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.

Membrane poration by antimicrobial peptides

Abstract: Antimicrobial peptides (AMPs) comprise a large family of peptides that include small cationic peptides, such as magainins, which permeabilize lipid membranes Previous atomistic level simulations of magainin-H2 peptides show that they act by forming toroidal transmembrane pores However, due to the atomistic level of description, these simulations were necessarily limited to small system sizes and sub-microsecond time scales Here, we study the long-time relaxation properties of these pores by evolving the systems using a coarse-grain (CG) description The disordered nature and the topology of the atomistic pores are maintained at the CG level The peptides sample different orientations but at any given time, only a few peptides insert into the pore Key states observed at the CG level are subsequently back-transformed to the atomistic level using a resolutiontransformation protocol The configurations sampled at the CG level are stable in the atomistic simulation The effect of helicity on pore stability is investigated at the CG level and we find that partial helicity is required to form stable pores We also show that the current CG scheme can be used to study spontaneous poration by magainin-H2 peptides Overall, our simulations provide a multi-scale view of a fundamental biophysical membrane process involving a complex interplay between peptides and lipids

Test Selection and Coverage Based on CTM and Metric Spaces

Abstract: One of the main open issues in testing and in particular in conformance testing is finding a good way of measuring the quality of the testing activity. With other words after performing a given quantity of tests, how much it is covered from the number of potential errors of the implementation under test (IUT). The present paper tries to build up a solution for this necessity. In (L. Feijs et al., 2002, N. Goga et al., 2004) we proposed a general framework for defining a coverage measure based on a distance measure between different behaviors of a system under test. In the current paper we apply this general theory to another domain, namely to CTM (classification tree method) that is usually used for the selection of the data for testing. As a case study we apply this technology for testing a software tool used for computer music generation

Architecture of a Non-Intrusive IoT System for Frailty Detection in Older People

Abstract: Early detection of frailty is one of the main challenges in the world we live in. Being aware of physiologic and behavior changes can predict and prevent the onset of mental complications for older people. By using modern technologies, one can get insights, which may help detection of different pathologies. In this paper, preliminary results for a novel system to detect early signs of frailty are presented. A prototype was developed and tested in laboratory conditions after requirements and functional capabilities were defined. The main advantages of the proposed architecture are the usage of commercial off-the-shelf (COTS) components and custom mechanisms of security to assure a high level of confidentiality and integrity of user-specific data. Other original elements are its easy-to-use and non-intrusive characteristics.

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...