Nicolae Goga

Bio: Nicolae Goga is an academic researcher from Politehnica University of Bucharest. The author has contributed to research in topics: Computer science & Ontology (information science). The author has an hindex of 14, co-authored 117 publications receiving 1328 citations. Previous affiliations of Nicolae Goga include Eindhoven University of Technology & University of Bucharest.

Semantic report search engine - Questor

Abstract: In this paper we present a novel report search engine which uses a dedicated ontology, employs natural language processing and acts as a recommender system. The work on the project has been financed by QUESTOR [1], an Eureka project. The aim of the project was to create an innovative product that will be used in large companies to lower the complexities in the report management workflow. The stated purpose was to be able to query the report management system in natural language, for example entering the question ”Give the situation of the procurements in the surgery department in May 2011”. When entering the question in the graphical user interface, the user is guided by contextual suggestions. The final question is analyzed using natural language processing and transformed in a semantic query language, SPARQL, that is executed on a metadata semantic repository. There, all the reports were indexed, using a domain specific ontology. In the first step all the matching reports are retrieved, the parameters are detected from the question and completed as values for the retrieved reports. Then the list of results is passed through a ranker, which orders the results based on their similarity score with the question. The rank of the chosen result is increased to favor that result in subsequent queries. QUESTOR also introduced a new feature: ad-hoc queries. If the question contains more parameters than there are available in the results, a new report is made in real time, using data from the metadata repository and from the report database. This feature was introduced during the development, at the request of the stakeholders. The paper is organized in the following way: a state of the art of the domain, the Questor architecture and algorithms, experimental data and conclusions.

Pain Relief using Virtual Reality

Abstract: A serious issue in the medical field is the treatment of patients affected by chronic pain, burns or recovery treatment after an accident or surgery. The regular treatment is providing the patient with opioid pain relievers medications that in a wide variety of cases leads to addiction. To prevent the partial use of pain reducing drugs in patients that suffer from minor to medium pain and delay their use as much as possible, we propose the use of Virtual Reality technology. Current technological advances have allowed virtual reality application to leave their mark in the medical sector by the use of different training simulators and applications that help the doctors experience from simulating a variety of surgeries. In this paper we present the effects of Virtual Reality immersion on patients that suffer mild to medium pain, as well as our knowledge in the implementation of a virtual reality application that can achieve a positive effect on this serious issue. A direct benefit of successfully creating an application would be the reduction in the amount of pain the patient feels. A second positive effect would be the decrease in the consumption of pain relievers and a better response of the patient to the recovery treatment without the risk of becoming depended on opioids.

Developing a novel algorithm for the computation of poisson's ratio using molecular dynamics for polymers

Abstract: This article presents a method for the computation of Poisson's ratio for an elastic material using molecular dynamic theory, based on an original algorithm and implemented in GROMACS environment. An overview of the theoretical approach (algorithm, computation formulas) is presented and also the simulation results. The simulation results for the chosen system (expanded polystyrene) are in agreement with the experimental results.

The knowledge-creating company : how Japanese companies create the dynamics of innovation

Abstract: How has Japan become a major economic power, a world leader in the automotive and electronics industries? What is the secret of their success? The consensus has been that, though the Japanese are not particularly innovative, they are exceptionally skilful at imitation, at improving products that already exist. But now two leading Japanese business experts, Ikujiro Nonaka and Hiro Takeuchi, turn this conventional wisdom on its head: Japanese firms are successful, they contend, precisely because they are innovative, because they create new knowledge and use it to produce successful products and technologies. Examining case studies drawn from such firms as Honda, Canon, Matsushita, NEC, 3M, GE, and the U.S. Marines, this book reveals how Japanese companies translate tacit to explicit knowledge and use it to produce new processes, products, and services.

Tools and Algorithms for the Construction and Analysis of Systems. Proc. TACAS 2009

Abstract: ing WS1S Systems to Verify Parameterized Networks . . . . . . . . . . . . 188 Kai Baukus, Saddek Bensalem, Yassine Lakhnech and Karsten Stahl FMona: A Tool for Expressing Validation Techniques over Infinite State Systems . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 204 J.-P. Bodeveix and M. Filali Transitive Closures of Regular Relations for Verifying Infinite-State Systems . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 220 Bengt Jonsson and Marcus Nilsson Diagnostic and Test Generation Using Static Analysis to Improve Automatic Test Generation . . . . . . . . . . . . . 235 Marius Bozga, Jean-Claude Fernandez and Lucian Ghirvu Efficient Diagnostic Generation for Boolean Equation Systems . . . . . . . . . . . . 251 Radu Mateescu Efficient Model-Checking Compositional State Space Generation with Partial Order Reductions for Asynchronous Communicating Systems . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 266 Jean-Pierre Krimm and Laurent Mounier Checking for CFFD-Preorder with Tester Processes . . . . . . . . . . . . . . . . . . . . . . . 283 Juhana Helovuo and Antti Valmari Fair Bisimulation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 299 Thomas A. Henzinger and Sriram K. Rajamani Integrating Low Level Symmetries into Reachability Analysis . . . . . . . . . . . . . 315 Karsten Schmidt Model-Checking Tools Model Checking Support for the ASM High-Level Language . . . . . . . . . . . . . . 331 Giuseppe Del Castillo and Kirsten Winter Table of

Improved Parameters for the Martini Coarse-Grained Protein Force Field

Abstract: The Martini coarse-grained force field has been successfully used for simulating a wide range of (bio)molecular systems. Recent progress in our ability to test the model against fully atomistic force fields, however, has revealed some shortcomings. Most notable, phenylalanine and proline were too hydrophobic, and dimers formed by polar residues in apolar solvents did not bind strongly enough. Here, we reparametrize these residues either through reassignment of particle types or by introducing embedded charges. The new parameters are tested with respect to partitioning across a lipid bilayer, membrane binding of Wimley–White peptides, and dimerization free energy in solvents of different polarity. In addition, we improve some of the bonded terms in the Martini protein force field that lead to a more realistic length of α-helices and to improved numerical stability for polyalanine and glycine repeats. The new parameter set is denoted Martini version 2.2.

Perspective on the Martini model.

Abstract: The Martini model, a coarse-grained force field for biomolecular simulations, has found a broad range of applications since its release a decade ago. Based on a building block principle, the model combines speed and versatility while maintaining chemical specificity. Here we review the current state of the model. We describe recent highlights as well as shortcomings, and our ideas on the further development of the model.

Computational Lipidomics with insane: A Versatile Tool for Generating Custom Membranes for Molecular Simulations

Abstract: For simulations of membranes and membrane proteins, the generation of the lipid bilayer is a critical step in the setup of the system. Membranes comprising multiple components pose a particular challenge, because the relative abundances need to be controlled and the equilibration of the system may take several microseconds. Here we present a comprehensive method for building membrane containing systems, characterized by simplicity and versatility. The program uses preset, coarse-grain lipid templates to build the membrane, and also allows on-the-fly generation of simple lipid types by specifying the headgroup, linker, and lipid tails on the command line. The resulting models can be equilibrated, after which a relaxed atomistic model can be obtained by reverse transformation. For multicomponent membranes, this provides an efficient means for generating equilibrated atomistic models. The method is called insane, an acronym for INSert membrANE. The program has been made available, together with the complemen...