Description Of Atomic Interactions Research Articles

Computational and experimental studies on the influence of theTrp-cage inter-residue interactions and other external factors on its structural and folding stability

<p indent=0mm>The major driving force of protein folding depends on their inter-residue interactions, especially for sidechain-sidechain interactions. The Trp-cage is a fast-folding mini-protein, which has already been acknowledged as an ideal model for tackling complicated folding-related problems of proteins. Although this protein model is merely composed of 20 amino acid residues, it exhibits an extremely complex interaction network between residues with different types of sidechain orientation. Because current force fields exhibit different degrees of accuracy inadequacies in the descriptions of atomic interactions, it remains a matter of debate at what stage of folding the helix, hydrophobic cluster and salt-bridge is being conclusively formed in its possible folding mechanisms. The structures and mutations of all the Trp-cage system reported since 2002 are summarized in this paper, and its two typical structures (TC5b and TC10b) are taken as examples to summarize the composition and types of their inter-residue interactions as well as the sidechain features and orientations. Meanwhile, the recent computational and experimental studies of several possible folding mechanisms are also generalized and discussed, and their relationships with simulation temperature and force field as well as the switching from one folding pathway to the other are also discussed in detail. Finally, the effects of numerous factors on structural stability and folding dynamics have been elaborately discussed, including different types of inter-residue interactions (such as salt-bridge, hydrophobic and hydrogen-bonding interactions) and environmental factors (such as temperature, pressure, pH and other potential factors). We also propose that the clarification of the above factors and their synergistic effects are beneficial not only to reveal the driving force of protein stabilization and rapid formation, but also to provide theoretical guidance for further structural regulation and optimal design.

New parameters of many-body potentials: studying the thermal and mechanical properties of noble metals

Abstract New parameters of nearest-neighbor EAM (1N-EAM), n-th neighbor EAM (NN-EAM), and the second-moment approximation to the tight-binding (TB-SMA) potentials are obtained by fitting experimental data at different temperatures. In comparison with the available many-body potentials, our results suggest that the 1N-EAM potential with the new parameters is the best description of atomic interactions in studying the thermal expansion of noble metals. For mechanical properties, it is suggested that the elastic constants should be calculated in the experimental zero-stress states for all three potentials. Furthermore, for NNEAM and TB-SMA potentials, the calculated results approach the experimental data as the range of the atomic interaction increases from the first-neighbor to the sixth-neighbor distance.

Atomistic modelling of diffusional phase transformations with elastic strain

Phase transformations in 2xxx series aluminium alloys (Al–Cu–Mg) are investigated withan off-lattice atomistic kinetic Monte Carlo simulation incorporating the effects of strainaround misfitting atoms and vacancies. Atomic interactions are modelled by Finnis–Sinclairpotentials constructed for these simulations. Vacancy diffusion is modelled bycomparing the energies of trial states, where the system is partially relaxed for eachtrial state. No special requirements are made about the description of atomicinteractions, making our approach suitable for more fundamentally based models such astight binding if sufficient computational resources are available. Only a limitedprecision is required for the energy of each trial state, determined by the value ofkBT. Since the change in the relaxation displacement field caused by a vacancy hop decays as1/r3, it is sufficient to determine the next move by relaxing only those atoms in a sphere offinite radius centred on the moving vacancy. However, once the next move has beenselected, the entire system is relaxed.Simulations of the early stages of phase separation in Al–Cu with elastic relaxation showan enhanced rate of clustering compared to those performed on the same system with arigid lattice.

Influence of non-glide stresses on plastic flow: from atomistic to continuum modeling

The Schmid law, which is accurate for face-centered-cubic (fcc) metals, assumes that only the shear stress acting in the slip plane in the slip direction controls the plastic deformation. Hence, it is implicitly assumed that the critical resolved shear stress (CRSS) for the slip is not affected by any other components of the applied stress tensor. This rule is almost ubiquitously utilized in large-scale continuum computations of plastically deforming single and polycrystals. On the other hand, in materials with more complex structures and for some orientations of the dislocation line the cores can spread onto several non-parallel planes. The most widely-known example is the screw dislocation in bcc metals, though this phenomenon is quite universal in structures that are not close packed. Signatures of such core configurations commonly include unexpected deformation modes and slip geometries, strong and unusual dependence of flow stresses on temperature and strain rate, a high Peierls stress, and, in general, a breakdown of the Schmid law. In this paper, we first summarize results of atomistic computer simulations of the response of 1/2〈1 1 1〉 screw dislocations to the applied shear stresses. The calculations have been made using central-force many-body potentials and tight-binding based bond-order potentials for molybdenum. While the core structure found is not the same for the two descriptions of atomic interactions, both lead to a very similar orientation dependence of the critical resolved shear stress for the dislocation motion which takes place along the most highly stressed {1 1 0} plane. This dependence reveals the break down of the Schmid law invoked by the effect of shear stresses acting in another {1 1 0} plane, which are called non-glide stresses. These results are then transferred to macroscopic level by formulating single crystal yield criteria that include the effects of non-glide components of the stress tensor. These criteria form a basis for multislip yield criteria and flow relations for continuum analyses. Using this approach we demonstrate that the effects of non-glide stresses that have their origin at the level of individual dislocations also have significant effect on polycrystalline response, including a significant tension-compression asymmetry.

Predicting peptide structures using NMR data and deterministic global optimization

The ability to analyze large molecular structures by NMR techniques requires efficient methods for structure calculation. Currently, there are several widely available methods for tackling these problems, which, in general, rely on the optimization of penalty-type target functions to satisfy the conformational restraints. Typically, these methods combine simulated annealing protocols with molecular dynamics and local minimization, either in distance or torsional angle space. In this work, both a novel formulation and algorithmic procedure for the solution of the NMR structure prediction problem is outlined. First, the unconstrained, penalty-type structure prediction problem is reformulated using nonlinear constraints, which can be individually enumerated for all, or subsets, of the distance restraints. In this way, the violation can be controlled as a constraint, in contrast to the usual penalty-type restraints. In addition, the customary simplified objective function is replaced by a full atom force field in the torsional angle space. This guarantees a better description of atomic interactions, which dictate the native structure of the molecule along with the distance restraints. The second novel portion of this work involves the solution method. Rather than pursue the typical simulated annealing procedure, this work relies on a deterministic method, which theoretically guarantees that the global solution can be located. This branch and bound technique, based on the αBB algorithm, has already been successfully applied to the identification of global minimum energy structures of peptides modeled by full atom force fields. Finally, the approach is applied to the Compstatin structure prediction, and it is found to possess some important merits when compared to existing techniques. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 1354–1370, 1999

Predicting peptide structures using NMR data and deterministic global optimization

The ability to analyze large molecular structures by NMR techniques requires efficient methods for structure calculation. Currently, there are several widely available methods for tackling these problems, which, in general, rely on the optimization of penalty-type target functions to satisfy the conformational restraints. Typically, these methods combine simulated annealing protocols with molecular dynamics and local minimization, either in distance or torsional angle space. In this work, both a novel formulation and algorithmic procedure for the solution of the NMR structure prediction problem is outlined. First, the unconstrained, penalty-type structure prediction problem is reformulated using nonlinear constraints, which can be individually enumerated for all, or subsets, of the distance restraints. In this way, the violation can be controlled as a constraint, in contrast to the usual penalty-type restraints. In addition, the customary simplified objective function is replaced by a full atom force field in the torsional angle space. This guarantees a better description of atomic interactions, which dictate the native structure of the molecule along with the distance restraints. The second novel portion of this work involves the solution method. Rather than pursue the typical simulated annealing procedure, this work relies on a deterministic method, which theoretically guarantees that the global solution can be located. This branch and bound technique, based on the αBB algorithm, has already been successfully applied to the identification of global minimum energy structures of peptides modeled by full atom force fields. Finally, the approach is applied to the Compstatin structure prediction, and it is found to possess some important merits when compared to existing techniques. ©1999 John Wiley & Sons, Inc. J Comput Chem 20: 1354–1370, 1999

Atomic Level Studies of Dislocation Networks in Niobium-Sapphire Interfaces

In this paper we present atomistic modelling of the (0001) Al2 O 3 || (111) Nb interface using a simple description of atomic interactions. The goal is to reveal the influence of the strength of bonding between the two materials upon the misfit dislocations formed in Nb at or near the interface. The calculations show that two types of networks of misfit dislocations may be formed depending on the strength of bonding but only the triangular network with 1/2 dislocations occurs if the transport of material, for example by diffusion, can take place. This is, indeed, the network found by electron microscopic studies [1]. The core structure of the misfit dislocations also depends on the strength of bonding. Comparison of simulated high resolution electron microscope (HREM) images, based on the atomistic model, with observations leads to an excellent agreement for a reasonable strength of bonding and provides means for assessment of this physical quantity.

Pair Potentials in Atomistic Computer Simulations

Computer modeling of crystal defects ranges at present from generic empirical investigations to first-principle quantum-mechanical calculations (see, for example, References 1–4). Descriptions of atomic interactions in terms of pair potentials dominated such studies until the early 1980s, and many fundamental features of lattice defects and interfaces were revealed in these calculations. The generic results of these studies withstood the test of time, and calculations employing more sophisticated schemes usually confirmed their validity. An early example goes back to the late 1950s when Vineyard and co-workers pioneered the very first computer simulations in their studies of radiation damage. Empirical pair potentials were used in these investigations in which many fundamental, generic aspects of the effect of irradiation of crystalline materials by energetic particles were discovered.Such simple treatments of atomic interactions may appear totally inadequate from the point of view of pure physics. However, it must be recognized that the purpose of the majority of atomistic studies of lattice defects has been to elucidate atomic structure and atomic-level properties in materials with given: (a) crystal structure, (b) elastic properties and possibly phonon spectra, (c) values of certain material parameters such as vacancy formation energies and stacking fault energies, and (d) in alloys, alloying and ordering energies, and possibly antiphase boundary energies. This is in contrast with ab initio studies, the objective of which is to determine all these properties from first principles. These goals of atomistic studies are, of course, the same for all semi-empirical approaches discussed in this collection of articles. In general, the validity of the structural features of lattice defects found in calculations using empirical schemes is best guaranteed if they can be related to fitted material properties and are not sensitively dependent on the deails of the fittings and functional forms employed.

Structure of dislocation cores in metallic materials and its impact on their plastic behaviour

Whilst the dislocation core structure was investigated in the early days of the dislocation theory, the importance of core effects for understanding the basic features of plastic behaviour was first recognized in the case of bcc metals. At this time the first extensive computer modelling studies of dislocation cores were initiated. In this paper we show how the atomistic studies of dislocations advanced since these early calculations and how the basic ideas, developed at this time, apply when analysing deformation properties of other materials. Since a description of atomic interactions is the precursor of any atomistic calculations we first briefly describe the present status in this area, in particular the recently developed N-body potentials. Next, we discuss the concept of generalised stacking faults and associated energy-displacement surfaces (γ-surfaces). In this part we demonstrate how the symmetry considerations can be used to assess the existence of possible metastable planar faults which play a role in dislocation splitting. A general discussion of planar and non-planar dislocation cores then follows in which the dislocation splitting and core phenomena are combined into one notion. These general concepts are illustrated by results of recent studies of the dislocation cores in hcp metals and intermetallic compounds with L1 2 and DO 22 structures. Using these results we discuss the physical reasons for the following phenomena: preference for the prism slip in some hcp metals, anomalous positive temperature dependence of the yield stress for prism slip in beryllium, similar anomalous yield behaviour observed in L1 2 intermetallic compounds, such as Ni 3Al, existence of another class of L1 2 compounds with a strong temperature dependence of the yield stress at low temperatures, and brittleness of DO 22 compounds.

Atomic structure of (111) twist grain boundaries in f.c.c metals

Abstract In this paper we have studied the atomic structures of (111) twist boundaries and investigated the applicability of the structural unit model which has previously been established for tilt boundaries and (001) twist boundaries by Sutton and Vitek. The calculations were carried out using two different descriptions of interatomic forces. A pair potential for aluminium, for which the calculations were made at constant volume, and a many-body potential for gold, for which the calculations were performed at constant pressure. The atomic structures of all the boundaries studied were found to be very similar for both the descriptions of atomic interactions. This suggests that the principal features of the structure of (111) twist boundaries found in this study are common to all f.c.c. metals. At the same time it supports the conclusion that calculations employing pair potentials are fully capable of revealing the generic features of the structure of grain boundaries in metals. The results obtained here, indeed, show that structures of all the boundaries with misorientations between 0° and 21–79° (∊=21) are composed of units of the ideal lattice and/or the 1/6‘112’ stacking fault on (111) planes, and units of the ∊ = 21 boundary. Similarly, structures of boundaries with misorientations between 21–79° and 27–8° (X= 13), 27–8° and 38–21° (1=1) and 38–21° and 60° (Z = 3) can all be regarded as decomposed into units of the corresponding delimiting boundaries. Therefore we conclude that the atomic structure of (111) twist boundaries can well be understood in the framework of the structural unit model. A related aspect analysed here in detail is the dislocation content of these boundaries. This study shows both the general relation between dislocation content and atomic structure of the boundaries, which is an integral part of the structural unit model, and features specific to the dislocation networks present in the (111) twist boundaries. Furthermore, the dislocation content revealed by the atomistic calculations can be compared in several cases with transmission electron microscope (TEM) observations and the results are discussed in this context.

Semiclassical Model of Atomic Interactions

The possibility of obtaining approximate solutions to atomic interaction problems by using a drastically simplified version of the quantum-mechanical atomic model is discussed. The atom on this simplified model is regarded as a point-charge nucleus enclosed by a thin, spherical, uniformly charged electron shell. The model allows a description of atomic interactions on an essentially classical basis and gives fairly realistic expressions for the dissociation energy of homonuclear diatomic molecules and for certain other interaction parameters. It is concluded that the model provides a tool helpful for discussions of interatomic forces and effects associated with these forces.