Molecular dynamics mechanisms

Adaptation of molecular dynamics/mechanics, ab initio approaches to polymer blend problems. 

There is, of course, a mass of rather direct evidence on orientation at the liquid-vapor interface, much of which is at least implicit in this chapter and in Chapter IV. The methods of statistical mechanics are applicable to the calculation of surface orientation of assymmetric molecules, usually by introducing an angular dependence to the inter-molecular potential function (see Refs. 67, 68, 77 as examples). Widom has applied a mean-held approximation to a lattice model to predict the tendency of AB molecules to adsorb and orient perpendicular to the interface between phases of AA and BB [78]. In the case of water, a molecular dynamics calculation concluded that the surface dipole density corresponded to a tendency for surface-OH groups to point toward the vapor phase [79]. 

We have alluded to the comrection between the molecular PES and the spectroscopic Hamiltonian. These are two very different representations of the molecular Hamiltonian, yet both are supposed to describe the same molecular dynamics. Furthemrore, the PES often is obtained via ab initio quairtum mechanical calculations while the spectroscopic Hamiltonian is most often obtained by an empirical fit to an experimental spectrum. Is there a direct link between these two seemingly very different ways of apprehending the molecular Hamiltonian and dynamics And if so, how consistent are these two distinct ways of viewing the molecule ... 

There are also approaches [, and M] to control that have had marked success and which do not rely on quantum mechanical coherence. These approaches typically rely explicitly on a knowledge of the internal molecular dynamics, both in the design of the experiment and in the achievement of control. So far, these approaches have exploited only implicitly the very simplest types of bifiircation phenomena, such as the transition from local to nonnal stretch modes. If fiittlier success is achieved along these lines m larger molecules, it seems likely that deliberate knowledge and exploitation of more complicated bifiircation phenomena will be a matter of necessity. 

In equilibrium statistical mechanics, one is concerned with the thennodynamic and other macroscopic properties of matter. The aim is to derive these properties from the laws of molecular dynamics and thus create a link between microscopic molecular motion and thennodynamic behaviour. A typical macroscopic system is composed of a large number A of molecules occupying a volume V which is large compared to that occupied by a molecule ... 

Progress in the theoretical description of reaction rates in solution of course correlates strongly with that in other theoretical disciplines, in particular those which have profited most from the enonnous advances in computing power such as quantum chemistry and equilibrium as well as non-equilibrium statistical mechanics of liquid solutions where Monte Carlo and molecular dynamics simulations in many cases have taken on the traditional role of experunents, as they allow the detailed investigation of the influence of intra- and intemiolecular potential parameters on the microscopic dynamics not accessible to measurements in the laboratory. No attempt, however, will be made here to address these areas in more than a cursory way, and the interested reader is referred to the corresponding chapters of the encyclopedia. 

Leforestier C et ak 1991 Time-dependent quantum mechanical methods for molecular dynamics J. Comput. Phys. 94 59-80... 

At any geometry g.], the gradient vector having components d EjJd Q. provides the forces (F. = -d Ej l d 2.) along each of the coordinates Q-. These forces are used in molecular dynamics simulations which solve the Newton F = ma equations and in molecular mechanics studies which are aimed at locating those geometries where the F vector vanishes (i.e. tire stable isomers and transition states discussed above). 

Tuckerman M E and Hughes A 1998 Path integral molecular dynamics a computational approach to quantum statistical mechanics Classical and Quantum Dynamics In Condensed Phase Simulations ed B J Berne, G Ciccotti and D F Coker (Singapore World Scientific) pp 311-57... 

A comprehensive introduction to the field, covering statistical mechanics, basic Monte Carlo, and molecular dynamics methods, plus some advanced techniques, including computer code. 

A comprehensive and up-to-date introduction to the ideas of molecular dynamics and Monte Carlo, with statistical mechanical background, advanced teclmiques and case studies, supported by a Web page for software download. 

The complexity of polymeric systems make tire development of an analytical model to predict tlieir stmctural and dynamical properties difficult. Therefore, numerical computer simulations of polymers are widely used to bridge tire gap between tire tlieoretical concepts and the experimental results. Computer simulations can also help tire prediction of material properties and provide detailed insights into tire behaviour of polymer systems. A simulation is based on two elements a more or less detailed model of tire polymer and a related force field which allows tire calculation of tire energy and tire motion of tire system using molecular mechanisms, molecular dynamics, or Monte Carlo teclmiques 1631. 

Equation (C3.5.3) shows tire VER lifetime can be detennined if tire quantum mechanical force-correlation Emotion is computed. However, it is at present impossible to compute tliis Emotion accurately for complex systems. It is straightforward to compute tire classical force-correlation Emotion using classical molecular dynamics (MD) simulations. Witli tire classical force-correlation function, a quantum correction factor Q is needed 5,... 

Information about critical points on the PES is useful in building up a picture of what is important in a particular reaction. In some cases, usually themially activated processes, it may even be enough to describe the mechanism behind a reaction. However, for many real systems dynamical effects will be important, and the MEP may be misleading. This is particularly true in non-adiabatic systems, where quantum mechanical effects play a large role. For example, the spread of energies in an excited wavepacket may mean that the system finds an intersection away from the minimum energy point, and crosses there. It is for this reason that molecular dynamics is also required for a full characterization of the system of interest. 

Prenkel, D. Pree energy computation and first order phase transitions. In Molecular Dynamic Simulation of Statistical Mechanical Systems, Enrico Fermi Summer School, Varenna 1985, G. Ciccotti and W. Hoover, eds. North Holland, Amsterdam (1986) 43-65. 

Berendsen, H.J.C., Postma, J.P.M., Van Gunsteren, W.F. Statistical mechanics and molecular dynamics The calculation of free energy, in Molecular Dynamics and Protein Structure, J. Hermans, ed.. Polycrystal Book Service, PO Box 27, Western Springs, 111., USA, (1985) 43-46. 

Field, M.J., Bash, P.A., Karplus, M. A combined quantum mechanical and molecular mechanical potential for molecular dynamics simulations. J. Comput. Chem. 11 (1990) 700-733. 

Bala, P., Grochowsky, R, Lesyng, B., McCammon, J.A. Quantum-classical molecular dynamics. Models and applications. In Quantum mechanical simulation methods for studying biological systems, D. Bicout and M. Field, eds. Springer, Berlin (1996) 119-156. 

Cao, J., Voth, G.A. The formulation of quantum statistical mechanics based on the Feynman path centroid density. I. Equilibrium properties. J. Chem. Phys. 100 (1994) 5093-5105 II Dynamical properties. J. Chem. Phys. 100 (1994) 5106-5117 III. Phase space formalism and nalysis of centroid molecular dynamics. J. Chem. Phys. 101 (1994) 6157-6167 IV. Algorithms for centroid molecular dynamics. J. Chem. Phys. 101 (1994) 6168-6183 V. Quantum instantaneous normal mode theory of liquids. J. Chem. Phys. 101 (1994) 6184 6192. 

The simulations also revealed that flapping motions of one of the loops of the avidin monomer play a crucial role in the mechanism of the unbinding of biotin. The fluctuation time for this loop as well as the relaxation time for many of the processes in proteins can be on the order of microseconds and longer (Eaton et al., 1997). The loop has enough time to fluctuate into an open state on experimental time scales (1 ms), but the fluctuation time is too long for this event to take place on the nanosecond time scale of simulations. To facilitate the exit of biotin from its binding pocket, the conformation of this loop was altered (Izrailev et al., 1997) using the interactive molecular dynamics features of MDScope (Nelson et al., 1995 Nelson et al., 1996 Humphrey et al., 1996). 

Zigmond, 1988). The ATP-hydrolysis that accompanies actin polymerization, ATP —> ADP + Pj, and the subsequent release of the cleaved phosphate (Pj) are believed to act as a clock (Pollard et ah, 1992 Allen et ah, 1996), altering in a time-dependent manner the mechanical properties of the filament and its propensity to depolymerize. Molecular dynamics simulations suggested a so-called back door mechanism for the hydrolysis reaction ATP ADP - - Pj in which ATP enters the actin from one side, ADP leaves from the same side, but Pj leaves from the opposite side, the back door (Wriggers and Schulten, 1997b). This hypothesis can explain the effect of the toxin phalloidin which blocks the exit of the putative back door pathway and, thereby, delays Pi release as observed experimentally (Dancker and Hess, 1990). 

Wriggers and Schulten, 1998] Wriggers, W., and Schulten, K. Investigating a back door mechanism of actin phosphate release by steered molecular dynamics. Biophys. J. Submitted. 

In molecular mechanics and molecular dynamics studies of proteins, assig-ment of standard, non-dynamical ionization states of protein titratable groups is a common practice. This assumption seems to be well justified because proton exchange times between protein and solution usually far exceed the time range of the MD simulations. We investigated to what extent the assumed protonation state of a protein influences its molecular dynamics trajectory, and how often our titration algorithm predicted ionization states identical to those imposed on the groups, when applied to a set of structures derived from a molecular dynamics trajectory [34]. As a model we took the bovine... 

Yoshida, H. Recent Progress in the Theory and Application of Symplectic Integrators. Celestial Mechanics and Dynamical Astronomy 56 (1993) 27-43 Trobec, R., Merzel, F., Janezic, D. On the Complexity of Parallel Symplectic Molecular Dynamics Algorithms. J. Chem. Inf. Comput. Sci. 37 (1997) 1055-1062... 

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