Atomistic Simulation Study Research Articles

Deformation behaviors and inverse Hall-Petch effect in nanoindentation of silicon: An atomistic simulation study with experimental validation

In this research, the unique perspectives on deformation behaviors of monocrystalline and polycrystalline silicon materials in nanoindentation are studied by the atomistic simulation approach. First, the validity of molecular dynamics (MD) simulation model for nanoindentation is verified by comparing the indentation morphology and force of simulation with those of nanoindentation experiment on monocrystalline silicon using atomic force microscopy (AFM). Further simulation on nanoindentation of polycrystalline silicon reveals the intriguing phenomena such as phase transformation and the effect of grain size. The indentation force with respect to indentation depth is analyzed for the monocrystalline silicon and polycrystalline silicon with grain size ranging from 20.48 nm to 6.45 nm. Inverse Hall-Petch effect, which indicates that stress decreases with the decrease of grain size, is observed in the nanoindentation process of silicon. The grain boundary-induced stress during indentation process hardly affects the formation of bct-5 silicon significantly, but it is responsible for the reduced formation of β‑silicon. The amount of bct-5 silicon atoms at the maximum indentation depth is not significantly different among the polycrystalline cases. On the other hand, the amount of bct-5 atoms of monocrystalline silicon is 14–18% less than that of polycrystalline silicon. In addition, it is discovered that residual indentation morphology and residual phase transformation are not significantly affected by the grain size. As such, this research reflects the rare efforts that bring direct validation to atomistic simulation of nanomanufacturing and provide analysis on deformation and phase transformation under various grain sizes for silicon nanoindentation.

Influence of surface stress on the mechanical response of nanoporous metals studied by an atomistically informed continuum model

The influence of surface stresses on the deformation behavior of nanoporous metals is considered to be the main reason for the tension-compression asymmetry observed in atomistic simulation studies of nanoporous metals. While it is difficult to differentiate between the contributions of linear and non-linear elasticity, dislocation activity, topology and surface stresses from atomistic simulations, continuum mechanics allow to disentangle these effects by systematically varying the applied constitutive relations. In this study, we investigate the elastic response of a nanoporous Au and Ag structure, both by molecular statics simulations and an elastic continuum model, which includes surface stresses and elastic anisotropy. The 3-dimensional periodic atomistic nanoporous structure is triangulated and transferred to the continuum model, where periodicity, elastic anisotropy, and surface stresses are considered. The results show that surface stress acts as a mechanical pre-load and that the elastic response is sensitive to the loading direction. An asymmetric behavior is observed in the elastic regime. Moreover, we show that sites, where dislocation activity is starting, show high von Mises stresses.

Robust finite-temperature magnetization dynamics in ferrimagnetic Gdx(FeCo)1−x (x = 0 ∼ 0.44) nanospheres across angular-momentum and magnetization compensation points: An atomistic model simulation

We explored robust magnetization dynamics in ferrimagnetic Gdx(FeCo)1−x nanospheres of Gd compositions ranging from x = 0 to 0.44 at finite T = 0 – 1200 K temperatures using two-sublattice atomistic simulations based on the stochastic Landau-Lifshitz-Gilbert equation. It was found that the magnetization compensation and angular-momentum compensation temperatures vary remarkably with x and that the former temperature is always lower than the latter. Also, it was found that neither compensation temperature exists below a specific Gd composition of x = 0.22, but above which, both exist and increase with x. The ferromagnetic resonance (FMR) frequency remarkably increases at the angular momentum compensation composition, whereas the FMR frequency does not reach zero at the magnetization compensation composition. The significant difference in the FMR frequency between the two characteristic compensation points is ascribed to the contrasting effective gyromagnetic ratios of Gd and FeCo. Our present atomistic simulation study well reproduced the earlier experimental observations of such dynamic behaviors at both the angular-momentum and magnetization compensation points, which observations cannot be explained by the existing Kittel and Wangsness models. This work provides a better understanding of robust dynamic behaviors of ferrimagnetic nanospheres as functions of temperature and constituent sublattice composition, especially at and near the characteristic compensation points.

Translocation of Endo-Functionalized Molecular Tubes across Different Lipid Bilayers: Atomistic Molecular Dynamics Simulation Study.

Various artificial receptors, such as calixarenes, cyclodextrins, cucurbit[n]urils, and their acyclic compounds, pliiar[n]arenes, deep cavitands, and molecular tweezers, can permeate the lipid membranes and they are used as drug carriers to improve the drug solubility, stability, and bioavailability. Inspired by these, we have employed atomistic molecular dynamics simulation to examine the effects of endo-functionalized molecular tubes or naphthotubes (host-1a and host-1b) on seven different types of model lipid bilayers and the permeation properties of these receptors through these model lipid bilayers. Lipid types include six model lipid bilayers (POPC, POPE, DOPC, POPG, DPPE, POPE/POPG) and one realistic membrane (Yeast). We observe that these receptors are spontaneously translocated toward these model lipid bilayer head regions and do not proceed further into these lipid bilayer tail regions (reside at the interface between lipid head and lipid tail region), except for the DPPE-containing systems. In the DPPE model lipid bilayer-containing systems (1a-dppe and 1b-dppe), receptor molecules are only adsorbed on the bilayer surface and reside at the interface between lipid head and water. This finding is also supported by the biased free-energy profiles of these translocation processes. Passive transport of these receptors may be possible through these model lipid bilayers (due to low barrier height), except for DPPE bilayer-containing systems (that have a very high energy barrier at the center). The results from these simulations provide insight into the biocompatibility of host-1a or host-1b in microscopic detail. Based on this work, more research is needed to fully comprehend the role of these synthesized receptors as a prospective drug carrier.

Genetic Algorithms Applied to Thermodynamic Rational Design of Mimetic Antibodies Based on the GB1 Domain of Streptococcal Protein G: An Atomistic Simulation Study.

The development of mimetic antibodies (MA) capable of combining the high affinity and selectivity of antibodies with the small size of the peptides has enormous potential for applications in current biotechnology. In this work, we demonstrate that in silico MA design is possible through genetic algorithms (GA) developed from shell scripts capable of combining software commonly used for atomistic simulation. Our results demonstrate that, using the GB1 domain of the streptococcal G protein as a model, it is possible to optimize the molecular recognition capacity of a large MA population in a few generations. In the first case, GA was able to generate 10 MA with binding free energy (BFE) less than the vascular endothelial cell growth factor conjugated with the fms-type tyrosine kinase receptor. In the second case, it generated 13 MA with BFE less than that of the hepatitis C-E2 viral envelope conjugate with the antibody. Through the GA developed in this work, we demonstrate the use of a new protocol, capable of guiding experimental methods for the design of bioactive peptides that can assist in the development of new therapeutic molecules.

Numerical simulation of outgassing characteristics of microchannel plate glass

Outgassing of internal materials is one of the main factors that cause vacuum deterioration of low-light-level image intensifiers and shorten their lifetime (especially storage lifetime). To perceive the attenuation mechanism of the vacuum degree of image intensifiers from the microscopic view, the outgassing characteristics of lead silicate glass used for the fabrication of microchannel plates (MCPs), which are the core components of image intensifiers, were numerically simulated by giant canonical Monte Carlo and molecular dynamics methods. A glass structure model of the third-generation MCPs was constructed, and the diffusion coefficients and molecular motion trajectories of hydrogen, carbon dioxide, carbon monoxide, water vapor, oxygen, and methane gases, together with their outgassing rates and cumulative outgassing amounts, were calculated based on the condensed-phase optimized molecular potentials for atomistic simulation studies force field. The calculation results show that the rising temperature of MCP glass augments the diffusion coefficients of these gases, which makes the outgassing rates increase in the initial stage but then decrease relatively quickly. Among these six kinds of gas molecules, hydrogen molecules have the largest skip distance and the highest diffusion coefficient because MCP glass can supply more effective diffusion paths for the gas molecules with a relatively small size. When an MCP glass lies in vacuum, first, the cumulative outgassing amounts of various gases from it increase rapidly and then gradually reach stable values, and the cumulative outgassing amount of hydrogen tends to reach a stable value faster than that of other gases due to its highest diffusion coefficient.

Atomistic Simulation Study of Impacts of Surface Carrier Scatterings on Carrier Transport in Pt Nanosheets

The understanding of carrier transport in metal nanostructures is indispensable for the development of nanoelectronics. In particular, Pt nanostructures have been intensively studied to realize gas sensors based on adsorbate-induced surface electron scattering. Conventionally, electron scattering at the surface of metal nanostructures has been phenomenologically described by a single specularity parameter. In this work, surface electron scattering was quantitatively studied through molecular dynamics simulations, followed by density functional nonequilibrium Green’s function calculations. Although the extracted specularity parameters qualitatively agreed with empirically treated diffusive scattering at the O-covered Pt surface and specular scattering at the H-covered Pt surface, our atomistic calculation revealed an increase in resistivity owing to H adsorption on thin Pt(111) nanosheets.

Atomistic simulation study of the adsorptive separation of hydrogen sulphide/alkane mixtures on all-silica zeolites

ABSTRACT The selective separation of the aggressive hydrogen sulphide gas from industrial streams is highly important from environmental and economic aspects. Capture of this substance from industrial gases of light hydrocarbons by all-silica zeolites can be an eco-friendly alternative to the other common absorption/adsorption procedures. The adsorption from binary mixtures of hydrogen sulphide and light alkanes (H2S/CH4, H2S/C2H6, and H2S/C3H8) on preselected all-silica zeolites was studied by atomistic simulations, using a recently developed force field for hydrogen sulphide. In addition to four experimental all-silica zeolite frameworks (DDR, CHA, ACO, CAS), three of their hypothetical relatives were also drawn into the investigations. The smaller pore size zeolites (ACO, CAS, and particularly one of the hypothetical zeolites) showed remarkable separation performances under real ambient conditions. Among the examined structural details of the studied frameworks, the calculated realistic pore size distributions proved the most appropriate in attempts to unravel the connection between adsorption selectivities and framework structural properties. The investigations were completed by a necessary demonstration of the translational accessibility of the inner cages of the smaller pore size zeolites.

Elastic and plastic deformation behavior of helium nano-bubbled single crystal copper: An atomistic simulation study

The mechanical properties, particularly, yield strength and ductility of metals, exposed under irradiation usually degrade due to generation of primary and secondary defects such as dislocations, vacancies, gas-bubbles, etc. Using atomistic simulations, we have shown that irradiation-induced Helium gas-bubbles are not always detrimental and can contribute to the plastic deformation that leads to improved strength and ductility of the host metal. However, the inter-bubble distance plays a strong role on controlling the mechanisms that operate during elastic and plastic deformation. When the inter-bubble distance is comparatively low (order of 3–4 nm), the copper nanopillar hosting He gas-bubbles exhibits lower yield strength but improved strain hardening rate, and ductility, via coalescence of bubbles that leads to a homogeneous plastic flow. In contrast, higher inter-bubble distance, order of 10 nm, shows a higher yield stress, large stress drop after yielding, and shear localization via shear band formation and bubble fragmentation. Similar inter-bubble distance dependent plasticity mechanisms in He nano-bubbled copper have also been observed in recent in-situ transmission electron microscopy experiments.

Deformation behavior of a model high entropy alloy from atomistic simulations

This paper reports atomistic simulation studies of deformation behavior in a model quinary high entropy FCC alloy. The simulations are based on empirical interatomic potentials and use massively parallel molecular dynamics techniques at the atomistic level to study the deformation mechanisms. The studies consider columnar polycrystalline samples containing pure tilt grain boundaries with random misorientations around the [110] crystallographic axis. Virtual tensile tests were performed and the material response analyzed using various techniques, focusing on the role that the local composition in the random alloy plays in the deformation mechanisms. Overall plastic response correlates well with the values of unstable stacking faults given by the potential, and it is therefore not meaningful to compare deformation response with that of any of the single components. The more meaningful comparison is with a corresponding “average atom” material that has the same average properties but no local randomness. The main effect of the random composition fluctuations is to make dislocation glide more difficult. These fluctuations also result in lower twin to stacking fault ratios in the deformed samples. The complex high entropy alloy presents a higher strength, and overall less plastic deformation for the same levels of stress. This is mostly driven by the fact that the dislocations emitted from the grain boundaries do not glide as easily in the random alloy as they do in the average atom material.

Unassisted photocatalytic H2O2 production under visible light by fluorinated polymer-TiO2 heterojunction

• Surface shielding of inorganic photocatalyst by hydrophobic organic photocatalyst. • Restrict the self-oxidation of photogenerated H 2 O 2 , and maximize the H 2 O 2 production. • A potential strategy for sustainable H 2 O 2 production from natural resources (sun, water, and air). • The atomistic simulation studies substantiate the hydrophobicity induced H 2 O 2 production. • A facile yet effective approach for solar H 2 O 2 production over inorganic/organic heterojunction. Photocatalytic H 2 O 2 production is one of the most promising methods because it is a safe and sustainable technique. However, the inactiveness of inorganic photocatalysts (TiO 2 ) under visible light irradiation and severe photodecomposition of H 2 O 2 on their surfaces result in low performance for solar H 2 O 2 production. Here, we report for the first time, a hydrophobic organic/inorganic (polymer/TiO 2 ) heterojunction photocatalyst, which not only can utilize visible light, but also suppress H 2 O 2 decomposition. In the absence of a hole scavenger, the photogenerated H 2 O 2 concentration of the poly(9,9-dioctylfluorene-alt-benzothiadiazole) (PFBT)/TiO 2 heterojunction photocatalyst (67 µM) was >70 times higher than that of pristine PFBT polymer. Further, improvement of polymer hydrophobicity by fluorine substitution results in enhanced photogenerated H 2 O 2 concentration (110.4 µM) on (Poly(9,9-dioctyl fluorine-alt-difluorobenzothiadiazole) (PF2FBT)/TiO 2 ). The atomistic simulation studies substantiate that the low adsorption energy of H 2 O 2 on the heterojunction and the surface shielding of TiO 2 induced by the hydrophobicity of the fluorinated polymers significantly improve H 2 O 2 production.

ATP-Magnesium Coordination: Protein Structure-Based Force Field Evaluation and Corrections.

In the numerous molecular recognition and catalytic processes across biochemistry involving adenosine triphosphate (ATP), the common bioactive form is its magnesium chelate, ATP·Mg2+. In aqueous solution, two chelation geometries predominate, distinguished by bidentate and tridentate Mg2+–phosphate coordination. These are approximately isoenergetic but separated by a high energy barrier. Force field-based atomistic simulation studies of this complex require an accurate representation of its structure and energetics. Here we focused on the energetics of ATP·Mg2+ coordination. Applying an enhanced sampling scheme to circumvent prohibitively slow sampling of transitions between coordination modes, we observed striking contradictions between Amber and CHARMM force field descriptions, most prominently in opposing predictions of the favored coordination mode. Through further configurational free energy calculations, conducted against a diverse set of ATP·Mg2+–protein complex structures to supplement otherwise limited experimental data, we quantified systematic biases for each force field. The force field calculations were strongly predictive of experimentally observed coordination modes, enabling additive corrections to the coordination free energy that deliver close agreement with experiment. We reassessed the applicability of the thus corrected force field descriptions of ATP·Mg2+ for biomolecular simulation and observed that, while the CHARMM parameters display an erroneous preference for overextended triphosphate configurations that will affect many common biomolecular simulation applications involving ATP, the force field energy landscapes broadly agree with experimental measurements of solution geometry and the distribution of ATP·Mg2+ structures found in the Protein Data Bank. Our force field evaluation and correction approach, based on maximizing consistency with the large and heterogeneous collection of structural information encoded in the PDB, should be broadly applicable to many other systems.

Void growth via dislocation pileup impingement on grain boundary

The effect of edge dislocations, impinging on grain boundary in fcc Fe near a preexisting void on the volume of this void, was studied using MD simulation. It was found that virtually unlimited growth of the void via this mechanism is possible under certain conditions. To the best of our knowledge this is the first atomistic simulation study, demonstrating feasibility of this void growth mechanism.

Polymer Electrolytes in Strong External Electric Fields: Modification of Structure and Dynamics

We present the results from an extensive atomistic molecular dynamics simulation study of poly(ethylene oxide) (PEO) doped with various amounts of lithium-bis(trifluoromethane)sulfonimide (LiTFSI) salt under the influence of external electric field strengths up to $1\,$V/nm. The motivation stems from recent experimental reports on the nonlinear response of mobilities to the application of an electric field in such electrolyte systems and arising speculations on field-induced alignment of the polymer chains, creating channel-like structures that facilitate ion passage. Hence, we systematically examine the electric field impact on the lithium coordination environment, polymer structure as well as ionic transport properties and further present a procedure to quantify the susceptibility of both structural and dynamical observables to the external field. Our investigation reveals indeed a coiled-to-stretched transformation of the PEO strands along with a concurrent nonlinear behavior of the dynamic properties. However, from studying the temporal response of the unperturbed electrolyte system to field application we are able to exclude a structurally conditioned enhancement of ion transport and surprisingly observe a slowing down. A microscopic understanding is supplied.

Wetting Transitions in the ATP Synthase C-Subunit Ring, a Large-Conductance Ion Channel

Apart from its known role in proton transport, the mammalian ATP synthase c-subunit ring (Fo domain) has been observed in recent electrophysiology experiments to form a high-conductance voltage-gated ion channel (∼1.5 nS). Yet, the ring's hydrophobic central lumen has been assumed to be dry, precluding a physical explanation for the observed conductance. We present an atomistic molecular dynamics simulation study of lumen wetting for mammalian and yeast c-subunit rings. Consistent with prior work, we find that the ∼12 Å diameter yeast ring remains dry on the several-hundred-nanosecond timescale of the simulations. In contrast, the narrower, ∼8 Å diameter, mammalian ring undergoes rapid (∼50 ns) liquid-vapor transitions, forming a transient but continuous water column across the lumen. Modifying the charge on the glutamate residues of the proton-transport pathway at the membrane-protein interface affects the duration and extent of lumen wetting, as do in silico mutations at various sites. The wetting variations are qualitatively consistent with electrophysiology experimental findings for wild-type and mutant forms of the mammalian c-subunit ring. We are encouraged to think that the simulations will serve as a valuable “computational microscope” for understanding how charge conductance can occur in the ATP synthase c-subunit ring. To determine the mechanism of wetting and its modulation, we are pursuing analysis of the surface hydrophobicity of the lumen lining and its response to the mutations. The simulation finding of reversible lumen wetting is supported by published work indicating c-subunit ring wetting in the intact ATP synthase. New experiments and published data additionally indicate that the Fo domain may exist at least partly dissociated from its F1 counterpart. ATP synthase c-subunit ring wetting, therefore, has implications with respect to osmotic swelling and the enigmatic mitochondrial permeability transition.

Magnesium Coordination of ATP - Force Field Evaluation and Structure-Driven Correction

In the numerous molecular recognition and catalytic processes across biochemistry involving adenosine triphosphate (ATP), the common bioactive form is its magnesium chelate, ATP.Mg2+. In aqueous solution, two chelation geometries predominate, with Mg contacting either the terminal beta and gamma phosphate groups (bidentate) or all three (tridentate). These subforms are approximately isoenergetic, but separated by a high energy barrier. Force field-based atomistic simulation studies of this complex require an accurate representation of its structure and energetics. Here we focused on the energetics of ATP.Mg2+ coordination. With unbiased molecular dynamics simulation showing prohibitively slow interconversion, we devised an enhanced sampling scheme to calculate free energy differences between different Mg2+-phosphate configurations. We observed striking contradictions between Amber and CHARMM force field descriptions, most prominently in opposing predictions of the favoured coordination mode. Through further configurational free energy calculations, conducted against a diverse set of ATP.Mg2+-protein complex structures to supplement otherwise limited experimental data, we observed systematic biases for each force field. However, the force field calculations were strongly predictive of experimentally observed coordination modes, enabling additive corrections to the coordination free energy that deliver close agreement with experiment. Reassessing the applicability of the corrected force field descriptions of ATP.Mg2+ for biomolecular simulation, we observe that calculated properties broadly agree with experimental measurements of solution geometry and the distribution of ATP.Mg2+ structures found in the Protein Data Bank. However, while the corrected Amber force field appears to reproduce both bidentate and tridentate configurations, CHARMM displays an erroneous preference triphosphate overextension. This will affect the interpretation of simulations of bidentate ATP.Mg2+, which comprises the majority of PDB structures.

Atomistic simulation and spectroscopy study of the Eu-doped NaCdPO4 compound

Atomistic simulation based on lattice energy minimization was performed to study the defect process caused by europium in the NaCdPO4 structure. The calculations suggest that the most favorable intrinsic defect type is formed by cation anti-site defect, in which Na+ and Cd2+ ions exchange positions. The calculation also reveals that doping by Eu3+ on the Cd site is the most energetically favorable. Charge compensation by NaCdʼ anti-site defect is probable. Crystal field parameters are then calculated and used to obtain the 7F1 sublevels of the Eu3+, which we use to discuss the local symmetry of the Eu3+.

The Origin of Activation of Non-basal Slip in Mg-Ce Dilute Alloy: An Atomistic Simulation Study

Mg-Ce alloys have been attracting attention because a small amount of Ce addition improves the ductility of Mg at room temperature. When Ce is added, non-basal slip related to improved ductility has been observed. However, the mechanism for activating non-basal slip by Ce has not been understood. In this study, the effect of Ce on slip behavior in Mg is investigated using a molecular dynamics simulation and interatomic potentials for pure Ce and Mg-Ce binary systems have been developed based on the second nearest-neighbor modified embedded-atom method formalism for molecular dynamics simulations. It is found that a small amount of Ce addition has little effect on the critical resolved shear stress (CRSS) of the pyramidal II slip, but significantly increases the CRSS of the basal and prismatic slip. Consequently, it reduces the CRSS anisotropy among slip systems and activates the non-basal slip. This study suggests that reduced CRSS anisotropy due to the difference in the solute-dislocation binding tendency among slip systems can be the reason for the non-basal slip activation, providing a guideline for Mg alloy design to improve the alloy’s ductility.

Anionic Tuning of Zeolite Crystallization

Zeolites are of great industrial relevance as catalysts, adsorbents, and ion-exchangers and typically synthesized under hydrothermal conditions. Rational regulation of their crystallization process...

Effects of surface modification of Nano-SiO2 imbedded in organic matrix on interfacial accumulation of water molecules: an atomistic simulation study

Silica nanoparticles are used as additives to organic coatings to modify their properties. The interface of inorganic nanoparticles with an organic matrix can be a preferred location for accumulation of water. Surface treatment of nanoparticles with 3-glycidoxypropyltrimethylsilane (silane) is one way to reduce the water accumulation. In this work, using atomistic simulations (MD), we studied the effects of silane treatment on accumulation of water at the interface of nanoparticles. Three different epoxy phases and two methods of deposition of water were simulated. Water molecules were studied at two locations: (i) the interface of nanoparticles, and (ii) in the matrix of coatings. Additionally, the changes in the organic matrix due to surface treatment of nanoparticles were studied. The simulations show how silane treatment affects the interactions of water with nanoparticles in different epoxies, and also how silane treatment reduces the water accumulation in an organic matrix with nanoparticles.