Molecular dynamics kinetic cycle

Molecular-dynamics (MD) simulations [14, 17, 18] provide one way of taking a model of a complex structure to an energy minimum. In an MD simulation, the atoms in the starting model are assigned random initial velocities consistent with the total kinetic energy at a chosen temperature, and are allowed to move for a brief interval of time (typically 1 or 2 fs) the forces on each atom then are evaluated from the first derivatives of the potential-energy function (Eq. B6.1.18) with respect to the coordinates, and the resulting accelerations are calculated and used to update the velocities. The system is allowed to move for another interval, the forces are reevaluated, and this cycle is iterated many times with periodic corrections... 

The life cycle of these organelles, their kinetics and molecular cargo, the molecular motors driving their transport and the substrates along which these movements track constitute interrelated aspects of what is broadly termed axonal transport. A primary aim of this chapter is to provide an understanding of this form of intraneuronal traffic. Achieving this goal requires an appreciation of the dynamics and structure of the relevant neuronal components and structures. Studies of how cellular structures and components move from where they are synthesized to where they are utilized comprise an... 

The available data from emulsion polymerization systems have been obtained almost exclusively through manual, off-line analysis of monomer conversion, emulsifier concentration, particle size, molecular weight, etc. For batch systems this results in a large expenditure of time in order to sample with sufficient frequency to accurately observe the system kinetics. In continuous systems a large number of samples are required to observe interesting system dynamics such as multiple steady states or limit cycles. In addition, feedback control of any process variable other than temperature or pressure is impossible without specialized on-line sensors. This note describes the initial stages of development of two such sensors, (one for the monitoring of reactor conversion and the other for the continuous measurement of surface tension), and their implementation as part of a computer data acquisition system for the emulsion polymerization of methyl methacrylate. 

Enzymes are flexible moieties whose structures exhibit dynamic fluctuations on a wide range of timescales. This inherent mobility of a protein fold was shown to be manifested in the various steps constituting the catalytic cycle. The nature of this linkage between protein structure movement and function undoubtedly is complex and might involve the formation of a coupled network of interactions that bring the substrate closer, orient it properly, and provide a favorable electrostatic environment in which the chemical reaction can occur (45). However, the molecular details that link the catalytic chemistry to key kinetic, electronic, and structural events have remained elusive because of the difficulties associated with probing time-dependent, structure-function aspects of enzymatic reactions. 

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