Self-healing of cracks during ductile regime machining of silicon: Insights from molecular dynamics simulation

During nanoindentation and ductile-regime machining of silicon, a phenomenon known as “self-healing” takes place in that the microcracks, microfractures, and small spallings generated during the machining are filled by the plastically flowing ductile phase of silicon. However, this phenomenon has not been observed in simulation studies. In this work, using a long-range potential function, molecular dynamics simulation was used to provide an improved explanation of this mechanism. A unique phenomenon of brittle cracking was discovered, typically inclined at an angle of 45° to 55° to the cut surface, leading to the formation of periodic arrays of nanogrooves being filled by plastically flowing silicon during cutting. This observation is supported by the direct imaging. The simulated X-ray diffraction analysis proves that in contrast to experiments, Si-I to Si-II (beta tin) transformation during ductile-regime cutting is highly unlikely and solid-state amorphisation of silicon caused solely by the machining stress rather than the cutting temperature is the key to its brittle-ductile transition observed during the MD simulations

Molecular dynamics studies of trinucleotide repeat DNA involved in neurodegenerative disorders.

Expansion of trinucleotide repeat DNA of the classes CAG�·CTG, CGG�·CCG and GAA�·TTC are found to be associated with several neurodegenerative disorders. Different mechanisms have been attributed to the expansion of triplets, mainly involving the formation of alternate secondary structures by such repeats. This paper reports the molecular dynamics simulation of triplet repeat DNA sequences to study the basic structural features of DNA that are responsible for the formation of structures such as hairpins and slip-strand DNA leading to expansion. All the triplet repeat sequences studied were found to be more flexible compared to the control sequence unassociated with disease. Moreover, flexibility was found to be in the order CAG�·CTG > CGG�·CCG = GAA�·TTC, the highly flexible CAG�·CTG repeat being the most common cause of neurodegenerative disorders. In another simulation, a single G�·C to T�·A mutation at the 9th position of the CAG�·CTG repeat exhibited a reduction in bending compared to the pure 15-mer CAGâ�¢CTG repeat. EPM1 dodecamer repeat associated with the pathogenesis of progressive myoclonus epilepsy was also simulated and showed flexible nature suggesting a similar expansion mechanism.

Molecular Dynamics of HIV1-Integrase in Complex with 93del - A Structural Perspective on the Mechanism of Inhibition

HIV1 integrase is an important target for the antiviral therapy. Guanine-rich quadruplex, such as 93del, have been shown to be potent inhibitors of this enzyme and thus representing a new class of antiviral agents. Although X-ray and NMR structures of HIV1 integrase and 93del have been reported, there is no structural information of the complex and the mechanism of inhibition still remains unexplored. A number of computational methods including automated protein-DNA docking and molecular dynamics simulation in explicit solvent were used to model the binding of 93del to HIV1 integrase. Analysis of the dynamic behaviour of the complex using principal components analysis and elastic network modelling techniques allow us to understand how the binding of 93del aptamer and its interactions with key residues affect the intrinsic motions of the catalytic loops by stabilising them in catalytically inactive conformations. Such insights into the structural mechanism of inhibition can aid in improving the design of anti-HIV aptamers.

Development of complex classical force fields through force matching to ab initio data: Application to a room-temperature ionic liquid

Recent experimental neutron diffraction data and ab initio molecular dynamics simulation of the ionic liquid dimethylimidazolium chloride ([dmim]Cl) have provided a structural description of the system at the molecular level. However, partial radial distribution functions calculated from the latter, when compared to previous classical simulation results, highlight some limitations in the structural description offered by force fieldbased simulations. With the availability of ab initio data it is possible to improve the classical description of [dmim]Cl by using the force matching approach, and the strategy for fitting complex force fields in their original functional form is discussed. A self-consistent optimization method for the generation of classical potentials of general functional form is presented and applied, and a force field that better reproduces the observed first principles forces is obtained. When used in simulation, it predicts structural data which reproduces more faithfully that observed in the ab initio studies. Some possible refinements to the technique, its application, and the general suitability of common potential energy functions used within many ionic liquid force fields are discussed.

Evidence of Short-Range Screening in Shock-Compressed Aluminum Plasma

We have investigated the angular variation in elastic x-ray scattering from a dense, laser-shock-compressed aluminum foil. A comparison of the experiment with simulations using an embedded atom potential in a molecular dynamics simulation shows a significantly better agreement than simulations based on an unscreened one-component plasma model. These data illustrate, experimentally, the importance of screening for the dense plasma static structure factor.

A molecular model for drug binding to tandem repeats of telomeric G-quadruplexes.

The extreme 3'-ends of human telomeres consist of 150–250 nucleotides of single-stranded DNA sequence together with associated proteins. Small-molecule ligands can compete with these proteins and induce a conformational change in the DNA to a four-stranded quadruplex arrangement, which is also no longer a substrate for the telomerase enzyme. The modified telomere ends provide signals to the DNA-damage-response system and trigger senescence and apoptosis. Experimental structural data are available on such quadruplex complexes comprising up to four telomeric DNA repeats, but not on longer systems that are more directly relevant to the single-stranded overhang in human cells. The present paper reports on a molecular modelling study that uses Molecular Dynamics simulation methods to build dimer and tetramer quadruplex repeats. These incorporate ligand-binding sites and are models for overhang–ligand complexes.

Phase Behaviour, Interactions, and Structural Studies of (Amines+Ionic Liquids) Binary Mixtures

We present a study on the phase equilibrium behaviour of binary mixtures containing two 1-alkyl-3-methylimidazolium bis{(trifluoromethyl)sulfonyl}imide-based ionic liquids, [Cnmim] [NTf2] (n=2 and 4), mixed with diethylamine or triethylamine as a function of temperature and composition using different experimental techniques. Based on this work, two systems showing an LCST and one system with a possible hourglass shape are measured. Their phase behaviours are then correlated and predicted by using Flory–Huggins equations and the UNIQUAC method implemented in Aspen. The potential of the COSMO-RS methodology to predict the phase equilibria was also tested for the binary systems studied. However, this methodology is unable to predict the trends obtained experimentally, limiting its use for systems involving amines in ionic liquids. The liquid-state structure of the binary mixture ([C2mim] [NTf2]+diethylamine) is also investigated by molecular dynamics simulation and neutron diffraction. Finally, the absorption of gaseous ethane by the ([C2mim][NTf2]+diethylamine) binary mixture is determined and compared with that observed in the pure solvents.

Simplifying the representation of complex free-energy landscapes using sketch-map

A new scheme, sketch-map, for obtaining a low-dimensional representation of the region of phase space explored during an enhanced dynamics simulation is proposed. We show evidence, from an examination of the distribution of pairwise distances between frames, that some features of the free-energy surface are inherently high-dimensional. This makes dimensionality reduction problematic because the data does not satisfy the assumptions made in conventional manifold learning algorithms We therefore propose that when dimensionality reduction is performed on trajectory data one should think of the resultant embedding as a quickly sketched set of directions rather than a road map. In other words, the embedding tells one about the connectivity between states but does not provide the vectors that correspond to the slow degrees of freedom. This realization informs the development of sketch-map, which endeavors to reproduce the proximity information from the high-dimensionality description in a space of lower dimensionality even when a faithful embedding is not possible.

Pinning down the solid-state polymorphism of the ionic liquid [bmim][PF6]

The solid-state polymorphism of the ionic liquid 1-butyl-3-methylimidazolium hexafluorophosphate, [bmim][PF6], has been investigated via low-temperature and high-pressure crystallisation experiments. The samples have been characterised by single-crystal X-ray diffraction, optical microscopy and Raman spectroscopy. The solid-state phase behaviour of the compound is confirmed and clarified with respect to previous phase diagrams. The structures of the previously reported gamma-form, which essentially exhibits a G'T cation conformation, as well as those of the elusive beta- and alpha-forms, are reported. Crystals of the beta-phase are twinned and the structure is heavily disordered; the cation conformation in this form is predominantly TT, though significant contributions from other less frequently encountered conformers are also observed at low temperature and high pressure. The cation conformation in the alpha-form is GT; the presence of the G'T conformer at 193 K in this phase can be eliminated on cooling to 100 K. Whilst X-ray structural data are overall in good agreement with previous interpretations based on Raman and NMR studies, they also reveal a more subtle interplay of intermolecular interactions, which give rise to a wider range of conformers than previously considered.

Anisotropy of single crystal 3C-SiC during nanometric cutting

3C–SiC (the only polytype of SiC that resides in a diamond cubic lattice structure) is a relatively new material that exhibits most of the desirable engineering properties required for advanced electronic applications. The anisotropy exhibited by 3C–SiC during its nanometric cutting is significant, and the potential for its exploitation has yet to be fully investigated. This paper aims to understand the influence of crystal anisotropy of 3C–SiC on its cutting behaviour. A molecular dynamics simulation model was developed to simulate the nanometric cutting of single-crystal 3C–SiC in nine (9) distinct combinations of crystal orientations and cutting directions, i.e. (1?1?1) <-1?1?0>, (1?1?1) <-2?1?1>, (1?1?0) <-1?1?0>, (1?1?0) <0?0?1>, (1?1?0) <1?1?-2>, (0?0?1) <-1?1?0>, (0?0?1) <1?0?0>, (1?1?-2) <1?-1?0> and (1?-2?0) <2?1?0>.

In order to ensure the reliability of the simulation results, two separate simulation trials were carried out with different machining parameters. In the first trial, a cutting tool rake angle of -25°, d/r (uncut chip thickness/cutting edge radius) ratio of 0.57 and cutting velocity of 10 m s-1 were used whereas a second trial was done using a cutting tool rake angle of -30°, d/r ratio of 1 and cutting velocity of 4 m s-1. Both the trials showed similar anisotropic variation.

The simulated orthogonal components of thrust force in 3C–SiC showed a variation of up to 45%, while the resultant cutting forces showed a variation of 37%. This suggests that 3C–SiC is highly anisotropic in its ease of deformation. These results corroborate with the experimentally observed anisotropic variation of 43.6% in Young's modulus of 3C–SiC. The recently developed dislocation extraction algorithm (DXA) [1, 2] was employed to detect the nucleation of dislocations in the MD simulations of varying cutting orientations and cutting directions. Based on the overall analysis, it was found that 3C–SiC offers ease of deformation on either (1?1?1) <-1?1?0>, (1?1?0) <0?0?1>, or (1?0?0) <1?0?0> setups.

Shear instability of nanocrystalline silicon carbide during nanometric cutting

The shear instability of the nanoscrystalline 3C-SiC during nanometric cutting at a cutting speed of 100?m/s has been investigated using molecular dynamics simulation. The deviatoric stress in the cutting zone was found to cause sp3-sp2 disorder resulting in the local formation of SiC-graphene and Herzfeld-Mott transitions of 3C-SiC at much lower transition pressures than that required under pure compression. Besides explaining the ductility of SiC at 1500?K, this is a promising phenomenon in general nanoscale engineering of SiC. It shows that modifying the tetrahedral bonding of 3C-SiC, which would otherwise require sophisticated pressure cells, can be achieved more easily by introducing non-hydrostatic stress conditions.

Influence of microstructure on the cutting behaviour of silicon

We use molecular dynamics simulation to study the mechanisms of plasticity during cutting of monocrystalline and polycrystalline silicon. Three scenarios are considered: (i) cutting a single crystal silicon workpiece with a single crystal diamond tool, (ii) cutting a polysilicon workpiece with a single crystal diamond tool, and (iii) cutting a single crystal silicon workpiece with a polycrystalline diamond tool. A long-range analytical bond order potential is used in the simulations, providing a more accurate picture of the atomic-scale mechanisms of brittle fracture, ductile plasticity, and structural changes in silicon. The MD simulation results show a unique phenomenon of brittle cracking typically inclined at an angle of 45° to 55° to the cut surface, leading to the formation of periodic arrays of nanogrooves in monocrystalline silicon, which is a new insight into previously published results. Furthermore, during cutting, silicon is found to undergo solid-state directional amorphisation without prior Si-I to Si-II (beta tin) transformation, which is in direct contrast to many previously published MD studies on this topic. Our simulations also predict that the propensity for amorphisation is significantly higher in single crystal silicon than in polysilicon, signifying that grain boundaries eases the material removal process.

Topical Review: The current understanding on the diamond machining of silicon carbide

The Glenn Research Centre of NASA, USA (www.grc.nasa.gov/WWW/SiC/, silicon carbide electronics) is in pursuit of realizing bulk manufacturing of silicon carbide (SiC), specifically by mechanical means. Single point diamond turning (SPDT) technology which employs diamond (the hardest naturally-occurring material realized to date) as a cutting tool to cut a workpiece is a highly productive manufacturing process. However, machining SiC using SPDT is a complex process and, while several experimental and analytical studies presented to date aid in the understanding of several critical processes of machining SiC, the current knowledge on the ductile behaviour of SiC is still sparse. This is due to a number of simultaneously occurring physical phenomena that may take place on multiple length and time scales. For example, nucleation of dislocation can take place at small inclusions that are of a few atoms in size and once nucleated, the interaction of these nucleations can manifest stresses on the micrometre length scales. The understanding of how stresses manifest during fracture in the brittle range, or dislocations/phase transformations in the ductile range, is crucial in understanding the brittle–ductile transition in SiC. Furthermore, there is a need to incorporate an appropriate simulation-based approach in the manufacturing research on SiC, owing primarily to the number of uncertainties in the experimental research that includes wear of the cutting tool, poor controllability of the nano-regime machining scale (effective thickness of cut), and coolant effects (interfacial phenomena between the tool, workpiece/chip and coolant), etc. In this review, these two problems are combined together to posit an improved understanding on the current theoretical knowledge on the SPDT of SiC obtained from molecular dynamics simulation.

Flow due to multiple jets downstream of a barrage: Experiments, 3-D CFD and depth-averaged modelling

The flow through and downstream of a row of seven open draft tubes in a barrage has been investigated through laboratory experiments in a wide flume, a three-dimensional (3D) computational fluid dynamics simulation, and a two-dimensional depth-averaged computation. Agreement between the experiments and the 3D modeling is shown to be good, including the prediction of an asymmetric Coandă effect. One aim is to determine the distance downstream at which depth-averaged modeling provides a reasonable prediction; this is shown to be approximately 20 tube diameters downstream of the barrage. Upstream of this, the depth-averaged modeling inaccurately predicts water level, bed shear, and the 3D flow field. The 3D model shows that bed shear stress can be markedly magnified near the barrage, particularly where the jets become attached.

Twinning anisotropy of tantalum during nanoindentation

Unlike other BCC metals, the plastic deformation of nanocrystalline Tantalum during compression is regulated by deformation twinning. Whether or not this twinning exhibits anisotropy was investigated through simulation of displacement-controlled nanoindentation test using molecular dynamics simulation. MD data was found to correlate well with the experimental data in terms of surface topography and hardness measurements. The mechanism of the transport of material was identified due to the formation and motion of prismatic dislocations loops (edge dislocations) belonging to the 1/2<111> type and <100> type Burgers vector family. Further analysis of crystal defects using a fully automated dislocation extraction algorithm (DXA) illuminated formation and migration of twin boundaries on the (110) and (111) orientation but not on the (010) orientation and most importantly after retraction all the dislocations disappeared on the (110) orientation suggesting twinning to dominate dislocation nucleation in driving plasticity in tantalum. A significant finding was that the maximum shear stress (critical Tresca stress) in the deformation zone exceeded the theoretical shear strength of tantalum (Shear modulus/ 2π~10.03 GPa) on the (010) orientation but was lower than it on the (110) and the (111) orientations. In light to this, the conventional lore of assuming the maximum shear stress being 0.465 times the mean contact pressure was found to break down at atomic scale.