Atomic-level simulations

In an atomic level simulation, the bond stretch vibrations are usually the fastest motions in the molecular dynamics of biomolecules, so the evolution of the stretch vibration is taken as the reference propagator with the smallest time step. The nonbonded interactions, including van der Waals and electrostatic forces, are the slowest varying interactions, and a much larger time-step may be used. The bending, torsion and hydrogen-bonding forces are treated as intermediate time-scale interactions. 

Ding H-Q, N Karasawa and W A Goddard III 1992a. Atomic Level Simulations on a Milhon Particles The Cell Multipole Method for Coulomb and London Nonbonding Interactions. Journal of Chemical Physics 97 4309-4315. 

Atomic-level simulation has been used extensively in the study of friction, not simply as a means of supplementing experimental studies, but... 

A typical model system used in tribological simulations is shown in Figure 8. In this system, two walls are separated by a fluid and shear is applied by pulling the top wall with an external device, whereas the bottom wall is held fixed. In atomic-level simulations, the two walls correspond to atomically discrete surfaces and the fluid is composed of atoms or molecules, which represent lubricants or contaminants. 

Molecular dynamics simulations are attractive because they can provide not only quantitative information about rates and pathways of reactions, but also valuable insight into the details of ho y the chemistry occurs. Furthermore, a dynamical treatment is required if the statistical assumption is not valid. Yet another reason for interest in explicit atomic-level simulations of the gas-phase reactions is that they contribute to the formulation of condensed-phase models and, of course, are needed if one is to include the initial stages of the vapor-phase chemistry in the simulations of the decomposition of energetic materials. These and other motivations have lead to a lot of efforts to develop realistic atomic-level models that can be used in MD simulations of the decomposition of gas-phase energetic molecules. 

Modifications to the crystal structure of choice are necessary before starting any atomic-level simulations. The critical points to consider in order to prepare the best biophysical system with the X REL1 crystal structure are presented here (see Note 1). 

Finally, protonation states of all titratable residues should be determined before any atomic-level simulation. Several programs, such as WHATIF (16) and PROPKA (17-19) (see Notes 5 and 6), exist to predict protonation states of standard residues. 

Because numerous programs are available to pursue atomic-level simulations and docking, we do not review in detail the input parameters of each program here. We instead list the available programs and refer the reader to the manuals of each program for specific details. Additionally, we present the published atomic-level simulation and docking studies on T REL1 to provide the reader with specific examples. 

Jorgensen WL, J Tirado-Rives (2005) Potential energy functions for atomic-level simulations of water and organic and biomolecular systems. Proc. Natl. Acad. Sci. U. S. A. 102 (19) 6665—6670... 

Atom Level Simulations of a Million Particles The Cell Multipole Method for Coulomb and London Nonbond Interactions. 

H.-Q. Ding, N. Karasawa, and W. A. Goddard III, Atomic level simulations on a million particles The cell multipole method for Coulomb and London nonbond interactions, J. Chem. Phys., 97 (1992), 4309-4315. 

Schelling, P.K., S.R. Phillpot, and P. Keblinski, Comparison of Atomic-Level Simulation Methods for Computing Thermal Conductivity. Physical Review B, 2002. 65 p. 144306/1-12. 

Atomic level simulations and electronic structure calculations are necessary to understand the mechanisms and physical properties for these molecule/bulk interfacial CTs. However, unfortunately, a simple extension of standard theoretical models for homogeneous CTs is not always useful. While there are several difficulties in developing theoretical models (ideally possible to combine ah initio techniques) for interfacial CTs, the fundamental difficulties result from (i) the total system size often being (semi-) infinite (ii) the coexistence of locality and nonlocality in excited electron... 

One of the most important points of contact between models like those described above and experiment is the use of transmission electron microscopy to examine grain boundaries. In particular, there is a well-established tradition of effecting direct comparisons between the outcome of a given atomic-level simulation of... 

Atomic-Level Simulation of Grain Boundary Structure... 

In Chapter 4, Professor Donald W. Brenner and his co-workers Olga A. Shenderova and Denis A. Areshkin explore density functional theory and quantum-based analytic interatomic forces as they pertain to simulations of materials. The study of interfaces, fracture, point defects, and the new area of nanotechnology can be aided by atomistic simulations. Atom-level simulations require the use of an appropriate force field model because quantum mechanical calculations, although useful, are too compute-intensive for handling large systems or long simulation times. For these cases, analytic potential energy functions can be used to provide detailed information. Use of reliable quantum mechanical models to derive the functions is explained in this chapter. 

Towards the Atomic-level Simulation of Water-in-Crude Oil Membranes... 

Once the computer resources advanced far enough to allow their atomic-level simulation, few interfacial phenomena have attracted more attention from researches in the field of molecular modeling as the transport of small molecules in lipid bilayers. Simulation of unassisted transport of water (11) and ions (12) study of energetic and structural effects... 

Schematic illustration of the membrane electrode assembly (MEA) of a PEM fuel cell (top) and details which have been subjected to modeling and simulation work described in the following chapters. Atomic level simulations have been performed for water and proton transport within the hydrophilic domaine of hydrated ionomers and for the electrochemical processes taking place at the electrocatalysts surfaces. The latter include the introduction of polarizable solvents and electrostatic potential variations. Mesoscale modeling is aiming at a better description and understanding of the development of ionomer microstructures.

A central challenge for atomic level simulations of minerals is to be able to model the crystal structure, thermodynamics and atom transport. Clearly, if the same technique is employed then the underlying relationships between these properties can be examined. There are two atomistic simulation techniques that have been used to model these three properties for minerals, lattice dynamics (LD) and molecular dynamics (MD). The aim of this chapter is to describe these techniques and show, via a series of examples, how these methods can be applied. 

Relatively recent advancements have been made in the understanding of heterogeneous ORR catalysis using the combination of molecular and atomic level simulation tools, nanoscale fabrication methods, and nanoscale characterization techniques. For example, the early experimental work of Markovic [17], combined with the important theoretical work of Nprskov [18], Mavrakakis [19], Neurock [20], and others, has now given a deeper understanding not only of the thermodynamics involved in the ORR, and the likely cause of the associated overpotential. 

Hybrid Methods for Atomic-Level Simulations Spanning Multiple-Length Scales in the Solid State... 

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