interactions. The strengths of OH···O/π interactions, but not those of CH···π, show large variations. Even though an aromatic residue has a large variety of POs to interact with a saccharide, distinct preferences are found due to anomeric and epimeric differences. An aromatic residue can interact from either the a- or b-face of Glc, but only through the b-face with Gal, its C4-epimer. In contrast, stacking interaction with Man (C2-epimer of Glc) requires the participation of the -CH(2)OH group and free rotation of this group, as is observed in solution, precludes all modes of stacking interactions. It is also found that an aromatic residue can be strategically placed either to discriminate or to accommodate (i) anomers of Glc and of Fuc and (ii) Gal/Fuc. Thus, analysis of the optimized geometries of by far the largest number of complexes, and with six different saccharides, at this level of theory has given insights into how Nature cleverly uses aromatic residues to fine tune saccharide specificities of proteins. These are of immense utility for protein engineering and protein design studies.

  18. Identification of amino acid residues involved in the interaction between measles virus Haemagglutin (MVH) and its human cell receptor (signaling lymphocyte activation molecule, SLAM).

    Science.gov (United States)

    Xu, Qin; Zhang, Peng; Hu, Chunling; Liu, Xin; Qi, Yipeng; Liu, Yingle

    2006-07-31

    Signaling lymphocyte activation molecule (SLAM; also known as CD150) is a newly identified cellular receptor for measles virus (MV). The interaction between MV Haemagglutin (MVH) and SLAM is an initial step for MV entry. We have identified several novel SLAM binding sites at residues S429, T436 and H437 of MVH protein and MVH mutants in these residues dramatically decrease the ability to interaction with the cell surface SLAM and fail to coprecipitation with SLAM in vivo as well as malfunction in syncytium formation. At the same time, K58, S59 and H61 of SLAM was also identified to be critical for MVH and SLAM binding. Further, these residues may be useful targets for the development of measles therapy.

  19. Program in C for studying characteristic properties of two-body interactions in the framework of spectral distribution theory

    CERN Document Server

    Launey, K D; Dytrych, T; Draayer, J P

    2014-01-01

    We present a program in C that employs spectral distribution theory for studies of characteristic properties of a many-particle quantum-mechanical system and the underlying few-body interaction. In particular, the program focuses on two-body nuclear interactions given in a JT-coupled harmonic oscillator basis and calculates correlation coefficients, a measure of similarity of any two interactions, as well as Hilbert-Schmidt norms specifying interaction strengths. An important feature of the program is its ability to identify the monopole part (centroid) of a 2-body interaction, as well as its 'density-dependent' one-body and two-body part, thereby providing key information on the evolution of shell gaps and binding energies for larger nuclear systems. As additional features, we provide statistical measures for 'density-dependent' interactions, as well as a mechanism to express an interaction in terms of two other interactions. This, in turn, allows one to identify, e.g., established features of the nuclear in...

  20. Critical body residues linked to octanol-water partitioning, organism composition, and LC50 QSARs: meta-analysis and model.

    Science.gov (United States)

    Hendriks, A Jan; Traas, Theo P; Huijbregts, Mark A J

    2005-05-01

    To protect thousands of species from thousands of chemicals released in the environment, various risk assessment tools have been developed. Here, we link quantitative structure-activity relationships (QSARs) for response concentrations in water (LC50) to critical concentrations in organisms (C50) by a model for accumulation in lipid or non-lipid phases versus water Kpw. The model indicates that affinity for neutral body components such as storage fat yields steep Kpw-Kow relationships, whereas slopes for accumulation in polar phases such as proteins are gentle. This pattern is confirmed by LC50 QSARs for different modes of action, such as neutral versus polar narcotics and organochlorine versus organophosphor insecticides. LC50 QSARs were all between 0.00002 and 0.2Kow(-1). After calibrating the model with the intercepts and, for the first time also, with the slopes of the LC50 QSARs, critical concentrations in organisms C50 are calculated and compared to an independent validation data set. About 60% of the variability in lethal body burdens C50 is explained by the model. Explanations for differences between estimated and measured levels for 11 modes of action are discussed. In particular, relationships between the critical concentrations in organisms C50 and chemical (Kow) or species (lipid content) characteristics are specified and tested. The analysis combines different models proposed before and provides a substantial extension of the data set in comparison to previous work. Moreover, the concept is applied to species (e.g., plants, lean animals) and substances (e.g., specific modes of action) that were scarcely studied quantitatively so far.

  1. Brain process for perception of the "out of the body" tactile illusion for virtual object interaction.

    Science.gov (United States)

    Lee, Hye Jin; Lee, Jaedong; Kim, Chi Jung; Kim, Gerard J; Kim, Eun-Soo; Whang, Mincheol

    2015-04-01

    "Out of the body" tactile illusion refers to the phenomenon in which one can perceive tactility as if emanating from a location external to the body without any stimulator present there. Taking advantage of such a tactile illusion is one way to provide and realize richer interaction feedback without employing and placing actuators directly at all stimulation target points. However, to further explore its potential, it is important to better understand the underlying physiological and neural mechanism. As such, we measured the brain wave patterns during such tactile illusion and mapped out the corresponding brain activation areas. Participants were given stimulations at different levels with the intention to create veridical (i.e., non-illusory) and phantom sensations at different locations along an external hand-held virtual ruler. The experimental data and analysis indicate that both veridical and illusory sensations involve, among others, the parietal lobe, one of the most important components in the tactile information pathway. In addition, we found that as for the illusory sensation, there is an additional processing resulting in the delay for the ERP (event-related potential) and involvement by the limbic lobe. These point to regarding illusion as a memory and recognition task as a possible explanation. The present study demonstrated some basic understanding; how humans process "virtual" objects and the way associated tactile illusion is generated will be valuable for HCI (Human-Computer Interaction).

  2. Modelling of fluid-structure interaction with multiphase viscous flows using an immersed-body method

    Science.gov (United States)

    Yang, P.; Xiang, J.; Fang, F.; Pavlidis, D.; Latham, J.-P.; Pain, C. C.

    2016-09-01

    An immersed-body method is developed here to model fluid-structure interaction for multiphase viscous flows. It does this by coupling a finite element multiphase fluid model and a combined finite-discrete element solid model. A coupling term containing the fluid stresses is introduced within a thin shell mesh surrounding the solid surface. The thin shell mesh acts as a numerical delta function in order to help apply the solid-fluid boundary conditions. When used with an advanced interface capturing method, the immersed-body method has the capability to solve problems with fluid-solid interfaces in the presence of multiphase fluid-fluid interfaces. Importantly, the solid-fluid coupling terms are treated implicitly to enable larger time steps to be used. This two-way coupling method has been validated by three numerical test cases: a free falling cylinder in a fluid at rest, elastic membrane and a collapsing column of water moving an initially stationary solid square. A fourth simulation example is of a water-air interface with a floating solid square being moved around by complex hydrodynamic flows including wave breaking. The results show that the immersed-body method is an effective approach for two-way solid-fluid coupling in multiphase viscous flows.

  3. Immobile survival of motoneuron (SMN) protein stored in Cajal bodies can be mobilized by protein interactions.

    Science.gov (United States)

    Förthmann, Benjamin; Brinkmann, Hella; Ratzka, Andreas; Stachowiak, Michal K; Grothe, Claudia; Claus, Peter

    2013-07-01

    Reduced levels of survival of motoneuron (SMN) protein lead to spinal muscular atrophy, but it is still unknown how SMN protects motoneurons in the spinal cord against degeneration. In the nucleus, SMN is associated with two types of nuclear bodies denoted as gems and Cajal bodies (CBs). The 23 kDa isoform of fibroblast growth factor-2 (FGF-2(23)) is a nuclear protein that binds to SMN and destabilizes the SMN-Gemin2 complex. In the present study, we show that FGF-2(23) depletes SMN from CBs without affecting their general structure. FRAP analysis of SMN-EGFP in CBs demonstrated that the majority of SMN in CBs remained mobile and allowed quantification of fast, slow and immobile nuclear SMN populations. The potential for SMN release was confirmed by in vivo photoconversion of SMN-Dendra2, indicating that CBs concentrate immobile SMN that could have a specialized function in CBs. FGF-2(23) accelerated SMN release from CBs, accompanied by a conversion of immobile SMN into a mobile population. Furthermore, FGF-2(23) caused snRNP accumulation in CBs. We propose a model in which Cajal bodies store immobile SMN that can be mobilized by its nuclear interaction partner FGF-2(23), leading to U4 snRNP accumulation in CBs, indicating a role for immobile SMN in tri-snRNP assembly.

  4. Determining High-Quality Critical Body Residues for Multiple Species and Chemicals by Applying Improved Experimental Design and Data Interpretation Concepts

    DEFF Research Database (Denmark)

    van der Heijden, Stephan A.; Hermens, Joop L. M.; Sinnige, Theo L.

    2015-01-01

    Ecotoxicological effect data are generally expressed as effective concentrations in the external exposure medium and do thus not account for differences in chemical uptake, bioavailability, and metabolism, which can introduce substantial data variation. The Critical Body Residue (CBR) concept...... provides clear advantages, because it links effects directly to the internal exposure. Using CBRs instead of external concentrations should therefore reduce variability. For compounds that act via narcosis even a constant CBR has been proposed. Despite the expected uniformity, CBR values......-defined test protocol for accurately and precisely measuring CBR data, involving improved (passive) dosing, sampling, and processing of organisms. The chemicals 1,2,4-trichlorobenzene, 1,2,3,4-tetrachlorobenzene, 2,3,4-trichloroaniline, 2,3,5,6-tetrachloroaniline, 4-chloro-3-methylphenol, pentylbenzene, pyrene...

  5. Survival, growth, and body residues of hyalella azteca (Saussure) exposed to fipronil contaminated sediments from non-vegetated and vegetated microcosms.

    Science.gov (United States)

    Kröger, Robert; Lizotte, Richard E; Moore, Matthew T

    2009-09-01

    We assessed chronic effects of fipronil and metabolite contaminated sediments from non-vegetated and Thallia dealbata vegetated wetland microcosms on Hyalella azteca during wet and dry exposures. Mean sediment concentrations (ng g(-1)) ranged from 0.72-1.26, 0.01-0.69, 0.07-0.23, and 0.49-7.87 for fipronil, fipronil-sulfide, fipronil-sulfone, and fipronil-desulfinyl, respectively. No significant differences in animal survival or growth were observed between non-vegetated and vegetated microcosms during wet or dry exposures. Mean animal body residue concentrations (ng g(-1)) ranged from 28.4-77.6, 0-30.7, and 8.3-43.8 for fipronil, fipronil-sulfide, and fipronil-sulfone. Fipronil-desulfinyl was not detected in any animal samples.

  6. Mechanisms underlying rhythmic locomotion: interactions between activation, tension and body curvature waves

    Science.gov (United States)

    Chen, Jun; Friesen, W. Otto; Iwasaki, Tetsuya

    2012-01-01

    SUMMARY Undulatory animal locomotion arises from three closely related propagating waves that sweep rostrocaudally along the body: activation of segmental muscles by motoneurons (MNs), strain of the body wall, and muscle tension induced by activation and strain. Neuromechanical models that predict the relative propagation speeds of neural/muscle activation, muscle tension and body curvature can reveal crucial underlying control features of the central nervous system and the power-generating mechanisms of the muscle. We provide an analytical explanation of the relative speeds of these three waves based on a model of neuromuscular activation and a model of the body–fluid interactions for leech anguilliform-like swimming. First, we deduced the motoneuron spike frequencies that activate the muscle and the resulting muscle tension during swimming in intact leeches from muscle bending moments. Muscle bending moments were derived from our video-recorded kinematic motion data by our body–fluid interaction model. The phase relationships of neural activation and muscle tension in the strain cycle were then calculated. Our study predicts that the MN activation and body curvature waves have roughly the same speed (the ratio of curvature to MN activation speed ≈0.84), whereas the tension wave travels about twice as fast. The high speed of the tension wave resulting from slow MN activation is explained by the multiplicative effects of MN activation and muscle strain on tension development. That is, the product of two slower waves (activation and strain) with appropriate amplitude, bias and phase can generate a tension wave with twice the propagation speed of the factors. Our study predicts that (1) the bending moment required for swimming is achieved by minimal MN spike frequency, rather than by minimal muscle tension; (2) MN activity is greater in the mid-body than in the head and tail regions; (3) inhibitory MNs not only accelerate the muscle relaxation but also reduce

  7. The Relationship between Body Movements and Qualities of Social Interaction between a Boy with Severe Developmental Disabilities and His Caregiver

    Science.gov (United States)

    Dammeyer, Jesper; Koppe, Simo

    2013-01-01

    Research in social interaction and nonverbal communication among individuals with severe developmental disabilities also includes the study of body movements. Advances in analytical technology give new possibilities for measuring body movements more accurately and reliably. One such advance is the Qualisys Motion Capture System (QMCS), which…

  8. The Relationship between Body Movements and Qualities of Social Interaction between a Boy with Severe Developmental Disabilities and His Caregiver

    Science.gov (United States)

    Dammeyer, Jesper; Koppe, Simo

    2013-01-01

    Research in social interaction and nonverbal communication among individuals with severe developmental disabilities also includes the study of body movements. Advances in analytical technology give new possibilities for measuring body movements more accurately and reliably. One such advance is the Qualisys Motion Capture System (QMCS), which…

  9. Small-world networks of residue interactions in the Abl kinase complexes with cancer drugs: topology of allosteric communication pathways can determine drug resistance effects.

    Science.gov (United States)

    Tse, A; Verkhivker, G M

    2015-07-01

    The human protein kinases play a fundamental regulatory role in orchestrating functional processes in complex cellular networks. Understanding how conformational equilibrium between functional kinase states can be modulated by ligand binding or mutations is critical for quantifying molecular basis of allosteric regulation and drug resistance. In this work, molecular dynamics simulations of the Abl kinase complexes with cancer drugs (Imatinib and Dasatinib) were combined with structure-based network modeling to characterize dynamics of the residue interaction networks in these systems. The results have demonstrated that structural architecture of kinase complexes can produce a small-world topology of the interaction networks. Our data have indicated that specific Imatinib binding to a small number of highly connected residues could lead to network-bridging effects and allow for efficient allosteric communication, which is mediated by a dominant pathway sensitive to the unphosphorylated Abl state. In contrast, Dasatinib binding to the active kinase form may activate a broader ensemble of allosteric pathways that are less dependent on the phosphorylation status of Abl and provide a better balance between the efficiency and resilience of signaling routes. Our results have unveiled how differences in the residue interaction networks and allosteric communications of the Abl kinase complexes can be directly related to drug resistance effects. This study offers a plausible perspective on how efficiency and robustness of the residue interaction networks and allosteric pathways in kinase structures may be associated with protein responses to drug binding.

  10. Does Parental Divorce Moderate the Heritability of Body Dissatisfaction? An Extension of Previous Gene-Environment Interaction Effects

    Science.gov (United States)

    O’Connor, Shannon M.; Klump, Kelly L.; VanHuysse, Jessica L.; McGue, Matt; Iacono, William

    2015-01-01

    Objective Previous research suggests that parental divorce moderates genetic influences on body dissatisfaction. Specifically, the heritability of body dissatisfaction is higher in children of divorced versus intact families, suggesting possible gene-environment interaction effects. However, prior research is limited to a single, self-report measure of body dissatisfaction. The primary aim of the present study was to examine whether these findings extend to a different dimension of body dissatisfaction, body image perceptions. Method Participants were 1,534 female twins from the Minnesota Twin Family Study, ages 16–20 years. The Body Rating Scale (BRS) was used to assess body image perceptions. Results Although BRS scores were heritable in twins from divorced and intact families, the heritability estimates in the divorced group were not significantly greater than estimates in the intact group. However, there were differences in nonshared environmental effects, where the magnitude of these environmental influences was larger in the divorced as compared to the intact families. Discussion Different dimensions of body dissatisfaction (i.e., negative self-evaluation versus body image perceptions) may interact with environmental risk, such as parental divorce, in discrete ways. Future research should examine this possibility and explore differential gene x environment interactions using diverse measures. PMID:26314278

  11. Interactive effects of body position and perceived exertion during spinning exercises.

    Science.gov (United States)

    Rendos, Nicole K; Musto, Anthony A; Signorile, Joseph F

    2015-03-01

    Spinning is a popular group exercise taught in health and fitness facilities worldwide. Throughout a Spinning workout session, intensity is variable and is controlled by body position on the Spinning stationary cycle and perceived resistance. This study examined the effects of 3 body positions and 4 levels of perceived exertion (RPE) on cardiorespiratory response and vastus lateralis normalized electromyographical activity (NrmsEMGVL). Eleven participants (24.4 ± 6.3 years) with 3.2 ± 2.2 years of Spinning experience completed twelve 3-minute randomly assigned Spinning conditions across 4 separate testing days after an 8-hour fast. Conditions were determined by body position (seated, running, and standing climb [SC]) and RPE (low, low-medium, medium-high, and high). Cardiorespiratory data and NrmsEMGVL were recorded continuously during each Spinning condition. Respiratory rate and oxygen consumption were significantly higher for running and SC than seated, and minute ventilation was significantly higher for running than seated. All cardiorespiratory values were higher at medium-high and high RPE, than low or medium-low RPE, and high RPE generated higher respiratory rate and respiratory exchange ratio than medium-high RPE. Significant body position × RPE interactions were observed for heart rate (HR) and NrmsEMGVL with running and SC producing higher HRs than seated at low and high RPE, and running producing higher NrmsEMGVL than seated at low RPE. Results indicate that running and SC provide the greatest cardiorespiratory responses, and maximal efforts are not needed for these responses. Additionally, HR seems to be a poor marker of oxygen consumption, especially at high RPEs.

  12. Terminology for the body in social interaction, as appearing in papers published in the journal 'Research on Language and Social Interaction', 1987-2013

    DEFF Research Database (Denmark)

    Nevile, Maurice Richard

    2016-01-01

    This is a list of terms referring generally to the body in descriptions and analyses of social interaction, as used by authors in papers published in ROLSI. The list includes over 200 items, grouped according to common phrasing and within alphabetical order. The list was compiled in preparation...... for the review paper: Nevile, M. (2015) The embodied turn in research on language and social interaction. Research on Language and Social Interaction,48(2): 121-151....

  13. [Effect of mutations and modifications of amino acid residues on zinc-induced interaction of the metal-binding domain of β-amyloid with DNA].

    Science.gov (United States)

    Khmeleva, S A; Mezentsev, Y V; Kozin, S A; Mitkevich, V A; Medvedev, A E; Ivanov, A S; Bodoev, N V; Makarov, A A; Radko, S P

    2015-01-01

    Interaction of intranuclear β-amyloid with DNA is considered to be a plausible mechanism of Alzheimer's disease pathogenesis. The interaction of single- and double-stranded DNA with synthetic peptides was analyzed using surface plasmon resonance. The peptides represent the metal-binding domain of β-amyloid (amino acids 1-16) and its variants with chemical modifications and point substitutions of amino acid residues which are associated with enhanced neurotoxicity of β-amyloid in cell tests. It has been shown that the presence of zinc ions is necessary for the interaction of the peptides with DNA in solution. H6R substitution has remarkably reduced the ability of domain 1-16 to bind DNA. This is in accordance with the supposition that the coordination of a zinc ion by amino acid residues His6, Glu11, His13, and His14 of the β-amyloid metal-binding domain results in the occurrence of an anion-binding site responsible for the interaction of the domain with DNA. Zinc-induced dimerization and oligomerization of domain 1-16 associated with phosphorylation of Ser8 and the presence of unblocked amino- and carboxy-terminal groups have resulted in a decrease of peptide concentrations required for detection of the peptide-DNA interaction. The presence of multiple anion-binding sites on the dimers and oligomers is responsible for the enhancement of the peptide-DNA interaction. A substitution of the negatively charged residue Asp7 for the neutral residue Asn in close proximity to the anion-binding site of the domain 1-16 of Aβ facilitates the electrostatic interaction between this site and phosphates of a polynucleotide chain, which enhances zinc-induced binding to DNA.

  14. Influence of nuclear interactions in body tissues on tumor dose in carbon-ion radiotherapy

    Energy Technology Data Exchange (ETDEWEB)

    Inaniwa, T., E-mail: taku@nirs.go.jp; Kanematsu, N. [Medical Physics Research Program, Research Center for Charged Particle Therapy, National Institute of Radiological Sciences, Anagawa 4-9-1, Inage-ku, Chiba 263-8555 (Japan); Tsuji, H.; Kamada, T. [Hospital, Research Center for Charged Particle Therapy, National Institute of Radiological Sciences, 4-9-1 Anagawa, Inage-ku, Chiba 263-8555 (Japan)

    2015-12-15

    Purpose: In carbon-ion radiotherapy treatment planning, the planar integrated dose (PID) measured in water is applied to the patient dose calculation with density scaling using the stopping power ratio. Since body tissues are chemically different from water, this dose calculation can be subject to errors, particularly due to differences in inelastic nuclear interactions. In recent studies, the authors proposed and validated a PID correction method for these errors. In the present study, the authors used this correction method to assess the influence of these nuclear interactions in body tissues on tumor dose in various clinical cases. Methods: Using 10–20 cases each of prostate, head and neck (HN), bone and soft tissue (BS), lung, liver, pancreas, and uterine neoplasms, the authors first used treatment plans for carbon-ion radiotherapy without nuclear interaction correction to derive uncorrected dose distributions. The authors then compared these distributions with recalculated distributions using the nuclear interaction correction (corrected dose distributions). Results: Median (25%/75% quartiles) differences between the target mean uncorrected doses and corrected doses were 0.2% (0.1%/0.2%), 0.0% (0.0%/0.0%), −0.3% (−0.4%/−0.2%), −0.1% (−0.2%/−0.1%), −0.1% (−0.2%/0.0%), −0.4% (−0.5%/−0.1%), and −0.3% (−0.4%/0.0%) for the prostate, HN, BS, lung, liver, pancreas, and uterine cases, respectively. The largest difference of −1.6% in target mean and −2.5% at maximum were observed in a uterine case. Conclusions: For most clinical cases, dose calculation errors due to the water nonequivalence of the tissues in nuclear interactions would be marginal compared to intrinsic uncertainties in treatment planning, patient setup, beam delivery, and clinical response. In some extreme cases, however, these errors can be substantial. Accordingly, this correction method should be routinely applied to treatment planning in clinical practice.

  15. Performance-Driven Hybrid Full-Body Character Control for Navigation and Interaction in Virtual Environments

    Science.gov (United States)

    Mousas, Christos; Anagnostopoulos, Christos-Nikolaos

    2017-06-01

    This paper presents a hybrid character control interface that provides the ability to synthesize in real-time a variety of actions based on the user's performance capture. The proposed methodology enables three different performance interaction modules: the performance animation control that enables the direct mapping of the user's pose to the character, the motion controller that synthesizes the desired motion of the character based on an activity recognition methodology, and the hybrid control that lies within the performance animation and the motion controller. With the methodology presented, the user will have the freedom to interact within the virtual environment, as well as the ability to manipulate the character and to synthesize a variety of actions that cannot be performed directly by him/her, but which the system synthesizes. Therefore, the user is able to interact with the virtual environment in a more sophisticated fashion. This paper presents examples of different scenarios based on the three different full-body character control methodologies.

  16. Human UBL5 protein interacts with coilin and meets the Cajal bodies.

    Science.gov (United States)

    Svéda, Martin; Castorálová, Markéta; Lipov, Jan; Ruml, Tomáš; Knejzlík, Zdeněk

    2013-06-28

    UBL5 protein, a structural homologue of ubiquitin, was shown to be involved in pre-mRNA splicing and transcription regulation in yeast and Caenorhabditis elegans, respectively. However, role of the UBL5 human orthologue is still elusive. In our study, we observed that endogenous human UBL5 that was localized in the nucleus, partially associates with Cajal bodies (CBs), nuclear domains where spliceosomal components are assembled. Simultaneous expression of exogenous UBL5 and coilin resulted in their nuclear colocalization in HeLa cells. The ability of UBL5 to interact with coilin was proved by GST pull-down assay using coilin that was either in vitro translated or extracted from HEK293T cells. Further, our results showed that the UBL5-coilin interaction was not influenced by coilin phosphorylation. These results suggest that UBL5 could be targeted to CBs via its interaction with coilin. Relation between human UBL5 protein and CBs is in the agreement with current observations about yeast orthologue Hub1 playing important role in alternative splicing.

  17. Interactive Effects of Physical Fitness and Body Mass Index on the Risk of Hypertension.

    Science.gov (United States)

    Crump, Casey; Sundquist, Jan; Winkleby, Marilyn A; Sundquist, Kristina

    2016-02-01

    High body mass index (BMI) and low physical fitness are risk factors for hypertension, but their interactive effects are unknown. Elucidation of interactions between these modifiable risk factors may help inform more effective interventions in susceptible subgroups. To determine the interactive effects of BMI and physical fitness on the risk of hypertension in a large national cohort. This cohort study included all 1,547,189 military conscripts in Sweden from January 1, 1969, through December 31, 1997 (97%-98% of all 18-year-old men nationwide each year), who were followed up through December 31, 2012 (maximum age, 62 years). Data analysis was conducted August 1 through August 15, 2015. Standardized aerobic capacity, muscular strength, and BMI measurements obtained at a military conscription examination. Hypertension identified from outpatient and inpatient diagnoses. A total of 93,035 men (6.0%) were diagnosed with hypertension in 39.7 million person-years of follow-up. High BMI and low aerobic capacity (but not muscular strength) were associated with increased risk of hypertension, independent of family history and socioeconomic factors (BMI, overweight or obese vs normal: incidence rate ratio, 2.51; 95% CI, 2.46-2.55; P fitness, even among persons with normal BMI.

  18. Interaction between smoking and body mass index and risk of oral clefts

    DEFF Research Database (Denmark)

    Wehby, George L; Uribe, Lina M Moreno; Wilcox, Allen J

    2017-01-01

    PURPOSE: To examine maternal smoking and body mass index (BMI) interactions in contributing to risk of oral clefts. METHODS: We studied 4935 cases and 10,557 controls from six population-based studies and estimated a pooled logistic regression of individual-level data, controlling for study fixed...... effects and individual-level risk factors. RESULTS: We found a significant negative smoking-BMI interaction, with cleft risk with smoking generally declining with higher BMI. For all clefts combined, the odds ratio for smoking was 1.61 (95% confidence interval [CI]: 1.39-1.86) at BMI 17 (underweight), 1.......47 (95% CI: 1.34-1.62) at BMI 22 (normal weight), 1.35 (95% CI: 1.22-1.48) at BMI 27 (overweight), 1.21 (95% CI: 1.04-1.41) at BMI 33 (obese), and 1.13 (95% CI: 0.92-1.38) at BMI 37 (very obese). A negative interaction was also observed for isolated clefts and across cleft types but was more pronounced...

  19. Aerodynamic Interactions Between Contralateral Wings and Between Wings and Body of a Model Insect at Hovering and Small Speed Motions

    Institute of Scientific and Technical Information of China (English)

    LIANG Bin; SUN Mao

    2011-01-01

    In this paper,we study the aerodynamic interactions between the contralateral wings and between the body and wings of a model insect,when the insect is hovering and has various translational and rotational motions,using the method numerically solving the Navier-Stokes equations over moving overset grids.The aerodynamic interactional effects are identified by comparing the results of a complete model insect,the corresponding wing pair,single wing and body without the wings.Horizontal,vertical and lateral translations and roll,pitch and yaw rotations at small speeds are considered.The results indicate that for the motions considered,both the interaction between the contralateral wings and the interaction between the body and wings are weak.The changes in the forces and moments of a wing due to the contralateral wing interaction,of the wings due to the presence of the body,and of the body due to the presence of the wings are generally less than 4.5%.Results show that aerodynamic forces of wings and body can be measured or computed separately in the analysis of flight stability and control of hovering insects.

  20. Circuit design for multi-body interactions in superconducting quantum annealing systems with applications to a scalable architecture

    Science.gov (United States)

    Chancellor, N.; Zohren, S.; Warburton, P. A.

    2017-06-01

    Quantum annealing provides a way of solving optimization problems by encoding them as Ising spin models which are implemented using physical qubits. The solution of the optimization problem then corresponds to the ground state of the system. Quantum tunneling is harnessed to enable the system to move to the ground state in a potentially high non-convex energy landscape. A major difficulty in encoding optimization problems in physical quantum annealing devices is the fact that many real world optimization problems require interactions of higher connectivity, as well as multi-body terms beyond the limitations of the physical hardware. In this work we address the question of how to implement multi-body interactions using hardware which natively only provides two-body interactions. The main result is an efficient circuit design of such multi-body terms using superconducting flux qubits in which effective N-body interactions are implemented using N ancilla qubits and only two inductive couplers. It is then shown how this circuit can be used as the unit cell of a scalable architecture by applying it to a recently proposed embedding technique for constructing an architecture of logical qubits with arbitrary connectivity using physical qubits which have nearest-neighbor four-body interactions. It is further shown that this design is robust to non-linear effects in the coupling loops, as well as mismatches in some of the circuit parameters.

  1. A conserved interaction that is essential for the biogenesis of histone locus bodies.

    Science.gov (United States)

    Yang, Xiao-cui; Sabath, Ivan; Kunduru, Lalitha; van Wijnen, Andre J; Marzluff, William F; Dominski, Zbigniew

    2014-12-05

    Nuclear protein, ataxia-telangiectasia locus (NPAT) and FLICE-associated huge protein (FLASH) are two major components of discrete nuclear structures called histone locus bodies (HLBs). NPAT is a key co-activator of histone gene transcription, whereas FLASH through its N-terminal region functions in 3' end processing of histone primary transcripts. The C-terminal region of FLASH contains a highly conserved domain that is also present at the end of Yin Yang 1-associated protein-related protein (YARP) and its Drosophila homologue, Mute, previously shown to localize to HLBs in Drosophila cells. Here, we show that the C-terminal domain of human FLASH and YARP interacts with the C-terminal region of NPAT and that this interaction is essential and sufficient to drive FLASH and YARP to HLBs in HeLa cells. Strikingly, only the last 16 amino acids of NPAT are sufficient for the interaction. We also show that the C-terminal domain of Mute interacts with a short region at the end of the Drosophila NPAT orthologue, multi sex combs (Mxc). Altogether, our data indicate that the conserved C-terminal domain shared by FLASH, YARP, and Mute recognizes the C-terminal sequence of NPAT orthologues, thus acting as a signal targeting proteins to HLBs. Finally, we demonstrate that the C-terminal domain of human FLASH can be directly joined with its N-terminal region through alternative splicing. The resulting 190-amino acid MiniFLASH, despite lacking 90% of full-length FLASH, contains all regions necessary for 3' end processing of histone pre-mRNA in vitro and accumulates in HLBs. © 2014 by The American Society for Biochemistry and Molecular Biology, Inc.

  2. Interaction between the FTO gene, body mass index and depression: meta-analysis of 13701 individuals.

    Science.gov (United States)

    Rivera, Margarita; Locke, Adam E; Corre, Tanguy; Czamara, Darina; Wolf, Christiane; Ching-Lopez, Ana; Milaneschi, Yuri; Kloiber, Stefan; Cohen-Woods, Sara; Rucker, James; Aitchison, Katherine J; Bergmann, Sven; Boomsma, Dorret I; Craddock, Nick; Gill, Michael; Holsboer, Florian; Hottenga, Jouke-Jan; Korszun, Ania; Kutalik, Zoltan; Lucae, Susanne; Maier, Wolfgang; Mors, Ole; Müller-Myhsok, Bertram; Owen, Michael J; Penninx, Brenda W J H; Preisig, Martin; Rice, John; Rietschel, Marcella; Tozzi, Federica; Uher, Rudolf; Vollenweider, Peter; Waeber, Gerard; Willemsen, Gonneke; Craig, Ian W; Farmer, Anne E; Lewis, Cathryn M; Breen, Gerome; McGuffin, Peter

    2017-08-01

    BackgroundDepression and obesity are highly prevalent, and major impacts on public health frequently co-occur. Recently, we reported that having depression moderates the effect of the FTO gene, suggesting its implication in the association between depression and obesity.AimsTo confirm these findings by investigating the FTO polymorphism rs9939609 in new cohorts, and subsequently in a meta-analysis.MethodThe sample consists of 6902 individuals with depression and 6799 controls from three replication cohorts and two original discovery cohorts. Linear regression models were performed to test for association between rs9939609 and body mass index (BMI), and for the interaction between rs9939609 and depression status for an effect on BMI. Fixed and random effects meta-analyses were performed using METASOFT.ResultsIn the replication cohorts, we observed a significant interaction between FTO, BMI and depression with fixed effects meta-analysis (β = 0.12, P = 2.7 × 10(-4)) and with the Han/Eskin random effects method (P = 1.4 × 10(-7)) but not with traditional random effects (β = 0.1, P = 0.35). When combined with the discovery cohorts, random effects meta-analysis also supports the interaction (β = 0.12, P = 0.027) being highly significant based on the Han/Eskin model (P = 6.9 × 10(-8)). On average, carriers of the risk allele who have depression have a 2.2% higher BMI for each risk allele, over and above the main effect of FTOConclusionsThis meta-analysis provides additional support for a significant interaction between FTO, depression and BMI, indicating that depression increases the effect of FTO on BMI. The findings provide a useful starting point in understanding the biological mechanism involved in the association between obesity and depression. © The Royal College of Psychiatrists 2017.

  3. Relationships between body condition score change, prior mid-lactation phenotypic residual feed intake, and hyperketonemia onset in transition dairy cows.

    Science.gov (United States)

    Rathbun, Francesca M; Pralle, Ryan S; Bertics, Sandra J; Armentano, Louis E; Cho, K; Do, C; Weigel, Kent A; White, Heather M

    2017-05-01

    Extensive efforts have been made to identify more feed-efficient dairy cows, yet it is unclear how selection for feed efficiency will influence metabolic health. The objectives of this research were to determine the relationships between residual feed intake (RFI), a measure of feed efficiency, body condition score (BCS) change, and hyperketonemia (HYK) incidence. Blood and milk samples were collected twice weekly from cows 5 to 18 d postcalving for a total of 4 samples. Hyperketonemia was diagnosed at a blood β-hydroxybutyrate (BHB) ≥1.2 mmol/L and cows were treated upon diagnosis. Dry period, calving, and final blood sampling BCS was recorded. Prior mid-lactation production, body weight, body weight change, and dry matter intake (DMI) data were used to determine RFI phenotype, calculated as the difference between observed DMI and predicted DMI. The maximum BHB concentration (BHBmax) for each cow was used to group cows into HYK or not hyperketonemic. Lactation number, BCS, and RFI data were analyzed with linear and quadratic orthogonal contrasts. Of the 570 cows sampled, 19.7% were diagnosed with HYK. The first positive HYK test occurred at 9 ± 0.9 d postpartum and the average BHB concentration at the first positive HYK test was 1.53 ± 0.14 mmol/L. In the first 30 d postpartum, HYK-positive cows had increased milk yield and fat concentration, decreased milk protein concentration, and decreased somatic cell count. Cows with a dry BCS ≥4.0, or that lost 1 or more BCS unit across the transition to lactation period, had greater BHBmax than cows with lower BCS. Prior-lactation RFI did not alter BHBmax. Avoiding over conditioning of dry cows and subsequent excessive fat mobilization during the transition period may decrease HYK incidence; however, RFI during a prior lactation does not appear to be associated with HYK onset. Copyright © 2017 American Dairy Science Association. Published by Elsevier Inc. All rights reserved.

  4. Periodically driven interacting electrons in one dimension: Many-body Floquet approach

    Science.gov (United States)

    Puviani, M.; Manghi, F.

    2016-10-01

    We propose a method to study the time evolution of correlated electrons driven by a harmonic perturbation. Combining Floquet formalism to include the time-dependent field and cluster perturbation theory to solve the many-body problem in the presence of short-range correlations, we treat the electron double dressing, by photons and by e -e interactions, on the same footing. We apply the method to an extended Hubbard chain at half occupation, and we show that in the regime of small field frequency and for given values of field strength, the zero-mode Floquet band is no longer gapped and the system recovers a metallic state. Our results are indicative of an omnipresent mechanism for insulator-to-metal transitions in one-dimensional systems.

  5. Hydrodynamic interactions between two bodies in waves in 3D time domain

    Institute of Scientific and Technical Information of China (English)

    WANG Jian-fang; LI Ji-de; CAI Xin-gong; TIAN Ming-qi; Hao Jin-feng

    2005-01-01

    In this paper, a 3D time domain technique is adopted to calculate the coupled hydrodynamic interaction between two bodies without flare in waves. For verifying the code, two same cylinders are selected to calculate coupled hydrodynamic effects by comparison with the results obtained by 3D frequency method which has been proved to be efficient for solving such problems. In order to improve efficiency of calculation, the effect of history time has been discussed, and an improved method is presented. Moreover, the effect of lateral separation distance is also discussed in detail. The technique developed here may serve as a more rigorous tool to analyze the related transient problems of two ships doing underway replenishment in waves.

  6. Particle-hole configuration interaction and many-body perturbation theory: application to Hg+

    CERN Document Server

    Berengut, J C

    2016-01-01

    The combination of configuration interaction and many-body perturbation theory methods (CI+MBPT) is extended to non-perturbatively include configurations with electron holes below the designated Fermi level, allowing us to treat systems where holes play an important role. For example, the method can treat valence-hole systems like Ir$^{17+}$, particle-hole excitations in noble gases, and difficult transitions such as the $6s \\rightarrow 5d^{-1}6s^2$ optical clock transition in Hg$^+$. We take the latter system as our test case for the method and obtain very good accuracy (~1%) for the low-lying transition energies. The $\\alpha$-dependence of these transitions is calculated and used to reinterpret the existing best laboratory limits on the time-dependence of the fine-structure constant.

  7. The influence of print exposure on the body-object interaction effect in visual word recognition.

    Science.gov (United States)

    Hansen, Dana; Siakaluk, Paul D; Pexman, Penny M

    2012-01-01

    We examined the influence of print exposure on the body-object interaction (BOI) effect in visual word recognition. High print exposure readers and low print exposure readers either made semantic categorizations ("Is the word easily imageable?"; Experiment 1) or phonological lexical decisions ("Does the item sound like a real English word?"; Experiment 2). The results from Experiment 1 showed that there was a larger BOI effect for the low print exposure readers than for the high print exposure readers in semantic categorization, though an effect was observed for both print exposure groups. However, the results from Experiment 2 showed that the BOI effect was observed only for the high print exposure readers in phonological lexical decision. The results of the present study suggest that print exposure does influence the BOI effect, and that this influence varies as a function of task demands.

  8. The Influence of Print Exposure on the Body-Object Interaction Effect in Visual Word Recognition

    Directory of Open Access Journals (Sweden)

    Dana eHansen

    2012-05-01

    Full Text Available We examined the influence of print exposure on the body-object interaction (BOI effect in visual word recognition. High print exposure readers and low print exposure readers either made semantic categorizations (Is the word easily imageable?; Experiment 1 or phonological lexical decisions (Does the item sound like a real English word?; Experiment 2. The results from Experiment 1 showed that there was a larger facilitatory BOI effect for the low print exposure readers than for the high print exposure readers in semantic categorization, though an effect was observed for both print exposure groups. However, the results from Experiment 2 showed that a facilitatory BOI effect was observed only for the high print exposure readers in phonological lexical decision. The results of the present study suggest that print exposure does influence the BOI effect, and that this influence varies as a function of task demands.

  9. Desorption electrospray ionization-based imaging of interaction between vascular graft and human body.

    Science.gov (United States)

    Bodzon-Kulakowska, Anna; Drabik, Anna; Mystkowska, Joanna; Chlabicz, Michal; Gacko, Marek; Dabrowski, Jan R; Mielczarek, Przemyslaw; Silberring, Jerzy; Suder, Piotr

    2016-01-01

    The desorption electrospray ionization-mass spectrometry imaging (DESI-MSI) is known as a fast and convenient MS-based method for lipid imaging in various biological materials. Here, we applied this technique to visualize lipid distribution in a vascular graft removed from a patient's body. This is a good example of the DESI system capabilities toward imaging of interaction between artificial material and living tissues. Detailed analysis allowed for visualization of the spatial distribution of selected lipids in this implanted, artificial material. Not only DESI-MSI allowed visualization of lipid distribution in the investigated material but also enabled identification of the detected molecular species using MS/MS. Here, this technique was successfully used to evaluate the saturation and spatial distribution of endogenous lipids in the artificial vascular graft. Unambiguous identification of the lipids was done with the aid of fragmentation procedure. We also showed that various lipids localize preferably in graft material or internal plaque existing inside the graft.

  10. Screened test-charge - electron interaction including many-body effects in two and three dimensions

    Science.gov (United States)

    Gold, A.; Ghazali, A.

    1997-05-01

    Bound states of a negatively charged test particle and an electron are studied by incorporating many-body effects (exchange and correlation) in the screening function of an interacting electron gas via the local-field correction. Using a variational method and a matrix-diagonalization method we determine the energies and the wave functions of the ground state and the excited states as functions of the electron density for three-dimensional and two-dimensional systems. For high electron density no bound states are found. Below a critical density the number and the energy of the bound states increase with decreasing electron density. We also present results for bound-state energies of a positively charged test particle with an electron, and compare them with results obtained within the random-phase approximation where the local-field correction is ignored.

  11. Strain field of interstitial hydrogen atom in body-centered cubic iron and its effect on hydrogen-dislocation interaction

    OpenAIRE

    Wang, Shuai; Takahashi, Keisuke; Hashimoto, Naoyuki; Isobe, Shigehito; Ohnuki, Somei

    2013-01-01

    Effect of hydrogen in body-centered cubic iron is explored by using the density function theory. Hydrogen atoms increase the concentration of free electrons in the simulation cell and have bonding interaction with Fe atom. Caused by anisotropic strain components of hydrogen atoms in the tetrahedral sites, elastic interaction for hydrogen with screw dislocation has been found. The dependence of hydrogen-screw dislocation interaction on hydrogen concentration is confirmed by repeated stress rel...

  12. Dipicrylamine Modulates GABAρ1 Receptors through Interactions with Residues in the TM4 and Cys-Loop Domains.

    Science.gov (United States)

    Limon, Agenor; Estrada-Mondragón, Argel; Ruiz, Jorge M Reyes; Miledi, Ricardo

    2016-04-01

    Dipicrylamine (DPA) is a commonly used acceptor agent in Förster resonance energy transfer experiments that allows the study of high-frequency neuronal activity in the optical monitoring of voltage in living cells. However, DPA potently antagonizes GABAA receptors that contain α1 and β2 subunits by a mechanism which is not clearly understood. In this work, we aimed to determine whether DPA modulation is a general phenomenon of Cys-loop ligand-gated ion channels (LGICs), and whether this modulation depends on particular amino acid residues. For this, we studied the effects of DPA on human homomeric GABAρ1, α7 nicotinic, and 5-HT3A serotonin receptors expressed in Xenopus oocytes. Our results indicate that DPA is an allosteric modulator of GABAρ1 receptors with an IC50 of 1.6 µM, an enhancer of α7 nicotinic receptors at relatively high concentrations of DPA, and has little, if any, effect on 5-HT3A receptors. DPA antagonism of GABAρ1 was strongly enhanced by preincubation, was slightly voltage-dependent, and its washout was accelerated by bovine serum albumin. These results indicate that DPA modulation is not a general phenomenon of LGICs, and structural differences between receptors may account for disparities in DPA effects. In silico modeling of DPA docking to GABAρ1, α7 nicotinic, and 5-HT3A receptors suggests that a hydrophobic pocket within the Cys-loop and the M4 segment in GABAρ1, located at the extracellular/membrane interface, facilitates the interaction with DPA that leads to inhibition of the receptor. Functional examinations of mutant receptors support the involvement of the M4 segment in the allosteric modulation of GABAρ1 by DPA.

  13. Curvilinear Immersed Boundary Method for Simulating Fluid Structure Interaction with Complex 3D Rigid Bodies.

    Science.gov (United States)

    Borazjani, Iman; Ge, Liang; Sotiropoulos, Fotis

    2008-08-10

    The sharp-interface CURVIB approach of Ge and Sotiropoulos [L. Ge, F. Sotiropoulos, A Numerical Method for Solving the 3D Unsteady Incompressible Navier-Stokes Equations in Curvilinear Domains with Complex Immersed Boundaries, Journal of Computational Physics 225 (2007) 1782-1809] is extended to simulate fluid structure interaction (FSI) problems involving complex 3D rigid bodies undergoing large structural displacements. The FSI solver adopts the partitioned FSI solution approach and both loose and strong coupling strategies are implemented. The interfaces between immersed bodies and the fluid are discretized with a Lagrangian grid and tracked with an explicit front-tracking approach. An efficient ray-tracing algorithm is developed to quickly identify the relationship between the background grid and the moving bodies. Numerical experiments are carried out for two FSI problems: vortex induced vibration of elastically mounted cylinders and flow through a bileaflet mechanical heart valve at physiologic conditions. For both cases the computed results are in excellent agreement with benchmark simulations and experimental measurements. The numerical experiments suggest that both the properties of the structure (mass, geometry) and the local flow conditions can play an important role in determining the stability of the FSI algorithm. Under certain conditions unconditionally unstable iteration schemes result even when strong coupling FSI is employed. For such cases, however, combining the strong-coupling iteration with under-relaxation in conjunction with the Aitken's acceleration technique is shown to effectively resolve the stability problems. A theoretical analysis is presented to explain the findings of the numerical experiments. It is shown that the ratio of the added mass to the mass of the structure as well as the sign of the local time rate of change of the force or moment imparted on the structure by the fluid determine the stability and convergence of the FSI

  14. Penis size interacts with body shape and height to influence male attractiveness.

    Science.gov (United States)

    Mautz, Brian S; Wong, Bob B M; Peters, Richard A; Jennions, Michael D

    2013-04-23

    Compelling evidence from many animal taxa indicates that male genitalia are often under postcopulatory sexual selection for characteristics that increase a male's relative fertilization success. There could, however, also be direct precopulatory female mate choice based on male genital traits. Before clothing, the nonretractable human penis would have been conspicuous to potential mates. This observation has generated suggestions that human penis size partly evolved because of female choice. Here we show, based upon female assessment of digitally projected life-size, computer-generated images, that penis size interacts with body shape and height to determine male sexual attractiveness. Positive linear selection was detected for penis size, but the marginal increase in attractiveness eventually declined with greater penis size (i.e., quadratic selection). Penis size had a stronger effect on attractiveness in taller men than in shorter men. There was a similar increase in the positive effect of penis size on attractiveness with a more masculine body shape (i.e., greater shoulder-to-hip ratio). Surprisingly, larger penis size and greater height had almost equivalent positive effects on male attractiveness. Our results support the hypothesis that female mate choice could have driven the evolution of larger penises in humans. More broadly, our results show that precopulatory sexual selection can play a role in the evolution of genital traits.

  15. Identification of an anchor residue for CheA-CheY interactions in the chemotaxis system of Escherichia coli.

    Science.gov (United States)

    Thakor, Hemang; Nicholas, Sarah; Porter, Ian M; Hand, Nicole; Stewart, Richard C

    2011-08-01

    Transfer of a phosphoryl group from autophosphorylated CheA (P-CheA) to CheY is an important step in the bacterial chemotaxis signal transduction pathway. This reaction involves CheY (i) binding to the P2 domain of P-CheA and then (ii) acquiring the phosphoryl group from the P1 domain. Crystal structures indicated numerous side chain interactions at the CheY-P2 binding interface. To investigate the individual contributions of the P2 side chains involved in these contacts, we analyzed the effects of eight alanine substitution mutations on CheA-CheY binding interactions. An F214A substitution in P2 caused ∼1,000-fold reduction in CheA-CheY binding affinity, while Ala substitutions at other P2 positions had small effects (E171A, E178A, and I216A) or no detectable effects (H181A, D202A, D207A, and C213A) on binding affinity. These results are discussed in relation to previous in silico predictions of hot-spot and anchor positions at the CheA-CheY interface. We also investigated the consequences of these mutations for chemotaxis signal transduction in living cells. CheA(F214A) was defective in mediating localization of CheY-YFP to the large clusters of signaling proteins that form at the poles of Escherichia coli cells, while the other CheA variants did not differ from wild-type (wt) CheA (CheA(wt)) in this regard. In our set of mutants, only CheA(F214A) exhibited a markedly diminished ability to support chemotaxis in motility agar assays. Surprisingly, however, in FRET assays that monitored receptor-regulated production of phospho-CheY, CheA(F214A) (and each of the other Ala substitution mutants) performed just as well as CheA(wt). Overall, our findings indicate that F214 serves as an anchor residue at the CheA-CheY interface and makes an important contribution to the binding energy in vitro and in vivo; however, loss of this contribution does not have a large negative effect on the overall ability of the signaling pathway to modulate P-CheY levels in response to

  16. Effects of three-body interactions in the parametric and modulational instabilities of Bose–Einstein condensates

    Energy Technology Data Exchange (ETDEWEB)

    Wamba, Etienne, E-mail: wambaetienne@yahoo.fr [Laboratory of Mechanics, Department of Physics, Faculty of Science, University of Yaounde I, P.O. Box 812, Yaounde (Cameroon); Mohamadou, Alidou, E-mail: mohdoufr@yahoo.fr [Condensed Matter Laboratory, Department of Physics, Faculty of Science, University of Douala, P.O. Box 24157, Douala (Cameroon); The Abdus Salam International Center for Theoretical Physics, P.O. Box 586, Strada Costiera, 11, I-34014 Trieste (Italy); Ekogo, Thierry B. [Departement de Physique, Université des Sciences et Techniques de Masuku, B.P. 943, Franceville (Gabon); Atangana, Jacque [High Teachers Training College of Yaounde, P.O. Box 47, Yaounde (Cameroon); Kofane, Timoleon C. [Laboratory of Mechanics, Department of Physics, Faculty of Science, University of Yaounde I, P.O. Box 812, Yaounde (Cameroon); The Abdus Salam International Center for Theoretical Physics, P.O. Box 586, Strada Costiera, 11, I-34014 Trieste (Italy)

    2011-11-21

    The parametric modulational instability for a discrete nonlinear Schrödinger equation with a cubic–quintic nonlinearity is analyzed. This model describes the dynamics of BECs, with both two- and three-body interatomic interactions trapped in an optical lattice. We identify and discuss the salient features of the three-body interaction in the parametric modulational instability. It is shown that the three-body interaction term can both, shift as well as narrow the window of parametric instability, and also change the behavior of a modulationally stable and parametrically unstable BEC with attractive two-body interaction. We explore this instability through the multiple-scale analysis and identify it numerically. The effect of the three body losses have also been investigated. -- Highlights: ► The parametric MI for the 1D GPE with a cubic–quintic nonlinearity is analyzed. ► The two- and three-body recombination and time-dependent scattering length is considered. ► We generate bright matter waves soliton through MI.

  17. Classifying a Person's Degree of Accessibility From Natural Body Language During Social Human-Robot Interactions.

    Science.gov (United States)

    McColl, Derek; Jiang, Chuan; Nejat, Goldie

    2017-02-01

    For social robots to be successfully integrated and accepted within society, they need to be able to interpret human social cues that are displayed through natural modes of communication. In particular, a key challenge in the design of social robots is developing the robot's ability to recognize a person's affective states (emotions, moods, and attitudes) in order to respond appropriately during social human-robot interactions (HRIs). In this paper, we present and discuss social HRI experiments we have conducted to investigate the development of an accessibility-aware social robot able to autonomously determine a person's degree of accessibility (rapport, openness) toward the robot based on the person's natural static body language. In particular, we present two one-on-one HRI experiments to: 1) determine the performance of our automated system in being able to recognize and classify a person's accessibility levels and 2) investigate how people interact with an accessibility-aware robot which determines its own behaviors based on a person's speech and accessibility levels.

  18. The nature of three-body interactions in DFT: Exchange and polarization effects

    Science.gov (United States)

    Hapka, Michał; Rajchel, Łukasz; Modrzejewski, Marcin; Schäffer, Rainer; Chałasiński, Grzegorz; Szcześniak, Małgorzata M.

    2017-08-01

    We propose a physically motivated decomposition of density functional theory (DFT) 3-body nonadditive interaction energies into the exchange and density-deformation (polarization) components. The exchange component represents the effect of the Pauli exclusion in the wave function of the trimer and is found to be challenging for density functional approximations (DFAs). The remaining density-deformation nonadditivity is less dependent upon the DFAs. Numerical demonstration is carried out for rare gas atom trimers, Ar2-HX (X = F, Cl) complexes, and small hydrogen-bonded and van der Waals molecular systems. None of the tested semilocal, hybrid, and range-separated DFAs properly accounts for the nonadditive exchange in dispersion-bonded trimers. By contrast, for hydrogen-bonded systems, range-separated DFAs achieve a qualitative agreement to within 20% of the reference exchange energy. A reliable performance for all systems is obtained only when the monomers interact through the Hartree-Fock potential in the dispersion-free Pauli blockade scheme. Additionally, we identify the nonadditive second-order exchange-dispersion energy as an important but overlooked contribution in force-field-like dispersion corrections. Our results suggest that range-separated functionals do not include this component, although semilocal and global hybrid DFAs appear to imitate it in the short range.

  19. The Neural Correlates of the Body-Object Interaction Effect in Semantic Processing

    Directory of Open Access Journals (Sweden)

    Ian Scott Hargreaves

    2012-02-01

    Full Text Available The semantic richness dimension referred to as body-object interaction (BOI measures perceptions of the ease with which people can physically interact with words’ referents. Previous studies have shown facilitated lexical and semantic processing for words rated high in BOI (e.g., belt than for words rated low in BOI (e.g., sun (e.g., Siakaluk, Pexman, Sears, Wilson, Locheed, & Owen, 2008b. These BOI effects have been taken as evidence that embodied information is relevant to word recognition. However, to date there is no evidence linking BOI manipulations to differences in the utilization of perceptual or sensorimotor areas of the brain. The current study used event-related fMRI to examine the neural correlates of BOI in a semantic categorization task (SCT. Sixteen healthy adults participated. Results showed that high BOI words were associated with activation in the left inferior parietal lobule (supramarginal gyrus, BA 40, a sensory association area involved in kinesthetic memory. These results provide evidence that the BOI dimension captures sensorimotor information, and that this contributes to semantic processing.

  20. Adolescent-parent interactions and communication preferences regarding body weight and weight management: a qualitative study

    Directory of Open Access Journals (Sweden)

    Howlett Sarah A

    2010-02-01

    Full Text Available Abstract Background This study aimed to canvass the nature of adolescent-parent interactions about weight, particularly overweight, and to explore ideas of how to foster supportive discussions regarding weight, both in the home and with family doctors. Methods A market research company was contracted to recruit and conduct a series of separate focus groups with adolescents and unrelated parents of adolescents from low-middle socio-economic areas in Sydney and a regional centre, Australia. Group discussions were audio recorded, transcribed, and then a qualitative content analysis of the data was performed. Results Nine focus groups were conducted; two were held with girls (n = 13, three with boys (n = 18, and four with parents (20 mothers, 12 fathers. Adolescent and parent descriptions of weight-related interactions could be classified into three distinct approaches: indirect/cautious (i.e. focus on eating or physical activity behaviors without discussing weight specifically; direct/open (i.e. body weight was discussed; and never/rarely discussing the subject. Indirect approaches were described most frequently by both adolescents and parents and were generally preferred over direct approaches. Parents and adolescents were circumspect but generally supportive of the potential role for family doctors to monitor and discuss adolescent weight status. Conclusions These findings have implications for developing acceptable messages for adolescent and family overweight prevention and treatment interventions.

  1. Effect of divergence in residual feed intake on feeding behavior, blood metabolic variables, and body composition traits in growing beef heifers.

    Science.gov (United States)

    Kelly, A K; McGee, M; Crews, D H; Fahey, A G; Wylie, A R; Kenny, D A

    2010-01-01

    This study examined the relationship of feed efficiency and performance with feeding behavior, blood metabolic variables, and various body composition measurements in growing beef heifers. Individual DMI and growth were measured in yearling Limousin x Holstein-Friesian heifers [n = 86; initial BW = 191.8 (SD = 37) kg] fed a TMR diet comprising 70:30 concentrate:corn silage on a DM basis (ME of 2.65 Mcal/kg of DM; DM of 580 g/kg) for 82 d. Meal duration (min/d) and meal frequency (events/d) were calculated for each animal on a daily basis using an Insentec computerized feeding system. Physical measurements as well as ultrasonic fat and muscle depths were recorded on 3 equally spaced occasions during the experimental period. Blood samples were collected by jugular venipuncture on 4 equally spaced occasions and analyzed for plasma concentrations of IGF-I, insulin, leptin, and various metabolites. Phenotypic residual feed intake (RFI) was calculated for all animals as the residuals from a multiple regression model regressing DMI on ADG and midtest BW(0.75). Overall, ADG, DMI, feed conversion ratio (FCR), and RFI were 1.51 (SD = 0.13), 6.74 (SD = 0.99), 4.48 (SD = 0.65), and 0.00 (SD = 0.48) kg/d, respectively. Residual feed intake was positively correlated with DMI (r = 0.47) and FCR (r = 0.46), but not with ADG or midtest BW. Positive correlations (ranging from r = 0.27 to r = 0.63) were estimated between ultrasonic measures of final lumbar fat and lumbar fat accretion over the test period and DMI, FCR, and RFI. The inclusion of gain in lumbar fat to the base RFI model increased R(2) (0.77 vs. 0.80) value for the degree of variation in DMI not explained by midtest BW and ADG alone. The Pearson rank correlation between RFI and carcass-adjusted RFI (RFI(c)) was high (r = 0.93). From the plasma analytes measured, NEFA (r = -0.21; P glucose:insulin (r = -0.23), NEFA (r = -0.32), and beta-hydroxybutyrate (r = 0.25) were associated with FCR. However, systemic IGF-I and

  2. Stability and phase transition of localized modes in Bose–Einstein condensates with both two- and three-body interactions

    Energy Technology Data Exchange (ETDEWEB)

    Bai, Xiao-Dong; Ai, Qing; Zhang, Mei; Xiong, Jun, E-mail: junxiong@bnu.edu.cn; Yang, Guo-Jian; Deng, Fu-Guo

    2015-09-15

    We investigate the stability and phase transition of localized modes in Bose–Einstein Condensates (BECs) in an optical lattice with the discrete nonlinear Schrödinger model by considering both two- and three-body interactions. We find that there are three types of localized modes, bright discrete breather (DB), discrete kink (DK), and multi-breather (MUB). Moreover, both two- and three-body on-site repulsive interactions can stabilize DB, while on-site attractive three-body interactions destabilize it. There is a critical value for the three-body interaction with which both DK and MUB become the most stable ones. We give analytically the energy thresholds for the destabilization of localized states and find that they are unstable (stable) when the total energy of the system is higher (lower) than the thresholds. The stability and dynamics characters of DB and MUB are general for extended lattice systems. Our result is useful for the blocking, filtering, and transfer of the norm in nonlinear lattices for BECs with both two- and three-body interactions.

  3. Elicitin-Induced Distal Systemic Resistance in Plants is Mediated Through the Protein-Protein Interactions Influenced by Selected Lysine Residues.

    Science.gov (United States)

    Uhlíková, Hana; Obořil, Michal; Klempová, Jitka; Šedo, Ondrej; Zdráhal, Zbyněk; Kašparovský, Tomáš; Skládal, Petr; Lochman, Jan

    2016-01-01

    Elicitins are a family of small proteins with sterol-binding activity that are secreted by Phytophthora and Pythium sp. classified as oomycete PAMPs. Although α- and β-elicitins bind with the same affinity to one high affinity binding site on the plasma membrane, β-elicitins (possessing 6-7 lysine residues) are generally 50- to 100-fold more active at inducing distal HR and systemic resistance than the α-isoforms (with only 1-3 lysine residues). To examine the role of lysine residues in elicitin biological activity, we employed site-directed mutagenesis to prepare a series of β-elicitin cryptogein variants with mutations on specific lysine residues. In contrast to direct infiltration of protein into leaves, application to the stem revealed a rough correlation between protein's charge and biological activity, resulting in protection against Phytophthora parasitica. A detailed analysis of proteins' movement in plants showed no substantial differences in distribution through phloem indicating differences in consequent apoplastic or symplastic transport. In this process, an important role of homodimer formation together with the ability to form a heterodimer with potential partner represented by endogenous plants LTPs is suggested. Our work demonstrates a key role of selected lysine residues in these interactions and stresses the importance of processes preceding elicitin recognition responsible for induction of distal systemic resistance.

  4. Elicitin-induced distal systemic resistance in plants is mediated through the protein-protein interactions influenced by selected lysine residues

    Directory of Open Access Journals (Sweden)

    Hana eUhlíková

    2016-02-01

    Full Text Available Elicitins are a family of small proteins with sterol-binding activity that are secreted by Phytophthora and Pythium spp. classified as oomycete PAMPs. Although alfa- and beta-elicitins bind with the same affinity to one high affinity binding site on the plasma membrane, beta-elicitins (possessing 6-7 lysine residues are generally 50- to 100-fold more active at inducing distal HR and systemic resistance than the alfa-isoforms (with only 1-3 lysine residues.To examine the role of lysine residues in elicitin biological activity, we employed site-directed mutagenesis to prepare a series of beta-elicitin cryptogein variants with mutations on specific lysine residues. In contrast to direct infiltration of protein into leaves, application to the stem revealed a rough correlation between protein’s charge and biological activity, resulting in protection against Phytophthora parasitica. A detailed analysis of proteins’ movement in plants showed no substantial differences in distribution through phloem indicating differences in consequent apoplastic or symplastic transport. In this process, an important role of homodimer formation together with the ability to form a heterodimer with potential partner represented by endogenous plants LTPs is suggested. Our work demonstrates a key role of selected lysine residues in these interactions and stresses the importance of processes preceding elicitin recognition responsible for induction of distal systemic resistance.

  5. The presence of modifiable residues in the core peptide part of precursor nisin is not crucial for precursor nisin interactions with NisB- and NisC.

    Directory of Open Access Journals (Sweden)

    Rustem Khusainov

    Full Text Available Precursor nisin is a model posttranslationally modified precursor lantibiotic that can be structurally divided into a leader peptide sequence and a modifiable core peptide part. The nisin core peptide clearly plays an important role in the precursor nisin-nisin modification enzymes interactions, since it has previously been shown that the construct containing only the nisin leader sequence is not sufficient to pull-down the nisin modification enzymes NisB and NisC. Serines and threonines in the core peptide part are the residues that NisB specifically dehydrates, and cysteines are the residues that NisC stereospecifically couples to the dehydrated amino acids. Here, we demonstrate that increasing the number of negatively charged residues in the core peptide part of precursor nisin, which are absent in wild-type nisin, does not abolish binding of precursor nisin to the modification enzymes NisB and NisC, but dramatically decreases the antimicrobial potency of these nisin mutants. An unnatural precursor nisin variant lacking all serines and threonines in the core peptide part and an unnatural precursor nisin variant lacking all cysteines in the core peptide part still bind the nisin modification enzymes NisB and NisC, suggesting that these residues are not essential for direct interactions with the nisin modification enzymes NisB and NisC. These results are important for lantibiotic engineering studies.

  6. Coiled-coil interaction of N-terminal 36 residues of cyclase-associated protein with adenylyl cyclase is sufficient for its function in Saccharomyces cerevisiae ras pathway.

    Science.gov (United States)

    Nishida, Y; Shima, F; Sen, H; Tanaka, Y; Yanagihara, C; Yamawaki-Kataoka, Y; Kariya, K; Kataoka, T

    1998-10-23

    In the budding yeast Saccharomyces cerevisiae, association with the 70-kDa cyclase-associated protein (CAP) is required for proper response of adenylyl cyclase to Ras proteins. We show here that a small segment comprising the N-terminal 36 amino acid residues of CAP is sufficient for association with adenylyl cyclase as well as for its function in the Ras-adenylyl cyclase pathway as assayed by the ability to confer RAS2(Val-19)-dependent heat shock sensitivity to yeast cells. The CAP-binding site of adenylyl cyclase was mapped to a segment of 119 amino acid residues near its C terminus. Both of these regions contained tandem repetitions of a heptad motif alphaXXalphaXXX (where alpha represents a hydrophobic amino acid and X represents any amino acid), suggesting a coiled-coil interaction. When mutants of CAP defective in associating with adenylyl cyclase were isolated by screening of a pool of randomly mutagenized CAP, they were found to carry substitution mutations in one of the key hydrophobic residues in the heptad repeats. Furthermore, mutations of the key hydrophobic residues in the heptad repeats of adenylyl cyclase also resulted in loss of association with CAP. These results indicate the coiled-coil mechanism as a basis of the CAP-adenylyl cyclase interaction.

  7. Kv channel gating requires a compatible S4-S5 linker and bottom part of S6, constrained by non-interacting residues.

    Science.gov (United States)

    Labro, Alain J; Raes, Adam L; Grottesi, Alessandro; Van Hoorick, Diane; Sansom, Mark S P; Snyders, Dirk J

    2008-12-01

    Voltage-dependent K(+) channels transfer the voltage sensor movement into gate opening or closure through an electromechanical coupling. To test functionally whether an interaction between the S4-S5 linker (L45) and the cytoplasmic end of S6 (S6(T)) constitutes this coupling, the L45 in hKv1.5 was replaced by corresponding hKv2.1 sequence. This exchange was not tolerated but could be rescued by also swapping S6(T). Exchanging both L45 and S6(T) transferred hKv2.1 kinetics to an hKv1.5 background while preserving the voltage dependence. A one-by-one residue substitution scan of L45 and S6(T) in hKv1.5 further shows that S6(T) needs to be alpha-helical and forms a "crevice" in which residues I422 and T426 of L45 reside. These residues transfer the mechanical energy onto the S6(T) crevice, whereas other residues in S6(T) and L45 that are not involved in the interaction maintain the correct structure of the coupling.

  8. The interaction between the superhero ideal and maladaptive perfectionism as predictors of unhealthy eating attitudes and body esteem.

    Science.gov (United States)

    Dour, Halina J; Theran, Sally A

    2011-01-01

    Unhealthy eating attitudes and poor body esteem often lead to adverse outcomes (e.g., eating disorders). Prior research has identified two risk factors for these outcomes--endorsement of the superhero ideal and maladaptive perfectionism--and has suggested that these factors may interact to predict unhealthy eating attitudes and body esteem. The current study examined the interaction between the superhero ideal and maladaptive perfectionism as predictors of unhealthy eating attitudes and body esteem among 161 12- to 14-year-olds (74 males, 87 females). Maladaptive perfectionism moderated the relation between endorsement of the superhero ideal and unhealthy eating attitudes for girls only, such that endorsement of the superhero ideal was significantly associated with unhealthy eating attitudes only for adolescents with high levels of maladaptive perfectionism. The moderation model was not significant for body esteem. Prevention strategies should focus on reducing endorsement of the superhero ideal when there are high levels of maladaptive perfectionism.

  9. Simple model for analyzing Efimov energy and three-body recombination of three identical bosons with van der Waals interactions

    Science.gov (United States)

    Li, Jing-Lun; Hu, Xue-Jin; Han, Yong-Chang; Cong, Shu-Lin

    2016-09-01

    We construct a simple model to calculate the trimer bound state energy ET(n ) and three-body recombination rate K30 of three identical bosons with van der Waals interaction without using any two- or three-body fitting parameter. Using this simple model, we investigate the influence of the van der Waals finite-range effect on ET(n ) and K30. Our calculation shows that the finite-range effect leads to the ground trimer state energy ET(0 ) not crossing the atom-dimer threshold, and the scaled three-body recombination rate K30/a4 deviating from the universal three-body theory. The results of our simple model agree within a few percent with other theoretical works with van der Waals interaction and also the experimental data.

  10. Water-soluble LYNX1 residues important for interaction with muscle-type and/or neuronal nicotinic receptors.

    Science.gov (United States)

    Lyukmanova, Ekaterina N; Shulepko, Mikhail A; Buldakova, Svetlana L; Kasheverov, Igor E; Shenkarev, Zakhar O; Reshetnikov, Roman V; Filkin, Sergey Y; Kudryavtsev, Denis S; Ojomoko, Lucy O; Kryukova, Elena V; Dolgikh, Dmitry A; Kirpichnikov, Mikhail P; Bregestovski, Piotr D; Tsetlin, Victor I

    2013-05-31

    Human LYNX1, belonging to the Ly6/neurotoxin family of three-finger proteins, is membrane-tethered with a glycosylphosphatidylinositol anchor and modulates the activity of nicotinic acetylcholine receptors (nAChR). Recent preparation of LYNX1 as an individual protein in the form of water-soluble domain lacking glycosylphosphatidylinositol anchor (ws-LYNX1; Lyukmanova, E. N., Shenkarev, Z. O., Shulepko, M. A., Mineev, K. S., D'Hoedt, D., Kasheverov, I. E., Filkin, S. Y., Krivolapova, A. P., Janickova, H., Dolezal, V., Dolgikh, D. A., Arseniev, A. S., Bertrand, D., Tsetlin, V. I., and Kirpichnikov, M. P. (2011) NMR structure and action on nicotinic acetylcholine receptors of water-soluble domain of human LYNX1. J. Biol. Chem. 286, 10618-10627) revealed the attachment at the agonist-binding site in the acetylcholine-binding protein (AChBP) and muscle nAChR but outside it, in the neuronal nAChRs. Here, we obtained a series of ws-LYNX1 mutants (T35A, P36A, T37A, R38A, K40A, Y54A, Y57A, K59A) and examined by radioligand analysis or patch clamp technique their interaction with the AChBP, Torpedo californica nAChR and chimeric receptor composed of the α7 nAChR extracellular ligand-binding domain and the transmembrane domain of α1 glycine receptor (α7-GlyR). Against AChBP, there was either no change in activity (T35A, T37A), slight decrease (K40A, K59A), and even enhancement for the rest mutants (most pronounced for P36A and R38A). With both receptors, many mutants lost inhibitory activity, but the increased inhibition was observed for P36A at α7-GlyR. Thus, there are subtype-specific and common ws-LYNX1 residues recognizing distinct targets. Because ws-LYNX1 was inactive against glycine receptor, its "non-classical" binding sites on α7 nAChR should be within the extracellular domain. Micromolar affinities and fast washout rates measured for ws-LYNX1 and its mutants are in contrast to nanomolar affinities and irreversibility of binding for α-bungarotoxin and similar

  11. Water-soluble LYNX1 Residues Important for Interaction with Muscle-type and/or Neuronal Nicotinic Receptors*

    Science.gov (United States)

    Lyukmanova, Ekaterina N.; Shulepko, Mikhail A.; Buldakova, Svetlana L.; Kasheverov, Igor E.; Shenkarev, Zakhar O.; Reshetnikov, Roman V.; Filkin, Sergey Y.; Kudryavtsev, Denis S.; Ojomoko, Lucy O.; Kryukova, Elena V.; Dolgikh, Dmitry A.; Kirpichnikov, Mikhail P.; Bregestovski, Piotr D.; Tsetlin, Victor I.

    2013-01-01

    Human LYNX1, belonging to the Ly6/neurotoxin family of three-finger proteins, is membrane-tethered with a glycosylphosphatidylinositol anchor and modulates the activity of nicotinic acetylcholine receptors (nAChR). Recent preparation of LYNX1 as an individual protein in the form of water-soluble domain lacking glycosylphosphatidylinositol anchor (ws-LYNX1; Lyukmanova, E. N., Shenkarev, Z. O., Shulepko, M. A., Mineev, K. S., D'Hoedt, D., Kasheverov, I. E., Filkin, S. Y., Krivolapova, A. P., Janickova, H., Dolezal, V., Dolgikh, D. A., Arseniev, A. S., Bertrand, D., Tsetlin, V. I., and Kirpichnikov, M. P. (2011) NMR structure and action on nicotinic acetylcholine receptors of water-soluble domain of human LYNX1. J. Biol. Chem. 286, 10618–10627) revealed the attachment at the agonist-binding site in the acetylcholine-binding protein (AChBP) and muscle nAChR but outside it, in the neuronal nAChRs. Here, we obtained a series of ws-LYNX1 mutants (T35A, P36A, T37A, R38A, K40A, Y54A, Y57A, K59A) and examined by radioligand analysis or patch clamp technique their interaction with the AChBP, Torpedo californica nAChR and chimeric receptor composed of the α7 nAChR extracellular ligand-binding domain and the transmembrane domain of α1 glycine receptor (α7-GlyR). Against AChBP, there was either no change in activity (T35A, T37A), slight decrease (K40A, K59A), and even enhancement for the rest mutants (most pronounced for P36A and R38A). With both receptors, many mutants lost inhibitory activity, but the increased inhibition was observed for P36A at α7-GlyR. Thus, there are subtype-specific and common ws-LYNX1 residues recognizing distinct targets. Because ws-LYNX1 was inactive against glycine receptor, its “non-classical” binding sites on α7 nAChR should be within the extracellular domain. Micromolar affinities and fast washout rates measured for ws-LYNX1 and its mutants are in contrast to nanomolar affinities and irreversibility of binding for α-bungarotoxin and

  12. An interactive three-dimensional virtual body structures system for anatomical training over the internet.

    Science.gov (United States)

    Temkin, Bharti; Acosta, Eric; Malvankar, Ameya; Vaidyanath, Sreeram

    2006-04-01

    The Visible Human digital datasets make it possible to develop computer-based anatomical training systems that use virtual anatomical models (virtual body structures-VBS). Medical schools are combining these virtual training systems and classical anatomy teaching methods that use labeled images and cadaver dissection. In this paper we present a customizable web-based three-dimensional anatomy training system, W3D-VBS. W3D-VBS uses National Library of Medicine's (NLM) Visible Human Male datasets to interactively locate, explore, select, extract, highlight, label, and visualize, realistic 2D (using axial, coronal, and sagittal views) and 3D virtual structures. A real-time self-guided virtual tour of the entire body is designed to provide detailed anatomical information about structures, substructures, and proximal structures. The system thus facilitates learning of visuospatial relationships at a level of detail that may not be possible by any other means. The use of volumetric structures allows for repeated real-time virtual dissections, from any angle, at the convenience of the user. Volumetric (3D) virtual dissections are performed by adding, removing, highlighting, and labeling individual structures (and/or entire anatomical systems). The resultant virtual explorations (consisting of anatomical 2D/3D illustrations and animations), with user selected highlighting colors and label positions, can be saved and used for generating lesson plans and evaluation systems. Tracking users' progress using the evaluation system helps customize the curriculum, making W3D-VBS a powerful learning tool. Our plan is to incorporate other Visible Human segmented datasets, especially datasets with higher resolutions, that make it possible to include finer anatomical structures such as nerves and small vessels. (c) 2006 Wiley-Liss, Inc.

  13. Estimating bioconcentration factors, lethal concentrations and critical body residues of metals in the mollusks Perna viridis and Mytilus edulis using ion characteristics.

    Science.gov (United States)

    van Kolck, Maurits; Huijbregts, Mark A J; Veltman, Karin; Jan Hendriks, A

    2008-02-01

    Quantitative structure-activity relationships (QSARs) for metal bioconcentration factors (BCF) and median acute lethal water concentrations (LC50) were developed for two species of mollusks, Perna viridis and Mytilus edulis. These endpoints were related to four metal ion characteristics, the covalent index (chi(2)(m)r) (r represents the ion radius in A), the softness index (sigma(p)), the hydrolysis constant (K(OH)) and the ionic index (Z(2)/r). The BCF and LC50 were significantly correlated to chi(m)(2)r. The coefficients of determination r(2) for the relationships with other metal descriptors were much lower. Critical body residue (CBR) QSARs were derived by multiplying the chi(2)(m)r-based BCF and LC50 regressions. The CBRs were independent of the covalent index chi(2)(m)r, as BCF and LC50 scaled to chi(2)(m)r with slope that had opposite signs. Comparison of the estimated CBRs with independent empirical values confirmed the predicted trends, but substantial deviations were noted too.

  14. Lattice chiral effective field theory with three-body interactions at next-to-next-to-leading order

    CERN Document Server

    Epelbaum, Evgeny; Lee, Dean; Meißner, Ulf-G

    2009-01-01

    We consider low-energy nucleons at next-to-next-to-leading order in lattice chiral effective field theory. Three-body interactions first appear at this order, and we discuss several methods for determining three-body interaction coefficients on the lattice. We compute the energy of the triton and low-energy neutron-deuteron scattering phase shifts in the spin-doublet and spin-quartet channels using Luescher's finite volume method. In the four-nucleon system we calculate the energy of the alpha particle using auxiliary fields and projection Monte Carlo.

  15. Dynamics and Matter-Wave Solitons in Bose-Einstein Condensates with Two- and Three-Body Interactions

    Directory of Open Access Journals (Sweden)

    Jing Chen

    2014-01-01

    Full Text Available By means of similarity transformation, this paper proposes the matter-wave soliton solutions and dynamics of the variable coefficient cubic-quintic nonlinear Schrödinger equation arising from Bose-Einstein condensates with time-dependent two- and three-body interactions. It is found that, under the effect of time-dependent two- and three-body interaction and harmonic potential with time-dependent frequency, the density of atom condensates will gradually diminish and finally collapse.

  16. Sensorimotor body-environment interaction serves to regulate emotional experience and exploratory behavior

    Directory of Open Access Journals (Sweden)

    Martin Dobricki

    2016-10-01

    Full Text Available Almost all living species regularly explore environments that they experience as pleasant, aversive, arousing or frightening. We postulate that such exploratory behavior and emotional experience both are regulated based on the interdependent perception of one’s body and stimuli that collectively define a spatial context such as a cliff. Here we examined this by testing if the interaction of the sensory input on one’s gait and the sensory input on the spatial context is modulating both the emotional experience of the environment and its exploration through head motion. To this end, we asked healthy humans to explore a life-sized Virtual Reality simulation of a forest glade by physically walking around in this environment on two narrow rectangular platforms connected by a plank. The platforms and the plank were presented such that they were either placed on ground or on the top of two high bridge piers. Hence, the forest glade was presented either as a “ground” or as a “height” context. Within these two spatial contexts the virtual plank was projected either on the rigid physical floor or onto a bouncy physical plank. Accordingly, the gait of our participants while they crossed the virtual plank was either “smooth” or “bouncy.” We found that in the height context bouncy gait compared to smooth gait increased the orientation of the head below the horizon and intensified the experience of the environment as negative. Whereas, within the ground context bouncy gait increased the orientation of the head towards and above the horizon and made that the environment was experienced as positive. Our findings suggest that the brain of healthy humans is using the interaction of the sensory input on their gait and the sensory input on the spatial context to regulate both the emotional experience of the environment and its exploration through head motion.

  17. Body space in social interactions: a comparison of reaching and comfort distance in immersive virtual reality.

    Directory of Open Access Journals (Sweden)

    Tina Iachini

    Full Text Available BACKGROUND: Do peripersonal space for acting on objects and interpersonal space for interacting with con-specifics share common mechanisms and reflect the social valence of stimuli? To answer this question, we investigated whether these spaces refer to a similar or different physical distance. METHODOLOGY: Participants provided reachability-distance (for potential action and comfort-distance (for social processing judgments towards human and non-human virtual stimuli while standing still (passive or walking toward stimuli (active. PRINCIPAL FINDINGS: Comfort-distance was larger than other conditions when participants were passive, but reachability and comfort distances were similar when participants were active. Both spaces were modulated by the social valence of stimuli (reduction with virtual females vs males, expansion with cylinder vs robot and the gender of participants. CONCLUSIONS: These findings reveal that peripersonal reaching and interpersonal comfort spaces share a common motor nature and are sensitive, at different degrees, to social modulation. Therefore, social processing seems embodied and grounded in the body acting in space.

  18. Energy dissipation end states of the sphere restricted planar three-body problem with collisional interaction

    Science.gov (United States)

    Gabriel, T. S. J.; Scheeres, D. J.

    2016-11-01

    We perform a large number of gravitational granular mechanics simulations to investigate the role of energy dissipation in the sphere-restricted planar three-body problem where, for a given angular momentum, multiple end-state configurations are available to the system. For the case of three equal spheres, previous studies have mapped all relative equilibria of the problem as a function of angular momentum. We find trends in the production of end states as a function of angular momentum and dissipation parameters, as well as outline the dynamical-mechanical interactions that generate these results. For strongly dissipative systems a relationship between the minimum energy function of the system and the end-state dynamics is uncovered. In particular, the likelihood of achieving one end state over another is largely governed by the geometrical projection of the minimum energy function. In contrast, for systems with low-energy dissipation the end state becomes a function of the relative depth of the different energy wells available to the system. This study highlights the importance of having well-defined dissipative properties of a gravitational granular system, such as those used to study the dynamics of rubble pile asteroids and planetary rings.

  19. The Role of Many-Body Dispersion Interactions in Molecular Crystal Polymorphism

    Science.gov (United States)

    Leiserowitz, Leslie; Marom, Noa; Distasio, Robert A., Jr.; Atalla, Viktor; Levchenko, Sergey; Kapishnikov, Sergey; Chelikowsky, James R.; Tkatchenko, Alexandre

    2012-02-01

    Molecular crystals often have several polymorphs that are close in energy (few meV per molecule), but possess very different physical and chemical properties. Treating polymorphism from first principles has been a long standing problem because conventional density-functional theory (DFT) lacks a proper description of long-range dispersion interactions that govern the structure and energetics of molecular crystals. Here we assess the effect of the many-body dispersion (MBD) energy on the structure and relative energies of the polymorphs of benchmark molecular crystals: glycine, alanine, and para-diiodobenzene. This is accomplished by using the recently developed first-principles DFT+MBD method [A. Tkatchenko, R.A. DiStasio Jr., R. Car, M. Scheffler, submitted], based on the earlier Tkatchenko-Scheffler (TS) dispersion correction [PRL 102, 073005 (2009)]. We show that the non-additive MBD energy plays a crucial role in making qualitatively and quantitatively accurate predictions for the structure and relative energies of polymorphs.

  20. Manifestation of many-body interactions in the integer quantum Hall effect regime

    Science.gov (United States)

    Oswald, Josef; Römer, Rudolf A.

    2017-09-01

    We use the self-consistent Hartree-Fock approximation for numerically addressing the integer quantum Hall (IQH) regime in terms of many-body physics at higher Landau levels (LL). The results exhibit a strong tendency to avoid the simultaneous existence of partly filled spin-up and spin-down LLs. Partly filled LLs appear as a mixture of coexisting regions of full and empty LLs. We obtain edge stripes with approximately constant filling factor ν close to half-odd filling at the boundaries between the regions of full and empty LLs, which we explain in terms of the g -factor enhancement as a function of a locally varying ν across the compressible stripes. The many-particle interactions follow a behavior as it would result from applying Hund's rule for the occupation of the spin split LLs. The screening of the disorder and edge potential appears significantly reduced as compared to screening based on a Thomas-Fermi approximation. For addressing carrier transport, we use a nonequilibrium network model (NNM) that handles the lateral distribution of the experimentally injected nonequilibrium chemical potentials μ .

  1. A Structured Mesh Euler and Interactive Boundary Layer Method for Wing/Body Configurations

    Institute of Scientific and Technical Information of China (English)

    Li Jie; Zhou Zhou

    2008-01-01

    To compute transonic flows over a complex 3D aircraft configuration, a viscous/inviscid interaction method is developed by coupling an integral boundary-layer solver with an Eluer solver in a "semi-inverse" manner. For the turbulent bonndary-layer, an integral method using Green's lag equation is coupled with the outer inviscid flow. A blowing velocity approach is used to simulate the displacement effects of the boundary layer. To predict the aerodynamic drag, it is developed a numerical technique called far-field method that is based on the momentum theorem, in which the total drag is divided into three component drags, i.e. viscous, induced and wave-formed. Consequently, it can provide more physical insight into the drag sources than the oflen-used surface integral technique.The drag decomposition can be achieved with help of the second law of thermodynamics, which implies that entropy increases and total pressure decreases only across shock wave along a streamline of an inviscid non-isentropic flow. This method has been applied to the DLR-F4 wing/body configuration showing results in good agreement with the wind tunnel data.

  2. Quartet correlations in N = Z nuclei induced by realistic two-body interactions

    Energy Technology Data Exchange (ETDEWEB)

    Sambataro, M. [Istituto Nazionale di Fisica Nucleare - Sezione di Catania, Catania (Italy); Sandulescu, N. [National Institute of Physics and Nuclear Engineering, Bucharest-Magurele (Romania)

    2017-03-15

    Two variational quartet models previously employed in a treatment of pairing forces are extended to the case of a general two-body interaction. One model approximates the nuclear states as a condensate of identical quartets with angular momentum J = 0 and isospin T = 0 while the other let these quartets to be all different from each other. With these models we investigate the role of alpha-like quartet correlations both in the ground state and in the lowest J = 0, T = 0 excited states of even-even N = Z nuclei in the sd -shell. We show that the ground-state correlations of these nuclei can be described to a good extent in terms of a condensate of alpha-like quartets. This turns out to be especially the case for the nucleus {sup 32}S for which the overlap between this condensate and the shell model wave function is found close to one. In the same nucleus, a similar overlap is found also in the case of the first excited 0{sup +} state. No clear correspondence is observed instead between the second excited states of the quartet models and the shell model eigenstates in all the cases examined. (orig.)

  3. Body Space in Social Interactions: A Comparison of Reaching and Comfort Distance in Immersive Virtual Reality

    Science.gov (United States)

    Iachini, Tina; Coello, Yann; Frassinetti, Francesca; Ruggiero, Gennaro

    2014-01-01

    Background Do peripersonal space for acting on objects and interpersonal space for interacting with con-specifics share common mechanisms and reflect the social valence of stimuli? To answer this question, we investigated whether these spaces refer to a similar or different physical distance. Methodology Participants provided reachability-distance (for potential action) and comfort-distance (for social processing) judgments towards human and non-human virtual stimuli while standing still (passive) or walking toward stimuli (active). Principal Findings Comfort-distance was larger than other conditions when participants were passive, but reachability and comfort distances were similar when participants were active. Both spaces were modulated by the social valence of stimuli (reduction with virtual females vs males, expansion with cylinder vs robot) and the gender of participants. Conclusions These findings reveal that peripersonal reaching and interpersonal comfort spaces share a common motor nature and are sensitive, at different degrees, to social modulation. Therefore, social processing seems embodied and grounded in the body acting in space. PMID:25405344

  4. Gravitational self-force corrections to two-body tidal interactions and the effective one-body formalism

    CERN Document Server

    Bini, Donato

    2014-01-01

    Tidal interactions have a significant influence on the late dynamics of compact binary systems, which constitute the prime targets of the upcoming network of gravitational-wave detectors. We refine the theoretical description of tidal interactions (hitherto known only to the second post-Newtonian level) by extending our recently developed analytic self-force formalism, for extreme mass-ratio binary systems, to the computation of several tidal invariants. Specifically, we compute, to linear order in the mass ratio and to the 7.5$^{\\rm th}$ post-Newtonian order, the following tidal invariants: the square and the cube of the gravitoelectric quadrupolar tidal tensor, the square of the gravitomagnetic quadrupolar tidal tensor, and the square of the gravitoelectric octupolar tidal tensor. Our high-accuracy analytic results are compared to recent numerical self-force tidal data by Dolan et al. \\cite{Dolan:2014pja}, and, notably, provide an analytic understanding of the light ring asymptotic behavior found by them. W...

  5. Residues essential for Panton-Valentine leukocidin S component binding to its cell receptor suggest both plasticity and adaptability in its interaction surface.

    Directory of Open Access Journals (Sweden)

    Benoit-Joseph Laventie

    Full Text Available Panton-Valentine leukocidin (PVL, a bicomponent staphylococcal leukotoxin, is involved in the poor prognosis of necrotizing pneumonia. The present study aimed to elucidate the binding mechanism of PVL and in particular its cell-binding domain. The class S component of PVL, LukS-PV, is known to ensure cell targeting and exhibits the highest affinity for the neutrophil membrane (Kd∼10(-10 M compared to the class F component of PVL, LukF-PV (Kd∼10(-9 M. Alanine scanning mutagenesis was used to identify the residues involved in LukS-PV binding to the neutrophil surface. Nineteen single alanine mutations were performed in the rim domain previously described as implicated in cell membrane interactions. Positions were chosen in order to replace polar or exposed charged residues and according to conservation between leukotoxin class S components. Characterization studies enabled to identify a cluster of residues essential for LukS-PV binding, localized on two loops of the rim domain. The mutations R73A, Y184A, T244A, H245A and Y250A led to dramatically reduced binding affinities for both human leukocytes and undifferentiated U937 cells expressing the C5a receptor. The three-dimensional structure of five of the mutants was determined using X-ray crystallography. Structure analysis identified residues Y184 and Y250 as crucial in providing structural flexibility in the receptor-binding domain of LukS-PV.

  6. Host-specific enzyme-substrate interactions in SPM-1 metallo-β-lactamase are modulated by second sphere residues.

    Directory of Open Access Journals (Sweden)

    Lisandro J González

    2014-01-01

    Full Text Available Pseudomonas aeruginosa is one of the most virulent and resistant non-fermenting Gram-negative pathogens in the clinic. Unfortunately, P. aeruginosa has acquired genes encoding metallo-β-lactamases (MβLs, enzymes able to hydrolyze most β-lactam antibiotics. SPM-1 is an MβL produced only by P. aeruginosa, while other MβLs are found in different bacteria. Despite similar active sites, the resistance profile of MβLs towards β-lactams changes from one enzyme to the other. SPM-1 is unique among pathogen-associated MβLs in that it contains "atypical" second sphere residues (S84, G121. Codon randomization on these positions and further selection of resistance-conferring mutants was performed. MICs, periplasmic enzymatic activity, Zn(II requirements, and protein stability was assessed. Our results indicated that identity of second sphere residues modulates the substrate preferences and the resistance profile of SPM-1 expressed in P. aeruginosa. The second sphere residues found in wild type SPM-1 give rise to a substrate selectivity that is observed only in the periplasmic environment. These residues also allow SPM-1 to confer resistance in P. aeruginosa under Zn(II-limiting conditions, such as those expected under infection. By optimizing the catalytic efficiency towards β-lactam antibiotics, the enzyme stability and the Zn(II binding features, molecular evolution meets the specific needs of a pathogenic bacterial host by means of substitutions outside the active site.

  7. Interactions between residue placement and earthworm ecological strategy affect aggregate turnover and N2O dynamics in agricultural soil

    NARCIS (Netherlands)

    Giannopoulos, G.; Pulleman, M.M.; Groenigen, van J.W.

    2010-01-01

    Previous laboratory studies using epigeic and anecic earthworms have shown that earthworm activity can considerably increase nitrous oxide (N2O) emissions from crop residues in soils. However, the universality of this effect across earthworm functional groups and its underlying mechanisms remain unc

  8. What Is an Attractive Body? Using an Interactive 3D Program to Create the Ideal Body for You and Your Partner

    Science.gov (United States)

    Crossley, Kara L.; Cornelissen, Piers L.; Tovée, Martin J.

    2012-01-01

    What is the ideal body size and shape that we want for ourselves and our partners? What are the important physical features in this ideal? And do both genders agree on what is an attractive body? To answer these questions we used a 3D interactive software system which allows our participants to produce a photorealistic, virtual male or female body. Forty female and forty male heterosexual Caucasian observers (females mean age 19.10 years, s.d. 1.01; 40 males mean age 19.84, s.d. 1.66) set their own ideal size and shape, and the size and shape of their ideal partner using the DAZ studio image manipulation programme. In this programme the shape and size of a 3D body can be altered along 94 independent dimensions, allowing each participant to create the exact size and shape of the body they want. The volume (and thus the weight assuming a standard density) and the circumference of the bust, waist and hips of these 3D models can then be measured. The ideal female body set by women (BMI = 18.9, WHR = 0.70, WCR = 0.67) was very similar to the ideal partner set by men, particularly in their BMI (BMI = 18.8, WHR = 0.73, WCR = 0.69). This was a lower BMI than the actual BMI of 39 of the 40 women. The ideal male body set by the men (BMI = 25.9, WHR = 0.87, WCR = 0.74) was very similar to the ideal partner set by the women (BMI = 24.5, WHR = 0.86, WCR = 0.77). This was a lower BMI than the actual BMI of roughly half of the men and a higher BMI than the other half. The results suggest a consistent preference for an ideal male and female body size and shape across both genders. The results also suggest that both BMI and torso shape are important components for the creation of the ideal body. PMID:23209791

  9. Combined adverse effects of maternal smoking and high body mass index on heart development in offspring : evidence for interaction?

    NARCIS (Netherlands)

    Baardman, M.E.; Kerstjens-Frederikse, W.S.; Corpeleijn, E.; de Walle, H.E.K.; Hofstra, R.M.W.; Berger, R.M.F.; Bakker, M.K.

    2012-01-01

    Objective To study the influence of a possible interaction between maternal smoking and high body mass index (BMI) on the occurrence of specific congenital heart anomalies (CHA) in offspring. Design Case-control study. Setting Data from a population-based birth defects registry in the Netherlands. P

  10. A computational study of the wing-wing and wing-body interactions of a model insect

    Institute of Scientific and Technical Information of China (English)

    Xin Yu; Mao Sun

    2009-01-01

    The aerodynamic interaction between the contralateral wings and between the body and wings of a model insect are studied, by using the method of numerically solving the Navier-Stokes equations over moving overset grids, under typical hovering and forward flight conditions. Both the interaction between the contralateral wings and the interaction between the body and wings are very weak, e.g. at hovering, changes in aerodynamic forces of a wing due to the present of the other wing are less than 3% and changes in aerodynamic forces of the wings due to presence of thebody are less than 2%. The reason for this is as following. During each down-or up-stroke, a wing produces a vortexring, which induces a relatively large jet-like flow inside the ring but very small flow outside the ring. The vortex tings of the left and right wings are on the two sides of the body. Thus one wing is outside vortex ring of the other wing and the body is outside the vortex rings of the left and right wings, resulting in the weak interactions.

  11. Modulational Instability of (1+1)-Dimensional Bose-Einstein Condensate with Three-Body Interatomic Interaction

    Institute of Scientific and Technical Information of China (English)

    WU Lei; ZHANG Jie-Fang

    2007-01-01

    The modulational instability of Bose-Einstein condensate with three-body interatomic interaction and external harmonic trapping potential is investigated. Both of our analytical and numerical results show that the external potential will either cause the excitation of modulationally unstable modes or restrain the modulationally unstable modes from growing.

  12. Insensitivity of the Yrast Spectra of Even-Even Nuclei to the T=0 two-body interaction matrix elements

    CERN Document Server

    Robinson, S J Q; Robinson, Shadow J.Q.; Zamick, Larry

    2002-01-01

    Calculations of the spectra of various even-even nuclei in the fp shell ($^{44}$Ti, $^{46}$Ti, $^{48}$Cr, and $^{50}$Cr) are performed with two sets of two-body interaction matrix elements. The first set consists of the matrix elements of the FPD6 interaction. The second set have the same T=1 two-body matrix elements as the FPD6 interaction, but all the T=0 two-body matrix elements are set equal to zero. Despite the drastic differences between the two interactions, the spectra they yield are very similar and indeed it is difficult to say which set gives a better fit to experiment. That the results for the yrast spectra are insensitive to the presence or absence of T=0 two-body matrix elements is surprising because the only bound two nucleon system has T=0, namely the deuteron. Also there is the general folklore that T=0 matrix elements are responsible for nuclear collectivity. Electric quadrupole transition rates are also examined. It is found that the reintroduction of T=0 matrix elements leads to an enhance...

  13. Exact results for Casimir interactions between dielectric bodies: The weak-coupling or van der Waals Limit

    CERN Document Server

    Milton, Kimball A; Wagner, Jef

    2008-01-01

    In earlier papers we have applied multiple scattering techniques to calculate Casimir forces due to scalar fields between different bodies described by delta function potentials. When the coupling to the potentials became weak, closed-form results were obtained. We simplify this weak-coupling technique and apply it to the case of tenuous dielectric bodies, in which case the method involves the summation of van der Waals (Casimir-Polder) interactions. Once again exact results for finite bodies can be obtained. We present closed formulas describing the interaction between spheres and between cylinders, and between an infinite plate and a retangular slab of finite size. For such a slab, we consider the torque acting on it, and find non-trivial equilibrium points can occur.

  14. Use of Two-Body Correlated Basis Functions with van der Waals Interaction to Study the Shape-Independent Approximation for a Large Number of Trapped Interacting Bosons

    Science.gov (United States)

    Lekala, M. L.; Chakrabarti, B.; Das, T. K.; Rampho, G. J.; Sofianos, S. A.; Adam, R. M.; Haldar, S. K.

    2017-01-01

    We study the ground-state and the low-lying excitations of a trapped Bose gas in an isotropic harmonic potential for very small (˜ 3) to very large (˜ 10^7 ) particle numbers. We use the two-body correlated basis functions and the shape-dependent van der Waals interaction in our many-body calculations. We present an exhaustive study of the effect of inter-atomic correlations and the accuracy of the mean-field equations considering a wide range of particle numbers. We calculate the ground-state energy and the one-body density for different values of the van der Waals parameter C6 . We compare our results with those of the modified Gross-Pitaevskii results, the correlated Hartree hypernetted-chain equations (which also utilize the two-body correlated basis functions), as well as of the diffusion Monte Carlo for hard sphere interactions. We observe the effect of the attractive tail of the van der Waals potential in the calculations of the one-body density over the truly repulsive zero-range potential as used in the Gross-Pitaevskii equation and discuss the finite-size effects. We also present the low-lying collective excitations which are well described by a hydrodynamic model in the large particle limit.

  15. Residual Symmetry and Explicit Soliton-Cnoidal Wave Interaction Solutions of the (2+1)-Dimensional KdV-mKdV Equation

    Science.gov (United States)

    Cheng, Wenguang; Li, Biao

    2016-04-01

    The truncated Painlevé method is developed to obtain the nonlocal residual symmetry and the Bäcklund transformation for the (2+1)-dimensional KdV-mKdV equation. The residual symmetry is localised after embedding the (2+1)-dimensional KdV-mKdV equation to an enlarged one. The symmetry group transformation of the enlarged system is computed. Furthermore, the (2+1)-dimensional KdV-mKdV equation is proved to be consistent Riccati expansion (CRE) solvable. The soliton-cnoidal wave interaction solution in terms of the Jacobi elliptic functions and the third type of incomplete elliptic integral is obtained by using the consistent tanh expansion (CTE) method, which is a special form of CRE.

  16. Simulations of collisions between N-body classical systems in interaction; Simulations de collisions entre systemes classiques a n-corps en interaction

    Energy Technology Data Exchange (ETDEWEB)

    Morisseau, Francois [Laboratoire de Physique Corpusculaire de CAEN, ENSICAEN, Universite de Caen Basse-Normandie, UFR des Sciences, 6 bd Marechal Juin, 14050 Caen Cedex (France)

    2006-05-15

    The Classical N-body Dynamics (CNBD) is dedicated to the simulation of collisions between classical systems. The 2-body interaction used here has the properties of the Van der Waals potential and depends on just a few parameters. This work has two main goals. First, some theoretical approaches assume that the dynamical stage of the collisions plays an important role. Moreover, colliding nuclei are supposed to present a 1. order liquid-gas phase transition. Several signals have been introduced to show this transition. We have searched for two of them: the bimodality of the mass asymmetry and negative heat capacity. We have found them and we give an explanation of their presence in our calculations. Second, we have improved the interaction by adding a Coulomb like potential and by taking into account the stronger proton-neutron interaction in nuclei. Then we have figured out the relations that exist between the parameters of the 2-body interaction and the properties of the systems. These studies allow us to fit the properties of the classical systems to those of the nuclei. In this manuscript the first results of this fit are shown. (author)

  17. Mobile Brain/Body Imaging (MoBI) of Physical Interaction with Dynamically Moving Objects

    Science.gov (United States)

    Jungnickel, Evelyn; Gramann, Klaus

    2016-01-01

    The non-invasive recording and analysis of human brain activity during active movements in natural working conditions is a central challenge in Neuroergonomics research. Existing brain imaging approaches do not allow for an investigation of brain dynamics during active behavior because their sensors cannot follow the movement of the signal source. However, movements that require the operator to react fast and to adapt to a dynamically changing environment occur frequently in working environments like assembly-line work, construction trade, health care, but also outside the working environment like in team sports. Overcoming the restrictions of existing imaging methods would allow for deeper insights into neurocognitive processes at workplaces that require physical interactions and thus could help to adapt work settings to the user. To investigate the brain dynamics accompanying rapid volatile movements we used a visual oddball paradigm where participants had to react to color changes either with a simple button press or by physically pointing towards a moving target. Using a mobile brain/body imaging approach (MoBI) including independent component analysis (ICA) with subsequent backprojection of cluster activity allowed for systematically describing the contribution of brain and non-brain sources to the sensor signal. The results demonstrate that visual event-related potentials (ERPs) can be analyzed for simple button presses and physical pointing responses and that it is possible to quantify the contribution of brain processes, muscle activity and eye movements to the signal recorded at the sensor level even for fast volatile arm movements with strong jerks. Using MoBI in naturalistic working environments can thus help to analyze brain dynamics in natural working conditions and help improving unhealthy or inefficient work settings. PMID:27445747

  18. Extraction of user's navigation commands from upper body force interaction in walker assisted gait

    Directory of Open Access Journals (Sweden)

    Pons José L

    2010-08-01

    Full Text Available Abstract Background The advances in technology make possible the incorporation of sensors and actuators in rollators, building safer robots and extending the use of walkers to a more diverse population. This paper presents a new method for the extraction of navigation related components from upper-body force interaction data in walker assisted gait. A filtering architecture is designed to cancel: (i the high-frequency noise caused by vibrations on the walker's structure due to irregularities on the terrain or walker's wheels and (ii the cadence related force components caused by user's trunk oscillations during gait. As a result, a third component related to user's navigation commands is distinguished. Results For the cancelation of high-frequency noise, a Benedict-Bordner g-h filter was designed presenting very low values for Kinematic Tracking Error ((2.035 ± 0.358·10-2 kgf and delay ((1.897 ± 0.3697·101ms. A Fourier Linear Combiner filtering architecture was implemented for the adaptive attenuation of about 80% of the cadence related components' energy from force data. This was done without compromising the information contained in the frequencies close to such notch filters. Conclusions The presented methodology offers an effective cancelation of the undesired components from force data, allowing the system to extract in real-time voluntary user's navigation commands. Based on this real-time identification of voluntary user's commands, a classical approach to the control architecture of the robotic walker is being developed, in order to obtain stable and safe user assisted locomotion.

  19. The proteins of intra-nuclear bodies: a data-driven analysis of sequence, interaction and expression

    Directory of Open Access Journals (Sweden)

    Bodén Mikael

    2010-04-01

    Full Text Available Abstract Background Cajal bodies, nucleoli, PML nuclear bodies, and nuclear speckles are morpohologically distinct intra-nuclear structures that dynamically respond to cellular cues. Such nuclear bodies are hypothesized to play important regulatory roles, e.g. by sequestering and releasing transcription factors in a timely manner. While the nucleolus and nuclear speckles have received more attention experimentally, the PML nuclear body and the Cajal body are still incompletely characterized in terms of their roles and protein complement. Results By collating recent experimentally verified data, we find that almost 1000 proteins in the mouse nuclear proteome are known to associate with one or more of the nuclear bodies. Their gene ontology terms highlight their regulatory roles: splicing is confirmed to be a core activity of speckles and PML nuclear bodies house a range of proteins involved in DNA repair. We train support-vector machines to show that nuclear proteins contain discriminative sequence features that can be used to identify their intra-nuclear body associations. Prediction accuracy is highest for nucleoli and nuclear speckles. The trained models are also used to estimate the full protein complement of each nuclear body. Protein interactions are found primarily to link proteins in the nuclear speckles with proteins from other compartments. Cell cycle expression data provide support for increased activity in nucleoli, nuclear speckles and PML nuclear bodies especially during S and G2 phases. Conclusions The large-scale analysis of the mouse nuclear proteome sheds light on the functional organization of physically embodied intra-nuclear compartments. We observe partial support for the hypothesis that the physical organization of the nucleus mirrors functional modularity. However, we are unable to unambiguously identify proteins' intra-nuclear destination, suggesting that critical drivers behind of intra-nuclear translocation are yet to

  20. Role of the SUMO-interacting motif in HIPK2 targeting to the PML nuclear bodies and regulation of p53

    Energy Technology Data Exchange (ETDEWEB)

    Sung, Ki Sa; Lee, Yun-Ah [Department of Biological Sciences, Sungkyunkwan University, Suwon 440-746 (Korea, Republic of); Kim, Eui Tae [Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon 440-746 (Korea, Republic of); Lee, Seung-Rock [Department of Biochemistry, Research Center for Aging and Geriatrics, Research Institute of Medical Sciences, Chonnam National University Medical School, Gwangju 501-190 (Korea, Republic of); Ahn, Jin-Hyun [Department of Molecular Cell Biology, Samsung Biomedical Research Institute, Sungkyunkwan University School of Medicine, Suwon 440-746 (Korea, Republic of); Choi, Cheol Yong, E-mail: choicy@skku.ac.kr [Department of Biological Sciences, Sungkyunkwan University, Suwon 440-746 (Korea, Republic of)

    2011-04-15

    Homeodomain-interacting protein kinase 2 (HIPK2) is a key regulator of various transcription factors including p53 and CtBP in the DNA damage signaling pathway. PML-nuclear body (NB) is required for HIPK2-mediated p53 phosphorylation at Ser46 and induction of apoptosis. Although PML-NB targeting of HIPK2 has been shown, much is not clear about the molecular mechanism of HIPK2 recruitment to PML-NBs. Here we show that HIPK2 colocalizes specifically with PML-I and PML-IV. Mutational analysis showed that HIPK2 recruitment to PML-IV-NBs is mediated by the SUMO-interaction motifs (SIMs) of both PML-IV and HIPK2. Wild-type HIPK2 associated with SUMO-conjugated PML-IV at a higher affinity than with un-conjugated PML-IV, while the association of a HIPK2 SIM mutant with SUMO-modified PML-IV was impaired. In colony formation assays, HIPK2 strongly suppressed cell proliferation, but HIPK2 SIM mutants did not. In addition, activation and phosphorylation of p53 at the Ser46 residue were impaired by HIPK2 SIM mutants. These results suggest that SIM-mediated HIPK2 targeting to PML-NBs is crucial for HIPK2-mediated p53 activation and induction of apoptosis.

  1. Probing the acidic residue within the integrin binding site of laminin-511 that interacts with the metal ion-dependent adhesion site of α6β1 integrin.

    Science.gov (United States)

    Taniguchi, Yukimasa; Li, Shaoliang; Takizawa, Mamoru; Oonishi, Eriko; Toga, Junko; Yagi, Emiko; Sekiguchi, Kiyotoshi

    2017-06-03

    Laminins are major cell-adhesive proteins of basement membranes that interact with integrins in a divalent cation-dependent manner. Laminin-511 consists of α5, β1, and γ1 chains, of which three laminin globular domains of the α5 chain (α5/LG1-3) and a Glu residue in the C-terminal tail of chain γ1 (γ1-Glu1607) are required for binding to integrins. However, it remains unsettled whether the Glu residue in the γ1 tail is involved in integrin binding by coordinating the metal ion in the metal ion-dependent adhesion site of β1 integrin (β1-MIDAS), or by stabilizing the conformation of α5/LG1-3. To address this issue, we examined whether α5/LG1-3 contain an acidic residue required for integrin binding that is as critical as the Glu residue in the γ1 tail; to achieve this, we undertook exhaustive alanine substitutions of the 54 acidic residues present in α5/LG1-3 of the E8 fragment of laminin-511 (LM511E8). Most of the alanine mutants possessed α6β1 integrin binding activities comparable with wild-type LM511E8. Alanine substitution for α5-Asp3198 and Asp3219 caused mild reduction in integrin binding activity, and that for α5-Asp3218 caused severe reduction, possibly resulting from conformational perturbation of α5/LG1-3. When α5-Asp3218 was substituted with asparagine, the resulting mutant possessed significant binding activity to α6β1 integrin, indicating that α5-Asp3218 is not directly involved in integrin binding through coordination with the metal ion in β1-MIDAS. Given that substitution of γ1-Glu1607 with glutamine nullified the binding activity to α6β1 integrin, these results, taken together, support the possibility that the critical acidic residue coordinating the metal ion in β1-MIDAS is Glu1607 in the γ1 tail, but no such residue is present in α5/LG1-3. Copyright © 2017 Elsevier Inc. All rights reserved.

  2. Exploring the molecular mechanism of cross-resistance to HIV-1 integrase strand transfer inhibitors by molecular dynamics simulation and residue interaction network analysis.

    Science.gov (United States)

    Xue, Weiwei; Jin, Xiaojie; Ning, Lulu; Wang, Meixia; Liu, Huanxiang; Yao, Xiaojun

    2013-01-28

    The rapid emergence of cross-resistance to the integrase strand transfer inhibitors (INSTIs) has become a serious problem in the therapy of human immunodeficiency virus type 1 (HIV-1) infection. Understanding the detailed molecular mechanism of INSTIs cross-resistance is therefore critical for the development of new effective therapy against cross-resistance. On the basis of the homology modeling constructed structure of tetrameric HIV-1 intasome, the detailed molecular mechanism of the cross-resistance mutation E138K/Q148K to three important INSTIs (Raltegravir (RAL, FDA approved in 2007), Elvitegravir (EVG, FDA approved in 2012), and Dolutegravir (DTG, phase III clinical trials)) was investigated by using molecular dynamics (MD) simulation and residue interaction network (RIN) analysis. The results from conformation analysis and binding free energy calculation can provide some useful information about the detailed binding mode and cross-resistance mechanism for the three INSTIs to HIV-1 intasome. Binding free energy decomposition analysis revealed that Pro145 residue in the 140s 1oop (Gly140 to Gly149) of the HIV-1 intasome had strong hydrophobic interactions with INSTIs and played an important role in the binding of INSTIs to HIV-1 intasome active site. A systematic comparison and analysis of the RIN proves that the communications between the residues in the resistance mutant is increased when compared with that of the wild-type HIV-1 intasome. Further analysis indicates that residue Pro145 may play an important role and is relevant to the structure rearrangement in HIV-1 intasome active site. In addition, the chelating ability of the oxygen atoms in INSTIs (e.g., RAL and EVG) to Mg(2+) in the active site of the mutated intasome was reduced due to this conformational change and is also responsible for the cross-resistance mechanism. Notably, the cross-resistance mechanism we proposed could give some important information for the future rational design of novel

  3. Molecular modeling and residue interaction network studies on the mechanism of binding and resistance of the HCV NS5B polymerase mutants to VX-222 and ANA598.

    Science.gov (United States)

    Xue, Weiwei; Jiao, Pingzu; Liu, Huanxiang; Yao, Xiaojun

    2014-04-01

    Hepatitis C virus (HCV) NS5B protein is an RNA-dependent RNA polymerase (RdRp) with essential functions in viral genome replication and represents a promising therapeutic target to develop direct-acting antivirals (DAAs). Multiple nonnucleoside inhibitors (NNIs) binding sites have been identified within the polymerase. VX-222 and ANA598 are two NNIs targeting thumb II site and palm I site of HCV NS5B polymerase, respectively. These two molecules have been shown to be very effective in phase II clinical trials. However, the emergence of resistant HCV replicon variants (L419M, M423T, I482L mutants to VX-222 and M414T, M414L, G554D mutants to ANA598) has significantly decreased their efficacy. To elucidate the molecular mechanism about how these mutations influenced the drug binding mode and decreased drug efficacy, we studied the binding modes of VX-222 and ANA598 to wild-type and mutant polymerase by molecular modeling approach. Molecular dynamics (MD) simulations results combined with binding free energy calculations indicated that the mutations significantly altered the binding free energy and the interaction for the drugs to polymerase. The further per-residue binding free energy decomposition analysis revealed that the mutations decreased the interactions with several key residues, such as L419, M423, L474, S476, I482, L497, for VX-222 and L384, N411, M414, Y415, Q446, S556, G557 for ANA598. These were the major origins for the resistance to these two drugs. In addition, by analyzing the residue interaction network (RIN) of the complexes between the drugs with wild-type and the mutant polymerase, we found that the mutation residues in the networks involved in the drug resistance possessed a relatively lower size of topology centralities. The shift of betweenness and closeness values of binding site residues in the mutant polymerase is relevant to the mechanism of drug resistance of VX-222 and ANA598. These results can provide an atomic-level understanding about

  4. Chemical modification of the urokinase-type plasminogen activator and its receptor using tetranitromethane. Evidence for the involvement of specific tyrosine residues in both molecules during receptor-ligand interaction

    DEFF Research Database (Denmark)

    Ploug, M; Rahbek-Nielsen, H; Ellis, V

    1995-01-01

    ., Ellis, V., & Danø, K. (1994) Biochemistry 33, 8991-8997]. To identify residues engaged in the uPAR-uPA interaction, we have performed a "protein-protein footprinting" study on preformed uPAR-GFD complexes by chemical modification with tetranitromethane. All six tyrosine residues in uPAR and the single...

  5. Interaction of clothing and body mass index affects validity of air displacement plethysmography in adults

    Science.gov (United States)

    Objective: Examine the effect of alternate clothing schemes on validity of Bod Pod to estimate percent body fat (BF) compared to dual x-ray absorptiometry (DXA), and determine if these effects differ by body mass index (BMI). Design: Cross-sectional Subjects: 132 healthy adults aged 19-81 classifi...

  6. The same periplasmic ExbD residues mediate in vivo interactions between ExbD homodimers and ExbD-TonB heterodimers.

    Science.gov (United States)

    Ollis, Anne A; Postle, Kathleen

    2011-12-01

    The TonB system couples cytoplasmic membrane proton motive force to TonB-gated outer membrane transporters for active transport of nutrients into the periplasm. In Escherichia coli, cytoplasmic membrane proteins ExbB and ExbD promote conformational changes in TonB, which transmits this energy to the transporters. The only known energy-dependent interaction occurs between the periplasmic domains of TonB and ExbD. This study identified sites of in vivo homodimeric interactions within ExbD periplasmic domain residues 92 to 121. ExbD was active as a homodimer (ExbD(2)) but not through all Cys substitution sites, suggesting the existence of conformationally dynamic regions in the ExbD periplasmic domain. A subset of homodimeric interactions could not be modeled on the nuclear magnetic resonance (NMR) structure without significant distortion. Most importantly, the majority of ExbD Cys substitutions that mediated homodimer formation also mediated ExbD-TonB heterodimer formation with TonB A150C. Consistent with the implied competition, ExbD homodimer formation increased in the absence of TonB. Although ExbD D25 was not required for their formation, ExbD dimers interacted in vivo with ExbB. ExbD-TonB interactions required ExbD transmembrane domain residue D25. These results suggested a model where ExbD(2) assembled with ExbB undergoes a transmembrane domain-dependent transition and exchanges partners in localized homodimeric interfaces to form an ExbD(2)-TonB heterotrimer. The findings here were also consistent with our previous hypothesis that ExbD guides the conformation of the TonB periplasmic domain, which itself is conformationally dynamic.

  7. The Same Periplasmic ExbD Residues Mediate In Vivo Interactions between ExbD Homodimers and ExbD-TonB Heterodimers ▿ †

    Science.gov (United States)

    Ollis, Anne A.; Postle, Kathleen

    2011-01-01

    The TonB system couples cytoplasmic membrane proton motive force to TonB-gated outer membrane transporters for active transport of nutrients into the periplasm. In Escherichia coli, cytoplasmic membrane proteins ExbB and ExbD promote conformational changes in TonB, which transmits this energy to the transporters. The only known energy-dependent interaction occurs between the periplasmic domains of TonB and ExbD. This study identified sites of in vivo homodimeric interactions within ExbD periplasmic domain residues 92 to 121. ExbD was active as a homodimer (ExbD2) but not through all Cys substitution sites, suggesting the existence of conformationally dynamic regions in the ExbD periplasmic domain. A subset of homodimeric interactions could not be modeled on the nuclear magnetic resonance (NMR) structure without significant distortion. Most importantly, the majority of ExbD Cys substitutions that mediated homodimer formation also mediated ExbD-TonB heterodimer formation with TonB A150C. Consistent with the implied competition, ExbD homodimer formation increased in the absence of TonB. Although ExbD D25 was not required for their formation, ExbD dimers interacted in vivo with ExbB. ExbD-TonB interactions required ExbD transmembrane domain residue D25. These results suggested a model where ExbD2 assembled with ExbB undergoes a transmembrane domain-dependent transition and exchanges partners in localized homodimeric interfaces to form an ExbD2-TonB heterotrimer. The findings here were also consistent with our previous hypothesis that ExbD guides the conformation of the TonB periplasmic domain, which itself is conformationally dynamic. PMID:21984795

  8. Computational modeling of blast wave interaction with a human body and assessment of traumatic brain injury

    Science.gov (United States)

    Tan, X. G.; Przekwas, A. J.; Gupta, R. K.

    2017-07-01

    The modeling of human body biomechanics resulting from blast exposure poses great challenges because of the complex geometry and the substantial material heterogeneity. We developed a detailed human body finite element model representing both the geometry and the materials realistically. The model includes the detailed head (face, skull, brain and spinal cord), the neck, the skeleton, air cavities (lungs) and the tissues. Hence, it can be used to properly model the stress wave propagation in the human body subjected to blast loading. The blast loading on the human was generated from a simulated C4 explosion. We used the highly scalable solvers in the multi-physics code CoBi for both the blast simulation and the human body biomechanics. The meshes generated for these simulations are of good quality so that relatively large time-step sizes can be used without resorting to artificial time scaling treatments. The coupled gas dynamics and biomechanics solutions were validated against the shock tube test data. The human body models were used to conduct parametric simulations to find the biomechanical response and the brain injury mechanism due to blasts impacting the human body. Under the same blast loading condition, we showed the importance of inclusion of the whole body.

  9. Effect of three-body interaction on hot asymmetric nuclear matter

    Institute of Scientific and Technical Information of China (English)

    Li Zeng-Hua; Zuo Wei; Lu Guang-Cheng

    2004-01-01

    The properties of hot asymmetric nuclear matter are studied in the framework of the finite temperature BruecknerHartree-Fock theory that is extended to include the contribution of microscopic three-body forces. We give the variation of the critical temperature with the asymmetry parameter and show the effect brought by this three-body repulsive potential on the value of the critical asymmetry of the phase transition for asymmetric nuclear matter. Owing to the additional repulsion provided by three-body forces, this value decreases. In addition, the domain of mechanical instability for hot nuclear matter is also indicated, which gradually shrinks with increasing asymmetry and temperature.

  10. Optimal definition of inter-residual contact in globular proteins based on pairwise interaction energy calculations, its robustness, and applications.

    Science.gov (United States)

    Fačkovec, Boris; Vondrášek, Jiří

    2012-10-25

    Although a contact is an essential measurement for the topology as well as strength of non-covalent interactions in biomolecules and their complexes, there is no general agreement in the definition of this feature. Most of the definitions work with simple geometric criteria which do not fully reflect the energy content or ability of the biomolecular building blocks to arrange their environment. We offer a reasonable solution to this problem by distinguishing between "productive" and "non-productive" contacts based on their interaction energy strength and properties. We have proposed a method which converts the protein topology into a contact map that represents interactions with statistically significant high interaction energies. We do not prove that these contacts are exclusively stabilizing, but they represent a gateway to thermodynamically important rather than geometry-based contacts. The process is based on protein fragmentation and calculation of interaction energies using the OPLS force field and relies on pairwise additivity of amino acid interactions. Our approach integrates the treatment of different types of interactions, avoiding the problems resulting from different contributions to the overall stability and the different effect of the environment. The first applications on a set of homologous proteins have shown the usefulness of this classification for a sound estimate of protein stability.

  11. Critical body residues, Michaelis-Menten analysis of bioaccumulation, lethality and behaviour as endpoints of waterborne Ni toxicity in two teleosts.

    Science.gov (United States)

    Leonard, Erin M; Marentette, Julie R; Balshine, Sigal; Wood, Chris M

    2014-03-01

    Traditionally, water quality guidelines/criteria are based on lethality tests where results are expressed as a function of waterborne concentrations (e.g. LC50). However, there is growing interest in the use of uptake and binding relationships, such as biotic ligand models (BLM), and in bioaccumulation parameters, such as critical body residue values (e.g. CBR50), to predict metal toxicity in aquatic organisms. Nevertheless, all these approaches only protect species against physiological death (e.g. mortality, failed recruitment), and do not consider ecological death which can occur at much lower concentrations when the animal cannot perform normal behaviours essential for survival. Therefore, we investigated acute (96 h) Ni toxicity in two freshwater fish species, the round goby (Neogobius melanostomus) and rainbow trout (Oncorhynchus mykiss) and compared LC, BLM, and CBR parameters for various organs, as well as behavioural responses (spontaneous activity). In general, round goby were more sensitive. Ni bioaccumulation displayed Michaelis-Menten kinetics in most tissues, and round goby gills had lower Kd (higher binding affinity) but similar Bmax (binding site density) values relative to rainbow trout gills. Round goby also accumulated more Ni than did trout in most tissues at a given exposure concentration. Organ-specific 96 h acute CBR values tended to be higher in round goby but 96 h acute CBR50 and CBR10 values in the gills were very similar in the two species. In contrast, LC50 and LC10 values were significantly higher in rainbow trout. With respect to BLM parameters, gill log KNiBL values for bioaccumulation were higher by 0.4-0.8 log units than the log KNiBL values for toxicity in both species, and both values were higher in goby (more sensitive). Round goby were also more sensitive with respect to the behavioural response, exhibiting a significant decline of 63-75 % in movements per minute at Ni concentrations at and above only 8 % of the LC50 value

  12. Structures of Cytochrome b 5 Mutated at the Charged Surface-Residues and Their Interactions with Cytochrome c

    Institute of Scientific and Technical Information of China (English)

    WU,Jian(邬键); WANG,Yun-Hua(王韵华); GAN,Jian-Hua(甘建华); WANG,Wen-Hu(王文虎); SUN,Bing-Yun(孙炳耘); HUANG,Zhong-Xian(黄仲贤); XIA,Zong-Xiang(夏宗芗)

    2002-01-01

    Glu44, Glu48, Glu56 and Asp60 are the negatively charged residues located at the molecular surface of cytochrome b5@Two mutants of cytochrome b5 were prepared, in which two or all of these four residues were mutated to alanines. The mutations give rise to slightly positive shifts of the redox potentials of cytochrome b5 and obvious decrease of the cytochrome b5-cytochrome c binding constants and electron transfer rates. The crystal structures of the two mutants were determined at 0.18 nm resolution, showing no alteration in overall structures and exhibiting slight chages in the local conformations around the mutation sites as compared with the wild-type protein. Based on the crystal structure of the quadruple-site mutant, a model for the binding of this mutant with cytochrome c is proposed, which involves the salt bridges from Glu37, Glu38 and heme propionate of cytochrome b5 to three lysines of cytochrome c and can well account for the properties and behaviors of this mutant.

  13. Two-body state with p -wave interaction in a one-dimensional waveguide under transversely anisotropic confinement

    Science.gov (United States)

    Gao, Tian-You; Peng, Shi-Guo; Jiang, Kaijun

    2015-04-01

    We theoretically study two atoms with p -wave interaction in a one-dimensional waveguide, investigating how the transverse anisotropy of the confinement affects the two-body state, especially the properties of the resonance. For a bound-state solution, we find there are a total of three two-body bound states due to the richness of the orbital magnetic quantum number of the p -wave interaction, while only one bound state is supported by the s -wave interaction. Two of them become nondegenerate due to the breaking of the rotation symmetry under a transversely anisotropic confinement. For a scattering solution, the effective one-dimensional scattering amplitude and scattering length are derived. We find the position of the p -wave confinement-induced resonance shifts apparently versus the transverse anisotropy. In addition, a two-channel mechanism for the confinement-induced resonance in a one-dimensional waveguide is generalized to the p -wave interaction, which was previously proposed only for the s -wave interaction. All our calculations are based on the parametrization of the 40K-atom experiments and can thus be confirmed in future experiments.

  14. DYNAMIC CHARACTERISTIC ANALYSIS OF A 3-D SEMI-SUBMERGED BODY AS A FLUID-STRUCTURE INTERACTION SYSTEM

    Institute of Scientific and Technical Information of China (English)

    徐刚; 任文敏

    2004-01-01

    An Arnoldi's method with new iteration pattern, which was designed for solving a large unsymmetric eigenvalue problem introduced by displacement-pressure FE (Finite Element) pattern of a fluid-structure interaction system, was adopted here to get the dynamic characteristics of the semi-submerged body. The new iteration pattern could be used efficiently to obtain the Arnoldi's vectors in the shift-frequency technique, which was used for the zero-frequency problem. Numerical example showed that the fluid-structure interaction is one of the important factors to the dynamic characteristics of large semi-submerged thin-walled structures.

  15. Crossover dynamics of dispersive shocks in Bose-Einstein condensates characterized by two- and three-body interactions

    KAUST Repository

    Crosta, M.

    2012-04-10

    We show that the perturbative nonlinearity associated with three-atom interactions, competing with standard two-body repulsive interactions, can change dramatically the evolution of one-dimensional (1D) dispersive shock waves in a Bose-Einstein condensate. In particular, we prove the existence of a rich crossover dynamics, ranging from the formation of multiple shocks regularized by nonlinear oscillations culminating in coexisting dark and antidark matter waves to 1D-soliton collapse. For a given scattering length, all these different regimes can be accessed by varying the density of atoms in the condensate.

  16. Experimental investigations on the magneto-hydro-dynamic interaction around a blunt body in a hypersonic unseeded air flow

    Science.gov (United States)

    Cristofolini, Andrea; Borghi, Carlo A.; Neretti, Gabriele; Schettino, Antonio; Trifoni, Eduardo; Battista, Francesco; Passaro, Andrea; Baccarella, Damiano

    2012-11-01

    This paper deals with the experimental investigation on the MHD (magneto-hydro-dynamic or magneto-fluid-dynamic) interaction around a test body immersed into a hypersonic unseeded air flow. The experiments have been carried out in the CIRA plasma wind tunnel SCIROCCO. Two test conditions have been utilized for the experiments with a total pressure of 2.5 and 2.3 bar respectively, a total specific enthalpy of 16 and 12.1 MJ/kg respectively. The air flow was accelerated in the nozzle up to Mach 10. The magnetic induction field is generated by an electromagnet enclosed in the test body and reaches a 0.8 T maximum value in the interaction region.

  17. Analytical determination of the two-body gravitational interaction potential at the 4th post-Newtonian approximation

    CERN Document Server

    Bini, Donato

    2013-01-01

    We complete the analytical determination, at the 4th post-Newtonian approximation, of the main radial potential describing the gravitational interaction of two bodies within the effective one-body formalism. The (non logarithmic) coefficient a_5 (nu) measuring this 4th post-Newtonian interaction potential is found to be linear in the symmetric mass ratio nu. Its nu-independent part a_5 (0) is obtained by an analytical gravitational self-force calculation that unambiguously resolves the formal infrared divergencies which currently impede its direct post-Newtonian calculation. Its nu-linear part a_5 (nu) - a_5 (0) is deduced from recent results of Jaranowski and Sch\\"afer, and is found to be significantly negative.

  18. The water hexamer: three-body interactions, structures, energetics, and OH-stretch spectroscopy at finite temperature.

    Science.gov (United States)

    Tainter, C J; Skinner, J L

    2012-09-14

    Using a newly developed and recently parameterized classical empirical simulation model for water that involves explicit three-body interactions, we determine the eleven most stable isomers of the water hexamer. We find that the lowest energy isomer is one of the cage structures, in agreement with far-IR and microwave experiments. The energy ordering for the binding energies is cage > glove > book > bag > chair > boat > chaise, and energies relative to the cage are in good agreement with CCSD(T) calculations. The three-body contributions to the cage, book, and chair are also in reasonable agreement with CCSD(T) results. The energy of each isomer results from a delicate balance involving the number of hydrogen bonds, the strain of these hydrogen bonds, and cooperative and anti-cooperative three-body interactions, whose contribution we can understand simply from the form of the three-body interactions in the simulation model. Oxygen-oxygen distances in the cage and book isomers are in good agreement with microwave experiments. Hydrogen-bond distances depend on both donor and acceptor, which can again be understood from the three-body model. Fully anharmonic OH-stretch spectra are calculated for these low-energy structures, and compared with shifted harmonic results from ab initio and density functional theory calculations. Replica-exchange molecular dynamics simulations were performed from 40 to 194 K, which show that the cage isomer has the lowest free energy from 0 to 70 K, and the book isomer has the lowest free energy from 70 to 194 K. OH-stretch spectra were calculated between 40 and 194 K, and results at 40, 63, and 79 K were compared to recent experiments, leading to re-assignment of the peaks in the experimental spectra. We calculate local OH-stretch cumulative spectral densities for different donor-acceptor types and compare to analogous results for liquid water.

  19. A cation-π interaction at a phenylalanine residue in the glycine receptor binding site is conserved for different agonists

    DEFF Research Database (Denmark)

    Pless, Stephan Alexander; Hanek, Ariele P; Price, Kerry L

    2011-01-01

    . In the current study, we investigated whether the lower efficacy agonists of the human GlyR β-alanine and taurine also form cation-π interactions with Phe159. By incorporating a series of unnatural amino acids, we found cation-π interactions between Phe159 and the amino groups of β-alanine and taurine....... The strengths of these interactions were significantly weaker than for glycine. Modeling studies suggest that β-alanine and taurine are orientated subtly differently in the binding pocket, with their amino groups further from Phe159 than that of glycine. These data therefore show that similar agonists can have...... similar but not identical orientations and interactions in the binding pocket and provide a possible explanation for the lower potencies of β-alanine and taurine....

  20. New body mass estimates of British Pleistocene wolves: Palaeoenvironmental implications and competitive interactions

    Science.gov (United States)

    Flower, L. O. H.

    2016-10-01

    Body mass was reconstructed for early Middle Pleistocene Canis mosbachensis and late Middle to Late Pleistocene Canis lupus from key assemblages in Britain, to explore the presence of temporal size variability and whether size fluctuations were related to changes in climate and environment or to differences in Pleistocene carnivore community structure. Using the well-known body mass predictor of lower carnassial (m1) tooth length, combined with an extant canid dataset incorporating 25 species, least squares regression was used to assess allometric scaling prior to modelling the relationship between body mass and m1 length, producing a new predictive equation of Pleistocene canid body mass. The medium-sized C. mosbachensis had relatively stable body mass, with remarkable consistency in size compared to populations in the late Early Pleistocene of Europe. Periodical fluctuations in climatic conditions had a minimal effect on C. mosbachensis size over time, with the terrestrial connection between Britain and mainland Europe at this time key in promoting body mass stability by enabling movement away from less favourable conditions and to follow prey into refugia. Overall changes in carnivore guild structure were of minimal influence to C. mosbachensis in Britain, as the continued predominance of larger carnivores, in particular a larger canid, effectively constrained C. mosbachensis. In contrast, the body mass of larger-sized C. lupus was highly temporally varied, with an increasing size trend evident into the Devensian. Similar body size in the penultimate interglacial (MIS 7) and Middle Devensian (MIS 3) populations likely reflects palaeoenvironmental similarity and comparable carnivore community and prey spectrums, with larger predators effectively constraining C. lupus. However, the severely cold conditions of the Early Devensian (MIS 5a) may have caused a Bergmannian response in wolves, leading to their comparatively much larger size, with C. lupus further

  1. FTO Genotype Interacts with Improvement in Aerobic Fitness on Body Weight Loss During Lifestyle Intervention.

    Science.gov (United States)

    Sailer, Corinna; Schmid, Vera; Fritsche, Louise; Gerter, Tsvetelina; Machicao, Fausto; Niess, Andreas; Häring, Hans-Ulrich; Stefan, Norbert; Fritsche, Andreas; Heni, Martin

    2016-01-01

    Not every participant responds with a comparable body weight loss to lifestyle intervention, despite the same compliance. Genetic factors may explain parts of this difference. Variation in fat mass and obesity-associated gene (FTO) is the strongest common genetic determinant of body weight. The aim of the present study was to evaluate the impact of FTO genotype differences in the link between improvement of fitness and reduction of body weight during a lifestyle intervention. We genotyped 292 healthy subjects for FTO rs8050136. Participants underwent a 9-month lifestyle intervention. Before and after intervention, aerobic fitness was tested by bicycle (VO2max) and treadmill spiroergometry (individual anaerobic threshold (IAT), subgroup of N = 192). Participants lost body weight (p fitness lost significantly less body weight. Our data reveal that genetic variation in FTO impacts on body weight reduction during lifestyle intervention only in subjects with marked improvement in aerobic fitness. © 2016 The Author(s) Published by S. Karger GmbH, Freiburg.

  2. Ground state spin 0{sup +} dominance of many-body systems with random interactions and related topics

    Energy Technology Data Exchange (ETDEWEB)

    Arima, A.; Yoshinaga, N.; Zhao, Y.M

    2003-07-14

    In this talk we shall show our recent results in understanding the spin{sup parity} 0{sup +} ground state (0 g.s.) dominance of many-body systems. We propose a simple approach to predict the spin I g.s. probabilities which does not require the diagonalization of a Hamiltonian with random interactions. Some findings related to the 0 g.s. dominance will also be discussed.

  3. Dynamical stabilization of the body centered cubic phase in lanthanum and thorium by phonon-phonon interaction

    Energy Technology Data Exchange (ETDEWEB)

    Souvatzis, P; Rudin, S P [Theoretical Division, Los Alamos National Laboratory, Los Alamos, NM 87545 (United States); Bjoerkman, T; Eriksson, O [Department of Physics, Uppsala University, Box 530, SE-75121, Uppsala (Sweden); Andersson, P [FOI, Swedish Defence Research Agency, SE-164 90 Stockholm (Sweden); Katsnelson, M I [Institute for Molecules and Materials, Radboud University Nijmegen, NL-6525 ED, Nijmegen (Netherlands)], E-mail: petros.souvatzis@gmail.com

    2009-04-29

    A recently developed self-consistent ab initio lattice dynamical method has been applied to the high temperature body centered cubic (bcc) phase of La and Th, which are dynamically unstable at low temperatures. The bcc phase of these metals is found to be stabilized by phonon-phonon interactions. The calculated high temperature phonon frequencies for La are found to be in good agreement with the corresponding experimental data.

  4. β- transitions of 16 7N9 → 16 8O8 with optimized SDI residual interaction using pnTDA and TDA approximations

    Science.gov (United States)

    Pahlavani, M. R.; Firoozi, B.

    2015-11-01

    Within a developed particle-hole approach, a systematic study of the β- transition from the ground state of the 16N nucleus to the ground and some exited states of the 16O nucleus has been carried out. The energy spectrum and the wave functions of pure configuration of the 16N and 16O nuclei are numerically obtained using the mean-field shell model with respect to the Woods-Saxon nuclear potential accompanying spin-orbit and Coulomb interaction. Considering SDI residual interaction, mixed configuration of ground and excited pnTDA and TDA states are extracted for the aforementioned nucleus. These energy spectra and corresponding eigenstates are highly correspondent to the experimental energy spectrum and eigenstates after adjusting the residual potential parameters using the Nelder-Mead (NM) algorithm. In this approach, the endpoint energy, log ft and the partial half-lives of some possible transitions are calculated. The obtained results using the optimized SDI approach are reasonably close to the available experimental data.

  5. Adsorption of charged protein residues on an inorganic nanosheet: Computer simulation of LDH interaction with ion channel

    Science.gov (United States)

    Tsukanov, Alexey A.; Psakhie, Sergey G.

    2016-08-01

    Quasi-two-dimensional and hybrid nanomaterials based on layered double hydroxides (LDH), cationic clays, layered oxyhydroxides and hydroxides of metals possess large specific surface area and strong electrostatic properties with permanent or pH-dependent electric charge. Such nanomaterials may impact cellular electrostatics, changing the ion balance, pH and membrane potential. Selective ion adsorption/exchange may alter the transmembrane electrochemical gradient, disrupting potential-dependent cellular processes. Cellular proteins as a rule have charged residues which can be effectively adsorbed on the surface of layered hydroxide based nanomaterials. The aim of this study is to attempt to shed some light on the possibility and mechanisms of protein "adhesion" an LDH nanosheet and to propose a new direction in anticancer medicine, based on physical impact and strong electrostatics. An unbiased molecular dynamics simulation was performed and the combined process free energy estimation (COPFEE) approach was used.

  6. Identification and characterization of protein interactions in the mammalian mRNA processing body using a novel two-hybrid assay

    Energy Technology Data Exchange (ETDEWEB)

    Bloch, Donald B., E-mail: bloch@helix.mgh.harvard.edu; Nobre, Rita A.; Bernstein, Gillian A.; Yang, Wei-Hong

    2011-09-10

    Components of the mRNA processing body (P-body) regulate critical steps in mRNA storage, transport, translation and degradation. At the core of the P-body is the decapping complex, which removes the 5' cap from de-adenylated mRNAs and mediates an irreversible step in mRNA degradation. The assembly of P-bodies in Saccharomyces cerevisiae, Arabidopsis thaliana and Drosophila melanogaster has been previously described. Less is known about the assembly of mammalian P-bodies. To investigate the interactions that occur between components of mammalian P-bodies, we developed a fluorescence-based, two-hybrid assay system. The assay depends on the ability of one P-body component, fused to an exogenous nuclear localization sequence (NLS), to recruit other P-body components to the nucleus. The assay was used to investigate interactions between P-body components Ge-1, DCP2, DCP1, EDC3, RAP55, and RCK. The results of this study show that the modified two-hybrid assay can be used to identify protein interactions that occur in a macromolecular complex. The assay can also be used to efficiently detect protein interaction domains. The results provide important insights into mammalian P-body assembly and demonstrate similarities, and critical differences, between P-body assembly in mammalian cells compared with that of other species. -- Research highlights: {yields} A two-hybrid assay was developed to study interactions in macromolecular complexes. {yields} The assay was applied to interactions between components of mRNA P-bodies. {yields} The assay effectively and efficiently identified protein interaction domains. {yields} P-body assembly in mammalian cells differs from that in other species.

  7. Disrupting the Acyl Carrier Protein/SpoT interaction in vivo: identification of ACP residues involved in the interaction and consequence on growth.

    Directory of Open Access Journals (Sweden)

    Sandra Angelini

    Full Text Available In bacteria, Acyl Carrier Protein (ACP is the central cofactor for fatty acid biosynthesis. It carries the acyl chain in elongation and must therefore interact successively with all the enzymes of this pathway. Yet, ACP also interacts with proteins of diverse unrelated function. Among them, the interaction with SpoT has been proposed to be involved in regulating ppGpp levels in the cell in response to fatty acid synthesis inhibition. In order to better understand this mechanism, we screened for ACP mutants unable to interact with SpoT in vivo by bacterial two-hybrid, but still functional for fatty acid synthesis. The position of the selected mutations indicated that the helix II of ACP is responsible for the interaction with SpoT. This suggested a mechanism of recognition similar to one used for the enzymes of fatty acid synthesis. Consistently, the interactions tested by bacterial two-hybrid of ACP with fatty acid synthesis enzymes were also affected by the mutations that prevented the interaction with SpoT. Yet, interestingly, the corresponding mutant strains were viable, and the phenotypes of one mutant suggested a defect in growth regulation.

  8. Sperm-egg interaction is mediated by a sperm-associated body in quail.

    Science.gov (United States)

    Rabbani, M Golam; Sasanami, Tomohiro; Mori, Makoto; Yoshizaki, Norio

    2006-01-01

    The present study describes the holes in the inner vitelline membrane of fertile eggs of the quail Coturnix japonica, which remain after the spermatozoa pass through. It was shown that the light-microscopically observable 'holes' correspond mostly to electron-microscopically defined 'disks', and, to a lesser extent (about 5%), real holes. Immunofluorescent staining of the vitelline membranes with an antiquail ZPC antiserum was used to discriminate the holes from the disks light-microscopically. Over 96% of holes were accompanied by calcium-coated sperm-associated bodies, indicating a close relationship between the two. There was no preferential localization of the disks, holes or sperm-associated bodies in the vitelline membrane around the egg. The sperm-associated bodies bound with the spermatozoa at the posterior end of sperm flagella. Incubation of the inner vitelline membranes, isolated from the largest follicles, with spermatozoa resulted in production only of the disks, whereas the holes (about 9%) were produced when the sperm-associated bodies were added to the system. It was suggested that the sperm-associated bodies assist fertile spermatozoa in binding to the inner vitelline membrane, making holes in the membrane and passing through them in fertile eggs.

  9. Interaction between leading and trailing edge vortex shedding: effects of bluff body geometry

    Science.gov (United States)

    Taylor, Zachary; Kopp, Gregory; Gurka, Roi

    2011-11-01

    Elongated bluff bodies are distinguished from shorter bluff bodies (e.g., circular cylinders) by the fact that they have separating-reattaching flow at the leading edge as well as having vortex shedding at the trailing edge. Engineering examples of these bodies include heat exchanger fins and long-span suspension bridges. We have performed experiments on elongated bluff bodies of varying geometry. These experiments have been performed at Reynolds numbers O(104) based on the thickness of the model. Both surface pressure measurements (using 512 simultaneously sampled pressure taps) and PIV are used to quantify the flow fields of these bodies. The leading edge separation angle is controlled by changing the leading edge geometry. It is observed that the size of the leading edge separation bubble increases with increasing leading edge separation angle. As the size of the leading edge separation bubble increases, it is shown to continually decrease the shedding frequency for a given elongation ratio. It is suggested that the shedding frequency is diminished because the trailing edge vortex shedding is affected by the structures being shed from the leading edge separation bubble. The implications of this competition between leading and trailing edge flows will be explored.

  10. Importance of a Conserved Lys/Arg Residue for Ligand/PDZ Domain Interactions as Examined by Protein Semisynthesis

    DEFF Research Database (Denmark)

    Pedersen, Søren W; Moran, Griffin E; Sereikaité, Vita

    2016-01-01

    drug targets for diseases (in the brain in particular), so understanding the molecular details of PDZ domain interactions is of fundamental importance. PDZ domains bind to a protein partner at either a C-terminal peptide or internal peptide motifs. Here, we examined the importance of a conserved Lys......PDZ domains are ubiquitous small protein domains that are mediators of numerous protein-protein interactions, and play a pivotal role in protein trafficking, synaptic transmission, and the assembly of signaling-transduction complexes. In recent years, PDZ domains have emerged as novel and exciting...

  11. Thermal QRPA equations with finite rank separable approximation for residual forces based on the Skyrme type interactions

    CERN Document Server

    Dzhioev, Alan A

    2011-01-01

    The approach to study properties of charge-exchange excitations in hot nuclei is presented. The approach is based on the extension of the finite rank separable approximation for Skyrme interactions to finite temperatures employing the TFD formalism. We present the formulae to obtain charge-exchange strength distributions within the Thermal Quasiparticle Random Phase Approximation (TQRPA).

  12. The translation initiation factor 3 subunit eIF3K interacts with PML and associates with PML nuclear bodies

    Energy Technology Data Exchange (ETDEWEB)

    Salsman, Jayme; Pinder, Jordan; Tse, Brenda [Department of Pathology, Dalhousie University, P.O. Box 15000, Halifax, Nova Scotia, Canada B3H 4R2 (Canada); Corkery, Dale [Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia (Canada); Dellaire, Graham, E-mail: dellaire@dal.ca [Department of Pathology, Dalhousie University, P.O. Box 15000, Halifax, Nova Scotia, Canada B3H 4R2 (Canada); Department of Biochemistry and Molecular Biology, Dalhousie University, Halifax, Nova Scotia (Canada)

    2013-10-15

    The promyelocytic leukemia protein (PML) is a tumor suppressor protein that regulates a variety of important cellular processes, including gene expression, DNA repair and cell fate decisions. Integral to its function is the ability of PML to form nuclear bodies (NBs) that serve as hubs for the interaction and modification of over 90 cellular proteins. There are seven canonical isoforms of PML, which encode diverse C-termini generated by alternative pre-mRNA splicing. Recruitment of specific cellular proteins to PML NBs is mediated by protein–protein interactions with individual PML isoforms. Using a yeast two-hybrid screen employing peptide sequences unique to PML isoform I (PML-I), we identified an interaction with the eukaryotic initiation factor 3 subunit K (eIF3K), and in the process identified a novel eIF3K isoform, which we term eIF3K-2. We further demonstrate that eIF3K and PML interact both in vitro via pull-down assays, as well as in vivo within human cells by co-immunoprecipitation and co-immunofluorescence. In addition, eIF3K isoform 2 (eIF3K-2) colocalizes to PML bodies, particularly those enriched in PML-I, while eIF3K isoform 1 associates poorly with PML NBs. Thus, we report eIF3K as the first known subunit of the eIF3 translation pre-initiation complex to interact directly with the PML protein, and provide data implicating alternative splicing of both PML and eIF3K as a possible regulatory mechanism for eIF3K localization at PML NBs. - Highlights: • The PML-I C-terminus, encoded by exon 9, interacts with translation factor eIF3K. • We identify a novel eIF3K isoform that excludes exon 2 (eIF3K-2). • eIF3K-2 preferentially associates with PML bodies enriched in PML-I vs. PML-IV. • Alternative splicing of eIF3K regulates association with PML bodies.

  13. Site-directed mutagenesis of amino acid residues of D1 protein interacting with phosphatidylglycerol affects the function of plastoquinone QB in photosystem II.

    Science.gov (United States)

    Endo, Kaichiro; Mizusawa, Naoki; Shen, Jian-Ren; Yamada, Masato; Tomo, Tatsuya; Komatsu, Hirohisa; Kobayashi, Masami; Kobayashi, Koichi; Wada, Hajime

    2015-12-01

    Recent X-ray crystallographic analysis of photosystem (PS) II at 1.9-Å resolution identified 20 lipid molecules in the complex, five of which are phosphatidylglycerol (PG). In this study, we mutagenized amino acid residues S232 and N234 of D1, which interact with two of the PG molecules (PG664 and PG694), by site-directed mutagenesis in Synechocystis sp. PCC 6803 to investigate the role of the interaction in PSII. The serine and asparagine residues at positions 232 and 234 from the N-terminus were mutagenized to alanine and aspartic acid, respectively, and a mutant carrying both amino acid substitutions was also produced. Although the obtained mutants, S232A, N234D, and S232AN234D, exhibited normal growth, they showed decreased photosynthetic activities and slower electron transport from QA to QB than the control strain. Thermoluminescence analysis suggested that this slower electron transfer in the mutants was caused by more negative redox potential of QB, but not in those of QA and S2. In addition, the levels of extrinsic proteins, PsbV and PsbU, were decreased in PSII monomer purified from the S232AN234D mutant, while that of Psb28 was increased. In the S232AN234D mutant, the content of PG in PSII was slightly decreased, whereas that of monogalactosyldiacylglycerol was increased compared with the control strain. These results suggest that the interactions of S232 and N234 with PG664 and PG694 are important to maintain the function of QB and to stabilize the binding of extrinsic proteins to PSII.

  14. The tyrosine 343 residue of nucleophosmin (NPM)-anaplastic lymphoma kinase (ALK) is important for its interaction with SHP1, a cytoplasmic tyrosine phosphatase with tumor suppressor functions.

    Science.gov (United States)

    Hegazy, Samar A; Wang, Peng; Anand, Mona; Ingham, Robert J; Gelebart, Pascal; Lai, Raymond

    2010-06-25

    The cytoplasmic tyrosine phosphatase SHP1 has been shown to inhibit the oncogenic fusion protein nucleophosmin (NPM)-anaplastic lymphoma kinase (ALK), and loss of SHP1 contributes to NPM-ALK-mediated tumorigenesis. In this study, we aimed to further understand how SHP1 interacts and regulates NPM-ALK. We employed an in vitro model in which GP293 cells were transfected with various combinations of NPM-ALK (or mutants) and SHP1 (or mutants) expression vectors. We found that SHP1 co-immunoprecipitated with NPM-ALK, but not the enzymatically inactive NPM-ALK(K210R) mutant, or the mutant in which all three functionally important tyrosine residues (namely, Tyr(338), Tyr(342), and Tyr(343)) in the kinase activation loop (KAL) of ALK were mutated. Interestingly, whereas mutation of Tyr(338) or Tyr(342) did not result in any substantial change in the NPM-ALK/SHP1 binding (assessed by co-immunoprecipitation), mutation of Tyr(343) abrogated this interaction. Furthermore, the NPM-ALK/SHP1 binding was readily detectable when each of the remaining 8 tyrosine residues known to be phosphorylated were mutated. Although the expression of SHP1 effectively reduced the level of tyrosine phosphorylation of NPM-ALK, it did not affect that of the NPM-ALK(Y343F) mutant. In soft agar clonogenic assay, SHP1 expression significantly reduced the tumorigenicity of NPM-ALK but not that of NPM-ALK(Y343F). In conclusion, we identified Tyr(343) of NPM-ALK as the crucial site for mediating the NPM-ALK/SHP1 interaction. Our results also support the notion that the tumor suppressor effects of SHP1 on NPM-ALK are dependent on its ability to bind to this oncogenic protein.

  15. STUDY OF INTERACTION OF DRUGS WITH BODY-ALIKE MACROMOLECULE (POLYVINYLPYRROLIDONE BY ULTRA VIOLET SPECTROSCOPIC METHOD

    Directory of Open Access Journals (Sweden)

    AKHTAR SAEED

    2006-01-01

    Full Text Available UV-visible spectrophotometric technique was used to study the interaction of polyvinylpyrrolidone (PVP with co-solutes: phenol, benzoic acid, sodium benzoate, salicylic acid and acetyl salicylic acid in aqueous medium. Changes in the absorption spectra of the co-solutes were observed in the presence of PVP from 200 to 210 nm. The changes were attributed to interaction of PVP molecules with the co-solute molecules. As the concentration of the co-solute increased, a red shift in the bands was observed indicating an increase in interaction between PVP and the co-solute.

  16. Effect of dissolution/precipitation on the residual stress redistribution of plasma-sprayed hydroxyapatite coating on titanium substrate in simulated body fluid (SBF).

    Science.gov (United States)

    Rakngarm Nimkerdphol, Achariya; Otsuka, Yuichi; Mutoh, Yoshiharu

    2014-08-01

    The residual stress distributions in hydroxyapatite (HAp) coating with and without mixed hydroxyapatite/titanium (HAp/Ti) bond coating on commercially pure Titanium substrate (cp-Ti) were evaluated by Raman piezo-spectroscopy analysis. The Raman shifted position 962cm(-1), which is the symmetrical stretching of surrounded oxygen atoms with phosphorous atom ( [Formula: see text] ), was referred to analyses of stress dependency. The piezo-spectroscopic coefficient, which is a Raman shift value per stress (cm(-1)/GPa), was fitted from the result of four-points bending test of rectangular HAp bar and as-sprayed HAp on Zn plate. The calculated values were 3.89cm(-1)/GPa for the former and 7.11cm(-1)/GPa for the latter. By using these calibrations, the compressive residual stress in HAp coating with HAp/Ti bond coating (HA-B) has been found to be distributed in the range of -137MPa to -75MPa. For the heat-treated HAp coating (HA-B-HT) specimen, the compressive residual stresses placed in the range of -40--22MPa. The changes in the values of residual stress of the HAp coating after immersion in SBF were also evaluated. The residual stress in HA-WB specimens tend to change from compressive to tensile after 30 days immersion. The HA-B-HT specimens exhibited similar behavior and reached to zero stress after the immersion. The mechanism of the changes in residual stress would be the effect of stress redistribution around melted calcium phosphate particles to remained HAp splats.

  17. Second order corrections to mean field evolution for weakly interacting Bosons in the case of 3-body interactions

    CERN Document Server

    Chen, Xuwen

    2010-01-01

    In this paper, we consider the Hamiltonian evolution of N weakly interacting Bosons. Assuming triple collisions with singular potentials, its mean field approximation is given by a quintic Hartree equation. We construct a second order correction to the mean field approximation using a kernel k(t,x,y) and derive an evolution equation for k. We show the global existence for the resulting evolution equation for the correction and establish an apriori estimate comparing the approximation to the exact Hamiltonian evolution. Our error estimate is global and uniform in time. Comparing with the work in [20,11,12] where the error estimate grows in time, our approximation tracks the exact dynamics for all time with an error of the order O(1/$\\sqrt{N}$).

  18. Using Multimodal Learning Analytics to Identify Patterns of Interactions in a Body-Based Mathematics Activity

    Science.gov (United States)

    Smith, Carmen; King, Barbara; Gonzalez, Diana

    2016-01-01

    Elementary students' difficulties with angles in geometry are well documented, but we know little about how they conceptualize angles while solving problems and how their thinking changes over time. In this study, we examined 26 third and fourth grade students completing a body-based angle task supported by the Kinect for Windows. We used…

  19. Grab a Golgi: Laser trapping of golgi bodies reveals in vivo Interactions with the endoplasmic reticulum

    NARCIS (Netherlands)

    Sparkes, I.A.; Ketelaar, T.; Ruijter, de N.C.A.; Hawes, C.

    2009-01-01

    In many vacuolate plant cells individual Golgi bodies appear to be attached to tubules of the pleiomorphic cortical endoplasmic reticulum (ER) network. Such observations culminated in the controversial mobile secretory unit hypothesis to explain transport of cargo from the ER to Golgi via Golgi atta

  20. The Effect of Body Mass on the Shoe-Athlete Interaction

    Directory of Open Access Journals (Sweden)

    A. Tsouknidas

    2017-01-01

    Full Text Available Long-distance running is known to induce joint overloading and elevate cytokine levels, which are the hallmarks for a variety of running-related injuries. To address this, footwear systems incorporate cushioning midsoles to mitigate injurious mechanical loading. The aim of this study was to evaluate the effect of athlete body mass on the cushioning capacity of technical footwear. An artificial heel was prototyped to fit the impact pattern of a heel-strike runner and used to measure shock attenuation by an automated drop test. Impact mass and velocity were modulated to simulate runners of various body mass and speeds. The investigation provided refined insight on running-induced impact transmission to the human body. The examined midsole system was optimized around anthropometric data corresponding to an average (normal body mass. The results suggest that although modern footwear is capable of attenuating the shock waves occurring during foot strike, improper shoe selection could expose an athlete to high levels of peak stress that could provoke an abnormal cartilage response. The selection of a weight-specific cushioning system could provide optimum protection and could thus prolong the duration of physical exercise beneficial to maintaining a simulated immune system.

  1. Validation of a Wave-Body Interaction Model by Experimental Tests

    DEFF Research Database (Denmark)

    Ferri, Francesco; Kramer, Morten; Pecher, Arthur

    2013-01-01

    Within the wave energy field, numerical simulation has recently acquired a worldwide consent as being a useful tool, besides physical model testing. The main goal of this work is the validation of a numerical model by experimental results. The numerical model is based on a linear wave-body intera...

  2. project SENSE : multimodal simulation with full-body real-time verbal and nonverbal interactions

    NARCIS (Netherlands)

    Miri, Hossein; Kolkmeier, Jan; Taylor, Paul Jonathon; Poppe, Ronald; Heylen, Dirk; Poppe, Ronald; Meyer, John-Jules; Veltkamp, Remco; Dastani, Mehdi

    2016-01-01

    This paper presents a multimodal simulation system, project-SENSE, that combines virtual reality and full-body motion capture technologies with real-time verbal and nonverbal communication. We introduce the technical setup and employed hardware and software of a first prototype. We discuss the

  3. Maize root lectins mediate the interaction with Herbaspirillum seropedicae via N-acetyl glucosamine residues of lipopolysaccharides.

    Science.gov (United States)

    Balsanelli, Eduardo; Tuleski, Thalita Regina; de Baura, Valter Antonio; Yates, Marshall Geoffrey; Chubatsu, Leda Satie; Pedrosa, Fabio de Oliveira; de Souza, Emanuel Maltempi; Monteiro, Rose Adele

    2013-01-01

    Herbaspirillum seropedicae is a plant growth-promoting diazotrophic betaproteobacterium which associates with important crops, such as maize, wheat, rice and sugar-cane. We have previously reported that intact lipopolysaccharide (LPS) is required for H. seropedicae attachment and endophytic colonization of maize roots. In this study, we present evidence that the LPS biosynthesis gene waaL (codes for the O-antigen ligase) is induced during rhizosphere colonization by H. seropedicae. Furthermore a waaL mutant strain lacking the O-antigen portion of the LPS is severely impaired in colonization. Since N-acetyl glucosamine inhibits H. seropedicae attachment to maize roots, lectin-like proteins from maize roots (MRLs) were isolated and mass spectrometry (MS) analysis showed that MRL-1 and MRL-2 correspond to maize proteins with a jacalin-like lectin domain, while MRL-3 contains a B-chain lectin domain. These proteins showed agglutination activity against wild type H. seropedicae, but failed to agglutinate the waaL mutant strain. The agglutination reaction was severely diminished in the presence of N-acetyl glucosamine. Moreover addition of the MRL proteins as competitors in H. seropedicae attachment assays decreased 80-fold the adhesion of the wild type to maize roots. The results suggest that N-acetyl glucosamine residues of the LPS O-antigen bind to maize root lectins, an essential step for efficient bacterial attachment and colonization.

  4. Maize root lectins mediate the interaction with Herbaspirillum seropedicae via N-acetyl glucosamine residues of lipopolysaccharides.

    Directory of Open Access Journals (Sweden)

    Eduardo Balsanelli

    Full Text Available Herbaspirillum seropedicae is a plant growth-promoting diazotrophic betaproteobacterium which associates with important crops, such as maize, wheat, rice and sugar-cane. We have previously reported that intact lipopolysaccharide (LPS is required for H. seropedicae attachment and endophytic colonization of maize roots. In this study, we present evidence that the LPS biosynthesis gene waaL (codes for the O-antigen ligase is induced during rhizosphere colonization by H. seropedicae. Furthermore a waaL mutant strain lacking the O-antigen portion of the LPS is severely impaired in colonization. Since N-acetyl glucosamine inhibits H. seropedicae attachment to maize roots, lectin-like proteins from maize roots (MRLs were isolated and mass spectrometry (MS analysis showed that MRL-1 and MRL-2 correspond to maize proteins with a jacalin-like lectin domain, while MRL-3 contains a B-chain lectin domain. These proteins showed agglutination activity against wild type H. seropedicae, but failed to agglutinate the waaL mutant strain. The agglutination reaction was severely diminished in the presence of N-acetyl glucosamine. Moreover addition of the MRL proteins as competitors in H. seropedicae attachment assays decreased 80-fold the adhesion of the wild type to maize roots. The results suggest that N-acetyl glucosamine residues of the LPS O-antigen bind to maize root lectins, an essential step for efficient bacterial attachment and colonization.

  5. Analysis and Design Tools for Fluid-Structure Interaction with Multi-Body Flexible Structures Project

    Data.gov (United States)

    National Aeronautics and Space Administration — The overall objective of this proposal (Phases I and II) is to develop a robust and accurate solver for fluid-structure interaction computations capable of...

  6. Classical statistical mechanics of a few-body interacting spin model

    CERN Document Server

    Borgonovi, F

    1999-01-01

    We study the emergence of Boltzmann's law for the "single particle energy distribution" in a closed system of interacting classical spins. It is shown that for a large number of particles Boltzmann's law may occur, even if the interaction is very strong. Specific attention is paid to classical analogs of the average shape of quantum eigenstates and "local density of states", which are very important in quantum chaology. Analytical predictions are then compared with numerical data.

  7. Spring Chinook Salmon Interactions Indices and Residual/Precocial Monitoring in the Upper Yakima Basin; Yakima/Klickitat Fisheries Project Monitoring and Evaluation, 2001-2002 Annual Report.

    Energy Technology Data Exchange (ETDEWEB)

    Pearsons, Todd N.; James, Brenda B.; Johnson, Christopher L. (Washington Department of Fish and Wildlife, Olympia, WA)

    2003-05-01

    This report examines some of the factors that can influence the success of supplementation, which is currently being tested in the Yakima Basin using upper Yakima stock of spring chinook salmon. Supplementation success in the Yakima Basin is defined relative to four topic areas: natural production, genetics, ecological interactions, and harvest (Busack et al. 1997). The success of spring chinook salmon supplementation in the Yakima Basin is dependent, in part, upon fish culture practices and favorable physical and biological conditions in the natural environment (Busack et al. 1997). Shortfalls in either of these two topics (i.e., failure in culturing many fish that have high long-term fitness or environmental conditions that constrain spring chinook salmon production) will cause supplementation success to be limited. For example, inadvertent selection or propagation of spring chinook that residualize or precocially mature may hinder supplementation success. Spring chinook salmon that residualize (do not migrate during the normal migration period) may have lower survival rates than migrants and, additionally, may interact with wild fish and cause unacceptable impacts to non-target taxa. Large numbers of precocials (nonanadromous spawners) may increase competition for females and significantly skew ratios of offspring sired by nonanadromous males, which could result in more nonanadromous spring chinook in future generations. Conditions in the natural environment may also limit the success of spring chinook supplementation. For example, intra or interspecific competition may constrain spring chinook salmon production. Spring chinook salmon juveniles may compete with each other for food or space or compete with other species that have similar ecological requirements. Monitoring of spring chinook salmon residuals, precocials, prey abundance, carrying capacity, and competition will help researchers interpret why supplementation is working or not working (Busack et al

  8. Combining symmetry breaking and restoration with configuration interaction: a highly accurate many-body scheme applied to the pairing Hamiltonian

    CERN Document Server

    Ripoche, J; Gambacurta, D; Ebran, J -P; Duguet, T

    2016-01-01

    Background: Ab initio many-body methods have been developed over the past ten years to address mid-mass nuclei... As progress in the design of inter-nucleon interactions is made, further efforts must be made to tailor many-body methods. Methods: We formulate a truncated configuration interaction method that consists of diagonalizing the Hamiltonian in a highly truncated subspace of the total N-body Hilbert space. The reduced Hilbert space is generated via the particle-number projected BCS state along with projected seniority-zero two and four quasi-particle excitations. Furthermore, the extent by which the underlying BCS state breaks U(1) symmetry is optimized in presence of the projected two and four quasi-particle excitations... The quality of the newly designed method is tested against exact solutions of the so-called attractive pairing Hamiltonian problem. Results: By construction, the method reproduce exact results for N=2 and N=4. For N=(8,16,20) the error on the ground-state correlation energy is less ...

  9. A fraction of neurofibromin interacts with PML bodies in the nucleus of the CCF astrocytoma cell line

    Energy Technology Data Exchange (ETDEWEB)

    Godin, Fabienne; Villette, Sandrine; Vallee, Beatrice; Doudeau, Michel; Morisset-Lopez, Severine [Centre de Biophysique Moleculaire, Centre National de la Recherche Scientifique (CNRS), UPR 4301, Universite d' Orleans et INSERM, rue Charles Sadron, 45071 Orleans Cedex 2 (France); Ardourel, Maryvonne; Hevor, Tobias [Laboratoire de Neurobiologie, Universite d' Orleans, BP 6759, 45067 Orleans Cedex 2 (France); Pichon, Chantal [Centre de Biophysique Moleculaire, Centre National de la Recherche Scientifique (CNRS), UPR 4301, Universite d' Orleans et INSERM, rue Charles Sadron, 45071 Orleans Cedex 2 (France); Benedetti, Helene, E-mail: helene.benedetti@cnrs-orleans.fr [Centre de Biophysique Moleculaire, Centre National de la Recherche Scientifique (CNRS), UPR 4301, Universite d' Orleans et INSERM, rue Charles Sadron, 45071 Orleans Cedex 2 (France)

    2012-02-24

    Highlights: Black-Right-Pointing-Pointer We validate the use of specific anti-Nf1 antibodies for immunofluorescence studies. Black-Right-Pointing-Pointer We detect Nf1 in the cytoplasm and nucleus of CCF cells. Black-Right-Pointing-Pointer We demonstrate that Nf1 partially colocalizes with PML nuclear bodies. Black-Right-Pointing-Pointer We demonstrate that there is a direct interaction between a fraction of Nf1 and the PML bodies. -- Abstract: Neurofibromatosis type 1 is a common genetic disease that causes nervous system tumors, and cognitive deficits. It is due to mutations within the NF1 gene, which encodes the Nf1 protein. Nf1 has been shown to be involved in the regulation of Ras, cAMP and actin cytoskeleton dynamics. In this study, using immunofluorescence experiments, we have shown a partial nuclear localization of Nf1 in the astrocytoma cell line: CCF and we have demonstrated that Nf1 partially colocalizes with PML (promyelocytic leukemia) nuclear bodies. A direct interaction between Nf1 and the multiprotein complex has further been demonstrated using 'in situ' proximity ligation assay (PLA).

  10. Application of kidney inhibition swab tests to evaluate penicillin-G residues in sow tissues and body fluids following intramuscular injection

    Science.gov (United States)

    Kidney inhibition swab (KIS) tests, recently adapted by the US FSIS for antibiotics on-site screening, were employed to evaluate the depletion of penicillin-G residues from kidney, liver, muscle, serum, and urine of sows after intramuscular (IM) penicillin-G procaine administration. Sows (n=130; 22...

  11. Ionic interaction of myosin loop 2 with residues located beyond the N-terminal part of actin probed by chemical cross-linking.

    Science.gov (United States)

    Pliszka, Barbara; Martin, Brian M; Karczewska, Emilia

    2008-02-01

    To probe ionic contacts of skeletal muscle myosin with negatively charged residues located beyond the N-terminal part of actin, myosin subfragment 1 (S1) and actin split by ECP32 protease (ECP-actin) were cross-linked with 1-ethyl-3-(3-dimethylaminopropyl)carbodiimide (EDC). We have found that unmodified S1 can be cross-linked not only to the N-terminal part, but also to the C-terminal 36 kDa fragment of ECP-actin. Subsequent experiments performed on S1 cleaved by elastase or trypsin indicate that the cross-linking site in S1 is located within loop 2. This site is composed of Lys-636 and Lys-637 and can interact with negatively charged residues of the 36 kDa actin fragment, most probably with Glu-99 and Glu-100. Cross-links are formed both in the absence and presence of MgATP.P(i) analog, although the addition of nucleotide decreases the efficiency of the cross-linking reaction.

  12. Reaction mechanism of Zn2+-dependent d-serine dehydratase: role of a conserved tyrosine residue interacting with pyridine ring nitrogen of pyridoxal 5'-phosphate.

    Science.gov (United States)

    Ito, Tomokazu; Matsuoka, Mai; Koga, Kazushi; Hemmi, Hisashi; Yoshimura, Tohru

    2014-09-01

    d-Serine dehydratase from Saccharomyces cerevisiae (Dsd1p) is a pyridoxal 5'-phosphate (PLP)- and Zn(2+)-dependent enzyme that catalyzes the dehydration of d-serine to yield pyruvate and ammonia. Dsd1p uses the Tyr residue (Y203) to interact with the pyridine nitrogen of PLP, which is a unique feature of PLP enzymes. To investigate the role of Y203 in catalysis, a series of Y203 mutants was constructed and studied. Mutant enzymes possessing a non-polar or a basic residue instead of Y203 (Y203F, A, S and R) exhibited substantial levels of catalytic activity, and among these, the Y203F mutant had the least impact on catalytic activity. The Y203D exhibited a 10(5)-fold decrease in enzyme activity, and unlike wild-type enzyme, the mutant enzyme favoured the Cα reprotonation before hydroxyl group protonation. Our data show that the Y203 does not participate in the protonation of the pyridine nitrogen (N1) of PLP, and Dsd1p uses the cofactor in an N1-unprotonated state. The unprotonated N1 promotes elimination of the leaving group and evades Cα reprotonation before hydroxyl group protonation.

  13. Flow Control Behind Bluff Bodies through the Interaction of an Attached Resonant Flexible Tail

    Science.gov (United States)

    Shelley, Samuel; Smith, John; Hibbins, Alastair; Sambles, Roy; Horsley, Simon

    2016-11-01

    Steady uniform flow, incident upon a bluff body can separate downstream causing a wake to form, this leads to the periodic shedding of vortices behind the body. By adding a thin flexible tail to the rear of the body one may reduce the drag as well as change the vortex shedding frequency (VSF). In this work we model the flow past a cylinder, in the Laminar flow regime, with an attached tail, varying the length and stiffness of the tail to couple the resonant frequencies of the tail to the natural VSF of the structure. We use this to explore how the drag and VSF of the system change as we couple to different vibrational modes of the tail. On increasing tail length, or decreasing tail stiffness progressively on passing where the natural VSF of the cylinder and tail resonances couple we see sharp increases in both the drag and VSF, which both gradually decrease again. The effect of changing the shape of the end of the tail is also investigated by exploring tails with square, rounded and triangular trailing edges. Experiments are being conducted in water at a higher Reynolds number using a tail made out of Neoprene to confirm these modelling results. DSTL.

  14. Coilin, the signature protein of Cajal bodies, differentially modulates the interactions of plants with viruses in widely different taxa.

    Science.gov (United States)

    Shaw, Jane; Love, Andrew J; Makarova, Svetlana S; Kalinina, Natalia O; Harrison, Bryan D; Taliansky, Michael E

    2014-01-01

    Cajal bodies (CBs) are distinct nuclear bodies physically and functionally associated with the nucleolus. In addition to their traditional function in coordinating maturation of certain nuclear RNAs, CBs participate in cell cycle regulation, development, and regulation of stress responses. A key "signature" component of CBs is coilin, the scaffolding protein essential for CB formation and function. Using an RNA silencing (loss-of-function) approach, we describe here new phenomena whereby coilin also affects, directly or indirectly, a variety of interactions between host plants and viruses that have RNA or DNA genomes. Moreover, the effects of coilin on these interactions are manifested differently: coilin contributes to plant defense against tobacco rattle virus (tobravirus), tomato black ring virus (nepovirus), barley stripe mosaic virus (hordeivirus), and tomato golden mosaic virus (begomovirus). In contrast, with potato virus Y (potyvirus) and turnip vein clearing virus (tobamovirus), coilin serves to increase virus pathogenicity. These findings show that interactions with coilin (or CBs) may involve diverse mechanisms with different viruses and that these mechanisms act at different phases of virus infection. Thus, coilin (CBs) has novel, unexpected natural functions that may be recruited or subverted by plant viruses for their own needs or, in contrast, are involved in plant defense mechanisms that suppress host susceptibility to the viruses.

  15. Accurate and efficient quantum chemistry calculations for noncovalent interactions in many-body systems: the XSAPT family of methods.

    Science.gov (United States)

    Lao, Ka Un; Herbert, John M

    2015-01-15

    We present an overview of "XSAPT", a family of quantum chemistry methods for noncovalent interactions. These methods combine an efficient, iterative, monomer-based approach to computing many-body polarization interactions with a two-body version of symmetry-adapted perturbation theory (SAPT). The result is an efficient method for computing accurate intermolecular interaction energies in large noncovalent assemblies such as molecular and ionic clusters, molecular crystals, clathrates, or protein-ligand complexes. As in traditional SAPT, the XSAPT energy is decomposable into physically meaningful components. Dispersion interactions are problematic in traditional low-order SAPT, and two new approaches are introduced here in an attempt to improve this situation: (1) third-generation empirical atom-atom dispersion potentials, and (2) an empirically scaled version of second-order SAPT dispersion. Comparison to high-level ab initio benchmarks for dimers, water clusters, halide-water clusters, a methane clathrate hydrate, and a DNA intercalation complex illustrate both the accuracy of XSAPT-based methods as well as their limitations. The computational cost of XSAPT scales as O(N(3))-O(N(5)) with respect to monomer size, N, depending upon the particular version that is employed, but the accuracy is typically superior to alternative ab initio methods with similar scaling. Moreover, the monomer-based nature of XSAPT calculations makes them trivially parallelizable, such that wall times scale linearly with respect to the number of monomer units. XSAPT-based methods thus open the door to both qualitative and quantitative studies of noncovalent interactions in clusters, biomolecules, and condensed-phase systems.

  16. Unexpected alignment patterns in high-j intruder bands evidence for a strong residual neutron proton interaction

    Energy Technology Data Exchange (ETDEWEB)

    Wyss, R. (Joint Inst. for Heavy Ion Research, Oak Ridge, TN (USA)); Johnson, A. (Manne Siegbahn Inst. of Physics, Stockholm (Sweden) Royal Inst. of Tech., Stockholm (Sweden). Dept. of Physics I)

    1990-01-01

    The alignment of h{sub 11/12} protons in {nu}i{sub 13/2} intruder bands in mass A = 130 region is investigated. The lack of a clear h{sub 11/12} band crossing is compared with the alignment pattern of i{sub 13/2} neutrons in {pi}i{sub 13/2} intruder bands in mass A = 180 region. The very smooth rise in angular momentum in the intruder bands is related to a possible neutron proton interaction between the single intruder orbital and the aligned two-quasiparticle configuration. 36 refs., 3 figs.

  17. Residues of the UL25 Protein of Herpes Simplex Virus That Are Required for Its Stable Interaction with Capsids ▿

    OpenAIRE

    Cockrell, Shelley K.; Huffman, Jamie B.; Toropova, Katerina; James F Conway; Homa, Fred L.

    2011-01-01

    The herpes simplex virus 1 (HSV-1) UL25 gene product is a minor capsid component that is required for encapsidation, but not cleavage, of replicated viral DNA. UL25 is located on the capsid surface in a proposed heterodimer with UL17, where five copies of the heterodimer are found at each of the capsid vertices. Previously, we demonstrated that amino acids 1 to 50 of UL25 are essential for its stable interaction with capsids. To further define the UL25 capsid binding domain, we generated reco...

  18. Parasympathetic cardio-regulation during social interactions in individuals with obesity-The influence of negative body image.

    Science.gov (United States)

    Schrimpf, Anne; Kube, Jana; Neumann, Jane; Horstmann, Annette; Villringer, Arno; Gaebler, Michael

    2017-04-01

    Individuals with obesity in Western societies often face weight-related stigmatization and social exclusion. Recurrent exposure to prejudice and negative social feedback alters one's behavior in future social interactions. In this study, we aimed to investigate autonomic nervous system and affective responses to social interactions in individuals with obesity. Women and men with (n = 56) and without (n = 56) obesity participated in episodes of social inclusion and social exclusion using a virtual ball-tossing game. During the experiment, heart rate was measured and parasympathetic activity (overall high-frequency power and event-related cardiac slowing) was analyzed. Our results show that in novel social interactions, women with obesity, relative to the other groups, exhibited the strongest increase in parasympathetic activity. Furthermore, parasympathetic activity was related to a more negative body image in individuals with obesity, but not in lean individuals. Additionally, women with obesity reported a stronger decrease in mood after social exclusion than did the other participants. Our results demonstrate influences of objective and subjective bodily characteristics on parasympathetic cardio-regulation during social interactions. In particular, they show behavioral and physiological alterations during social interactions in women with obesity.

  19. Exploring Interacting Quantum Many-Body Systems by Experimentally Creating Continuous Matrix Product States in Superconducting Circuits

    Science.gov (United States)

    Eichler, C.; Mlynek, J.; Butscher, J.; Kurpiers, P.; Hammerer, K.; Osborne, T. J.; Wallraff, A.

    2015-10-01

    Improving the understanding of strongly correlated quantum many-body systems such as gases of interacting atoms or electrons is one of the most important challenges in modern condensed matter physics, materials research, and chemistry. Enormous progress has been made in the past decades in developing both classical and quantum approaches to calculate, simulate, and experimentally probe the properties of such systems. In this work, we use a combination of classical and quantum methods to experimentally explore the properties of an interacting quantum gas by creating experimental realizations of continuous matrix product states—a class of states that has proven extremely powerful as a variational ansatz for numerical simulations. By systematically preparing and probing these states using a circuit quantum electrodynamics system, we experimentally determine a good approximation to the ground-state wave function of the Lieb-Liniger Hamiltonian, which describes an interacting Bose gas in one dimension. Since the simulated Hamiltonian is encoded in the measurement observable rather than the controlled quantum system, this approach has the potential to apply to a variety of models including those involving multicomponent interacting fields. Our findings also hint at the possibility of experimentally exploring general properties of matrix product states and entanglement theory. The scheme presented here is applicable to a broad range of systems exploiting strong and tunable light-matter interactions.

  20. Gravothermal collapse of isolated self-interacting dark matter haloes: N-body simulation versus the fluid model

    CERN Document Server

    Koda, Jun

    2011-01-01

    Self-Interacting Dark Matter (SIDM) is a collisional form of cold dark matter (CDM), originally proposed to solve problems that arose when the collisionless CDM theory of structure formation was compared with observations of galaxies on small scales. The quantitative impact of the proposed elastic collisions on structure formation has been estimated previously by Monte Carlo N-body simulations and by a conducting fluid model, with apparently diverging results. To improve this situation, we make direct comparisons between new Monte Carlo N-body simulations and solutions of the conducting fluid model, for isolated SIDM haloes of fixed mass. This allows us to separate cleanly the effects of gravothermal relaxation from those of continuous mass accretion in an expanding background universe. When these two methods are previously applied to halo formation with cosmological boundary conditions, they disagreed by an order of magnitude about the size of the scattering cross section required to solve the so-called 'cus...

  1. Interactions of dietary protein and adiposity measures in relation to subsequent changes in body weight and waist circumference

    DEFF Research Database (Denmark)

    Ankarfeldt, Mikkel Z; Angquist, Lars; Jakobsen, Marianne Uhre

    2014-01-01

    OBJECTIVE: To investigate if dietary protein and degree of adiposity interacts in relation to change in body weight and waist circumference (WC) in the general population. METHODS: In total 22,433 middle-aged individuals with dietary assessment at baseline and anthropometry at baseline...... to changes in body weight (BW) and changes WC adjusted for change in BW. RESULTS: Baseline intake of protein was not significantly associated with changes in weight or waist circumference. Across the nine groups of baseline BMI and WCBMI there were no distinct trends in the associations between dietary...... protein, whether replacing carbohydrate or fat, and weight change. However, individuals in the highest tertile of baseline BMI (irrespective of baseline WCBMI ) had significantly inverse change in waist circumference when protein replaced carbohydrate, but not when protein replaced fat. CONCLUSION...

  2. Insight into the interactive residues between two domains of human somatic Angiotensin-converting enzyme and Angiotensin II by MM-PBSA calculation and steered molecular dynamics simulation.

    Science.gov (United States)

    Guan, Shan-shan; Han, Wei-wei; Zhang, Hao; Wang, Song; Shan, Ya-ming

    2016-01-01

    Angiotensin-converting enzyme (ACE), a membrane-bound zinc metallopeptidase, catalyzes the formation of Angiotensin-II (AngII) and the deactivation of bradykinin in the renin-angiotensin-aldosterone and kallikrein-kinin systems. As a hydrolysis product of ACE, AngII is regarded as an inhibitor and displays stronger competitive inhibition in the C-domain than the N-domain of ACE. However, the AngII binding differences between the two domains and the mechanisms behind AngII dissociation from the C-domain are rarely explored. In this work, molecular docking, Molecular Mechanics/Poisson-Boltzmann Surface Area calculation, and steered molecular dynamics (SMD) are applied to explore the structures and interactions in the binding or unbinding of AngII with the two domains of human somatic ACE. Calculated free energy values suggest that the C-domain-AngII complex is more stable than the N-domain-AngII complex, consistent with available experimental data. SMD simulation results imply that electrostatic interaction is dominant in the dissociation of AngII from the C-domain. Moreover, Gln106, Asp121, Glu123, and Tyr213 may be the key residues in the unbinding pathway of AngII. The simulation results in our work provide insights into the interactions between the two domains of ACE and its natural peptide inhibitor AngII at a molecular level. Moreover, the results provide theoretical clues for the design of new inhibitors.

  3. Potential of lignin from Canna edulis ker residue in the inhibition of α-d-glucosidase: Kinetics and interaction mechanism merging with docking simulation.

    Science.gov (United States)

    Xie, Fan; Gong, Shengxiang; Zhang, Wei; Wu, Jinhong; Wang, Zhengwu

    2017-02-01

    In this study, we extracted lignin from Canna edulis ker residue. Its chemical structure, inhibitory activity on α-d-glucosidase, and kinetics as well as interaction mechanism were investigated by using spectrum analysis and docking simulation. The isolated lignin was composed by guaiacyl and syringal units, and exhibited stronger inhibition on α-d-glucosidase than acarbose with the half maximal inhibitory concentration at 5.3±0.3μM. It was a non-competitive inhibitior with Km and Ki values of 0.53±0.02mM and 0.92±0.12μM, respectively. It could quench the intrinsic fluorescence of α-d-glucosidase through a static quenching mode. The calculated values of enthalpy and entropy change were 20.8±2.5kJmol(-1) and 172.7±0.8Jmol(-1)K(-1), respectively. There was a single binding site on α-d-glucosidase for lignin, and the binding distance was 3.2nm. The molecular docking analysis exhibited that the hydrogen bonds, hydropholic interaction, and van der Waals forces were the main forces for lignin bind to α-d-glucosidase. This work provides a new insight into the interaction between the lignin and α-d-glucosidase, which might be beneficial to type 2 diabetes with the application of lignin in functional food and pharmacy fields.

  4. Involvement of the catalytically important Asp54 residue of Mycobacterium smegmatis DevR in protein-protein interactions between DevR and DevS.

    Science.gov (United States)

    Lee, Ha-Na; Lee, Na-On; Ko, In-Jeong; Kim, Si Wouk; Kang, Beom Sik; Oh, Jeong-Il

    2013-06-01

    The DevSR two-component system in Mycobacterium smegmatis consists of the DevS histidine kinase and the DevR response regulator. It is a regulatory system that is involved in the adaptation of mycobacteria to hypoxic and NO stresses. Using the yeast two-hybrid assay and pull-down assay, it was demonstrated that the phosphoaccepting Asp (Asp54) of DevR is important for protein-protein interactions between DevR and DevS. The negative charge of Asp54 of DevR was shown to play an important role in protein-protein interactions between DevR and DevS. When the Lys104 residue, which is involved in transmission of conformational changes induced by phosphorylation of the response regulator, was replaced with Ala, the mutant form of DevR was not phosphorylated by DevS and functionally inactive in vivo. However, the K104A mutation in DevR only slightly affected protein-protein interactions between DevR and DevS. © 2013 Federation of European Microbiological Societies. Published by Blackwell Publishing Ltd. All rights reserved.

  5. All-atom molecular dynamics simulations reveal significant differences in interaction between antimycin and conserved amino acid residues in bovine and bacterial bc1 complexes.

    Science.gov (United States)

    Kokhan, Oleksandr; Shinkarev, Vladimir P

    2011-02-02

    Antimycin A is the most frequently used specific and powerful inhibitor of the mitochondrial respiratory chain. We used all-atom molecular dynamics (MD) simulations to study the dynamic aspects of the interaction of antimycin A with the Q(i) site of the bacterial and bovine bc(1) complexes embedded in a membrane. The MD simulations revealed considerable conformational flexibility of antimycin and significant mobility of antimycin, as a whole, inside the Q(i) pocket. We conclude that many of the differences in antimycin binding observed in high-resolution x-ray structures may have a dynamic origin and result from fluctuations of protein and antimycin between multiple conformational states of similar energy separated by low activation barriers, as well as from the mobility of antimycin within the Q(i) pocket. The MD simulations also revealed a significant difference in interaction between antimycin and conserved amino acid residues in bovine and bacterial bc(1) complexes. The strong hydrogen bond between antimycin and conserved Asp-228 (bovine numeration) was observed to be frequently broken in the bacterial bc(1) complex and only rarely in the bovine bc(1) complex. In addition, the distances between antimycin and conserved His-201 and Lys-227 were consistently larger in the bacterial bc(1) complex. The observed differences could be responsible for a weaker interaction of antimycin with the bacterial bc(1) complex.

  6. Investigation of interaction between alkoxy substituted phthalocyanines with different lengths of alkyl residue and bovine serum albumin

    Energy Technology Data Exchange (ETDEWEB)

    Lebedeva, Natalya Sh., E-mail: nsl@isc-ras.ru [G.A. Krestov Institute of Solution Chemistry of the Russian Academy of Sciences, Akademicheskaya, 1, 153045 Ivanovo (Russian Federation); Gubarev, Yury A.; Vyugin, Anatoly I. [G.A. Krestov Institute of Solution Chemistry of the Russian Academy of Sciences, Akademicheskaya, 1, 153045 Ivanovo (Russian Federation); Koifman, Oscar I. [Research Institute of Macroheterocycles of Ivanovo State University of Chemistry and Technology, 153000 Ivanovo (Russian Federation)

    2015-10-15

    Interaction between bovine serum albumin and alkoxy substituted phthalocyanines was studied by means of electron absorption spectroscopy, fluorescence spectroscopy and viscosimetry. The binding constants and binding distance were calculated. It was found that ZnPc(4-NH-CO-C{sub 6}H{sub 4}-OC{sub 10}H{sub 21}){sub 4} prevents twisting of BSA molecule and localizes between subdomains IB and IIA in protein globule. ZnPc(4-NH-CO-C{sub 6}H{sub 4}-OC{sub 6}H{sub 13}){sub 4} and ZnPc(4-NH-CO-C{sub 6}H{sub 4}-OC{sub 8}H{sub 17}){sub 4} are located on the outer surface of the protein globule. In the case of ZnPc(4-NH-CO-C{sub 6}H{sub 4}-OC{sub 3}H{sub 7}){sub 4} it can be assumed that the phthalocyanine molecule is in the immediate vicinity of the subdomains IB and IIA. - Highlights: • Interaction between bovine serum albumin and alkoxy substituted phthalocyanines was studied by means of electron absorption spectroscopy, fluorescence spectroscopy and viscosimetry. • The binding constants and binding distance were calculated by using the Scatchard method. • Photochemical characteristics of phthalocyanines of studied phthalocyanines are defined. • Localization of phthalocyanines on the protein globule is defined.

  7. Basic research on interactions of heavy metals with pharmaceutical substances with relevance to the environment and residual toxicology

    Energy Technology Data Exchange (ETDEWEB)

    Gaede, W.; Kuehnert, M.

    1986-01-01

    Studies were conducted into interactions between long-time exposure of rats to subtoxic doses of lead and copper and humic acids orally applied to them in parallel. Tests were based on established activities of erythrocytic delta-aminolaevulinic acid dehydratase and on the length of hexobarbital-induced sleep. Also investigated were the effects of heavy metal on the blood level of a sulphonamide (sulphaclomide). Lead and copper interactions under the impact of pharmaceutical substances (humic acids and sulphaclomide) produced affirmative evidence to the well-known depression of activity of delta-aminolaevulinic acid dehydratase. There was also a high probability that cytochrome-P-450 had been induced by lead and copper and, perhaps, by humic acids, as well. Enteral absorption of sulphaclomide was clearly affected by protein-denaturing and permeability-reducing action of heavy metals on the gastro-intestinal mucosa. That locally delimited action of lead and copper was widely offset under the impact of humic acids, and sulphaclomide levels in the blood were renormalised. The above findings are likely to suggest that in the context of environmental toxicology long-time exposure of warm-blooded animals to heavy metals may impair the therapeutic effectiveness of pharmaceuticals (sulphaclomide in this case).

  8. Interaction of biochar and organic residues from sugarcane industry in soil chemical attributes and greenhouse gases emissions.

    Science.gov (United States)

    Fernanda Abbruzzini, Thalita; Feola Conz, Rafaela; Pellegrino Cerri, Carlos Eduardo

    2014-05-01

    Researchers have highlighted the importance of providing soil quality in agricultural systems, besides mitigating greenhouse gases (GHG) emissions to the atmosphere and increasing soil carbon sequestration. Therefore, several studies have demonstrated the effectiveness of biochar as a soil conditioner, both in relation to increased C sequestration and improvements in soil chemical, physical and biological attributes, resulting in better conditions for plant growth. The aim of this study was to assess the impact of applying biochar produced from sugarcane straw to soils in relation to changes in soil chemical attributes and mitigation of greenhouse gases emissions into the atmosphere. To do so, we conducted a laboratory incubation under controlled environmental conditions (ie temperature and humidity) with and without the application of filter cake and vinasse (ie organic residues from sugarcane industry) and rates of biochar application (0, 10, 20 and 50 Mg ha-1). The fluxes of CO2, N2O and CH4 of each incubation unity were measured periodically (in days 1, 2, 5, 9, 13, 16, 20, 24, 28, 30, 47, 60, 91, 105, 123, 130, 138 and 150). Each treatment consisted of eight replicates with destructive samples evaluated at 30, 60, 90 and 150 days after incubation to characterize the chemical attributes of the incubated soil, besides GHG (CO2, N2O and CH4) emissions. In general, there was an increase in carbon dioxide (CO2) fluxes over time due to the application of filter cake and vinasse and increasing dose of biochar. Regarding nitrous oxide (N2O) emissions, there was an increase of 82.35% with the application of vinasse and filter cake compared to the control treatment. However, different doses of biochar (10, 20 and 50 Mg ha-1) reduced N2O emissions by 29, 38.7 and 70.9%, respectively. The methane (CH4) flux was negligible in all treatments. We observed improvements in soil chemical attributes, such as higher pH, a substantial increase in the soil CEC, reduced exchangeable

  9. Effect of many-body interactions on the bulk and interfacial phase behavior of a model colloid-polymer mixture.

    Science.gov (United States)

    Dijkstra, Marjolein; van Roij, René; Roth, Roland; Fortini, Andrea

    2006-04-01

    We study a model suspension of sterically stabilized colloidal particles and nonadsorbing ideal polymer coils, both in bulk and adsorbed against a planar hard wall. By integrating out the degrees of freedom of the polymer coils, we derive a formal expression for the effective one-component Hamiltonian of the colloids. We employ an efficient Monte Carlo simulation scheme for this mixture based on the exact effective colloid Hamiltonian; i.e., it incorporates all many-body interactions. The many-body character of the polymer-mediated effective interactions between the colloids yields bulk phase behavior and adsorption phenomena that differ substantially from those found for pairwise simple fluids. We determine the phase behavior for size ratios q=sigma(p)/sigma(c)=1, 0.6, and 0.1, where sigma(c) and sigma(p) denote the diameters of the colloids and polymer coils, respectively. For q=1 and 0.6, we find both a fluid-solid and a stable colloidal gas-liquid transition with an anomalously large bulk liquid regime caused by the many-body interactions. We compare the phase diagrams obtained from simulations with the results of the free-volume approach and with direct simulations of the true binary mixture. Although we did not simulate the polymer coils explicitly, we are able to obtain the three partial structure factors and radial distribution functions. We compare our results with those obtained from density functional theory and the Percus-Yevick approximation. We find good agreement between all results for the structure. We also study the mixture in contact with a single hard wall for q=1. Upon approach of the gas-liquid binodal, we find far from the triple point, three layering transitions in the partial wetting regime.

  10. The thermal expansion of a face-centered cubic lattice with central two-body interactions

    NARCIS (Netherlands)

    Bicknese, V.

    1965-01-01

    The thermal expansion e is calculated by minimizing the free energy, including the cubic and quartic phonon-interaction terms. The free energy is expanded to third order in e. The work is closely related to that of Maradudin and Maradudin, Flinn and Coldwell-Horsfall. The resulting formulas are appl

  11. Normal and friction stabilization techniques for interactive rigid body constraint-based contact force computations

    DEFF Research Database (Denmark)

    2010-01-01

    We present a novel, yet simple, method for stabilization of normal forces. A normal stabilization term, carefully designed from hypotheses about interactive usability, is added to the contact force problem. Further, we propose friction stabilization as a completely new stabilization paradigm in i...

  12. Cooperative Excitation and Many-Body Interactions in a Cold Rydberg Gas

    DEFF Research Database (Denmark)

    Viteau, Matthieu; Huillery, Paul; Bason, Mark George;

    2012-01-01

    The dipole blockade of Rydberg excitations is a hallmark of the strong interactions between atoms in these high-lying quantum states [ M. Saffman, T. G. Walker and K. Mølmer Rev. Mod. Phys. 82 2313 (2010); D. Comparat and P. Pillet J. Opt. Soc. Am. B 27 A208 (2010)]. One of the consequences of th...

  13. Movement and Sound: The Musical Language of Body Rhythms in Interaction.

    Science.gov (United States)

    Chapple, Eliot D.

    1981-01-01

    The language of the central nervous system (the brain) differs from logical structures of language. Sound and movement together make up the total response patterns of the individual. In order to investigate the properties of interaction rhythms, verbal and nonverbal, the expressive and performing arts must be understood. (JN)

  14. Relation between the change of density of states and the shape of the potential in two-body interactions

    Science.gov (United States)

    Gao, Bo

    2017-04-01

    We derive a general relation in two-body scattering theory that more directly relates the change of density of states (DDOS) due to interaction to the shape of the potential. The relation allows us to infer certain global properties of the DDOS from the global properties of the potential. In particular, we show that DDOS is negative at all energies and for all partial waves, for potentials that are more repulsive than +1 /r2 everywhere. This behavior represents a different class of global properties of DDOS from that described by the Levinson's theorem.

  15. Non-verbal Full Body Emotional and Social Interaction: A Case Study on Multimedia Systems for Active Music Listening

    Science.gov (United States)

    Camurri, Antonio

    Research on HCI and multimedia systems for art and entertainment based on non-verbal, full-body, emotional and social interaction is the main topic of this paper. A short review of previous research projects in this area at our centre are presented, to introduce the main issues discussed in the paper. In particular, a case study based on novel paradigms of social active music listening is presented. Active music listening experience enables users to dynamically mould expressive performance of music and of audiovisual content. This research is partially supported by the 7FP EU-ICT Project SAME (Sound and Music for Everyone, Everyday, Everywhere, Every Way, www.sameproject.eu).

  16. Unidimensional reduction of the 3D Gross-Pitaevskii equation with two- and three-body interactions

    CERN Document Server

    Cardoso, W B; Bazeia, D

    2010-01-01

    We deal with the three-dimensional Gross-Pitaevskii equation, which is used to describe a cloud of dilute bosonic atoms that interact under competing two- and three-body scattering potentials. We study the case where the cloud of atoms is strongly confined in two spatial dimensions, allowing us to build an unidimensional nonlinear equation, controlled by the nonlinearities and the confining potentials that trap the system along the longitudinal coordinate. We focus attention on specific limits, dictated by the cubic and quintic coefficients, and we implement numerical simulations to help us to quantify the validity of the procedure.

  17. [Anthropophobia: psychopathological approach to the interactions between body, inter-subjectivity and language].

    Science.gov (United States)

    Ogawa, T; Bouderlique, J

    1994-09-01

    Anthropophobia is the general term often taken as an equivalent to social phobia which comprises the several afflictions known in Europe under names like autodysosmophobia, scopophobia, erythrophobia, and olfactory reference syndrome, among others. Following a general introduction to anthropophobia, we will use three short observations to illustrate a phenomenological approach which shows both the confusion between the two dimensions of corpority and intersubjectivity and the specific relations joining body and language that are characteristic of this pathology. In addition to that, a psychoanalytical insight shows that anthropophobic patients possess traits that are specific to the intrusion complex and that reveal an evolutionary stage between narcissism and Oedipian phases.

  18. A three body state with J=3 in the ρB*B̅N* interaction

    Science.gov (United States)

    Fernandez-Soler, P.; Bayar, M.; Sun, Zhi-Feng; Oset, E.

    2016-11-01

    We study the ρB*B̅N* system solving the Faddeev equations in the fixed center approximation. The B*B̅N* system will be considered forming a cluster, and using the two-body ρB* unitarized scattering amplitudes in the local Hidden Gauge approach we find a new I(JPC) = 1(3-) state. The mass of the new state corresponds to a two particle invariant mass of the ρB* system close to the resonant energy of the B*2(5747), indicating that the role of this J = 2 resonance is important in the dynamical generation of the new state.

  19. Aromatic-aromatic interactions between residues in KCa3.1 pore helix and S5 transmembrane segment control the channel gating process.

    Science.gov (United States)

    Garneau, Line; Klein, Hélène; Lavoie, Marie-France; Brochiero, Emmanuelle; Parent, Lucie; Sauvé, Rémy

    2014-02-01

    The Ca(2+)-activated potassium channel KCa3.1 is emerging as a therapeutic target for a large variety of health disorders. One distinguishing feature of KCa3.1 is that the channel open probability at saturating Ca(2+) concentrations (Pomax) is low, typically 0.1-0.2 for KCa3.1 wild type. This observation argues for the binding of Ca(2+) to the calmodulin (CaM)-KCa3.1 complex, promoting the formation of a preopen closed-state configuration leading to channel opening. We have previously shown that the KCa3.1 active gate is most likely located at the level of the selectivity filter. As Ca(2+)-dependent gating of KCa3.1 originates from the binding of Ca(2+) to CaM in the C terminus, the hypothesis of a gate located at the level of the selectivity filter requires that the conformational change initiated in the C terminus be transmitted to the S5 and S6 transmembrane helices, with a resulting effect on the channel pore helix directly connected to the selectivity filter. A study was thus undertaken to determine to what extent the interactions between the channel pore helix with the S5 and S6 transmembrane segments contribute to KCa3.1 gating. Molecular dynamics simulations first revealed that the largest contact area between the pore helix and the S5 plus S6 transmembrane helices involves residue F248 at the C-terminal end of the pore helix. Unitary current recordings next confirmed that modulating aromatic-aromatic interactions between F248 and W216 of the S5 transmembrane helical segment and/or perturbing the interactions between F248 and residues in S6 surrounding the glycine hinge G274 cause important changes in Pomax. This work thus provides the first evidence for a key contribution of the pore helix in setting Pomax by stabilizing the channel closed configuration through aromatic-aromatic interactions involving F248 of the pore helix. We propose that the interface pore helix/S5 constitutes a promising site for designing KCa3.1 potentiators.

  20. A fully-immersive set-up for remote interaction and neurorehabilitation based on virtual body ownership

    Directory of Open Access Journals (Sweden)

    Daniel ePerez-Marcos

    2012-07-01

    Full Text Available Although telerehabilitation systems represent one of the most technologically appealing clinical solutions for the immediate future, they still present limitations that prevent their standardisation. Here we propose an integrated approach that includes three key and novel factors: (a fully immersive virtual environments, including virtual body representation and ownership; (b multimodal interaction with remote people and virtual objects including haptic interaction; and (c a physical representation of the patient at the hospital through embodiment agents (e.g., as a physical robot. The importance of secure and rapid communication between the nodes is also stressed and an example implemented solution is described. Finally, we discuss the proposed approach with reference to the existing literature and systems.

  1. Optimal undulating swimming for a single fish-like body and for a pair of interacting swimmers

    CERN Document Server

    Maertens, Audrey P; Triantafyllou, Michael S

    2016-01-01

    We establish through numerical simulation conditions for optimal undulatory propulsion for a single fish, and for a pair of hydrodynamically interacting fish, accounting for linear and angular recoil. We first employ systematic 2D simulations to identify conditions for minimal propulsive power of a self-propelled fish, and continue with targeted 3D simulations for a danio-like fish. We find that the Strouhal number, phase angle between heave and pitch at the trailing edge, and angle of attack are principal parameters. Angular recoil has significant impact on efficiency, while optimized body bending requires maximum bending amplitude upstream of the trailing edge. For 2D simulations, imposing a deformation based on measured displacement for carangiform swimming provides efficiency of 40%, which increases for an optimized profile to 57%; for a 3D fish, the corresponding increase is from 22% to 35%; all at Reynolds number 5000. Next, we turn to 2D simulation of two hydrodynamically interacting fish. We find that...

  2. Residuation theory

    CERN Document Server

    Blyth, T S; Sneddon, I N; Stark, M

    1972-01-01

    Residuation Theory aims to contribute to literature in the field of ordered algebraic structures, especially on the subject of residual mappings. The book is divided into three chapters. Chapter 1 focuses on ordered sets; directed sets; semilattices; lattices; and complete lattices. Chapter 2 tackles Baer rings; Baer semigroups; Foulis semigroups; residual mappings; the notion of involution; and Boolean algebras. Chapter 3 covers residuated groupoids and semigroups; group homomorphic and isotone homomorphic Boolean images of ordered semigroups; Dubreil-Jacotin and Brouwer semigroups; and loli

  3. Dust Interactions on Small Solar System Bodies and Technology Considerations for Exploration

    Science.gov (United States)

    Kobrick, Ryan,; Hoffman, Jeffrey; Pavone, Marco; Street, Kenneth; Rickman, Douglas

    2014-01-01

    Small-bodies such as asteroids and Mars' moons Phobos and Deimos have relatively unknown regolith environments. It is hypothesized that dust preserved in the regolith on the surfaces will have similar mechanical properties to lunar dust because of similar formation processes from micrometeorite bombardment, low relative gravity for slow settling times, and virtually no weathering because there is no atmosphere. This combination of processes infers that small-body dust particles will be highly angular and retain abrasive properties. The focus of this paper uses the mission architecture and engineering design for an asteroid hopper known as Hedgehog, a spherical spacecraft with several symmetric spikes used to aid with tumbling mobility in a low gravity environment. Dust abrasion considerations are highlighted throughout the paper relating to the lead authors' previous work, but act as an example of one of many important dust or regolith physical properties that need to be considered for future exploration. Measurable regolith properties are summarized in order to identify technologies that may be useful for exploration in terms of scientific return and spacecraft design. Previous instruments are summarized in this paper that could be used on the Hedgehog. Opportunities for hardware payloads are highlighted that include low mass solutions or dualpurpose instruments that can measure regolith or dust properties. Finally, dust mitigation suggestions are made for vehicles of this mobility profile.

  4. Interactive influence of biotic and abiotic cues on the plasticity of preferred body temperatures in a predator-prey system.

    Science.gov (United States)

    Smolinský, Radovan; Gvoždík, Lumír

    2012-09-01

    The ability to modify phenotypes in response to heterogeneity of the thermal environment represents an important component of an ectotherm's non-genetic adaptive capacity. Despite considerable attention being dedicated to the study of thermally-induced developmental plasticity, whether or not interspecific interactions shape the plastic response in both a predator and its prey remains unknown. We tested several predictions about the joint influence of predator/prey scents and thermal conditions on the plasticity of preferred body temperatures (T (p)) in both actors of this interaction, using a dragonfly nymphs-newt larvae system. Dragonfly nymphs (Aeshna cyanea) and newt eggs (Ichthyosaura alpestris) were subjected to fluctuating cold and warm thermal regimes (7-12 and 12-22°C, respectively) and the presence/absence of a predator or prey chemical cues. Preferred body temperatures were measured in an aquatic thermal gradient (5-33°C) over a 24-h period. Newt T (p) increased with developmental temperature irrespective of the presence/absence of predator cues. In dragonflies, thermal reaction norms for T (p) were affected by the interaction between temperature and prey cues. Specifically, the presence of newt scents in cold regime lowered dragonfly T (p). We concluded that predator-prey interactions influenced thermally-induced plasticity of T (p) but not in a reciprocal fashion. The occurrence of frequency-dependent thermal plasticity may have broad implications for predator-prey population dynamics, the evolution of thermal biology traits, and the consequences of sustaining climate change within ecological communities.

  5. Fine study on single sand body and measures for tapping the potential of residual oil during polymer flooding in Pubei reservoir of Daqing

    Science.gov (United States)

    Meng, Y. J.

    2016-08-01

    In order to effectively guide the narrow channel sand body oil fields to exploit, according to the sand body distribution characteristics and geological genesis of narrow channel sand body oil fields, the type of single sand body is clarified. By means of identification of logging curves and correlation of well-tie profile, the internal structure of single sand body is recognized. and then the remaining oil genesis, distribution characteristics and the potential areas for polymer flooding are clarified by combining numerical simulation technology and dynamic analysis technology, and the remaining oil potential tapping method is designed by taking into consideration various factors including the characteristics of the remaining oil, reservoir property and product dynamic character. The result shows that the single sand body is divided into five types including multiphase channel superposition, distributary channel, single channel, sheet sand and lenticular sand. Potential remaining oil mainly are distributed in thick oil layers of multiphase channel superposition type and distributary channel type in which channel sands were developed and sedimentary environment are stable inner front facies and lake regressive inner front facies. The remaining oil is developed by optimizing the parameters of polymer flooding and combining many different measures. The study provides technical support for the efficient exploration for polymer flooding.

  6. Ab Initio No-Core Shell Model Calculations Using Realistic Two- and Three-Body Interactions

    Energy Technology Data Exchange (ETDEWEB)

    Navratil, P; Ormand, W E; Forssen, C; Caurier, E

    2004-11-30

    There has been significant progress in the ab initio approaches to the structure of light nuclei. One such method is the ab initio no-core shell model (NCSM). Starting from realistic two- and three-nucleon interactions this method can predict low-lying levels in p-shell nuclei. In this contribution, we present a brief overview of the NCSM with examples of recent applications. We highlight our study of the parity inversion in {sup 11}Be, for which calculations were performed in basis spaces up to 9{Dirac_h}{Omega} (dimensions reaching 7 x 10{sup 8}). We also present our latest results for the p-shell nuclei using the Tucson-Melbourne TM three-nucleon interaction with several proposed parameter sets.

  7. A deterministic projector configuration interaction approach for the ground state of quantum many-body systems

    CERN Document Server

    Zhang, Tianyuan

    2016-01-01

    In this work we propose a novel approach to solve the Schr\\"{o}dinger equation which combines projection onto the ground state with a path-filtering truncation scheme. The resulting projector configuration interaction (PCI) approach realizes a deterministic version of the full configuration interaction quantum Monte Carlo (FCIQMC) method [Booth, G. H.; Thom, A. J. W.; Alavi, A. J. Chem. Phys. 2009, 131, 054106]. To improve upon the linearized imaginary-time propagator, we develop an optimal projector scheme based on an exponential Chebyshev expansion in the limit of an infinite imaginary time step. After writing the exact projector as a path integral in determinant space, we introduce a path filtering procedure that truncates the size of the determinantal basis and approximates the Hamiltonian. The path filtering procedure is controlled by one real threshold that determines the accuracy of the PCI energy and is not biased towards any determinant. Therefore, the PCI approach can equally well describe static an...

  8. Accessing Rydberg-dressed interactions using many-body Ramsey dynamics

    CERN Document Server

    Mukherjee, Rick; Hazzard, Kaden R A

    2015-01-01

    We demonstrate that Ramsey spectroscopy can be used to observe Rydberg-dressed interactions. In contrast to many prior proposals, our scheme operates comfortably within experimentally measured lifetimes, and accesses a regime where quantum superpositions are crucial. The key idea is to build a spin-1/2 from one level that is Rydberg-dressed and another that is not. These levels may be hyperfine or long-lived electronic states. An Ising spin model governs the Ramsey dynamics, for which we derive an exact solution. Due to the structure of Rydberg interactions, the dynamics differs significantly from that in other spin systems. As one example, spin echo can increase the rate at which coherence decays. The results also apply to bare (undressed) Rydberg states as a special case, for which we quantitatively reproduce recent ultrafast experiments without fitting.

  9. Mean field propagation of infinite dimensional Wigner measures with a singular two-body interaction potential

    CERN Document Server

    Ammari, Zied

    2011-01-01

    We consider the quantum dynamics of many bosons systems in the mean field limit with a singular pair-interaction potential, including the attractive or repulsive Coulombic case in three dimensions. By using a measure transportation technique, we show that Wigner measures propagate along the nonlinear Hartree flow. Such property was previously proved only for bounded potentials in our previous works with a slightly different strategy.

  10. A New Application of Multi-Body System Dynamics in Vehicle-Road Interaction Simulation

    Institute of Scientific and Technical Information of China (English)

    RenWei-qun; ZhangYun-qing; JinGuo-dong

    2003-01-01

    In vehicle-road interaction simulation, multibody system (MBS) dynamics as well as the corresponding software ADAMS has been employed to model the nonlinear vehicle in more detail. The simulation method has been validated by the test data, and been compared to the former simple models. This method can be used for estimating the effects of dynamic tire forces and other vehicle features on road damage so that the “road-friendliness” can be assessed in vehicle design process.

  11. New results for two-neutrino double beta decay with large particle-particle two body proton-neutron interaction

    CERN Document Server

    Raduta, A A; Simkovic, F; Faessler, A; Faessler, Amand

    2001-01-01

    A model many-body Hamiltonian describing an heterogenous system of paired protons and paired neutrons and interacting among themselves through monopole particle-hole and monopole particle-particle interactions is used to study the double beta decay of Fermi type. The states are described by time dependent approaches choosing as trial functions coherent states of the symmetry groups underlying the model Hamiltonian. One formalism, VP1, is fully equivalent with the standard pnQRPA and therefore fails at a critical value of the particle-particle interaction strength while another one, VP2, corresponds to a two step BCS treatment, i.e. the proton quasiparticles are paired with the neutron quasiparticles. In this way a harmonic description for the double beta transition amplitude is provided for any strength of the particle-particle interaction. The approximation quality is judged by comparing the actual results with the exact result as well as with those corresponding to various truncations of the boson expanded ...

  12. Many-body Green’s function theory for electron-phonon interactions: Ground state properties of the Holstein dimer

    Energy Technology Data Exchange (ETDEWEB)

    Säkkinen, Niko; Leeuwen, Robert van [Department of Physics, Nanoscience Center, University of Jyväskylä, Survontie 9, 40014 Jyväskylä (Finland); Peng, Yang [Dahlem Center for Complex Quantum Systems and Fachbereich Physik, Freie Universität Berlin, 14195 Berlin (Germany); Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin-Dahlem (Germany); Appel, Heiko [Fritz-Haber-Institut der Max-Planck-Gesellschaft, Faradayweg 4-6, 14195 Berlin-Dahlem (Germany)

    2015-12-21

    We study ground-state properties of a two-site, two-electron Holstein model describing two molecules coupled indirectly via electron-phonon interaction by using both exact diagonalization and self-consistent diagrammatic many-body perturbation theory. The Hartree and self-consistent Born approximations used in the present work are studied at different levels of self-consistency. The governing equations are shown to exhibit multiple solutions when the electron-phonon interaction is sufficiently strong, whereas at smaller interactions, only a single solution is found. The additional solutions at larger electron-phonon couplings correspond to symmetry-broken states with inhomogeneous electron densities. A comparison to exact results indicates that this symmetry breaking is strongly correlated with the formation of a bipolaron state in which the two electrons prefer to reside on the same molecule. The results further show that the Hartree and partially self-consistent Born solutions obtained by enforcing symmetry do not compare well with exact energetics, while the fully self-consistent Born approximation improves the qualitative and quantitative agreement with exact results in the same symmetric case. This together with a presented natural occupation number analysis supports the conclusion that the fully self-consistent approximation describes partially the bipolaron crossover. These results contribute to better understanding how these approximations cope with the strong localizing effect of the electron-phonon interaction.

  13. Interaction between MyRIP and the actin cytoskeleton regulates Weibel-Palade body trafficking and exocytosis.

    Science.gov (United States)

    Conte, Ianina L; Hellen, Nicola; Bierings, Ruben; Mashanov, Gregory I; Manneville, Jean-Baptiste; Kiskin, Nikolai I; Hannah, Matthew J; Molloy, Justin E; Carter, Tom

    2016-02-01

    Weibel-Palade body (WPB)-actin interactions are essential for the trafficking and secretion of von Willebrand factor; however, the molecular basis for this interaction remains poorly defined. Myosin Va (MyoVa or MYO5A) is recruited to WPBs by a Rab27A-MyRIP complex and is thought to be the prime mediator of actin binding, but direct MyRIP-actin interactions can also occur. To evaluate the specific contribution of MyRIP-actin and MyRIP-MyoVa binding in WPB trafficking and Ca(2+)-driven exocytosis, we used EGFP-MyRIP point mutants with disrupted MyoVa and/or actin binding and high-speed live-cell fluorescence microscopy. We now show that the ability of MyRIP to restrict WPB movement depends upon its actin-binding rather than its MyoVa-binding properties. We also show that, although the role of MyRIP in Ca(2+)-driven exocytosis requires both MyoVa- and actin-binding potential, it is the latter that plays a dominant role. In view of these results and together with the analysis of actin disruption or stabilisation experiments, we propose that the role of MyRIP in regulating WPB trafficking and exocytosis is mediated largely through its interaction with actin rather than with MyoVa.

  14. LEDGIN-mediated Inhibition of Integrase–LEDGF/p75 Interaction Reduces Reactivation of Residual Latent HIV

    Directory of Open Access Journals (Sweden)

    Lenard S. Vranckx

    2016-06-01

    Full Text Available Persistence of latent, replication-competent Human Immunodeficiency Virus type 1 (HIV-1 provirus is the main impediment towards a cure for HIV/AIDS (Acquired Immune Deficiency Syndrome. Therefore, different therapeutic strategies to eliminate the viral reservoirs are currently being explored. We here propose a novel strategy to reduce the replicating HIV reservoir during primary HIV infection by means of drug-induced retargeting of HIV integration. A novel class of integration inhibitors, referred to as LEDGINs, inhibit the interaction between HIV integrase and the LEDGF/p75 host cofactor, the main determinant of lentiviral integration site selection. We show for the first time that LEDGF/p75 depletion hampers HIV-1 reactivation in cell culture. Next we demonstrate that LEDGINs relocate and retarget HIV integration resulting in a HIV reservoir that is refractory to reactivation by different latency-reversing agents. Taken together, these results support the potential of integrase inhibitors that modulate integration site targeting to reduce the likeliness of viral rebound.

  15. LEDGIN-mediated Inhibition of Integrase-LEDGF/p75 Interaction Reduces Reactivation of Residual Latent HIV.

    Science.gov (United States)

    Vranckx, Lenard S; Demeulemeester, Jonas; Saleh, Suha; Boll, Annegret; Vansant, Gerlinde; Schrijvers, Rik; Weydert, Caroline; Battivelli, Emilie; Verdin, Eric; Cereseto, Anna; Christ, Frauke; Gijsbers, Rik; Debyser, Zeger

    2016-06-01

    Persistence of latent, replication-competent Human Immunodeficiency Virus type 1 (HIV-1) provirus is the main impediment towards a cure for HIV/AIDS (Acquired Immune Deficiency Syndrome). Therefore, different therapeutic strategies to eliminate the viral reservoirs are currently being explored. We here propose a novel strategy to reduce the replicating HIV reservoir during primary HIV infection by means of drug-induced retargeting of HIV integration. A novel class of integration inhibitors, referred to as LEDGINs, inhibit the interaction between HIV integrase and the LEDGF/p75 host cofactor, the main determinant of lentiviral integration site selection. We show for the first time that LEDGF/p75 depletion hampers HIV-1 reactivation in cell culture. Next we demonstrate that LEDGINs relocate and retarget HIV integration resulting in a HIV reservoir that is refractory to reactivation by different latency-reversing agents. Taken together, these results support the potential of integrase inhibitors that modulate integration site targeting to reduce the likeliness of viral rebound.

  16. An exactly solvable two-body problem with retarded interactions and radiation reaction in classical electrodynamics

    Science.gov (United States)

    Rivera, R.; Villarroel, D.

    1997-11-01

    An exactly solvable two-body problem dealing with the Lorentz-Dirac equation is constructed in this paper. It corresponds to the motion of two identical charges rotating at opposite ends of a diameter, in a fixed circle, at constant angular velocity. The external electromagnetic field that allows this motion consists of a tangential time-independent electric field with a fixed value over the orbit circle, and a homogeneous time-independent magnetic field that points orthogonally to the orbit plane. Because of the geometrical symmetries of the charges' motion, in this case it is possible to obtain the rate of radiation emitted by the charges directly from the equation of motion. The rate of radiation is also calculated by studying the energy flux across a sphere of a very large radius, using the far retarded fields of the charges. Both calculations lead to the same result, in agreement with energy conservation.

  17. Spin-dependent two-body interactions from gravitational self-force computations

    CERN Document Server

    Bini, Donato; Geralico, Andrea

    2015-01-01

    We analytically compute, through the eight-and-a-half post-Newtonian order and the fourth-order in spin, the gravitational self-force correction to Detweiler's gauge invariant redshift function for a small mass in circular orbit around a Kerr black hole. Using the first law of mechanics for black hole binaries with spin [L.~Blanchet, A.~Buonanno and A.~Le Tiec, Phys.\\ Rev.\\ D {\\bf 87}, 024030 (2013)] we transcribe our results into a knowledge of various spin-dependent couplings, as encoded within the spinning effective-one-body model of T.~Damour and A.~Nagar [Phys.\\ Rev.\\ D {\\bf 90}, 044018 (2014)]. We also compare our analytical results to the (corrected) numerical self-force results of A.~G.~Shah, J.~L.~Friedman and T.~S.~Keidl [Phys.\\ Rev.\\ D {\\bf 86}, 084059 (2012)], from which we show how to directly extract physically relevant spin-dependent couplings.

  18. Cajal bodies and interchromatin granule clusters in cricket oocytes: composition, dynamics and interactions.

    Science.gov (United States)

    Stepanova, Irina S; Bogolyubov, Dmitry S; Skovorodkin, Ilya N; Parfenov, Vladimir N

    2007-03-01

    The organization and molecular composition of complicated Cajal bodies (CBs) and interchromatin granule clusters (IGCs) in oocytes of the house cricket, Acheta domesticus, were studied using immunofluorescent/confocal and Immunogold labeling/electron microscopy. In A. domesticus oocytes, the CB consists of the fibrillar matrix and a central cavity containing a predominantly granular body with insertions of tightly packed fibrillar material. The latter structure was identified as an "internal" IGC, since it is enriched with the SC35 protein, a marker for IGCs. The IGCs located outside the CB were also identified. Microinjections of the fluorescein-tagged U7 snRNA into the ooplasm showed the targeting of the U7 to the matrix of the CB. Some other essential CB components (coilin, snRNPs, fibrillarin) were found to be colocalized in the matrix of the CB. Neither confocal nor Immunogold microscopy revealed significant amounts of RNA polymerase II (pol II) in the CB of A. domesticus oocytes. The splicing factor SC35 was detected in the matrix of the CB. In oocytes treated with DRB, the amount of IGCs in the nucleoplasm increased significantly, granular and fibrillar components of IGCs were segregated, and the fibrillar areas accumulated pol II. Additionally, IG-like granules were shown to display on the surface of the CB probably due to a shifting from the internal IGC. We believe that in A. domesticus oocytes, CBs are involved in nuclear distribution of splicing factors, but their role in pol II transport is less significant. We also suggest that the formation of complicated CBs is a result of interconnection between two different nuclear domains, CBs and IGCs.

  19. Ultrafast photoelectron migration in dye-sensitized solar cells: Influence of the binding mode and many-body interactions

    Science.gov (United States)

    Hermann, G.; Tremblay, J. C.

    2016-11-01

    In the present contribution, the ultrafast photoinduced electron migration dynamics at the interface between an alizarin dye and an anatase TiO2 thin film is investigated from first principles. Comparison between a time-dependent many-electron configuration interaction ansatz and a single active electron approach sheds light on the importance of many-body effects, stemming from uniquely defined initial conditions prior to photoexcitation. Particular emphasis is put on understanding the influence of the binding mode on the migration process. The dynamics is analyzed on the basis of a recently introduced toolset in the form of electron yields, electronic fluxes, and flux densities, to reveal microscopic details of the electron migration mechanism. From the many-body perspective, insight into the nature of electron-electron and hole-hole interactions during the charge transfer process is obtained. The present results reveal that the single active electron approach yields quantitatively and phenomenologically similar results as the many-electron ansatz. Furthermore, the charge migration processes in the dye-TiO2 model clusters with different binding modes exhibit similar mechanistic pathways but on largely different time scales.

  20. A unified mathematical framework and an adaptive numerical method for fluid-structure interaction with rigid, deforming, and elastic bodies

    Science.gov (United States)

    Bhalla, Amneet Pal Singh; Bale, Rahul; Griffith, Boyce E.; Patankar, Neelesh A.

    2013-10-01

    Many problems of interest in biological fluid mechanics involve interactions between fluids and solids that require the coupled solution of momentum equations for both the fluid and the solid. In this work, we develop a mathematical framework and an adaptive numerical method for such fluid-structure interaction (FSI) problems in which the structure may be rigid, deforming, or elastic. We employ an immersed boundary (IB) formulation of the problem that permits us to avoid body conforming discretizations and to use fast Cartesian grid solvers. Rigidity and deformational kinematic constraints are imposed using a formulation based on distributed Lagrange multipliers, and a conventional IB method is used to describe the elasticity of the immersed body. We use Cartesian grid adaptive mesh refinement (AMR) to discretize the equations of motion and thereby obtain a solution methodology that efficiently captures thin boundary layers at fluid-solid interfaces as well as flow structures shed from such interfaces. This adaptive methodology is validated for several benchmark problems in two and three spatial dimensions. In addition, we use this scheme to simulate free swimming, including the maneuvering of a two-dimensional model eel and a three-dimensional model of the weakly electric black ghost knifefish.

  1. Body size affects the predatory interactions between introduced American Bullfrogs (Rana catesbeiana) and native anurans in China: An experimental study

    Science.gov (United States)

    Wang, Y.; Guo, Z.; Pearl, C.A.; Li, Y.

    2007-01-01

    Introduced American Bullfrogs (Rana catesbeiana) have established breeding populations in several provinces in China since their introduction in 1959. Although Bullfrogs are viewed as a potentially important predator of Chinese native anurans, their impacts in the field are difficult to quantify. We used two experiments to examine factors likely to mediate Bullfrog predation on native anurans. First, we examined effects of Bullfrog size and sex on daily consumption of a common Chinese native (Rana limnocharis). Second, we examined whether Bullfrogs consumed similar proportions of four Chinese natives: Black-Spotted Pond Frog (Rana nigromaculata), Green Pond Frog (Rana plancyi plancyi), Rice Frog (R. limnocharis), and Zhoushan Toad (Bufo bufo gargarizans). We found that larger Rana catesbeiana consumed more R. limnocharis per day than did smaller R. catesbeiana, and that daily consumption of R. limnocharis was positively related to R. catesbeiana body size. When provided with adults of four anurans that differed significantly in body size, R. catesbeiana consumed more individuals of the smallest species (R. limnocharis). However, when provided with similarly sized juveniles of the same four species, R. catesbeiana did not consume any species more than expected by chance. Our results suggest that body size plays an important role in the predatory interactions between R. catesbeiana and Chinese native anurans and that, other things being equal, smaller species and individuals are at greater risk of predation by R. catesbeiana. Copyright 2007 Society for the Study of Amphibians and Reptiles.

  2. Toward transferable interatomic van der Waals interactions without electrons: The role of multipole electrostatics and many-body dispersion

    Energy Technology Data Exchange (ETDEWEB)

    Bereau, Tristan, E-mail: bereau@mpip-mainz.mpg.de [Max-Planck-Institut für Polymerforschung, Ackermannweg 10, 55128 Mainz, Germany and Department of Chemistry, University of Basel, 4056 Basel (Switzerland); Lilienfeld, O. Anatole von [Department of Chemistry, Institute of Physical Chemistry, University of Basel, 4056 Basel, Switzerland and Argonne Leadership Computing Facility, Argonne National Laboratory, Argonne, Illinois 60439 (United States)

    2014-07-21

    We estimate polarizabilities of atoms in molecules without electron density, using a Voronoi tesselation approach instead of conventional density partitioning schemes. The resulting atomic dispersion coefficients are calculated, as well as many-body dispersion effects on intermolecular potential energies. We also estimate contributions from multipole electrostatics and compare them to dispersion. We assess the performance of the resulting intermolecular interaction model from dispersion and electrostatics for more than 1300 neutral and charged, small organic molecular dimers. Applications to water clusters, the benzene crystal, the anti-cancer drug ellipticine—intercalated between two Watson-Crick DNA base pairs, as well as six macro-molecular host-guest complexes highlight the potential of this method and help to identify points of future improvement. The mean absolute error made by the combination of static electrostatics with many-body dispersion reduces at larger distances, while it plateaus for two-body dispersion, in conflict with the common assumption that the simple 1/R{sup 6} correction will yield proper dissociative tails. Overall, the method achieves an accuracy well within conventional molecular force fields while exhibiting a simple parametrization protocol.

  3. Backbone and side chain NMR assignments of Geobacillus stearothermophilus ZapA allow identification of residues that mediate the interaction of ZapA with FtsZ.

    Science.gov (United States)

    Nogueira, Maria Luiza C; Sforça, Mauricio Luis; Chin, Yanni K-Y; Mobli, Mehdi; Handler, Aaron; Gorbatyuk, Vitaliy Y; Robson, Scott A; King, Glenn F; Gueiros-Filho, Frederico J; Zeri, Ana Carolina de Mattos

    2015-10-01

    Bacterial division begins with the formation of a contractile protein ring at midcell, which constricts the bacterial envelope to generate two daughter cells. The central component of the division ring is FtsZ, a tubulin-like protein capable of self-assembling into filaments which further associate into a higher order structure known as the Z ring. Proteins that bind to FtsZ play a crucial role in the formation and regulation of the Z ring. One such protein is ZapA, a widely conserved 21 kDa homodimeric protein that associates with FtsZ filaments and promotes their bundling. Although ZapA was discovered more than a decade ago, the structural details of its interaction with FtsZ remain unknown. In this work, backbone and side chain NMR assignments for the Geobacillus stearothermophilus ZapA homodimer are described. We titrated FtsZ into (15)N(2)H-ZapA and mapped ZapA residues whose resonances are perturbed upon FtsZ binding. This information provides a structural understanding of the interaction between FtsZ and ZapA.

  4. Effects of muscle dysmorphia, social comparisons and body schema priming on desire for social interaction: an experimental approach.

    Science.gov (United States)

    Schneider, Catharina; Agthe, Maria; Yanagida, Takuya; Voracek, Martin; Hennig-Fast, Kristina

    2017-06-15

    Muscle dysmorphia (MD) is a relatively young diagnosis referring to the desire for a high degree in lean muscle mass, while simultaneously believing that one is insufficiently muscular, mostly found in men. It goes along with a risk for social withdrawal to maintain rigid exercise and dietary regimen. The aim of the current study was thus, to explore differences in men with and without a risk for muscle dysmorphia regarding their desire for social interaction. Furthermore, we investigated potential effects of individual social comparison tendencies (the tendency to compare oneself with persons who are perceived to be superior or inferior to oneself on a certain dimension) and of one's own body schema on the desire for social interaction. One hundred physically active, college aged Austrian men were recruited via social media and flyers at fitness centers and the sports department of the University of Vienna. Participants were randomly assigned to a priming condition evoking their own body schema or a control condition and had to state their desire for social interaction with male or female stimulus persons of high or average attractiveness. We conducted a 2 (group of participant; men with vs. without a risk for MD) × 2 (priming condition; priming vs. non-priming) × 2 (attractiveness of stimulus person; highly attractive vs. less attractive) experimental design with different social comparison tendencies as covariates. Men with a risk for muscle dysmorphia showed lesser desire for social interaction than men without this risk, which can be seen as a risk factor for psychopathological outcomes. Generally, men with and without a risk for muscle dysmorphia did not differ with regard to their preferences for attractive stimulus persons as subjects for social interaction. We confirmed the notion that a tendency for downward social comparisons goes along with a diminished desire for social interaction. This study showed that men with a risk for muscle dysmorphia

  5. Underexpanded Supersonic Plume Surface Interactions: Applications for Spacecraft Landings on Planetary Bodies

    Science.gov (United States)

    Mehta, M.; Sengupta, A.; Renno, N. O.; Norman, J. W.; Gulick, D. S.

    2011-01-01

    Numerical and experimental investigations of both far-field and near-field supersonic steady jet interactions with a flat surface at various atmospheric pressures are presented in this paper. These studies were done in assessing the landing hazards of both the NASA Mars Science Laboratory and Phoenix Mars spacecrafts. Temporal and spatial ground pressure measurements in conjunction with numerical solutions at altitudes of approx.35 nozzle exit diameters and jet expansion ratios (e) between 0.02 and 100 are used. Data from steady nitrogen jets are compared to both pulsed jets and rocket exhaust plumes at Mach approx.5. Due to engine cycling, overpressures and the plate shock dynamics are different between pulsed and steady supersonic impinging jets. In contrast to highly over-expanded (e plumes, results show that there is a relative ground pressure load maximum for moderately underexpanded (e approx.2-5) jets which demonstrate a long collimated plume shock structure. For plumes with e much >5 (lunar atmospheric regime), the ground pressure is minimal due to the development of a highly expansive shock structure. We show this is dependent on the stability of the plate shock, the length of the supersonic core and plume decay due to shear layer instability which are all a function of the jet expansion ratio. Asymmetry and large gradients in the spatial ground pressure profile and large transient overpressures are predominantly linked to the dynamics of the plate shock. More importantly, this study shows that thruster plumes exhausting into martian environments possess the largest surface pressure loads and can occur at high spacecraft altitudes in contrast to the jet interactions at terrestrial and lunar atmospheres. Theoretical and analytical results also show that subscale supersonic cold gas jets adequately simulate the flow field and loads due to rocket plume impingement provided important scaling parameters are in agreement. These studies indicate the critical

  6. Direct Observation of Dynamical Quantum Phase Transitions in an Interacting Many-Body System

    Science.gov (United States)

    Jurcevic, P.; Shen, H.; Hauke, P.; Maier, C.; Brydges, T.; Hempel, C.; Lanyon, B. P.; Heyl, M.; Blatt, R.; Roos, C. F.

    2017-08-01

    The theory of phase transitions represents a central concept for the characterization of equilibrium matter. In this work we study experimentally an extension of this theory to the nonequilibrium dynamical regime termed dynamical quantum phase transitions (DQPTs). We investigate and measure DQPTs in a string of ions simulating interacting transverse-field Ising models. During the nonequilibrium dynamics induced by a quantum quench we show for strings of up to 10 ions the direct detection of DQPTs by revealing nonanalytic behavior in time. Moreover, we provide a link between DQPTs and the dynamics of other quantities such as the magnetization, and we establish a connection between DQPTs and entanglement production.

  7. Interacting quantum walkers: two-body bosonic and fermionic bound states

    Science.gov (United States)

    Krapivsky, P. L.; Luck, J. M.; Mallick, K.

    2015-11-01

    We investigate the dynamics of bound states of two interacting particles, either bosons or fermions, performing a continuous-time quantum walk on a one-dimensional lattice. We consider the situation where the distance between both particles has a hard bound, and the richer situation where the particles are bound by a smooth confining potential. The main emphasis is on the velocity characterizing the ballistic spreading of these bound states, and on the structure of the asymptotic distribution profile of their center-of-mass coordinate. The latter profile generically exhibits many internal fronts.

  8. Analytic solutions for Wheeler-Feynman interaction: Two bodies in straight-line motion

    Science.gov (United States)

    Stephas, Paul

    1992-02-01

    Analytic solutions are obtained for two point particles with any total energy that have charges of like sign and whose motions are confined to one dimension. These solutions are obtained by explicitly deriving the conserved quantities associated with Wheeler-Feynman interactions into forms that do not contain integrals but, rather, contain ``partial contributions'' to the momenta and potentials of particle two. The resulting conserved energy, momentum, and Lorentz momentum equations are separated in time to yield one set of equations with variables t1 and t2- (retarded) and another set with variables t1 and t1+ (advanced). These are solved to obtain auxiliary solutions x1r(t1) and x1a(t1), which are then combined for the case m1 = m2 to give the actual world lines x1(t1) and x2(t2). Comparison is made with a previous computer-generated exact solution for the same interaction and energy; good qualitative agreement is found, although some quantitative differences persist.

  9. A novel EB-1/AIDA-1 isoform, AIDA-1c, interacts with the Cajal body protein coilin

    Directory of Open Access Journals (Sweden)

    Hebert Michael D

    2005-04-01

    Full Text Available Abstract Background Cajal bodies (CBs are nuclear suborganelles that play a role in the biogenesis of small nuclear ribonucleoproteins (snRNPs, which are crucial for pre-mRNA splicing. Upon nuclear reentry, Sm-class snRNPs localize first to the CB, where the snRNA moiety of the snRNP is modified. It is not clear how snRNPs target to the CB and are released from this structure after their modification. Coilin, the CB marker protein, may participate in snRNP biogenesis given that it can interact with snRNPs and SMN. SMN is crucial for snRNP assembly and is the protein mutated in the neurodegenerative disease Spinal Muscular Atrophy. Coilin knockout mice display significant viability problems and altered CB formation. Thus characterization of the CB and its associated proteins will give insight into snRNP biogenesis and clarify the dynamic organization of the nucleus. Results In this report, we identify a novel protein isoform of EB-1/AIDA-1, termed AIDA-1c, that interacts with the CB marker protein, coilin. Northern and nested PCR experiments reveal that the AIDA-1c isoform is expressed in brain and several cancer cell lines. Competition binding experiments demonstrate that AIDA-1c competes with SmB' for coilin binding sites, but does not bind SMN. When ectopically expressed, AIDA-1c is predominantly nuclear with no obvious accumulations in CBs. Interestingly, another EB-1/AIDA-1 nuclear isoform, AIDA-1a, does not bind coilin in vivo as efficiently as AIDA-1c. Knockdown of EB-1/AIDA-1 isoforms by siRNA altered Cajal body organization and reduced cell viability. Conclusion These data suggest that specific EB-1/AIDA-1 isoforms, such as AIDA-1c, may participate in the regulation of nucleoplasmic coilin protein interactions in neuronal and transformed cells.

  10. Analysis of mechanical interaction between human gluteal soft tissue and body supports.

    Science.gov (United States)

    Then, C; Menger, J; Benderoth, G; Alizadeh, M; Vogl, T J; Hübner, F; Silber, G

    2008-01-01

    Pressure sores are the most common complication associated with patient immobilization. They develop through sustained localized tissue strain and stress, primarily caused by body supports. Modifying support design can reduce the risk and extent of pressure sore development with computational simulations helping to provide insight into tissue stress-strain distribution. Appropriate material parameters for human soft tissue and support material, as well as precise anatomical modelling, are indispensable in this process. A finite element (FE) model of the human gluteal region based on magnetic resonance imaging (MRI) data has been developed. In vivo human gluteal skin/fat and muscle long-term material parameters as well as open-cell polyurethane foam support long-term material parameters have been characterised. The Ogden form for slightly compressible materials was employed to describe human gluteal soft tissue behaviour. Altering support geometries and support materials, effects on human gluteal soft tissue could be quantified. FE-analysis indicated maximal tissue stress at the muscle-bone interface, not at the skin. Shear strain maxima were found in the muscle layer near the fat-muscle interface. Maximum compressive stress magnitude at the sacral bone depended strongly on the behaviour of the pelvic diaphragm musculature. We hypothesize that the compliance of the muscles forming the pelvic diaphragm govern the relative motion of the buttock tissue to the adjacent bone structure under compression, thus influencing tissue stress magnitudes.

  11. Towards Interactive Medical Content Delivery Between Simulated Body Sensor Networks and Practical Data Center.

    Science.gov (United States)

    Shi, Xiaobo; Li, Wei; Song, Jeungeun; Hossain, M Shamim; Mizanur Rahman, Sk Md; Alelaiwi, Abdulhameed

    2016-10-01

    With the development of IoT (Internet of Thing), big data analysis and cloud computing, traditional medical information system integrates with these new technologies. The establishment of cloud-based smart healthcare application gets more and more attention. In this paper, semi-physical simulation technology is applied to cloud-based smart healthcare system. The Body sensor network (BSN) of system transmit has two ways of data collection and transmission. The one is using practical BSN to collect data and transmitting it to the data center. The other is transmitting real medical data to practical data center by simulating BSN. In order to transmit real medical data to practical data center by simulating BSN under semi-physical simulation environment, this paper designs an OPNET packet structure, defines a gateway node model between simulating BSN and practical data center and builds a custom protocol stack. Moreover, this paper conducts a large amount of simulation on the real data transmission through simulation network connecting with practical network. The simulation result can provides a reference for parameter settings of fully practical network and reduces the cost of devices and personnel involved.

  12. Simulation of the fluid-structure-interaction of steam generator tubes and bluff bodies

    Energy Technology Data Exchange (ETDEWEB)

    Kuehlert, Karl [ANSYS, Inc. (United States)], E-mail: kue@fluent.com; Webb, Stephen [Sandia National Laboratories (United States); Schowalter, David; Holmes, William; Chilka, Amarvir; Reuss, Steve [ANSYS, Inc. (United States)

    2008-08-15

    The accuracy of computational fluid dynamics in simulating the cross-flow around a steam generator and the feasibility of a full scale coupled CFD/FEA fluid-structure-interaction (FSI) analysis is examined through successive validations. The study begins with a comparison between experiment and computation of flow within a stationary tube bank. Results from the simulation of an individual tube experiencing two-degree-of-freedom flow-induced vibration (at a Reynolds number of 3800) are then shown to compare favorably to experimental results. Finally, free vibration of a single cantilevered hydrofoil is simulated with comparison of mean square acceleration at resonant and non-resonant velocities, respectively. The magnitudes and frequencies of vibration are shown to be accurately captured.

  13. Performing Re-mediation in Graphical Cyberspace: Mediating Agency, Body and Identity in Virtual Interactional Practices

    DEFF Research Database (Denmark)

    McIlvenny, Paul

    and spectacular multi-media event raises many questions. How do we conceive of the recent developments in media technology and social computing that are impacting on what we have traditionally called 'the mass media'? How is interaction and talk mediated and adapted to new media genres? And how do participants...... the conference, avatar-embodied speakers using text chat performed to virtual audiences, 'webcams' (re)broadcast live video images of CNN and other remote sites, and a 'webcast' sent audiovisual representations captured by video camera of certain key participants in their physical locations. Such a novel...... construct and maintain senseful talk in a sometimes bewildering, 'inhabited', digitally re-mediated public environment? What is especially interesting about the cyberconference event is the ways in which participants themselves shaped their talk to constitute media spaces, presences and participation...

  14. Three-body bound states in dipole-dipole interacting Rydberg atoms

    CERN Document Server

    Kiffner, Martin; Jaksch, Dieter

    2013-01-01

    We show that the dipole-dipole interaction between three identical Rydberg atoms can give rise to bound trimer states. The microscopic origin of these states is fundamentally different from Efimov physics. Two stable trimer configurations exist where the atoms form the vertices of an equilateral triangle in a plane perpendicular to a static electric field. The triangle edge length typically exceeds $R\\approx 2\\,\\mu\\text{m}$, and each configuration is two-fold degenerate due to Kramers' degeneracy. The depth of the potential wells and the triangle edge length can be controlled by external parameters. We establish the Borromean nature of the trimer states, analyze the quantum dynamics in the potential wells and describe methods for their production and detection.

  15. Performing Re-mediation in Graphical Cyberspace: Mediating Agency, Body and Identity in Virtual Interactional Practices

    DEFF Research Database (Denmark)

    McIlvenny, Paul

    and spectacular multi-media event raises many questions. How do we conceive of the recent developments in media technology and social computing that are impacting on what we have traditionally called 'the mass media'? How is interaction and talk mediated and adapted to new media genres? And how do participants......Promoted as the first academic conference to be held completely in graphical cyberspace, Avatars 98 took place in November 1998. The virtual conference site was built and inhabited using software that supports multi-party presence over the Internet in a simulated, navigable environment. During...... construct and maintain senseful talk in a sometimes bewildering, 'inhabited', digitally re-mediated public environment? What is especially interesting about the cyberconference event is the ways in which participants themselves shaped their talk to constitute media spaces, presences and participation...

  16. SLIM: a Secured Lightweight Interactive Middleware for wireless body area network.

    Science.gov (United States)

    Waluyo, Agustinus Borgy; Pek, Isaac; Chen, Xiang; Yeoh, Wee-Soon

    2008-01-01

    Advances in wireless sensor technology have introduced a new dimension in healthcare computing. With miniaturized sensor devices, continuous medical monitoring of patients to detect transient life threatening conditions from daily activities has been made possible. This phenomenon will certainly improve the quality of life for a majority of people. However, the growing variety of sensor devices in the market, has made application developments very challenging. In light of this view, we are proposing SLIM, a lightweight middleware that shields the underlying differences in sensor technology from the application layer. SLIM is designed to simplify/accelerate application development while not simply providing common middleware functions (i.e. data acquisition and plug-and-play capability) but also others like security and interactive features. To support both indoor and outdoor activities, SLIM is built to reside on mobile devices. At the end of the paper, we will show the prototype of the proposed middleware including its functionalities when used with a mobile application.

  17. Association Between FTO Variant and Change in Body Weight and Its Interaction With Dietary Factors

    DEFF Research Database (Denmark)

    Vimaleswaran, Karani S; Angquist, Lars; Hansen, Rikke D;

    2012-01-01

    of being a weight-gainer (OR: 1.1; P = 0.045). We observed no interaction between FTO-rs9939609 and dietary fat, protein and carbohydrate, and GI on BMI and WC at baseline or on change in weight and WC. FTO-rs9939609 is associated with BMI and WC at baseline, but association with weight gain is weak......Although FTO is an established obesity-susceptibility locus, it remains unknown whether it influences weight change in adult life and whether diet attenuates this association. Therefore, we investigated the association of FTO-rs9939609 with changes in weight and waist circumference (WC) during 6.......8 years follow-up in a large-scale prospective study and examined whether these associations were modified by dietary energy percentage from fat, protein, carbohydrate, or glycemic index (GI). This study comprised data from five countries of European Prospective Investigation into Cancer and Nutrition...

  18. Nuclear Many-Body Theory of Electroweak Interactions with Nuclei at Intermediate Energies

    Energy Technology Data Exchange (ETDEWEB)

    Nieves, J. [Departamento de Fisica Moderna, Universidad de Granada, E-18071 Granada (Spain); Amaro, J.E. [Departamento de Fisica Moderna, Universidad de Granada, E-18071 Granada (Spain); Valverde, M. [Departamento de Fisica Moderna, Universidad de Granada, E-18071 Granada (Spain)

    2005-02-15

    The Quasi-Elastic (QE) contribution of the nuclear inclusive electron model developed in reference [Nucl. Phys. A627 (1997) 543; ibidem Nucl. Phys. A627 (1997) 598] is extended to the study of electroweak Charged Current (CC) induced nuclear reactions at intermediate energies of interest for future neutrino oscillation experiments. Long range nuclear (RPA) correlations, Final State Interaction (FSI) and Coulomb corrections are included within the model. RPA correlations are shown to play a crucial role in the whole range of neutrino energies, up to 500 MeV, studied in this work. Predictions for inclusive muon capture for different nuclei through the Periodic Table and for the reactions C12({nu}{sub {mu}},{mu}{sup -})X and C12({nu}{sub e},e{sup -})X near threshold are also given.

  19. A Deterministic Projector Configuration Interaction Approach for the Ground State of Quantum Many-Body Systems.

    Science.gov (United States)

    Zhang, Tianyuan; Evangelista, Francesco A

    2016-09-13

    In this work we propose a novel approach to solve the Schrödinger equation which combines projection onto the ground state with a path-filtering truncation scheme. The resulting projector configuration interaction (PCI) approach realizes a deterministic version of the full configuration interaction quantum Monte Carlo (FCIQMC) method [Booth, G. H.; Thom, A. J. W.; Alavi, A. J. Chem. Phys. 2009, 131, 054106]. To improve upon the linearized imaginary-time propagator, we develop an optimal projector scheme based on an exponential Chebyshev expansion in the limit of an infinite imaginary time step. After writing the exact projector as a path integral in determinant space, we introduce a path filtering procedure that truncates the size of the determinantal basis and approximates the Hamiltonian. The path filtering procedure is controlled by one real threshold that determines the accuracy of the PCI energy and is not biased toward any determinant. Therefore, the PCI approach can equally well describe static and dynamic electron correlation effects. This point is illustrated in benchmark computations on N2 at both equilibrium and stretched geometries. In both cases, the PCI achieves chemical accuracy with wave functions that contain less than 0.5% determinants of full CI space. We also report computations on the ground state of C2 with up to quaduple-ζ basis sets and wave functions as large as 200 million determinants, which allow a direct comparison of the PCI, FCIQMC, and density matrix renormalization group (DMRG) methods. The size of the PCI wave function grows modestly with the number of unoccupied orbitals, and its accuracy may be tuned to match that of FCIQMC and DMRG.

  20. An efficient conservative cut-cell method for rigid bodies interacting with viscous compressible flows

    Science.gov (United States)

    Schneiders, Lennart; Günther, Claudia; Meinke, Matthias; Schröder, Wolfgang

    2016-04-01

    A Cartesian cut-cell method for viscous flows interacting with freely moving boundaries is presented. The method enables a sharp resolution of the embedded boundaries and strictly conserves mass, momentum, and energy. A new explicit Runge-Kutta scheme (PC-RK) is introduced by which the overall computational time is reduced by a factor of up to 2.5. The new scheme is a predictor-corrector type reformulation of a popular class of Runge-Kutta methods which substantially reduces the computational effort for tracking the moving boundaries and subsequently reinitializing the solver impairing neither stability nor accuracy. The structural motion is computed by an implicit scheme with good stability properties due to a strong-coupling strategy and the conservative discretization of the flow solver at the material interfaces. A new formulation for the treatment of small cut cells is proposed with high accuracy and robustness for arbitrary geometries based on a weighted Taylor-series approach solved via singular-value decomposition. The efficiency and the accuracy of the new method are demonstrated for several three-dimensional cases of laminar and turbulent particulate flow. It is shown that the new method remains fully conservative even for large displacements of the boundaries leading to a fast convergence of the fluid-solid coupling while spurious force oscillations inherent to this class of methods are effectively suppressed. The results substantiate the good stability and accuracy properties of the scheme even on relatively coarse meshes.

  1. Mind-body interactions in pain: the neurophysiology of anxious and catastrophic pain-related thoughts.

    Science.gov (United States)

    Campbell, Claudia M; Edwards, Robert R

    2009-03-01

    The well-accepted biopsychosocial model proposes that the experience of pain and responses to it result from a complex interaction of biological, psychological, and social factors. However, the separation of these constructs is substantially artificial, and we presume that psychological processes have biological effects, that biological processes affect an individual's psychosocial environment, and so on. Considerable research has demonstrated that pain-coping strategies influence perceived pain intensity and physical functioning, and individual differences in styles of pain coping even shape the persistence of long-term pain complaints in some populations. A good deal of this coping research has focused on catastrophizing, which is a generally maladaptive cognitive and emotional mental set that involves feelings of helplessness when in pain, rumination about pain symptoms, and magnification of pain-related complaints. Collectively, catastrophizing has been consistently associated with heightened experiences of pain across a variety of samples. Although catastrophic thinking regarding pain-related symptoms is often classified under the "psychologic" category within the broader biopsychosocial model, we propose that catastrophizing exerts biologic effects that may account for some of its negative consequences. In general, the cognitive and affective processes captured within the construct of catastrophizing may exert effects on the neuromuscular, cardiovascular, immune, and neuroendocrine systems, and on the activity in the pain neuromatrix within the brain. The interface between pain-related neurobiology and processes such as pain-related catastrophizing represents an important avenue for future pain research.

  2. Isolation of soybean protein P34 from oil bodies using hydrophobic interaction chromatography

    Directory of Open Access Journals (Sweden)

    Seidel-Morgenstern Andreas

    2008-03-01

    Full Text Available Abstract Background Soybeans play a prominent role in allergologic research due to the high incidence of allergic reactions. For detailed studies on specific proteins it is necessary to have access to a large amount of pure substance. Results In this contribution, a method for purifying soybean (Glycine max protein P34 (also called Gly m Bd 30 K or Gly m 1 using hydrophobic interaction chromatography is presented. After screening experiments using 1 mL HiTrap columns, Butyl Sepharose 4 FF was selected for further systematic investigations. With this stationary phase, suitable operation conditions for two-step gradient elution using ammonium sulphate were determined experimentally. The separation conditions obtained in a small column could be scaled up successfully to column volumes of 7.5 and 75 mL, allowing for high product purities of almost 100% with a yield of 27% for the chromatographic separation step. Conditions could be simplified further using a onestep gradient, which gave comparable purification in a shorter process time. The identity of the purified protein was verified using in-gel digestion and mass spectrometry as well as immunological techniques. Conclusion With the technique presented it is possible to produce, within a short timeframe, pure P34, suitable for further studies where an example antigen is needed.

  3. Nonradiating normal modes in a classical many-body model of matter-radiation interaction

    Science.gov (United States)

    Carati, A.; Galgani, L.

    2003-08-01

    We consider a classical model of matter-radiation interaction, in which the matter is represented by a system of infinitely many dipoles on a one-dimensional lattice, and the system is dealt with in the so-called dipole ( linearized) approximation. We prove that there exist normal-mode solutions of the complete system, so that in particular the dipoles, though performing accelerated motions, do not radiate energy. This comes about in virtue of an exact compensation which we prove to occur, for each dipole, between the “radiation reaction force” and a part of the retarded forces due to all the other dipoles. This fact corresponds to a certain identity which we name after Oseen, since it occurs that this researcher did actually propose it, already in the year 1916. We finally make a connection with a paper of Wheeler and Feynman on the foundations of electrodynamics. It turns out indeed that the Oseen identity, which we prove here in a particular model, is in fact a weak form of a general identity that such authors were assuming as an independent postulate.

  4. Modeling the time-varying interaction between surface water and groundwater bodies

    Science.gov (United States)

    Gliege, Steffen; Steidl, Jörg; Lischeid, Gunnar; Merz, Christoph

    2016-04-01

    The countless kettle holes (small lakes) in the Late Pleistocene landscapes of Northern Europe have important ecological and hydrological functions. On the one hand they act as depressions in which water and solutes of mainly agriculturally used catchments accumulate. On the other hand they operate as biochemical reactors with respect to greenhouse gas emissions, carbon sequestration, and as major sinks for nutrients and contaminants. Even small kettle holes often are hydraulically connected to the uppermost groundwater system: Groundwater discharges into the kettle hole on one side, and the aquifer is recharged from the kettle hole water body on the other side. Thus kettle hole biogeochemical processes are both affected by groundwater and vice versa. Groundwater flow direction and velocity into and out of the kettle hole often is not stable over time. Groundwater flow direction might reverse at the downstream part, resulting in repeated recycling of groundwater and corresponding solute turnover within the kettle holes. A sound understanding of this intricate interplay is a necessary prerequisite for better understanding of the biogeochemistry of this terrestrial-aquatic interface. A numerical experiment was used to quantify the lateral solute exchange between a kettle hole and the surrounding groundwater. A vertical cross section through the real existing catchment of a kettle hole was chosen. Glacial till represents the lower boundary. The heterogeneity of the subsurface was reproduced by various parameterizations of the soil hydraulic properties as well as varying the thickness of the unconfined aquifer or the lateral boundary conditions. In total 24 different parameterizations were implemented in the modeling software HydroGeoSphere (HGS). HGS is suitable to calculate the fluid exchange between surface and subsurface simultaneously and in a physically based way. The simulation runs were done for the period from November 1994 to October 2014. All results were

  5. Biomolecule-Mineral Interactions in the Geochemical Environment on Early Earth and in the Human Body

    Science.gov (United States)

    Sahai, N.

    2011-12-01

    We worked on four projects consistent with the broad goals of the grant to investigate (i) the potential impacts of mineral surface chemistry and particle size on the stability and viability of cell membranes, bacteria and human cells and (ii) the influence of biomolecules on mineral nucleation and growth. The projects are of relevance to the origin and early evolution of life, biomineralization, medical mineralogy, and environmental biogeochemistry. The freedom enabled by the five-year grant to explore high-risk scientific areas, and the resulting high impact outcomes, cannot be overstated. We developed an almost entirely new field of Medical Mineralogyy and extended our concepts and knowledge-base to the potential roles of mineral surfaces in the evolution of protocells and the earliest cells. These exciting connections to medical mineralogy, and to the origin and evolution of life on early Earth are fascinating topics to the general public and even to other scientists, especially when the links to mineralogy and geochemistry are highlighted. In brief, we examined the stability of lipid bilayers representing model protocell membranes comprised of phospholipid bilayers with mineral surfaces. We found that the stability of lipid bilayers depends on mineral surface charge and increases as silica glass ~ quartz human either inadvertently as inhaled dusts or are inserted by design such as in components of orthopedic implants. It is important to know how the mineral surface properties affect the body's immune system response. We found that adhesion/detachment force of the Jurkat -line of T-lymphocytes increased as SiO2 glass ~ quartz < rutile (100) ~ mica (001) < polycrystalline corundum, and was related to the unraveling of cell surface glycoproteins, and to mineral surface charge. The studies described above have resulted in 23 peer-reviewed publications to date (published or in review or in prep.); one MSA volume and one Elements issue edited by the P.I.; trained

  6. Nonlinear phenomena in wave-body interaction: description and theoretical modeling; Les effets non-lineaires en interaction houle-structure et leur modelisation

    Energy Technology Data Exchange (ETDEWEB)

    Molin, B. [Ecole Generaliste d' Ingenieurs de Marseille, 13 (France)

    2006-03-15

    At first approximation, the study of wave interaction with fixed or floating bodies is carried out within a linear frame. However nonlinear effects are numerous and they have diverse origins: mechanical nonlinearities, variation in time of the wetted part of the hull, viscous phenomena (flow separation), nonlinear free surface equations. We focus here on the latter type of nonlinearities. Two different approaches are described, both being based on potential flow theory. Practical applications are given for two basic geometries: a vertical cylinder and a vertical plate, perpendicular to the wave direction. In the first approach, one proceeds through successive approximations, based on a perturbation series development. The first-order of approximation coincides with the linear theory. The main interest of the second-order of approximation, well mastered nowadays, is that it yields excitation loads in an enlarged frequency domain, encompassing most of the natural frequencies of the system considered. At third-order the complexity of the equations becomes dissuasive and few researchers have ventured there. We suggest that third-order (or tertiary) interactions, between incoming waves and reflected waves by the structure, can play a very important role, overlooked so far, in phenomena such as run-up or green water. In the second approach one integrates in time and space the nonlinear equations of the initial boundary value problem, with the free surface equations being exactly satisfied. In this way one obtains numerical equivalents of the physical wave-tanks. They are briefly described and some illustrative results are given. (authors)

  7. Combining symmetry breaking and restoration with configuration interaction: A highly accurate many-body scheme applied to the pairing Hamiltonian

    Science.gov (United States)

    Ripoche, J.; Lacroix, D.; Gambacurta, D.; Ebran, J.-P.; Duguet, T.

    2017-01-01

    Background: Ab initio many-body methods have been developed over the past ten years to address mid-mass nuclei. In their best current level of implementation, their accuracy is of the order of a few percent error on the ground-state correlation energy. Recently implemented variants of these methods are operating a breakthrough in the description of medium-mass open-shell nuclei at a polynomial computational cost while putting state-of-the-art models of internucleon interactions to the test. Purpose: As progress in the design of internucleon interactions is made, and as questions one wishes to answer are refined in connection with increasingly available experimental data, further efforts must be made to tailor many-body methods that can reach an even higher precision for an even larger number of observable quantum states or nuclei. The objective of the present work is to contribute to such a quest by designing and testing a new many-body scheme. Methods: We formulate a truncated configuration-interaction method that consists of diagonalizing the Hamiltonian in a highly truncated subspace of the total N -body Hilbert space. The reduced Hilbert space is generated via the particle-number projected BCS state along with projected seniority-zero two- and four-quasiparticle excitations. Furthermore, the extent by which the underlying BCS state breaks U(1 ) symmetry is optimized in the presence of the projected two- and four-quasiparticle excitations. This constitutes an extension of the so-called restricted variation after projection method in use within the frame of multireference energy density functional calculations. The quality of the newly designed method is tested against exact solutions of the so-called attractive pairing Hamiltonian problem. Results: By construction, the method reproduces exact results for N =2 and N =4 . For N =(8 ,16 ,20 ) , the error in the ground-state correlation energy is less than (0.006%, 0.1%, 0.15%) across the entire range of

  8. Polycyclic aromatic hydrocarbon body residues and lysosomal membrane destabilization in mussels exposed to the Dubai Star bunker fuel oil (intermediate fuel oil 380) spill in San Francisco Bay.

    Science.gov (United States)

    Hwang, Hyun-Min; Stanton, Beckye; McBride, Toby; Anderson, Michael J

    2014-05-01

    Following the spill of bunker fuel oil (intermediate fuel oil 380, approximately 1500-3000 L) into San Francisco Bay in October 2009, polycyclic aromatic hydrocarbon (PAH) concentrations in mussels from moderately oiled areas increased up to 87 554 ng/g (dry wt) and, 3 mo later, decreased to concentrations found in mussels collected prior to oiling, with a biological half-life of approximately 16 d. Lysosomal membrane destabilization increased in mussels with higher PAH body burdens.

  9. Interaction between genetic predisposition to adiposity and dietary protein in relation to subsequent change in body weight and waist circumference.

    Directory of Open Access Journals (Sweden)

    Mikkel Z Ankarfeldt

    Full Text Available Genetic predisposition to adiposity may interact with dietary protein in relation to changes of anthropometry.To investigate the interaction between genetic predisposition to higher body mass index (BMI, waist circumference (WC or waist-hip ratio adjusted for BMI (WHRBMI and dietary protein in relation to subsequent change in body weight (ΔBW or change in WC (ΔWC.Three different Danish cohorts were used. In total 7,054 individuals constituted the study population with information on diet, 50 single-nucleotide polymorphisms (SNPs associated with BMI, WC or WHRBMI, as well as potential confounders. Mean follow-up time was ∼5 years. Four genetic predisposition-scores were based on the SNPs; a complete-score including all selected adiposity- associated SNPs, and three scores including BMI, WC or WHRBMI associated polymorphisms, respectively. The association between protein intake and ΔBW or ΔWC were examined and interactions between SNP-score and protein were investigated. Analyses were based on linear regressions using macronutrient substitution models and meta-analyses.When protein replaced carbohydrate, meta-analyses showed no associations with ΔBW (41.0 gram/y/5 energy% protein, [95% CI: -32.3; 114.3] or ΔWC (<-0.1 mm/y/5 energy % protein, [-1.1; 1.1]. Similarly, there were no interactions for any SNP-scores and protein for either ΔBW (complete SNP-score: 1.8 gram/y/5 energy% protein/risk allele, [-7.0; 10.6] or ΔWC (complete SNP-score: <0.1 mm/y/5 energy% protein/risk allele, [-0.1; 0.1]. Similar results were seen when protein replaced fat.This study indicates that the genetic predisposition to general and abdominal adiposity, assessed by gene-scores, does not seem to modulate the influence of dietary protein on ΔBW or ΔWC.

  10. Interaction between Genetic Predisposition to Adiposity and Dietary Protein in Relation to Subsequent Change in Body Weight and Waist Circumference

    DEFF Research Database (Denmark)

    Ankarfeldt, Mikkel Z; Larsen, Sofus C; Angquist, Lars

    2014-01-01

    ) and dietary protein in relation to subsequent change in body weight (ΔBW) or change in WC (ΔWC). DESIGN: Three different Danish cohorts were used. In total 7,054 individuals constituted the study population with information on diet, 50 single-nucleotide polymorphisms (SNPs) associated with BMI, WC or WHRBMI......, as well as potential confounders. Mean follow-up time was ∼5 years. Four genetic predisposition-scores were based on the SNPs; a complete-score including all selected adiposity- associated SNPs, and three scores including BMI, WC or WHRBMI associated polymorphisms, respectively. The association between...... protein intake and ΔBW or ΔWC were examined and interactions between SNP-score and protein were investigated. Analyses were based on linear regressions using macronutrient substitution models and meta-analyses. RESULTS: When protein replaced carbohydrate, meta-analyses showed no associations with ΔBW (41...

  11. $B^+\\to K^-\\pi^+\\pi^+$: three-body final state interactions and $K\\pi$ isospin states

    CERN Document Server

    Nogueira, J H Alvarenga; Lourenço, O

    2016-01-01

    Final state interactions are considered to formulate the $B$ meson decay amplitude for the $K\\pi\\pi$ channel. The Faddeev decomposition of the Bethe-Salpeter equation is used in order to build a relativistic three-body model within the light-front framework. The S-wave scattering amplitude for the $K\\pi$ system is considered in the $1/2$ and $3/2$ isospin channels with the set of inhomogeneous integral equations solved perturbatively. In comparison with previous results for the $D$ meson decay in the same channel, one has to consider the different partonic processes, which build the source amplitudes, and the larger absorption to other decay channels appears, that are important features to be addressed. As in the $D$ decay case, the convergence of the rescattering perturbative series is also achieved with two-loop contributions.

  12. Experimental investigation of the generation of large-amplitude internal solitary wave and its interaction with a submerged slender body

    Science.gov (United States)

    Wei, Gang; Du, Hui; Xu, XiaoHui; Zhang, YuanMing; Qu, ZiYun; Hu, TianQun; You, YunXiang

    2014-01-01

    A principle of generating the nonlinear large-amplitude internal wave in a stratified fluid tank with large cross-section is proposed according to the `jalousie' control mode. A new wave-maker based on the principle was manufactured and the experiments on the generation and evolution of internal solitary wave were conducted. Both the validity of the new device and applicability range of the KdV-type internal soliton theory were tested. Furthermore, a measurement technique of hydrodynamic load of internal waves was developed. By means of accurately measuring slight variations of internal wave forces exerted on a slender body in the tank, their interaction characteristics were determined. It is shown that through establishing the similarity between the model scale in the stratified fluid tank and the full scale in the numerical simulation the obtained measurement results of internal wave forces are confirmed to be correct.

  13. Optical properties of azobenzene-functionalized self-assembled monolayers: Intermolecular coupling and many-body interactions

    Science.gov (United States)

    Cocchi, Caterina; Moldt, Thomas; Gahl, Cornelius; Weinelt, Martin; Draxl, Claudia

    2016-12-01

    In a joint theoretical and experimental work, the optical properties of azobenzene-functionalized self-assembled monolayers (SAMs) are studied at different molecular packing densities. Our results, based on density-functional and many-body perturbation theory, as well as on differential reflectance (DR) spectroscopy, shed light on the microscopic mechanisms ruling photo-absorption in these systems. While the optical excitations are intrinsically excitonic in nature, regardless of the molecular concentration, in densely packed SAMs intermolecular coupling and local-field effects are responsible for a sizable weakening of the exciton binding strength. Through a detailed analysis of the character of the electron-hole pairs, we show that distinct excitations involved in the photo-isomerization at low molecular concentrations are dramatically broadened by intermolecular interactions. Spectral shifts in the calculated DR spectra are in good agreement with the experimental results. Our findings represent an important step forward to rationalize the excited-state properties of these complex materials.

  14. Interactions between auditory and visual semantic stimulus classes: evidence for common processing networks for speech and body actions.

    Science.gov (United States)

    Meyer, Georg F; Greenlee, Mark; Wuerger, Sophie

    2011-09-01

    Incongruencies between auditory and visual signals negatively affect human performance and cause selective activation in neuroimaging studies; therefore, they are increasingly used to probe audiovisual integration mechanisms. An open question is whether the increased BOLD response reflects computational demands in integrating mismatching low-level signals or reflects simultaneous unimodal conceptual representations of the competing signals. To address this question, we explore the effect of semantic congruency within and across three signal categories (speech, body actions, and unfamiliar patterns) for signals with matched low-level statistics. In a localizer experiment, unimodal (auditory and visual) and bimodal stimuli were used to identify ROIs. All three semantic categories cause overlapping activation patterns. We find no evidence for areas that show greater BOLD response to bimodal stimuli than predicted by the sum of the two unimodal responses. Conjunction analysis of the unimodal responses in each category identifies a network including posterior temporal, inferior frontal, and premotor areas. Semantic congruency effects are measured in the main experiment. We find that incongruent combinations of two meaningful stimuli (speech and body actions) but not combinations of meaningful with meaningless stimuli lead to increased BOLD response in the posterior STS (pSTS) bilaterally, the left SMA, the inferior frontal gyrus, the inferior parietal lobule, and the anterior insula. These interactions are not seen in premotor areas. Our findings are consistent with the hypothesis that pSTS and frontal areas form a recognition network that combines sensory categorical representations (in pSTS) with action hypothesis generation in inferior frontal gyrus/premotor areas. We argue that the same neural networks process speech and body actions.

  15. Density-functional approach to the three-body dispersion interaction based on the exchange dipole moment.

    Science.gov (United States)

    Proynov, Emil; Liu, Fenglai; Gan, Zhengting; Wang, Matthew; Kong, Jing

    2015-08-28

    We implement and compute the density functional nonadditive three-body dispersion interaction using a combination of Tang-Karplus formalism and the exchange-dipole moment model of Becke and Johnson. The computation of the C9 dispersion coefficients is done in a non-empirical fashion. The obtained C9 values of a series of noble atom triplets agree well with highly accurate values in the literature. We also calculate the C9 values for a series of benzene trimers and find a good agreement with high-level ab initio values reported recently in the literature. For the question of damping of the three-body dispersion at short distances, we propose two damping schemes and optimize them based on the benzene trimers data, and the fitted analytic potentials of He3 and Ar3 trimers fitted to the results of high-level wavefunction theories available from the literature. Both damping schemes respond well to the optimization of two parameters.

  16. Interactive effects of family socioeconomic status and body mass index on depression in school-aged children.

    Science.gov (United States)

    Lin, Fu-Gong; Hsieh, Yu-Hsin; Tung, Ho-Jui

    2012-01-01

    Depression is an important health problem in children and the onset of depression is occurring at a younger age than previously suggested. The associations of being overweight and low socioeconomic status in childhood depression have been well documented; nevertheless few studies have addressed the combined effects of socioeconomic status and body weight, with depression in school-age children. We intended to examine if the relationship between socioeconomic status and childhood depression could be modified by abnormal body weight. A cross-sectional study was performed with a total of 559 subjects from 29 elementary schools in Taiwan. A depression scale was used to determine the depression status. Children receiving governmental monetary assistance for after-school class were categorized as being in the lower socioeconomic group. Data for depression-related demographic characteristics, family and school variables were collected. Children in the lower socioeconomic status group have a higher prevalence of depression (23.5%) than those in higher socioeconomic status groups(16.4%). Being overweight demonstrates the opposite effect on depression risk in the different socioeconomic groups. In lower socioeconomic families, the risk of depression in overweight children is three times higher than that for normal weight children; whereas in higher socioeconomic families, overweight children have a lower risk for depression than normal weight children. We concluded that a qualitative interactive effect existed between being overweight and socioeconomic status with childhood depression. More attention should be paid to overweight children from lower socioeconomic status families to prevent depression in school-age children.

  17. Residual undifferentiated cells during embryoid bodies differentiation of induced pluripotent stem cells%诱导的多潜能干细胞类胚体分化过程中残留未分化细胞的研究

    Institute of Scientific and Technical Information of China (English)

    王书军; 刁永力; 谷波; 于海洲; 葛乃航; 严晓鸥; 张文杰

    2011-01-01

    Objective To explore the residual undifferentiated cells during embryoid bodies differentiation of induced pluripotent stem cells. Methods Mouse iPS were firstly cultured in suspension to form embryoid bodies (Ebs).Twenty days later,Ebs were digested into single cells and then re-plated in standard iPS cells culture condition.The morphology of residual undifferentiated cells in Ebs was observed,while surface makers and in vitro redifferentiation potency of residual cells were examined by flow cytometry and immunofluorescent staining.The residual cells were expanded and subcutaneously injected into nude mice, and the specimens were harvested from the injection site for histological analysis 6 weeks after injection. Results A certain amount of residual undifferentiated cells in Ebs differentiated for 20 days, which displayed clonal morphology and expressed undifferentiated cell markers including SSEA-1,CD-9 and OCT-4.Amplified cells could form secondary Ebs in votro again,from which secondary undifferentiated cells could be re-expanded. Teratomas formed after amplified undifferentiated cells being injected into nude mice, which contain mature endoderm, mesoderm and ectoderm tissues. Conclusion A certain amount of undifferentiated cells exists in differentiated Ebs of iPS cells. The residual cells can differentiate again in vitro and vivo,and can residue again in the in vitro differentiation.%目的:探讨诱导的多潜能干细胞(induced pluripotent stem cells,iPS cells)通过类胚体长期分化后残留未分化细胞的特性.方法:小鼠iPS细胞株,体外类胚体分化20天后消化打散,重新给予iPS细胞常规培养液培养.观察扩增的残留细胞形态;流式细胞仪和免疫荧光染色检测和观察残留细胞表面标志物及体外再次分化能力.将残留细胞扩增后注射入裸鼠背部皮下,6周后注射部位取材进行大体和组织学检查.结果:分化20天的类胚体中存在残留未分化

  18. A macrocyclic HCV NS3/4A protease inhibitor interacts with protease and helicase residues in the complex with its full-length target

    Science.gov (United States)

    Schiering, Nikolaus; D’Arcy, Allan; Villard, Frederic; Simić, Oliver; Kamke, Marion; Monnet, Gaby; Hassiepen, Ulrich; Svergun, Dmitri I.; Pulfer, Ruth; Eder, Jörg; Raman, Prakash; Bodendorf, Ursula

    2011-01-01

    Hepatitis C virus (HCV) infection is a global health burden with over 170 million people infected worldwide. In a significant portion of patients chronic hepatitis C infection leads to serious liver diseases, including fibrosis, cirrhosis, and hepatocellular carcinoma. The HCV NS3 protein is essential for viral polyprotein processing and RNA replication and hence viral replication. It is composed of an N-terminal serine protease domain and a C-terminal helicase/NTPase domain. For full activity, the protease requires the NS4A protein as a cofactor. HCV NS3/4A protease is a prime target for developing direct-acting antiviral agents. First-generation NS3/4A protease inhibitors have recently been introduced into clinical practice, markedly changing HCV treatment options. To date, crystal structures of HCV NS3/4A protease inhibitors have only been reported in complex with the protease domain alone. Here, we present a unique structure of an inhibitor bound to the full-length, bifunctional protease-helicase NS3/4A and show that parts of the P4 capping and P2 moieties of the inhibitor interact with both protease and helicase residues. The structure sheds light on inhibitor binding to the more physiologically relevant form of the enzyme and supports exploring inhibitor-helicase interactions in the design of the next generation of HCV NS3/4A protease inhibitors. In addition, small angle X-ray scattering confirmed the observed protease-helicase domain assembly in solution. PMID:22160684

  19. A macrocyclic HCV NS3/4A protease inhibitor interacts with protease and helicase residues in the complex with its full-length target.

    Science.gov (United States)

    Schiering, Nikolaus; D'Arcy, Allan; Villard, Frederic; Simic, Oliver; Kamke, Marion; Monnet, Gaby; Hassiepen, Ulrich; Svergun, Dmitri I; Pulfer, Ruth; Eder, Jörg; Raman, Prakash; Bodendorf, Ursula

    2011-12-27

    Hepatitis C virus (HCV) infection is a global health burden with over 170 million people infected worldwide. In a significant portion of patients chronic hepatitis C infection leads to serious liver diseases, including fibrosis, cirrhosis, and hepatocellular carcinoma. The HCV NS3 protein is essential for viral polyprotein processing and RNA replication and hence viral replication. It is composed of an N-terminal serine protease domain and a C-terminal helicase/NTPase domain. For full activity, the protease requires the NS4A protein as a cofactor. HCV NS3/4A protease is a prime target for developing direct-acting antiviral agents. First-generation NS3/4A protease inhibitors have recently been introduced into clinical practice, markedly changing HCV treatment options. To date, crystal structures of HCV NS3/4A protease inhibitors have only been reported in complex with the protease domain alone. Here, we present a unique structure of an inhibitor bound to the full-length, bifunctional protease-helicase NS3/4A and show that parts of the P4 capping and P2 moieties of the inhibitor interact with both protease and helicase residues. The structure sheds light on inhibitor binding to the more physiologically relevant form of the enzyme and supports exploring inhibitor-helicase interactions in the design of the next generation of HCV NS3/4A protease inhibitors. In addition, small angle X-ray scattering confirmed the observed protease-helicase domain assembly in solution.

  20. Hydrophobic interaction between contiguous residues in the S6 transmembrane segment acts as a stimuli integration node in the BK channel

    Science.gov (United States)

    Carrasquel-Ursulaez, Willy; Contreras, Gustavo F.; Sepúlveda, Romina V.; Aguayo, Daniel; González-Nilo, Fernando

    2015-01-01

    Large-conductance Ca2+- and voltage-activated K+ channel (BK) open probability is enhanced by depolarization, increasing Ca2+ concentration, or both. These stimuli activate modular voltage and Ca2+ sensors that are allosterically coupled to channel gating. Here, we report a point mutation of a phenylalanine (F380A) in the S6 transmembrane helix that, in the absence of internal Ca2+, profoundly hinders channel opening while showing only minor effects on the voltage sensor active–resting equilibrium. Interpretation of these results using an allosteric model suggests that the F380A mutation greatly increases the free energy difference between open and closed states and uncouples Ca2+ binding from voltage sensor activation and voltage sensor activation from channel opening. However, the presence of a bulky and more hydrophobic amino acid in the F380 position (F380W) increases the intrinsic open–closed equilibrium, weakening the coupling between both sensors with the pore domain. Based on these functional experiments and molecular dynamics simulations, we propose that F380 interacts with another S6 hydrophobic residue (L377) in contiguous subunits. This pair forms a hydrophobic ring important in determining the open–closed equilibrium and, like an integration node, participates in the communication between sensors and between the sensors and pore. Moreover, because of its effects on open probabilities, the F380A mutant can be used for detailed voltage sensor experiments in the presence of permeant cations. PMID:25548136