Time scales applications

Lewis J W, Tilton R F, Einterz C M, Milder S J, Kuntz I D and Kliger D S 1985 New technique for measuring circular dichroism changes on a nanosecond time scale. Application to (carbonmonoxy)myoglobin and (carbonmonoxy)hemoglobin J. Rhys. Chem. 89 289-94... 

The uranium and thorium decay-series contain radioactive isotopes of many elements (in particular, U, Th, Pa, Ra and Rn). The varied geochemical properties of these elements cause nuclides within the chain to be fractionated in different geological environments, while the varied half-lives of the nuclides allows investigation of processes occurring on time scales from days to 10 years. U-series measurements have therefore revolutionized the Earth Sciences by offering some of the only quantitative constraints on time scales applicable to the physical processes that take place on the Earth. 

General Discussions. The vaporization configuration is shown in Figure la. For pure vaporization the "fiame is simply the ambience. We first present some general concepts and identify certain important time scales applicable to many situations pertaining to droplet vaporization. 

Shackleton N.J., Crowhurst S., Hagelberg T., Pisias N.G., Scheider D.A. (1995) A new Late Neogene time scale application to leg 138 sites. Proc. Ocean Drilling Prog. 138, 73-101. 

A promising technique is cavity ringdown laser absorption spectroscopy (307), in which the rate of decay of laser pulses injected into an optical cavity containing the sample is measured. Absorption sensitivities of 5 x 10-7 have been measured on a Ts time scale. Applications from the uv to the ir... 

Viscoelastic material such as polymers combine the characteristics of both elastic and viscous materials. They often exhibit elements of both Hookean elastic solid and pure viscous flow depending on the experimental time scale. Application of stresses of relatively long duration may cause some flow and irrecoverable (permanent) deformation, while a rapid shearing will induce elastic response in some polymeric fluids. Other examples of viscoelastic response include creep and stress relaxation, as described previously. 

T2—transverse relaxation times—allows the observation of the processes in 10 to 10 s time scale. Application of MAS technique, due to increasing the sensitivity, enables to extend the time scale to the range 10 to 10 s. 

Because of the generality of the symmetry principle that underlies the nonlinear optical spectroscopy of surfaces and interfaces, the approach has found application to a remarkably wide range of material systems. These include not only the conventional case of solid surfaces in ultrahigh vacuum, but also gas/solid, liquid/solid, gas/liquid and liquid/liquid interfaces. The infonnation attainable from the measurements ranges from adsorbate coverage and orientation to interface vibrational and electronic spectroscopy to surface dynamics on the femtosecond time scale. 

Many of the fiindamental physical and chemical processes at surfaces and interfaces occur on extremely fast time scales. For example, atomic and molecular motions take place on time scales as short as 100 fs, while surface electronic states may have lifetimes as short as 10 fs. With the dramatic recent advances in laser tecluiology, however, such time scales have become increasingly accessible. Surface nonlinear optics provides an attractive approach to capture such events directly in the time domain. Some examples of application of the method include probing the dynamics of melting on the time scale of phonon vibrations [82], photoisomerization of molecules [88], molecular dynamics of adsorbates [89, 90], interfacial solvent dynamics [91], transient band-flattening in semiconductors [92] and laser-induced desorption [93]. A review article discussing such time-resolved studies in metals can be found in... 

The example above of tire stopped-flow apparatus demonstrates some of tire requirements important for all fonns of transient spectroscopy. These are tire ability to provide a perturbation (pump) to tire physicochemical system under study on a time scale tliat is as fast or faster tlian tire time evolution of tire process to be studied, the ability to synclironize application of tire pump and tire probe on tliis time scale and tire ability of tire detection system to time resolve tire changes of interest. 

How does one monitor a chemical reaction tliat occurs on a time scale faster tlian milliseconds The two approaches introduced above, relaxation spectroscopy and flash photolysis, are typically used for fast kinetic studies. Relaxation metliods may be applied to reactions in which finite amounts of botli reactants and products are present at final equilibrium. The time course of relaxation is monitored after application of a rapid perturbation to tire equilibrium mixture. An important feature of relaxation approaches to kinetic studies is that tire changes are always observed as first order kinetics (as long as tire perturbation is relatively small). This linearization of tire observed kinetics means... 

We assume that the unbinding reaction takes place on a time scale long ( ompared to the relaxation times of all other degrees of freedom of the system, so that the friction coefficient can be considered independent of time. This condition is difficult to satisfy on the time scales achievable in MD simulations. It is, however, the most favorable case for the reconstruction of energy landscapes without the assumption of thermodynamic reversibility, which is central in the majority of established methods for calculating free energies from simulations (McCammon and Harvey, 1987 Elber, 1996) (for applications and discussion of free energy calculation methods see also the chapters by Helms and McCammon, Hermans et al., and Mark et al. in this volume). 

The first term represents the forces due to the electrostatic field, the second describes forces that occur at the boundary between solute and solvent regime due to the change of dielectric constant, and the third term describes ionic forces due to the tendency of the ions in solution to move into regions of lower dielectric. Applications of the so-called PBSD method on small model systems and for the interaction of a stretch of DNA with a protein model have been discussed recently ([Elcock et al. 1997]). This simulation technique guarantees equilibrated solvent at each state of the simulation and may therefore avoid some of the problems mentioned in the previous section. Due to the smaller number of particles, the method may also speed up simulations potentially. Still, to be able to simulate long time scale protein motion, the method might ideally be combined with non-equilibrium techniques to enforce conformational transitions. 

Abstract. Molecular dynamics (MD) simulations of proteins provide descriptions of atomic motions, which allow to relate observable properties of proteins to microscopic processes. Unfortunately, such MD simulations require an enormous amount of computer time and, therefore, are limited to time scales of nanoseconds. We describe first a fast multiple time step structure adapted multipole method (FA-MUSAMM) to speed up the evaluation of the computationally most demanding Coulomb interactions in solvated protein models, secondly an application of this method aiming at a microscopic understanding of single molecule atomic force microscopy experiments, and, thirdly, a new method to predict slow conformational motions at microsecond time scales. 

As an example for an efficient yet quite accurate approximation, in the first part of our contribution we describe a combination of a structure adapted multipole method with a multiple time step scheme (FAMUSAMM — fast multistep structure adapted multipole method) and evaluate its performance. In the second part we present, as a recent application of this method, an MD study of a ligand-receptor unbinding process enforced by single molecule atomic force microscopy. Through comparison of computed unbinding forces with experimental data we evaluate the quality of the simulations. The third part sketches, as a perspective, one way to drastically extend accessible time scales if one restricts oneself to the study of conformational transitions, which arc ubiquitous in proteins and are the elementary steps of many functional conformational motions. 

The previous application — in accord with most MD studies — illustrates the urgent need to further push the limits of MD simulations set by todays computer technology in order to bridge time scale gaps between theory and either experiments or biochemical processes. The latter often involve conformational motions of proteins, which typically occur at the microsecond to millisecond range. Prominent examples for functionally relevant conformatiotial motions... 

The upper hmit of a gas concentration measurement range is usually 1.5 to 2.5 times the applicable emission limit. If no span value is provided, a span value equivalent to 1.5 to 2.5 times the expected concentration is used. For convenience, the span value should correspond to 100 percent of the recorder scale. 

From shock compression of LiF to 13 GPa [68] these results demonstrate that X-ray diffraction can be applied to the study of shock-compressed solids, since diffraction effects can be observed. The fact that diffraction takes place at all implies that crystalline order can exist behind the shock front and the required readjustment to the shocked lattice configuration takes place on a time scale less than 20 ns. Another important experimental result is that the location of (200) reflection implies that the compression is isotropic i.e., shock compression moves atoms closer together in all directions, not just in the direction of shock propoagation. Similar conclusions are reached for shock-compressed single crystals of LiF, aluminum, and graphite [70]. Application of these experimental techniques to pyrolytic BN [71] result in a diffraction pattern (during compression) like that of wurtzite. 

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