MD of non-equilibrium processes

The thermalization is not always what we want. We may be interested in what happens, when a DNA molecule being anchored to a solid surface by one of its end functional groups is distorted by pulling the other end of the molecule. Such MD results may nowadays be compared to the corresponding experiment. 

And yet another example. A projectile hits a wall. The projectile is being composed of Lennard-Jones atoms (with some Sp and rg p, p. 287), we assume the same for the wall (for other values of the parameters, let us make the wall less 

Among more civil applications, we may think of the interaction of a drill and a steel plate, to plan better drills and better steel plates, as well as about other micro-tools which have a bright future. 

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The transmission coefficient has been computed here by using a positive flux formulation. The estimated value 0.44 0.05 is close to those obtained with classical MD simulations for related reactions. It illustrates the large amplitude of non-equilibrium effects on this process, especially if one considers that it is an upper limit to the transmission coefficient since we assume equilibrium at the transition state. Though this is a reasonable hypothesis, nonequilibrated situations may be also envisaged. Basically, this would increase the activation energy barrier modifying the exponential factor in the kinetic constant and contributing to a substantial transmission coefficient decrease. 

Monte Carlo (MC) methods can address the time gap problem of MD. The basis of MC methods is that the deterministic equations of the MD method are replaced by stochastic transitions for the slow processes in the system.3 MC methods are stochastic algorithms for exploring the system phase space although their implementation for equilibrium and non-equilibrium calculations presents some differences. 

Partial lipid extraction is considered as biologically important in several processes involving membranes, for example the fusion of membranes or enzymatic reactions with participation of phospholipids. To simulate this process, non-equilibrium or steered MD simulations can be used. This type of simulation was employed for the first time by Grubmuller et al. [96] to study the rupture of the binding in the strepta-vidin-biotin complex. Inspired by this pioneering work, similar studies have been undertaken to characterize the extraction of a phospholipid from the membrane. 

Normally, MD is performed at constant volume and constant total energy, yielding a microcanonical ensemble. For various reasons this is not very convenient and many approaches have appeared in the literature to yield a type of dynamics in which temperature and pressure are independent variables rather than derived properties. When MD is performed in non-equilibrium situations (NEMD non-equilibrium molecular dynamics) in order to study irreversible processes and transport properties, the... 

A modification of the Newtonian MD scheme with the purpose of generating a thermodynamical ensemble at constant temperature is called a thermostat algorithm. The use of a thermostat ean be motivated by one (or a number) of the following reasons (i) to match experimental conditions (most condensed-phase experiments are performed on thermostatized rather than isolated systems) (ii) to study temperature-dependent processes (e.g., determination of thermal coefficients, investigation of temperature-dependent conformational or phase transitions) (iii) to evacuate the heat in dissipative non-equilibrium MD simulations (e.g., computation of transport coefficients by viscous-flow or heat-flow simulations) (iv) to enhance the efficiency of a conformational search (e.g., high-temperature dynamics, simulated annealing) (v)... 

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