Electron cooling and Debye-Waller effect in photoexcited bismuth

By means of first principles calculations, we computed the effective electron-phonon coupling constant $G_0$ governing the electron cooling in photoexcited bismuth. $G_0$ strongly increases as a function of electron temperature, which can be traced back to the semi-metallic nature of bismuth. We also used a thermodynamical model to compute the time evolution of both electron and lattice temperatures following laser excitation. Thereby, we simulated the time evolution of (1 -1 0), (-2 1 1) and (2 -2 0) Bragg peak intensities measured by Sciaini et al [Nature 458, 56 (2009)] in femtosecond electron diffraction experiments. The effect of the electron temperature on the Debye-Waller factors through the softening of all optical modes across the whole Brillouin zone turns out to be crucial to reproduce the time evolution of these Bragg peak intensities

Nonthermal solid-to-solid phase transitions in tungsten

The ab initio calculations of phonon dispersions and nonthermal forces along structural deformation paths were used to study nonthermal solid-to-solid phase transitions in photoexcited tungsten. We assumed that electronic excitation can be described by an electronic temperature and demonstrated that nonthermal, i.e., caused purely by electronic excitation, bcc-to-fcc and bcc-to-hcp phase transitions can occur for electronic temperatures between 1.7 and 4.3 eV. These transitions result from soft modes along the Σ line of the Brillouin zone. Structural path calculations at different electronic temperatures indicate that both transitions are likely to take place in nonequilibrium conditions. We further predict that transient fcc and hcp phases of tungsten could be observed for several ps

Determination of the electron-phonon coupling constant in tungsten

We used two methods to determine the effective electron-phonon coupling constant (G 0) in tungsten. Our first principles calculations predict G 0 = 1.65 × 1017 W m−3 K−1. The temporal decay of the femtosecond-resolution optical reflectivity for a (100) surface of bulk W was measured using a pump-probe scheme and analysed using ab initio parameterised two temperature model, which includes both the effects of the electron-phonon coupling and thermal conduction into bulk. This analysis gives G 0 = 1.4(3) × 1017 W m−3 K−1, in good agreement with the theoretical prediction. The described effective method of calculating and measuring G0 in bulk materials can be easily extended to other metals

Entropy Driven Atomic Motion in Laser-Excited Bismuth

We introduce a thermodynamical model based on the two-temperature approach in order to fully understand the dynamics of the coherent A(1g) phonon in laser-excited bismuth. Using this model, we simulate the time evolution of (111) Bragg peak intensities measured by Fritz et al. [Science 315, 633 (2007)] in femtosecond x-ray diffraction experiments performed on a bismuth film for different laser fluences. The agreement between theoretical and experimental results is striking not only because we use fluences very close to the experimental ones but also because most of the model parameters are obtained from ab initio calculations performed for different electron temperatures

Determination of transient atomic structure of laser-excited materials from time-resolved diffraction data

The time evolution of the Bragg peaks of photo-excited gold nanofilms is measured using transmission ultrafast electron diffraction (UED) with 3.0 MeV electron pulses and the corresponding structure evolution is calculated using two-temperature molecular dynamics (2T-MD). The good agreement obtained between the measured and calculated Bragg peaks, over the full experimental timescale, enables the lattice temperature effects and the structural changes to be disentangled for the first time. The agreement demonstrates that 2T-MD is a reliable method for solving the inverse problem of structure determination of laser irradiated metals in UED measurements

Structural dynamics of laser-irradiated gold nanofilms

We performed relativistic ultrafast electron diffraction (UED) measurements of the structural dynamics of photoexcited gold nanofilms and developed an atomistic model, based on the two-temperature molecular dynamics (2T-MD) method, which allows us to make a direct comparison of the time evolutions of measured and calculated Bragg peaks. The quantitative agreement between the temporal evolutions of the experimental and theoretical Bragg peaks at all fluences suggests that the 2T-MD method provides a faithful atomistic representation of the structural evolution of photoexcited gold films. The results reveal the transition between slow heterogeneous melting at low absorbed photon fluence to rapid homogeneous melting at higher fluence and nonthermally driven melting at very high fluence. At high laser fluence, the time evolution of Bragg peaks calculated using the conventional 2T-MD model disagrees with experiment. We show that using an interatomic potential that directly depends on the electron temperature delivers a much better agreement with UED data. Finally, our ab initio calculations of phonon spectra suggest electronic bond softening, if the nanofilms can expand freely under electronic pressure, and bond hardening, if they are constrained in all three dimensions

Designing normative open virtual enterprises

This is an Accepted Manuscript of an article published by Taylor & Francis Group in Enterprise Information Systems on 23/03/2016, available online: http://www.tandfonline.com/10.1080/17517575.2015.1036927.[EN] There is an increasing interest on developing virtual enterprises in order to deal with the globalisation of the economy, the rapid growth of information technologies and the increase of competitiveness. In this paper we deal with the development of normative open virtual enterprises (NOVEs). They are systems with a global objective that are composed of a set of heterogeneous entities and enterprises that exchange services following a specific normative context. In order to analyse and design systems of this kind the multi-agent paradigm seems suitable because it offers a specific solution for supporting the social and contractual relationships between enterprises and for formalising their business processes. This paper presents how the Regulated Open Multiagent systems (ROMAS) methodology, an agent-oriented software methodology, can be used to analyse and design NOVEs. ROMAS offers a complete development process that allows identifying and formalising of the structure of NOVEs, their normative context and the interactions among their members. The use of ROMAS is exemplified by means of a case study that represents an automotive supply chain.This work was partially supported by the projects [PROMETEOII/2013/019], [TIN2012-36586-C03-01], [FP7-29493], [TIN2011-27652-C03-00] and [CSD2007-00022], and the CASES project within the 7th European Community Framework Programme [grant agreement number 294931].Garcia Marques, ME.; Giret Boggino, AS.; Botti Navarro, VJ. (2016). Designing normative open virtual enterprises. Enterprise Information Systems. 10(3):303-324. https://doi.org/10.1080/17517575.2015.1036927S303324103Cardoso, H. L., Urbano, J., Brandão, P., Rocha, A. P., & Oliveira, E. (2012). ANTE: Agreement Negotiation in Normative and Trust-Enabled Environments. Advances on Practical Applications of Agents and Multi-Agent Systems, 261-264. doi:10.1007/978-3-642-28786-2_33Chu, X. N., Tso, S. K., Zhang, W. J., & Li, Q. (2002). Partnership Synthesis for Virtual Enterprises. The International Journal of Advanced Manufacturing Technology, 19(5), 384-391. doi:10.1007/s001700200028Davidsson, P., & Jacobsson, A. (s. f.). Towards Norm-Governed Behavior in Virtual Enterprises. Studies in Computational Intelligence, 35-55. doi:10.1007/978-3-540-88071-4_3DeLoach, S. A., & Ojeda, J. C. G. (2010). O-MaSE: a customisable approach to designing and building complex, adaptive multi-agent systems. International Journal of Agent-Oriented Software Engineering, 4(3), 244. doi:10.1504/ijaose.2010.036984DI MARZO SERUGENDO, G., GLEIZES, M.-P., & KARAGEORGOS, A. (2005). Self-organization in multi-agent systems. The Knowledge Engineering Review, 20(2), 165-189. doi:10.1017/s0269888905000494Dignum, V. 2003. “A Model for Organizational Interaction: Based on Agents, Founded in Logic.” PhD diss., Utrecht University.Dignum, V., and F. Dignum. 2006.A Landscape of Agent Systems for the Real World. Technical Report 44-CS-2006-061. Utrecht: Institute of Information and Computing Sciences, Utrecht University.Dignum, V., Meyer, J.-J. C., Dignum, F., & Weigand, H. (2003). Formal Specification of Interaction in Agent Societies. Lecture Notes in Computer Science, 37-52. doi:10.1007/978-3-540-45133-4_4Garcia, E. 2013. “Engineering Regulated Open Multiagent Systems.” PhD diss., Universitat Politecnica de Valencia.Garcia, E., Giret, A., & Botti, V. (s. f.). Software Engineering for Service-Oriented MAS. Lecture Notes in Computer Science, 86-100. doi:10.1007/978-3-540-85834-8_9Garcia, E., Giret, A., & Botti, V. (2013). A Model-Driven CASE tool for developing and verifying regulated open MAS. Science of Computer Programming, 78(6), 695-704. doi:10.1016/j.scico.2011.10.009Garcia, E., Giret, A., & Botti, V. (2011). Evaluating software engineering techniques for developing complex systems with multiagent approaches. Information and Software Technology, 53(5), 494-506. doi:10.1016/j.infsof.2010.12.012Garcia, E., Giret, A., & Botti, V. (2011). Regulated Open Multi-Agent Systems Based on Contracts. Information Systems Development, 243-255. doi:10.1007/978-1-4419-9790-6_20Garcia, E., Giret, A., & Botti, V. (2014). ROMAS Methodology. Handbook on Agent-Oriented Design Processes, 331-369. doi:10.1007/978-3-642-39975-6_11Hollander, C. D., & Wu, A. S. (2011). The Current State of Normative Agent-Based Systems. Journal of Artificial Societies and Social Simulation, 14(2). doi:10.18564/jasss.1750HORLING, B., & LESSER, V. (2004). A survey of multi-agent organizational paradigms. The Knowledge Engineering Review, 19(4), 281-316. doi:10.1017/s0269888905000317Julian, V., Rebollo, M., Argente, E., Botti, V., Carrascosa, C., & Giret, A. (2009). Using THOMAS for Service Oriented Open MAS. Lecture Notes in Computer Science, 56-70. doi:10.1007/978-3-642-10739-9_5Luck, M., Barakat, L., Keppens, J., Mahmoud, S., Miles, S., Oren, N., … Taweel, A. (2011). Flexible Behaviour Regulation in Agent Based Systems. Lecture Notes in Computer Science, 99-113. doi:10.1007/978-3-642-22427-0_8Meneguzzi, F., Modgil, S., Oren, N., Miles, S., Luck, M., & Faci, N. (2012). Applying electronic contracting to the aerospace aftercare domain. Engineering Applications of Artificial Intelligence, 25(7), 1471-1487. doi:10.1016/j.engappai.2012.06.004Presley, A., Sarkis, J., Barnett, W., & Liles, D. (2001). International Journal of Flexible Manufacturing Systems, 13(2), 145-162. doi:10.1023/a:1011131417956Saeki, M., & Kaiya, H. (2008). 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Evaluating how agent methodologies support the specification of the normative environment through the development process

[EN] Due to the increase in collaborative work and the decentralization of processes in many domains, there is an expanding demand for large-scale, flexible and adaptive software systems to support the interactions of people and institutions distributed in heterogeneous environments. Commonly, these software applications should follow specific regulations meaning the actors using them are bound by rights, duties and restrictions. Since this normative environment determines the final design of the software system, it should be considered as an important issue during the design of the system. Some agent-oriented software engineering methodologies deal with the development of normative systems (systems that have a normative environment) by integrating the analysis of the normative environment of a system in the development process. This paper analyses to what extent these methodologies support the analysis and formalisation of the normative environment and highlights some open issues of the topic.This work is partially supported by the PROMETEOII/2013/019, TIN2012-36586-C03-01, FP7-29493, TIN2011-27652-C03-00, CSD2007-00022 projects, and the CASES project within the 7th European Community Framework Program under the grant agreement No 294931.Garcia Marques, ME.; Miles, S.; Luck, M.; Giret Boggino, AS. (2014). Evaluating how agent methodologies support the specification of the normative environment through the development process. Autonomous Agents and Multi-Agent Systems. 1-20. https://doi.org/10.1007/s10458-014-9275-zS120Cossentino, M., Hilaire, V., Molesini, A., & Seidita, V. (Eds.). (2014). Handbook on agent-oriented design processes (Vol. VIII, 569 p. 508 illus.). Berlin: Springer.Akbari, O. (2010). A survey of agent-oriented software engineering paradigm: Towards its industrial acceptance. 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Hingham, MA: Kluwer Academic Publishers.Botti, V., Garrido, A., Giret, A., & Noriega, P. (2011). The role of MAS as a decision support tool in a water-rights market. In Post-proceedings workshops AAMAS2011 (Vol. 7068, pp. 35–49). Berlin: Springer.Breaux, T. (2009). Exercising due diligence in legal requirements acquisition: A tool-supported, frame-based approach. In Proceedings of the IEEE international requirements engineering conference (pp. 225–230).Breaux, T. D., & Baumer, D. L. (2011). Legally reasonable security requirements: A 10-year ftc retrospective. Computers and Security, 30(4), 178–193.Breaux, T. D., Vail, M. W., & Anton, A. I. (2006). Towards regulatory compliance: Extracting rights and obligations to align requirements with regulations. In Proceedings of the 14th IEEE international requirements engineering conference, RE ’06 (pp. 46–55). Washington, DC: IEEE Computer Society.Bresciani, P., Perini, A., Giorgini, P., Giunchiglia, F., & Mylopoulos, J. (2004). Tropos: An agent-oriented software development methodology. Autonomous Agents and Multi-Agent Systems, 8(3), 203–236.Cardoso, H. L., & Oliveira, E. (2008). A contract model for electronic institutions. In COIN’07: Proceedings of the 2007 international conference on Coordination, organizations, institutions, and norms in agent systems III (pp. 27–40).Castor, A., Pinto, R. C., Silva, C. T. L. L., & Castro, J. (2004). Towards requirement traceability in tropos. In WER (pp. 189–200).Chopra, A., Dalpiaz, F., Giorgini, P., & Mylopoulos, J. (2009). Modeling and reasoning about service-oriented applications via goals and commitments. ICST conference on digital business.Cliffe, O., Vos, M., & Padget, J. (2006). Specifying and analysing agent-based social institutions using answer set programming. In O. Boissier, J. Padget, V. Dignum, G. Lindemann, E. Matson, S. Ossowski, J. Sichman, & J. Vázquez-Salceda (Eds.), Coordination, organizations, institutions, and norms in multi-agent systems. Lecture Notes in Computer Science (Vol. 3913, pp. 99–113). Springer. Berlin.Criado, N., Argente, E., Garrido, A., Gimeno, J. A., Igual, F., Botti, V., Noriega, P., & Giret, A. (2011). Norm enforceability in Electronic Institutions? In Coordination, organizations, institutions, and norms in agent systems VI (Vol. 6541, pp. 250–267). Springer.Dellarocas, C., & Klein, M. (2001). Contractual agent societies. In R. Conte & C. Dellarocas (Eds.), Social order in multiagent systems (Vol. 2, pp. 113–133)., Multiagent Systems, Artificial Societies, and Simulated Organizations New York: Springer.DeLoach, S. A. (2008). Developing a multiagent conference management system using the o-mase process framework. In Proceedings of the international conference on agent-oriented software engineering VIII (pp. 168–181).DeLoach, S. A., & Garcia-Ojeda, J. C. (2010). O-mase; a customisable approach to designing and building complex, adaptive multi-agent systems. 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Lecture Notes in Computer Science (Vol. 3346, pp. 181–198). Berlin: Springer.d’Inverno, M., Luck, M., Noriega, P., Rodriguez-Aguilar, J., & Sierra, C. (2012). Communicating open systems, 186, 38–94.Elsenbroich, C., & Gilbert, N. (2014). Agent-based modelling. In Modelling norms (pp. 65–84). Dordrecht: Springer.Esteva, M., Rosell, B., Rodriguez, J. A., & Arcos, J. L. (2004). AMELI: An agent-based middleware for electronic institutions. In AAMAS04 (pp. 236–243).Fenech, S., Pace, G. J., & Schneider, G. (2009). Automatic conflict detection on contracts. In Proceedings of the 6th international colloquium on theoretical aspects of computing, ICTAC ’09 (pp. 200–214).Garbay, C., Badeig, F., & Caelen, J. (2012). Normative multi-agent approach to support collaborative work in distributed tangible environments. In Proceedings of the ACM 2012 conference on computer supported cooperative work companion, CSCW ’12 (pp. 83–86). New York, NY: ACM.Garcia, E., Giret, A., & Botti, V. (2011). Regulated open multi-agent systems based on contracts. In Information Systems Development (pp. 243–255).Garcia, E., Tyson, G., Miles, S., Luck, M., Taweel, A., Staa, T. V., & Delaney, B. (2012). An analysis of agent-oriented engineering of e-health systems. In 13th international eorkshop on sgent-oriented software engineering (AOSE-AAMAS).Garcia, E., Tyson, G., Miles, S., Luck, M., Taweel, A., Staa, T. V., and Delaney, B. (2013). Analysing the Suitability of Multiagent Methodologies for e-Health Systems. In Agent-Oriented Software Engineering XIII, volume 7852, pages 134–150. Springer-Verlag.Garrido, A., Giret, A., Botti, V., & Noriega, P. (2013). mWater, a case study for modeling virtual markets. In New perspectives on agreement technologies (Vol. Law, Gover, pp. 563–579). Springer.Gteau, B., Boissier, O., & Khadraoui, D. (2006). Multi-agent-based support for electronic contracting in virtual enterprises. 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The GB Virus C (GBV-C) NS3 Serine Protease Inhibits HIV-1 Replication in a CD4+ T Lymphocyte Cell Line without Decreasing HIV Receptor Expression

Introduction: Persistent infection with GBV-C (GB Virus C), a non-pathogenic virus related to hepatitis C virus (HCV), prolongs survival in HIV infection. Two GBV-C proteins, NS5A and E2, have been shown previously to inhibit HIV replication in vitro. We investigated whether the GBV-C NS3 serine protease affects HIV replication. Results: GBV-C NS3 protease expressed in a human CD4+ T lymphocyte cell line significantly inhibited HIV replication. Addition of NS4A or NS4A/4B coding sequence to GBV-C NS3 increased the effect on HIV replication. Inhibition of HI

Simultaneous Identification of DNA and RNA Viruses Present in Pig Faeces Using Process-Controlled Deep Sequencing

Background: Animal faeces comprise a community of many different microorganisms including bacteria and viruses. Only scarce information is available about the diversity of viruses present in the faeces of pigs. Here we describe a protocol, which was optimized for the purification of the total fraction of viral particles from pig faeces. The genomes of the purified DNA and RNA viruses were simultaneously amplified by PCR and subjected to deep sequencing followed by bioinformatic analyses. The efficiency of the method was monitored using a process control consisting of three bacteriophages (T4, M13 and MS2) with different morphology and genome types. Defined amounts of the bacteriophages were added to the sample and their abundance was assessed by quantitative PCR during the preparation procedure. Results: The procedure was applied to a pooled faecal sample of five pigs. From this sample, 69,613 sequence reads were generated. All of the added bacteriophages were identified by sequence analysis of the reads. In total, 7.7 % of the reads showed significant sequence identities with published viral sequences. They mainly originated from bacteriophages (73.9%) and mammalian viruses (23.9%); 0.8 % of the sequences showed identities to plant viruses. The most abundant detected porcine viruses were kobuvirus, rotavirus C, astrovirus, enterovirus B, sapovirus and picobirnavirus. In addition, sequences with identities to the chimpanzee stool-associated circular ssDNA virus were identified. Whole genome analysis indicates that this virus, tentatively designated as pig stool-associated circular ssDNA virus (PigSCV), represents a novel pi