Simulation techniques, single molecule

Experimental techniques based on the application of mechanical forces to single molecules in small assemblies have been applied to study the binding properties of biomolecules and their response to external mechanical manipulations. Among such techniques are atomic force microscopy (AFM), optical tweezers, biomembrane force probe, and surface force apparatus experiments (Binning et al., 1986 Block and Svoboda, 1994 Evans et ah, 1995 Israelachvili, 1992). These techniques have inspired us and others (see also the chapters by Eichinger et al. and by Hermans et al. in this volume) to adopt a similar approach for the study of biomolecules by means of computer simulations. 

In this chapter, we review important concepts regarding vibrational spectroscopy with the STM. First, the basis of the technique will be introduced, together with some of the most relevant results produced up to date. It will be followed by a short description of experimental issues. The third section introduces theoretical approaches employed to simulate the vibrational excitation and detection processes. The theory provides a molecular-scale view of excitation processes, and can foresee the role of various parameters such as molecular symmetry, adsorption properties, or electronic structure of the adsorbate. Finally, we will describe current approaches to understand quenching dynamics via internal molecular pathways, leading to several kinds of molecular evolution. This has been named single-molecule chemistry. 

The polarizable point dipole model has also been used in Monte Carlo simulations with single particle moves.When using the iterative method, a whole new set of dipoles must be computed after each molecule is moved. These updates can be made more efficient by storing the distances between all the particles, since most of them are unchanged, but this requires a lot of memory. The many-body nature of polarization makes it more amenable to molecular dynamics techniques, in which all particles move at once, compared to Monte Carlo methods where typically only one particle moves at a time. For nonpolarizable, pairwise-additive models, MC methods can be efficient because only the interactions involving the moved particle need to be recalculated [while the other (N - 1) x (]V - 1) interactions are unchanged]. For polarizable models, all N x N interactions are, in principle, altered when one particle moves. Consequently, exact polarizable MC calculations can be... 

Dissipative particle dynamics (DPD) is a simulation technique initially developed for the simulation of complex fluids [18] and later extended for polymers. The DPD model consists of pointlike particles interacting with each other through a set of prescribed forces [19]. From a physical point of view, each dissipative particle is regarded not as a single atom or molecule but rather as a collection of atomic groups (molecules) that move in a coherent fashion. 

Figure 6. The first single-molecule optical spectra, showing use of the FM/Stark technique for pentacene in />-terphenyl. (a) Simulation of absorption line with (power-broadened) linewidth of 65 MHz. (b) Simulation of FM spectrum for (a), com = 75 MHz. (c) Simulation of FM/Stark line-shape, (d) single-molecule spectra at 592.423 nm, 512 averages, 8 traces overlaid, bar shows value of 2o)m = 150 MHz. (e) Average of traces in (d) with fit to the in-focus molecule (smooth curve), (f) Signal far off line at 597.514 nm. (g) Traces of SFSatthe O2 line center, 592.186 nm. After Ref. 1.

However, single molecule molecular dynamics for liquid crystal molecules can often be problematic. Many liquid crystal systems have torsional energy barriers in excess of 12 kJ mol separating conformations of similar energy (see Sec. 3.2.1). Such barriers can be difficult to cross during the course of a short MD simulation, and this can result in molecules becoming periodically trapped in regions of phase space. This has led to the development of stochastic dynamics techniques where random noise added to the equations of motion is de-... 

Single-chain-in-mean-field (SCMF) simulation [40-42, 86] is an approximate, computational method that retains the computational advantage of self-consistent field theory but additionally includes fluctuation effects because, in contrast to self-consistent theory, SCMF simulations aim at preserving the instantaneous description of the fluctuating interactions of a segment with its environment. In this partide-based simulation technique, one studies an ensemble of molecules in fluctuating, real, external fields. The explicit particle coordinates are the degrees of freedom and not the collective variables, densities and fields. 

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