Omar Gaci

The Small-World Model for Amino Acid Interaction Networks

In this paper we introduce the notion of protein interaction network. This is a graph whose verticesare the proteins amino acids and whose edges are the interactions between them. Using a graph theory approach, we identify a number of properties of these networks. We compare them to the general small-world network model and we analyze their hierarchical structure.

Node degree distribution in amino acid interaction networks

A protein interaction network is a graph whose vertices are the proteins amino acids and whose edges are the interactions between them. Using a graph theory approach, we study the properties of these networks. In particular, we are interested in the degree distribution and mean degree of the vertices. The results presented in this paper constitute the first steps of a new network approach to the protein folding problem.

Hubs identification in amino acids interaction networks

In this paper we introduce the notion of protein interaction network. This is a graph whose vertices are the proteins amino acids and whose edges are the interactions between them. Using a graph theory approach, we identify a number of properties of these networks. We compare them to the general scale-free network model and we analyze the existence of nodes with a high interaction level.

A Multi-Agent System to simulate storage activities in warehouse of chemical substances

Complex Adaptive System (CAS) provides a reliable framework to model and simulate behavioural dynamics. This paper proposes to reproduce storage activities in a warehouse of chemical substances. The warehouse is considered as a CAS and the physical persons are considered as software agents and constitute a Multi-Agent system, MAS. In this paper, the simulation of storage activities are reproduced using JADE platform that allows inter-agent communication via messages.

A Dynamic Risk Management in Chemical Substances Warehouses by an Interaction Network Approach

We propose to study activities of storages in a warehouse of chemical substances. Then, this warehouse is subject to restriction in business processes executed every day: operators must respect a segregation strategy which consists in avoiding any mixing of incompatible chemicals. To reproduce the actions of forklift operators, we propose a Multi-Agent System which is the support of CAS modelling. Then, during agent movements for handling pallets from their reception into their storage locations, we define a dynamic graphwhere the vertices represent agents in activities and edges measure the distance between agents. The study of this dynamic graph shows that the average mean distance remains weak meaning that agent are often close each other. From this observation, we deduce a strategy for a dynamic risk management that gives the priority to agents whose betweenness is superior to the other agents that handle pallets of incompatible chemicals.

Dynamic Risk Management Strategies with Communicating Objects in the Supply Chain of Chemical Substances Within the European Union

This chapter is organized as follows. Part 2 introduces briefly what supply chain management is and gives some definitions. Part 3 describes dangerous goods in logistics and notably the risks inherent to their storages. Current regulations such as CLP is presented, it provides a standard in the European Union to classify and identify dangerous goods. Risks relative to dangerous goods manipulation are presented, segregation strategies and storage constraints must be respected to maintain the security within awarehouse. In part 4, a risk study is lead to extract three scenarios that describe the domino effect consecutive to accidents. These scenario are treated further in part 5 when communicating objects are integrated at pallet level. Then, these smart items allow elaborating real-time risk assessment that contribute to detect early accident risks and to deploy emergency procedures to mitigate that risks.

A Study of Protein Structure Using Amino Acid Interaction Networks

Proteins are biological macromolecules participating in the large majority of processes which govern organisms. The roles played by proteins are varied and complex. Certain proteins, called enzymes, act as catalysts and increase several orders of magnitude, with a remarkable specificity, the speed of multiple chemical reactions essential to the organism survival. Proteins are also used for storage and transport of small molecules or ions, control the passage of molecules through the cell membranes, etc. Hormones, which transmit information and allow the regulation of complex cellular processes, are also proteins. Genome sequencing projects generate an ever increasing number of protein sequences. For example, the Human Genome Project has identified over 30,000 genes which may encode about 100,000 proteins. One of the first tasks when annotating a new genome is to assign functions to the proteins produced by the genes. To fully understand the biological functions of proteins, the knowledge of their structure is essential. In their natural environment, proteins adopt a native compact three-dimensional form. This process is called folding and is not fully understood. The process is a result of interactions between the proteins amino acids which form chemical bonds. In this paper we identify some of the properties of the network of interacting amino acids. We believe that understanding these networks can help to better understand the folding process. There exist different classifications of proteins according to their structure, such as CATH (Orengo, 1997) and SCOP (Murzin.1995). Proteins from the same class have similar structures and most often, similar functions. In this paper we show that structure classes can also be defined in the terms of the properties of amino acid networks.

Ant colony approach to predict amino acid interaction networks

In this paper we introduce the notion of protein interaction network. This is a graph whose vertices are the proteins amino acids and whose edges are the interactions between them. We consider the problem of reconstructing proteins interaction network from its amino acid sequence. An ant colony approach is used to solve this problem.

Dynamic Risk Assessment by Communicating Objects in Supply Chain of Chemicals

In this paper, a wireless sensor network is deployed to improve the security of goods, environment and persons along a supply chain manipulating chemicals in the European Union. Pallets are equipped with a RFID tag and a set of sensors that monitor in real-time the environment state. By defining and monitoring constraints that must satisfy pallet environments, a real-time risk assessment is proposed. Then, sensors send accident risks in case of unusual values to a centralized software. Supply chain actors responsible for goods are thus contacted and in parallel emergency services are contacted to plan and organize their interventions.

Sensors exploitation in supply chain management for French homeland security

The RESCUE-IT project is presented, the objective is the improvement of homeland security by the integration of RFID tags and wireless sensors in supply chain of chemicals in the European Union. Pallets are equipped with a RFID tag and a set of sensors that monitor in real-time the environment state. The collected data are transmitted to a software able to translate data into accident risks. The software is able to detect unusual values and to send alerts to the supply chain actor responsible for the goods. In parallel, alerts are sent to emergency services that can plan their interventions.