Molecular Dynamics Study of Ion Impact Phenomena and Compressive Stress in Thin Films

1993 ◽  
Vol 317 ◽  
Author(s):  
N.A. Marks ◽  
P. Guan ◽  
D.R. Mckenzie ◽  
B.A. PailThorpe
Keyword(s):  
Molecular Dynamics ◽  
Three Dimensional ◽  
Carbon Films ◽  
Loss Mechanism ◽  
Ion Energy ◽  
Lennard Jones ◽  
Impact Phenomena ◽  
Ion Impact ◽  
Dynamics Simulations ◽  
The Impact

ABSTRACTMolecular dynamics simulations of nickel and carbon have been used to study the phenomena due to ion impact. The nickel and carbon interactions were described using the Lennard-Jones and Stillinger-Weber potentials respectively. The phenomena occurring after the impact of 100 e V to 1 keV ions were studied in the nickel simulations, which were both two and three-dimensional. Supersonic focussed collision sequences (or focusons) were observed, and associated with these focusons were unexpected sonic bow waves, which were a major energy loss mechanism for the focuson. A number of 2D carbon films were grown and the stress in the films as a function of incident ion energy was Measured. With increasing energy the stress changed from tensile to compressive and reached a maximum around 50 eV, in agreement with experiment.

Molecular Dynamics Simulations of Structures of Amorphous Carbon Films via Deposition

2011 ◽  
Vol 194-196 ◽  
pp. 2220-2224
Author(s):  
Hui Qing Lan ◽  
Zheng Ling Kang
Keyword(s):  
Molecular Dynamics ◽  
Amorphous Carbon ◽  
Growth Dynamics ◽  
Carbon Films ◽  
Film Structure ◽  
Dynamics Simulation ◽  
Carbon Ions ◽  
Amorphous Carbon Films ◽  
Dynamics Simulations ◽  
The Impact

The growth of amorphous carbon films via deposition is investigated using molecular dynamics simulation with a modified Tersoff potential. The impact energy of carbon atoms ranges from 1 to 50 eV and the temperature of the diamond substrate is 300 K. The effects of the incident energy on the growth dynamics and film structure are studied in a detail. Simulation results show that the mobility of surface atoms in the cascade region is enhanced by impacting energetic carbon ions, especially at moderate energy, which favors the growth of denser and smoother films with better adhesion to the substrate. Our results agree qualitatively with the experimental observation.

Multicanonical Molecular Dynamics Simulation Study of the Liquid-Solid and Solid-Solid Transitions in Lennard-Jones Clusters

2011 ◽  
Author(s):  
Toshihiro Kaneko ◽  
Kenji Yasuoka ◽  
Ayori Mitsutake ◽  
Xiao Cheng Zeng
Keyword(s):  
Molecular Dynamics ◽  
Heat Capacity ◽  
Transition Temperature ◽  
Peak Position ◽  
Temperature Curve ◽  
Dynamics Simulation ◽  
Lennard Jones ◽  
Dynamics Simulations ◽  
First Time ◽  
Good Agreement

Multicanonical molecular dynamics simulations are applied, for the first time, to study the liquid-solid and solid-solid transitions in Lennard-Jones (LJ) clusters. The transition temperatures are estimated based on the peak position in the heat capacity versus temperature curve. For LJ31, LJ58 and LJ98, our results on the solid-solid transition temperature are in good agreement with previous ones. For LJ309, the predicted liquid-solid transition temperature is also in agreement with previous result.

Molecular Dynamics Simulations of High Energy Cascades in Iron

1994 ◽  
Vol 373 ◽  
Author(s):  
Roger E. Stoller
Keyword(s):  
Molecular Dynamics ◽  
Three Dimensional ◽  
High Energy ◽  
Dynamics Simulation ◽  
Method Of Molecular Dynamics ◽  
Energy Cascades ◽  
Iron Based ◽  
The Many ◽  
Property Changes ◽  
Dynamics Simulations

AbstractA series of high-energy, up to 20 keV, displacement cascades in iron have been investigated for times up to 200 ps at 100 K using the method of molecular dynamics simulation. Thesimulations were carried out using the MOLDY code and a modified version of the many-bodyinteratomic potential developed by Finnis and Sinclair. The paper focuses on those results obtained at the highest energies, 10 and 20 keV. The results indicate that the fraction of the Frenkel pairs surviving in-cascade recombination remains fairly high in iron and that the fraction of the surviving point defects that cluster is lower than in materials such as copper. In particular, vacancy clustering appears to be inhibited in iron. Some of the interstitial clusters were observed to exhibit an unexpectedly complex, three-dimensional morphology. The observations are discussed in terms of their relevance to microstructural evolution and mechanical property changes in irradiated iron-based alloys.

scholarly journals Exploiting correlated molecular-dynamics networks to counteract enzyme activity–stability trade-off

2018 ◽  
Vol 115 (52) ◽  
pp. E12192-E12200 ◽  
Author(s):  
Haoran Yu ◽  
Paul A. Dalby
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Active Site ◽  
Dynamic Networks ◽  
Aromatic Aldehydes ◽  
Active Site Residues ◽  
Trade Off ◽  
Highly Correlated ◽  
Dynamics Simulations ◽  
The Impact

The directed evolution of enzymes for improved activity or substrate specificity commonly leads to a trade-off in stability. We have identified an activity–stability trade-off and a loss in unfolding cooperativity for a variant (3M) of Escherichia coli transketolase (TK) engineered to accept aromatic substrates. Molecular dynamics simulations of 3M revealed increased flexibility in several interconnected active-site regions that also form part of the dimer interface. Mutating the newly flexible active-site residues to regain stability risked losing the new activity. We hypothesized that stabilizing mutations could be targeted to residues outside of the active site, whose dynamics were correlated with the newly flexible active-site residues. We previously stabilized WT TK by targeting mutations to highly flexible regions. These regions were much less flexible in 3M and would not have been selected a priori as targets using the same strategy based on flexibility alone. However, their dynamics were highly correlated with the newly flexible active-site regions of 3M. Introducing the previous mutations into 3M reestablished the WT level of stability and unfolding cooperativity, giving a 10.8-fold improved half-life at 55 °C, and increased midpoint and aggregation onset temperatures by 3 °C and 4.3 °C, respectively. Even the activity toward aromatic aldehydes increased up to threefold. Molecular dynamics simulations confirmed that the mutations rigidified the active-site via the correlated network. This work provides insights into the impact of rigidifying mutations within highly correlated dynamic networks that could also be useful for developing improved computational protein engineering strategies.

Molecular Dynamics Studies on the Growth and Structural Properties of Hydrogenated DLC Films

2008 ◽  
Vol 373-374 ◽  
pp. 108-112
Author(s):  
Yu Jun Zhang ◽  
Guang Neng Dong ◽  
Jun Hong Mao ◽  
You Bai Xie
Keyword(s):  
Molecular Dynamics ◽  
Structural Properties ◽  
Impact Energy ◽  
Frictional Coefficient ◽  
Carbon Films ◽  
Dynamics Simulation ◽  
Diamond Surface ◽  
Hydrogen Atoms ◽  
Molecular Configuration ◽  
The Impact

The novel frictional properties of hydrogenated DLC (Diamond-like Carbon) films have been reported for nearly ten years. But up to now, researchers still haven’t known the exact mechanism resulting in the super-low frictional performance of hydrogenated DLC films. Especially they have little knowledge on the molecular configuration and structural properties of these kinds of films. In this paper, CH3 radicals with different impact energies are selected as source species to deposit DLC films on diamond (100) by molecular dynamics simulation. Results show hydrogenated DLC films can be successfully obtained when impact energy is in an appropriate scope that is no less than 20eV. The depositing processes involve impinging diamond surface and bonding procedure. Some atoms, instead of bonding with substrate atoms, fly away from the diamond surface. Only suitable impact energy can improve the growth of the film. Within 30eV to 60eV, the maximum deposition ratio is attained. In addition, when carbon atoms act as the deposition sources, the deposition ratio is relatively higher. Furthermore, the authors find that species with higher concentration of carbon atoms in deposition sources lead to a better deposition rate. Carbon atoms are more reactive than hydrogen atoms. Then the relative densities of DLC films are calculated. The density curves indicate that the structures of the films vary obviously as the impact energy augments. The average relative density is generally monotone increase with the increment of impact energy. The hybridization of carbon atoms greatly affects the properties of hydrogenated DLC films. The transition between sp2 and sp3 will result in the graphitization and reduce the frictional coefficient when DLC films are used as tribo-pair in friction.

scholarly journals Shear-rate dependence of thermodynamic properties of the Lennard-Jones truncated and shifted fluid by molecular dynamics simulations

2021 ◽  
Author(s):  
Martin P. Lautenschlaeger ◽  
Hans Hasse
Keyword(s):  
Molecular Dynamics ◽  
Shear Stress ◽  
Shear Rate ◽  
Molecular Dynamics Simulations ◽  
Local Structure ◽  
Rate Dependence ◽  
Lennard Jones ◽  
Fluid Properties ◽  
Dynamics Simulations ◽  
Shear Rate Dependence

It was shown recently that using the two-gradient method, thermal, caloric, and transport properties of fluids under quasi-equilibrium conditions can be determined simultaneously from nonequilibrium molecular dynamics simulations. It is shown here that the influence of shear stresses on these properties can also be studied using the same method. The studied fluid is described by the Lennard-Jones truncated and shifted potential with the cut-off radius r*c = 2.5σ. For a given temperature T and density ρ, the influence of the shear rate on the following fluid properties is determined: pressure p, internal energy u, enthalpy h, isobaric heat capacity cp, thermal expansion coefficient αp, shear viscosity η, and self-diffusion coefficient D. Data for 27 state points in the range of T ∈ [0.7, 8.0] and ρ ∈ [0.3, 1.0] are reported for five different shear rates (γ ̇ ∈ [0.1,1.0]). Correlations for all properties are provided and compared with literature data. An influence of the shear stress on the fluid properties was found only for states with low temperature and high density. The shear-rate dependence is caused by changes in the local structure of the fluid which were also investigated in the present work. A criterion for identifying the regions in which a given shear stress has an influence on the fluid properties was developed. It is based on information on the local structure of the fluid. For the self-diffusivity, shear-induced anisotropic effects were observed and are discussed.

scholarly journals Systematic Finite-Temperature Reduction of Crystal Energy Landscapes.

2020 ◽  
Author(s):  
Nicholas Francia ◽  
Louise S. Price ◽  
Jonas Nyman ◽  
Sarah (Sally) Price ◽  
Matteo Salvalaglio
Keyword(s):  
Molecular Dynamics ◽  
Finite Temperature ◽  
Structure Prediction ◽  
Lattice Energy ◽  
Biased Sampling ◽  
Energy Landscapes ◽  
Polymorphic Transformations ◽  
Temperature And Pressure ◽  
Dynamics Simulations ◽  
The Impact

<p>Crystal structure prediction methods are prone to overestimate the number of potential polymorphs of organic molecules. In this work, we aim to reduce the overprediction by systematically applying molecular dynamics simulations and biased sampling methods to cluster subsets of structures that can easily interconvert at finite temperature and pressure. Following this approach, we rationally reduce the number of predicted putative polymorphs in CSP-generated crystal energy landscapes. This uses an unsupervised clustering approach to analyze independent finite-temperature molecular dynamics trajectories and hence identify a representative structure of each cluster of distinct lattice energy minima that are effectively equivalent at finite temperature and pressure. Biased simulations are used to reduce the impact of limited sampling time and to estimate the work associated with polymorphic transformations. We demonstrate the proposed systematic approach by studying the polymorphs of urea and succinic acid, reducing an initial set of over 100 energetically plausible CSP structures to 12 and 27 respectively, including the experimentally known polymorphs. The simulations also indicate the types of disorder and stacking errors that may occur in real structures.<br></p>

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