Constraint methods for determining pathways and free energy of activated processes

Activated processes from chemical reactions up to conformational transitions of large biomolecules are hampered by barriers which are overcome only by the input of some free energy of activation. Hence, the characteristic and rate-determining barrier regions are not sufficiently sampled by usual simulation techniques. Constraints on a reaction coordinate r have turned out to be a suitable means to explore difficult pathways without changing potential function, energy or temperature. For a dense sequence of values of r, the corresponding sequence of simulations provides a pathway for the process. As only one coordinate among thousands is fixed during each simulation, the pathway essentially reflects the system's internal dynamics. From mean forces the free energy profile can be calculated to obtain reaction rates and insight in the reaction mechanism. In the last decade, theoretical tools and computing capacity have been developed to a degree where simulations give impressive qualitative insight in the processes at quantitative agreement with experiments. Here, we give an introduction to reaction pathways and coordinates, and develop the theory of free energy as the potential of mean force. We clarify the connection between mean force and constraint force which is the central quantity evaluated, and discuss the mass metric tensor correction. Well-behaved coordinates without tensor correction are considered. We discuss the theoretical background and practical implementation on the example of the reaction coordinate of targeted molecular dynamics simulation. Finally, we compare applications of constraint methods and other techniques developed for the same purpose, and discuss the limits of the approach

Flow and particle deposition using an integrated CFD model of the respiratory system

This paper was presented at the 3rd Micro and Nano Flows Conference (MNF2011), which was held at the Makedonia Palace Hotel, Thessaloniki in Greece. The conference was organised by Brunel University and supported by the Italian Union of Thermofluiddynamics, Aristotle University of Thessaloniki, University of Thessaly, IPEM, the Process Intensification Network, the Institution of Mechanical Engineers, the Heat Transfer Society, HEXAG - the Heat Exchange Action Group, and the Energy Institute.In the present study a theoretical investigation on flow, particle motion, and deposition in the respiratory system is reported. An integrated computational model of the respiratory system is developed comprised of nine sequential computational blocks corresponding to the nasal cavity, the pharyngo-trachea, and a series of branches of the pulmonary system. Airflow during steady-state inhalation inside the human respiratory system was determined using computational fluid dynamics (CFD) for inlet velocities, vin = 1-20 m/s, corresponding to inhalation flow rates of 9 to 180 L/min, and particle deposition was examined in detail for particle sizes, D=1-20μm. Local deposition efficiencies as well as spatial distribution of deposited particles were found to be strongly dependent on the particle size and volumetric flow rate

Experimental and numerical investigation on mixing and axial dispersion in Taylor-Couette flow patterns

Taylor-Couette flows between two concentric cylinders have great potential applications in chemical engineering. They are particularly convenient for two-phase small scale devices enabling solvent extraction operations. An experimental device was designed with this idea in mind. It consists of two concentric cylinders with the inner one rotating and the outer one fixed. Moreover, a pressure driven axial flow can be superimposed. Taylor-Couette flow is known to evolve towards turbulence through a sequence of successive hydrodynamic instabilities. Mixing characterized by an axial dispersion coefficient is extremely sensitive to these flow bifurcations, which may lead to flawed modelling of the coupling between flow and mass transfer. This particular point has been studied using experimental and numerical approaches. Direct numerical simulations (DNS) of the flow have been carried out. The effective diffusion coefficient was estimated using particles tracking in the different Taylor-Couette regimes. Simulation results have been compared with literature data and also with our own experimental results. The experimental study first consists in visualizing the vortices with a small amount of particles (Kalliroscope) added to the fluid. Tracer residence time distribution (RTD) is used to determine dispersion coefficients. Both numerical and experimental results show a significant effect of the flow structure on the axial dispersion