Simulation graph model

Pastor, M., Perez, C., and Gago, F. (1997) Simulation of alternative binding modes in a structure-based QSAR study of HIV-1 protease inhibitors.. /. Mol. Graph. Model. 15, 364-371. 

The whole micropump is described in a bond graph model [43]. The pump is driven by a (square-wave) heat source. Simulation results of the pump actuation as well as the pump rate based on this model are given in Figs 22 and 23... 

Marelius J, Kolmodin K, Feierberg I, Aqvist J (1998) Q a molecular dynamics program for free energy calculations and empirical valence bond simulations in biomolecular systems. J Mol Graph Model 16(4-6) 213-225, 261... 

Lu SY, Jiang YJ, Zou JW, Wu TX (2011) Molecular modeling and molecular dynamics simulation studies on pyrrolopyrimidine-based alpha-helix mimetic as dual inhibitors of MDM2 and MDMX. J Mol Graph Model 30467-178... 

Verkhivker GM (2004) Computational analysis of ligand binding dynamics at the intermolecular hot spots with the aid of simulated tempering and binding free energy calculations, Mol J Graph Model, 22(5) 335-348... 

Wen EZ, Hsieh MJ, Kollman PA, Luo R (2004) Enhanced ab initio protein folding simulations in Poisson-Boltzmann molecular dynamics with self guiding forces, J Mol Graph Model, 22 415—424... 

Okamoto, Y. Generalized-ensemble algorithms Enhanced sampling techniques for Monte Carlo and molecular dynamics simulations. J. Mol. Graph. Model. 2004, 22, 425-39. 

El-Bastawissy E, Knaggs MH, Gilbert IH (2001) Molecular dynamics simulations of wild-type and point mutation human prion protein at normal and elevated temperature. J Mol Graph Model 20 145... 

Gsponer J, Ferrara P, Caflisch A (2001) Flexibility of the murine prion protein and its Asp 178 Asn mutant investigated by molecular dynamics simulations. J Mol Graph Model 20 169... 

Another application of the graph model is to derive equivalence for certain parts of the model. In analysis and simulation of the model, it is often desirable to combine several components to an equivalent single component. The overall reduction of a model to a minimal system will be of great value not only for computations but also for theoretical study of essential characteristics of the system and comparison to the traditional compartment modeling. The graph model will facilitate the development of such equivalence transformations. 

Beyond model development for the purpose of analysis and simulation of the dynamic or the frequency domain behaviour, bond graphs have also proven useful as a tool for model-based FDI in engineering systems represented by continuous time models. Only recently, bond graph model-based FDI has also been used for systems described by a hybrid model. Following common terminology a system will be called a hybrid system for short if its dynamic behaviour is appropriately described by a hybrid model. In Chap. 2.1 of [1] Kowalewski rightly remarks ... 

Bond Graph Models and Discrete Event Simulation... 

Simulation results in Fig.4.17 obtained by numerical evaluation of the coupled bond graph models in Fig. 4.16 confirm that residuals V2 and indicate this change in the behavioural model of the real circuit in accordance with the FSM in Table4.1. 

For this simulation, the residual sinks have been replaced by bond graph models depicted in Fig. 4.15. The simulation run performed with the dassl solver has used the... 

Borutzky, W. (2012). Bond graph modelling and simulation of fault scenarios in switched power electronic systems. Proceedings IMechE Part I J Systems and Control Engineering, (pp. 1381-1393). 

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