DFT-Derived Reactive Potentials for the Simulation of Activated Processes: the Case of CdTe and CdTe:S

We introduce a new ab initio derived reactive potential for the simulation of CdTe within density functional theory (DFT) and apply it to calculate both static and dynamical properties of a number of systems (bulk solid, defective structures, liquid, surfaces) at finite temperature. In particular, we also consider cases with low sulfur concentration (CdTe:S). The analysis of DFT and classical molecular dynamics (MD) simulations performed with the same protocol leads to stringent performance tests and to a detailed comparison of the two schemes. Metadynamics techniques are used to empower both Car-Parrinello and classical molecular dynamics for the simulation of activated processes. For the latter, we consider surface reconstruction and sulfur diffusion in the bulk. The same procedures are applied using previously proposed force fields for CdTe and CdTeS materials, thus allowing for a detailed comparison of the various schemes.

What Singles Out the G[8-5]C Intrastrand DNA Cross-Link? Mechanistic and Structural Insights from Quantum Mechanics/Molecular Mechanics Simulations

Chandan Patel

Naturally occurring intrastrand oxidative crosslink lesions have proven to be a potent source of endogenous DNA damage. Among the variety of lesions that can be formed and have been identified, G[8-5]C damage (in which the C8 atom of a guanine is covalently bonded to the CS atom of a nearby cytosine belonging to the same strand) occurs with a low incidence yet takes on special importance because of its high mutagenicity. Hybrid Car-Parrinello molecular dynamics simulations, rooted in density functional theory and coupled to molecular mechanics, have been performed to shed light on the cyclization process. The activation free energy of the reacting subsystem embedded in a solvated dodecamer is estimated to be similar to 12.4 kcal/mol, which is similar to 3 kcal/mol higher than the value for the prototypical G[8-5m]T lesion inferred employing the same theoretical framework [Garrec, 3., Patel, C., Rothlisberger, U., and Dumont, E. (2012) J. Am. Chem. Soc. 134, 2111-2119]. This study also situates the G[8-5m]mC lesion at an intermediate activation free energy (similar to 10.5 kcal/mol). The order of reactivity in DNA (T-center dot > mC(center dot) > C-center dot) is reversed compared to that in the reacting subsystems in the gas phase (C-center dot > mC(center dot) > T-center dot), stressing the crucial role of the solvated B-helix environment. The results of our simulations also characterize a more severe distortion for G[8-5]C than for methylene-bridged intrastrand cross-links.

Amer Chemical Soc2013

Object-oriented approach for dynamic system modelling and simulation

Adel Besrour

Software engineering always cares to provide solutions for building applications as close as possible to what they should be, according to the requirements and the final users needs. Systems behavior simulation is a very common application to virtually reproduce and often predict the real-world behavior. Simulation is one of the most operational research tool in a large variety of engineering and scientific domains: Transport, telecommunication, medicine, chemical processes, physics, etc. The complexity of such application is relative to the increasing complexity of the systems. In this context, it is relevant to bring together different tools and formalisms such as markovian chain, Petri nets, etc., to improve the existent approaches and so to answer the simulations performances needs. The principle objective of this thesis is to bring together techniques from software engineering and safety engineering in order to improve the state of the art of modeling and simulation of dynamic systems in the industrial context. In addressing this objective, this work initially involves defining the essential limitations of the used formalisms, methods and tools regarding from one hand the software engineering modeling and simulation techniques and from the other hand the existent risk analysis methodologies. This work is conducted with respect to the problem of danger identification, considering the context of the complex systems behavior and their interaction with the human operator. In software engineering, it is well known that Petri/high-level nets have attractive characteristics to be used in systems simulation and behavior prediction such as the natural graphical representation, and their well-defined semantic. They are well-suited for the description of complex situations with concurrency (interleaving and true concurrency depending on the underlying semantics), conflict and confusion. However, the absence of structuring capabilities has been one of the main criticisms raised against Petri nets/high-level nets. Thus, there have been many attempts to introduce structuring principles in nets of this kind [BCM88] [Kie89] [JR91]. The attractive characteristics of Petri/high-level nets have prompted researchers to enrich these formalisms with object-oriented features. CO-OPN (Concurrent Object-Oriented Petri Net) approach, brings together the power of both Petri/high-level nets and object-orientation techniques, it has been devised so as to offer an adequate framework for the specification and design of large scale concurrent system [BG91]. CO-OPN, as a powerful modeling tool, has been used in a limited way to simulate systems. This work aims to provide a CO-OPN extension to allow a more realistic systems' simulation. Actually, its simulator semantic uses to be a suitable approach for modeling near closed systems and software components, because they need to loose coupling with external world. But, when we model more realistic problems like industrial processes, where human interaction is a relevant event, this approach is not sufficient to catch all system activity attributes. Moreover, the CO-OPN interpretation process does not allow interaction with the object internal states. This work provides a new solution to overcome CO-OPN simulation limitations and a set of prototypes to assist dynamic systems simulations. Furthermore, this work has been conducted in a Risk Analysis (RA) context, a domain where computer-based simulations research are of utmost interest. Actually, classical approaches used to address complex workplace hazard in a limited way, using checklists or sequence models. Moreover, the use of single oriented methods, such as AEA (man-oriented), FMEA (machine oriented) or HAZOP (process oriented), is not satisfactory to overcome the increasing sophistication of industrial processes. The automation of a part of the analysis process as well as the multiple-oriented approach allowed by dynamic modeling may indeed enhance significantly the analysis completeness and reduce the time analyzing time. This work, based on Object Oriented Petri net formalism (CO-OPN), propose an alternative multi-oriented approach where existent methods limitations have been criticized to develop a dynamic model, MORM (Man-machine Occupational Risk Modeling). A real industrial system (metal wire making process) has been specified to implement the different approach steps (system identification, model application, system simulation, system analysis).

EPFL2005

Object-oriented approach for dynamic system modelling and simulation

Adel Besrour

EPFL2005