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Register a new userOrientation before destruction. A multiscale molecular dynamics study
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Authors
Anna Sinelnikova
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The emergence of ultra-fast X-ray free-electron lasers opens the possibility of imaging single molecules in the gas phase at atomic resolution. The main disadvantage of this imaging technique is the unknown orientation of the sample exposed to the X-ray beam, making the three dimensional reconstruction not trivial. Induced orientation of molecules prior to X-ray exposure can be highly beneficial, as it significantly reduces the number of collected diffraction patterns whilst improving the quality of the reconstructed structure. We present here the possibility of protein orientation using a time-dependent external electric field. We used ab initio simulations on Trp-cage protein to provide a qualitative estimation of the field strength required to break protein bonds, with 45 V/nm as a breaking point value. Furthermore, we simulated, in a classical molecular dynamics approach, the orientation of ubiquitin protein by exposing it to different time-dependent electric fields. The protein structure was preserved for all samples at the moment orientation was achieved, which we denote `orientation before destruction. Moreover, we find that the minimal field strength required to induce orientation within ten ns of electric field exposure, was of the order of 0.5 V/nm. Our results help explain the process of field orientation of proteins and can support the design of instruments for protein orientation.
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We report a molecular dynamics simulation of melting of tungsten (W) nanoparticles. The modified embedded atom method (MEAM) interatomic potentials are used to describe the interaction between tungsten atoms. The melting temperature of unsupported tungsten nanoparticles of different sizes are found to decrease as the size of the particles decreases. The melting temperature obtained in the present study is approximately a decreasing function of inverse radius, in a good agreement with the predictions of thermodynamic models. We also observed that the melting of a W nanoparticle is preceded by the premelting of its outer skin at a temperature lower than its melting temperature.
Molecular simulation is a scientific tool dealing with challenges in material science and biology. This is reflected in a permanent development and enhancement of algorithms within scientific simulation packages. Here, we present computational tools for multiscale modeling developed and implemented within the ESPResSo++ package. These include the latest applications of the adaptive resolution scheme, the hydrodynamic interactions through a lattice Boltzmann solvent coupled to particle-based molecular dynamics, the implementation of the hierarchical strategy for equilibrating long-chained polymer melts and a heterogeneous spatial domain decomposition. The software design of ESPResSo++ has kept its highly modular C++ kernel with a Python user interface. Moreover, it was enhanced by automatic scripts parsing configurations from other established packages providing scientists with a rapid setup possibility for their simulations.
Ebert et al. [Phys. Rev. Lett. 77, 3827 (1996)] have fractured icosahedral Al-Mn-Pd single crystals in ultrahigh vacuum and have investigated the cleavage planes in-situ by scanning tunneling microscopy (STM). Globular patterns in the STM-images were interpreted as clusters of atoms. These are significant structural units of quasicrystals. The experiments of Ebert et al. imply that they are also stable physical entities, a property controversially discussed currently. For a clarification we performed the first large scale fracture simulations on three-dimensional complex binary systems. We studied the propagation of mode I cracks in an icosahedral model quasicrystal by molecular dynamics techniques at low temperature. In particular we examined how the shape of the cleavage plane is influenced by the clusters inherent in the model and how it depends on the plane structure. Brittle fracture with no indication of dislocation activity is observed. The crack surfaces are rough on the scale of the clusters, but exhibit constant average heights for orientations perpendicular to high symmetry axes. From detailed analyses of the fractured samples we conclude that both, the plane structure and the clusters, strongly influence dynamic fracture in quasicrystals and that the clusters therefore have to be regarded as physical entities.
Pentadiamond is a recently proposed new carbon allotrope consisting of a network of pentagonal rings where both sp$^2$ and sp$^3$ hybridization are present. In this work we investigated the mechanical and electronic properties, as well as, the thermal stability of pentadiamond using DFT and fully atomistic reactive molecular dynamics (MD) simulations. We also investigated its properties beyond the elastic regime for three different deformation modes: compression, tensile and shear. The behavior of pentadiamond under compressive deformation showed strong fluctuations in the atomic positions which are responsible for the strain softening at strains beyond the linear regime, which characterizes the plastic flow. As we increase temperature, as expected, Youngs modulus values decrease, but this variation (up to 300 K) is smaller than 10% (from 347.5 to 313.6 GPa), but the fracture strain is very sensitive, varying from $sim$44% at 1K to $sim$5% at 300K.
Hydrogenated diamond has been regarded as a promising material in electronic device applications, especially in field-effect transistors (FETs). However, the quality of diamond hydrogenation has not yet been established, nor has the specific orientation that would provide the optimum hydrogen coverage. In addition, most theoretical work in the literature use models with 100% hydrogenated diamond surfaces to study electronic properties, which is far from the experimentally observed hydrogen coverage. In this work, we have carried out a detailed study using fully atomistic reactive molecular dynamics (MD) simulations on low indices diamond surfaces i.e. (001), (013), (110), (113) and (111) to evaluate the quality and hydrogenation thresholds on different diamond surfaces and their possible effects on electronic properties. Our simulation results indicate that the 100% surface hydrogenation in these surfaces is hard to achieve because of the steric repulsion between the terminated hydrogen atoms. Among all the considered surfaces, the (001), (110), and (113) surfaces incorporate a larger number of hydrogen atoms and passivate the surface dangling bonds. Our results on hydrogen stability also suggest that these surfaces with optimum hydrogen coverage are robust under extreme conditions and could provide homogeneous p-type surface conductivity in the diamond surfaces, a key requirement for high-field, high-frequency device applications.
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