Atomistic detail

Atomistically detailed models account for all atoms. The force field contains additive contributions specified in tenns of bond lengtlis, bond angles, torsional angles and possible crosstenns. It also includes non-bonded contributions as tire sum of van der Waals interactions, often described by Lennard-Jones potentials, and Coulomb interactions. Atomistic simulations are successfully used to predict tire transport properties of small molecules in glassy polymers, to calculate elastic moduli and to study plastic defonnation and local motion in quasi-static simulations [fy7, ( ]. The atomistic models are also useful to interiDret scattering data [fyl] and NMR measurements [70] in tenns of local order. 

Although the folding of short proteins has been simulated at the atomic level of detail [159,160], a simplified protein representation is often applied. Simplifications include using one or a few interaction centers per residue [161] as well as a lattice representation of a protein [162]. Some methods are hierarchical in that they begin with a simplified lattice representation and end up with an atomistic detailed molecular dynamics simulation [163]. 

From this short discussion, it is clear that atomistically detailed molecular dynamics or Monte Carlo simulations can provide a wealth of information on systems on a local molecular atomistic level. They can, in particular, address problems where small changes in chemical composition have a drastic effect. Since chemical detail is avoided in mesoscopic models, these can often capture such effects only indirectly. 

Adsorption of water on salt crystals plays a key role in many atmospheric and environmental processes. Alkah halides in particular play an important role in the first stages of drop growth in clouds. To understand the atomistic details of the wetting and dissolution processes that take place in these crystals, we apphed SPFM to the smdy of the adsorption of water vapor on single crystal surfaces and the role of surface defects, such as steps. 

From Atomistic Detailed Polymers to a Continuous Model. 56... 

Mapping Atomistically Detailed Models of Flexible Polymer Chains in Melts to Coarse-Grained Lattice Descriptions ... 

There is great interest in the development of methods that allow the identification of a reasonably good structure with which to start the simulation of dense atomistically detailed polymer systems. The problem of generating dense polymer systems is formidable due to the high density and the connectivity of polymer systems. For crystal structures this can be systematically achieved [33,34] for amorphous structures, however, there is no generally satisfactory method available. Two recent developments in methods for generating amorphous packing (Santos, Suter) are reviewed in Section 3. 

An atomistically detailed force field typically contains at least terms for describing the following types of interactions ... 

In this review, the state of the art of the bridging of the gap between quantum chemical, atomistic, coarse-grained (and almost macroscopic) models of polymers has been discussed. Simulations with coarse-grained models provide the promise of the equilibration of models of dense amorphous polymers, whereas such equilibration is extremely difficult if the models are expressed in fully atomistic detail. The review presents the status of this rapidly developing field as of the beginning of 1998. A few minor additions were incorporated in the page proof, early in 2000, in response to suggestions from the reviewer. 

What is clear is that the overall strategy, in which the computationally intensive equilibration is performed with a model that does not have atomistic detail, but which can nevertheless be unambiguously identified with a specific real system with atomistic detail, markedly increases the utility of simulations for polymer science. It provides access to much larger systems, and to phenomena that occur on much longer time scales than could be investigated with simulations in which full atomistic detail is retained throughout. 

One of the important limitations of these methods, in their current state of development, is the necessity to conduct a new coarse-graining for each new type of polymer that is simulated. Major opportunities to increase the utility of this class of simulations lie in the development of methods, which make the mapping to the coarse-grained structure (and the reverse-mapping back to the structure expressed in fully atomistic detail) as general (and painless) as possible when new polymers are treated. This area is the subject of continuing work by all four groups. 

Many solvents do not possess the simple structure that allows their effects to be modeled by the Langevin equation or generalized Langevin equation used earlier to calculate the TS trajectory [58, 111, 112]. Instead, they must be described in atomistic detail if their effects on the effective free energies (i.e., the time-independent properties) and the solvent response (i.e., the nonequilibrium or time-dependent properties) associated with the... 

Khandogin J, Chen J, Brooks CL III (2006) Exploring atomistic details of pH-dependent peptide folding. Proc Natl Acad Sci USA 103 18546-18550. 

The nonelectrostatic components of the free energy such as the energy of cavity formation AGcav or components that take into account atomistic details of the medium (interactions between atoms inside the cavity and those in the medium) are calculated using empirical approximations (see Reference 164 for review or 165 for recent developments). These terms are do not affect the SCF procedure since their dependence on electron density p is usually neglected. 

Numerous experimental studies have investigated the atomistic details of HE decomposition by examining the net products after thermal (low-pressure) decomposition (see, for example, Ref. 54). For RDX and HMX, the rate limiting reaction is most likely NO2 dissociation and a plethora of final products in the decomposition process have been isolated. Several theoretical studies have also... 

MD simulations have provided a unique molecular description of cholesterol-phospholipid interactions [31]. Atomistic simulations have succeeded in reproducing the condensing effect of cholesterol on phospholipid bilayers [32-34], With atomistic detail, many properties can be determined, such as the effect of cholesterol on lipid chain ordering or on hydrogen bond formation. Other simulations have focused on the interaction of cholesterol and SM [35-37], Aittoniemi et al. [38] showed that hydrogen bonding alone cannot explain the preferential interaction between cholesterol and SM compared to cholesterol and POPC. 

The structure of crystalline surfaces is described briefly in Sections 9.1 and 12.2.1 and in Appendix B. All surfaces have a tendency to undergo a roughening transition at elevated temperatures and so become general. Even though a considerable effort has been made, many aspects of the atomistic details of surface diffusion are still unknown.6... 

There are many kinds of polymerizing monomers used to make up copolymers. These differ in physical and chemical properties. One of the most important differences (essential features) is their solubility, that is, how much they like or dislike a solvent, e.g., water. Hence the chemical and atomistic details of different monomeric units may not be necessary to understand the properties of many two-letter copolymers. In what follows, we will mainly use the so-called HP model [31]. This two-letter model of a linear hydrophobic/hydrophilic macromolecule reflects the spirit of minimalist models, in that it is simple yet based on a physical principle. 

While these models match experimental data reasonably well at lower fields, recent experiments at higher magnetic fields of 3.4 and 9.2 T show enhancement values that are much higher than predicted with the currently employed theory.41,72,79 At these higher fields, the timescale of molecular interactions that give rise to Overhauser DNP effects is much shorter (sub-picoseconds to picoseconds) and thus should be more sensitive to the rotational diffusion dynamics of water, closely related to the atomistic details of the radical and solvent, instead of translational diffusion dynamics. These atomistic details are not accurately represented in the FFHS or rotational models (Equations (13) and (15)), implying that further work needs to be done to develop more accurate models. 

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