Landscaping

Figure B3.3.10. Contour plots of the free energy landscape associated with crystal niicleation for spherical particles with short-range attractions. The axes represent the number of atoms identifiable as belonging to a high-density cluster, and as being in a crystalline environment, respectively, (a) State point significantly below the metastable critical temperature. The niicleation pathway involves simple growth of a crystalline nucleus, (b) State point at the metastable critical temperature. The niicleation pathway is significantly curved, and the initial nucleus is liqiiidlike rather than crystalline. Thanks are due to D Frenkel and P R ten Wolde for this figure. For fiirther details see [189].

Wolynes P G 1996 Symmetry and the energy landscape of biomolecules Proc. Natl Acad. Sci. (USA) 93 14 249-55... 

Bryngelson J D, Onuchic J N, Socci N D and Wolynes P G 1995 Funnels, pathways, and the energy landscape of protein folding a synthesis Profe/ns 21 167-95... 

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). 

Figure 8 shows a one-dimensional sketch of a small fraction of that energy landscape (bold line) including one conformational substate (minimum) as well as, to the right, one out of the typically huge number of barriers separating this local minimum from other ones. Keeping this picture in mind the conformational dynamics of a protein can be characterized as jumps between these local minima. At the MD time scale below nanoseconds only very low barriers can be overcome, so that the studied protein remains in or close to its initial conformational substate and no predictions of slower conformational transitions can be made. 

Hans Prauenfelder, Sthephen G. Sligar, and Peter G. Wolynes. The energy landscape and motions of proteins. Science., 254 1598-1603, 1991. 

Fig. 5. The left hand side figure shows a contour plot of the potential energy landscape due to V4 with equipotential lines of the energies E = 1.5, 2, 3 (solid lines) and E = 7,8,12 (dashed lines). There are minima at the four points ( 1, 1) (named A to D), a local maximum at (0, 0), and saddle-points in between the minima. The right hand figure illustrates a solution of the corresponding Hamiltonian system with total energy E = 4.5 (positions qi and qs versus time t).

H and B J Berne 1999. Multicanonical Jump Walking A Method for Efficiently Sampling Rough Energy Landscapes. Journal of Chemical Physics 110 10299-10306. 

Fig. 10.27 Schematic representation of the energy landscape for protein folding. (Figure adapted from Onuchic ] N, Z Luthcy-Schulten and P Wolynes 1997. Theory of Protein Folding The Energy Landscape Perspective. Annual Reviews in Physical Chemistry 48 545-600.)...

Bryngelson J D, J N Onuchic, N D Socci and P G Wolynes 1995. Funnels, Pathways, and the Energy Landscape of Protein Folding A Synthesis. Proteins Structure, Function and Genetics 21 167-195. 

Meanwhile, in a stateiy iaboratory atop a hill, the second finest alchemist in the land cast her sight beyond her potions and upon the landscape below. The troubles in her land prompted her to speak aloud, "How have things come to this Although I am pleased for the good fortune that has come to my friends who contract and build dungeons, and who enforce the bee pollen laws, I cannot help but feel that...that...aw fucketh it ". And for no... 

The dominant role of petroleum in the chemical industry worldwide is reflected in the landscapes of, for example, the Ruhr Valley in Germany and the U.S. Texas/Louisiana Gulf Coast, where petrochemical plants coimected by extensive and complex pipeline systems dot the countryside. Any movement to a different feedstock would require replacement not only of the chemical plants themselves, but of the expensive infrastmcture which has been built over the last half of the twentieth century. Moreover, because petroleum is a Hquid which can easily be pumped, change to any of the soHd potential feedstocks (like coal and biomass) would require drastic changes in feedstock handling systems. 

Storage areas for maintenance, janitorial, and other service organizations must be provided. Safety items such as fire extinguishers, firehose cabinets, safety hoops on permanent ladders, guard rads, shielding for acid pumps, clearance for electric panel boards, etc, are needed. Manholes and cleanouts for sewer pipes within the facility as well as in the landscape and parking areas should be provided. 

Light-Duty Recreational Surfaces. Artificial surfaces intended for incidental recreational use, eg, swimming pool decks, patios, and landscaping, are designed primarily to provide a practical, durable, and attractive surface. Minimum cost is a prime consideration and has driven the quaUty of some such products to a low level. Most surfaces in this category utilize polypropylene ribbon and a tufted fabric constmction (see Olefin polymers, polypropylene). ... 

Many factors affect the mechanisms and kinetics of sorption and transport processes. For instance, differences in the chemical stmcture and properties, ie, ionizahility, solubiUty in water, vapor pressure, and polarity, between pesticides affect their behavior in the environment through effects on sorption and transport processes. Differences in soil properties, ie, pH and percentage of organic carbon and clay contents, and soil conditions, ie, moisture content and landscape position climatic conditions, ie, temperature, precipitation, and radiation and cultural practices, ie, crop and tillage, can all modify the behavior of the pesticide in soils. Persistence of a pesticide in soil is a consequence of a complex interaction of processes. Because the persistence of a pesticide can govern its availabiUty and efficacy for pest control, as weU as its potential for adverse environmental impacts, knowledge of the basic processes is necessary if the benefits of the pesticide ate to be maximized. 

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