Dynamics Study Of Structure Research Articles

Molecular Dynamics Study of Hydrogen Bond Structure and Tensile Strength for Hydrated Amorphous Cellulose.

Molecular dynamics (MD) simulations were conducted to investigate the hydrogen-bond (H-bond) structure and its impact on the tensile strength of hydrated amorphous cellulose. The study identifies a stable intramolecular H-bond between the hydroxyl group at position 3 and the ether oxygen at position 5 (OH3···O5). Intermolecularly, the hydroxyl groups at positions 2 (OH2) and 6 (OH6) form stable H-bonds. Young's modulus, maximum tensile strength, and corresponding strain were calculated as functions of moisture content, while the H-bond network, water cluster formation, and cellulose chain orientation during tensile simulations were analyzed to elucidate mechanical properties. The substitution effect of cellulose on Young's modulus is also examined, revealing that the substitution of OH3 for a hydrophobic group minimally affects Young's modulus, but substitutions at OH2 and OH6 significantly reduce tensile strength due to their roles as key intermolecular H-bond donor sites.

Molecular dynamics study of the interface fine structure and mechanical properties of Ni@SWCNT/Cu nanocrystalline composite materials

The use of carbon nanotubes (CNTs) as reinforcing phase in copper-based composites has been extensively studied. However, controlling the synthesis interface structure and explaining the nanoscale interface bonding mechanism through experimental methods still poses challenges. In this study, a model of single-walled carbon nanotube nanocrystalline copper composite was established based on molecular dynamics (MD) simulations to investigate the effects of grain boundaries and dislocations on the composite material. It was found that the addition of nickel atoms improved the interface bonding between carbon nanotubes and the copper matrix, reducing vacancies at the interface. Ni@SWCNT/Cu exhibited better mechanical properties. Structural changes and defect evolution during deformation were studied. The ultimate tensile strength of SWCNT/Cu and Ni@SWCNT/Cu composites increased by 62.29 % and 68.78 % respectively compared to nanocrystalline copper, while the Young's modulus increased by 25.91 % and 32.48 % respectively; moreover, the Young's modulus of these two composites increased by 45.24 % and 49.42 % respectively. Ni@SWCNT/Cu had the lowest wear rate and friction coefficient, with a minimum wear rate of 0.0055 and a minimum friction coefficient of 0.67, demonstrating better wear resistance. The effects of different friction speeds and depths of indentation on the friction performance of the composite materials were also investigated.

Ab initio molecular dynamics study of the local structures and migration behaviors of liquid Sb-based alloys

High-purity Sb is widely applied in the semiconductor industry, infrared detection and non-volatile memory. An in-depth knowledge of the local structure and related properties in liquid Sb-based alloys proves to be highly advantageous in the purification of Sb. In this work, an ab initio molecular dynamics simulation was used to study the local structures, dynamical properties, electronic structures and migration behaviors of liquid X-containing (X = As, Bi, Cu, Fe) Sb-based alloys. Among these solute atoms, the distribution coefficient of As/Bi is much larger than that of Cu/Fe. The results showed that the local structures around As/Bi are looser than those around Cu/Fe. The local structure around As/Bi contains a higher fraction of low-index bond pairs than that around Cu/Fe, and its local topological order of triples is closer to pure Sb melt. The coordination polyhedrons using As/Bi as the centered atom have more relaxed short-range order clusters than those using Cu/Fe as the centered atom. Different local structures and chemical effects may lead to different migration behaviors of solute atoms in the Sb melt.

X-ray and molecular dynamics study of the temperature-dependent structure of FLiNaK

The atomic structure of FLiNaK and its evolution with temperature are examined with x-ray scattering and molecular dynamics (MD) simulations in the temperature range 460–636 °C. In accord with previous studies, it’s observed that the average nearest-neighbor (NN) cation-anion coordination number increases with increasing cation size, going from ∼4 for Li-F to ∼6.4 for K-F. In addition, we find that there is a coupled change in local coordination geometry – going from tetrahedral for Li-F to octahedral for Na to very disordered quasi-cuboidal for K. The varying geometry and coordination distances for the cation-anion pairs cause a relatively constant F-F next-nearest neighbor (NNN) distance of approximately 3.1 Å. This relatively fixed distance allows the F anions to assume an overall correlated structure very similar to that of a hard-sphere liquid with an extended radius which is beyond the normal F ion size but reflects the cation-anion coordination requirements. Careful consideration of the evolution of the experimental atomic distribution functions with increasing temperature shows that the changes in correlation at each distance can be understood within the context of broadening asymmetric neighbor distributions. Within the temperature range studied, the evolution of F-F correlations with increasing temperature is consistent with changes expected in a hard-sphere liquid simply due to decreasing density.

Design and beam dynamics study of disk-loaded structure for muon LINAC

The disk-loaded structures (DLS) in the muon LINAC are under development for the J-PARC muon g–2/EDM experiment. Four DLSs with an accelerating gradient of 20 MV/m take charge of muon acceleration from 40 MeV to 212 MeV, which corresponds to 70% to 94% of the speed of light. The quasi-constant gradient type TM01-2π/3 mode DLSs with gradually varying disk spacing was designed and it was confirmed that the cumulative phase slip due to the mismatch between muon and phase velocity can be suppressed to less than 2 degrees at the frequency of 2592 MHz. In addition, the optimum synchronous phase and the lattice were investigated to satisfy the requirements of the total emittance less than 1.5π mm mrad and the momentum spread less than 0.1% in RMS.

Molecular dynamics study of structure and reactions at the hydroxylated Mg(0001)/bulk water interface.

A molecular level understanding of the aqueous Mg corrosion mechanism will be essential in developing improved alloys for battery electrodes, automobile parts, and biomedical implants. The structure and reactivity of the hydroxylated surface is expected to be key to the overall mechanism because (i) it is predicted to be the metastable surface state (rather than the bare surface) under a range of conditions and (ii) it provides a reasonable model for the outer corrosion film/water interface. We investigate the structure, interactions, and reactivity at the hydroxylated Mg(0001)/water interface using a combination of static Density Functional Theory calculations and second-generation Car-Parrinello ab initio molecular dynamics. We carry out detailed structural analyses into, among other properties, near-surface water orientations, favored adsorption sites, and near-surface hydrogen bonding behavior. Despite the short timescale (tens of ps) of our molecular dynamics run, we observe a cathodic water splitting event; the rapid timescale for this reaction is explained in terms of near-surface water structuring lowering the reaction barrier. Furthermore, we observe oxidation of an Mg surface atom to effectively generate a univalent Mg species (Mg+). Results are discussed in the context of understanding the Mg corrosion mechanism: For example, our results provide an explanation for the catalytic nature of the Mg corrosion film toward water splitting and a feasible mechanism for the generation of the univalent Mg species often proposed as a key intermediate.

Molecular dynamics study of special quasirandom structure of Zr-Nb alloys

Irradiation damage to zirconium alloys (e.g., zirconium niobium (Zr-Nb) alloy) is the key to the design of fission-reactor structural materials and fuel rod cladding materials. Atomic scale computational simulations such as molecular dynamics and first principles are often needed to understand the physical mechanism of irradiation damage. For the simulation of randomly substitutional solid solution, it is necessary to construct large-sized supercells that can reflect the random distribution characteristics of alloy elements. However, it is not suitable to use large-size supercells (such as ≥ 200 atoms) for first principle calculation, due to the large computational cost. Special quasirandom supercells (SQS) are usually used for first principles calculation. The SQS can partly reflect the random distribution characteristics of alloy elements, but it only corresponds to one configuration for specific components, hence whether this model can reflect the statistical average of multiple local configurations in a real randomly substitutional solid solution is still an open question, and needs further studying and verifying. Molecular dynamics (MD) simulation can be carried out on the randomly substitutional solid solution with a larger scale based on random substitution (RSS) method, these supercells include more local configurations. Therefore, the MD studies of Zr-Nb alloy are carried out for the RSS and SQS-extended supercells. The critical size of RSS supercell which can truly reflect the statistical properties of solid solution alloy is determined. Then the lattice constant, formation energy and energy-volume relationship of SQS-extended supercell of Zr-Nb alloy and a series of RSS supercells are calculated and compared. The results show that the lattice constants, the formation energy and energy volume curves of the solid solution obtained by SQS supercell simulation are close to a series of corresponding statistical values of the physical properties of RSS supercells, so the SQS supercells can be used to study the random substitution of solid solution alloys.

Interfacial structures and acidity constants of goethite from first-principles Molecular Dynamics simulations

Abstract In this paper, we report a first-principles Molecular Dynamics (FPMD) study of interfacial structures and acidity constants of goethite. The pKa values of the groups on (010), (110), and (021) surfaces (space group Pbnm) are derived with the FPMD based vertical energy gap technique. The results indicate that major reactive groups include ≡Fe2OH2 and ≡FeOH2 on (010), ≡FeOH2, ≡Fe3OLH, and ≡Fe3OUH on (110), and ≡FeOhH2 and ≡Fe2OH on (021). The interfacial structures were characterized in detail with a focus on the hydrogen bonding environment. With the calculated pKa values, the point of zero charges (PZCs) of the three surfaces are derived and the overall PZC range of goethite is found to be consistent with the experiment. We further discuss the potential applications of these results in future studies toward understanding the environmental processes of goethite.

Molecular Dynamics Study of Structure, Folding, and Aggregation of Poly-PR and Poly-GR Proteins

Poly-proline-arginine (poly-PR) and poly-glycine-arginine (poly-GR) proteins are believed to be the most toxic dipeptide repeat (DPR) proteins that are expressed by the hexanucleotide repeat expansion mutation in C9ORF72, which are associated with amyotrophic lateral sclerosis (ALS) and frontotemporal dementia (FTD) diseases. Their structural information and mechanisms of toxicity remain incomplete, however. Using molecular dynamics simulation and all-atom model of proteins, we study folding and aggregation of both poly-PR and poly-GR. The results indicate formation of double-helix structure during the aggregation of poly-PR into dimers, whereas no stable aggregate is formed during the aggregation of poly-GR; the latter only folds into α-helix and double-helix structures that are similar to those formed in the folding of poly-glycine-alanine (poly-GA) protein. Our findings are consistent with the experimental data indicating that poly-PR and poly-GR are less likely to aggregate because of the hydrophilic arginine residues within their structures. Such characteristics could, however, in some respect facilitate migration of the DPR proteins between and within cells and, at the same time, give proline residues the benefits of activating the receptors that regulate ionotropic effect in neurons, resulting in death or malfunction of neurons because of the abnormal increase or decrease of the ion transmission. This may explain the neurotoxicities of poly-PR and poly-GR associated with many neurodegenerative diseases. To our knowledge, this is the first molecular dynamics simulation of the phenomena involving poly-PR and poly-GR proteins.

Molecular Dynamics Study of Ionomer Aggregate Structure during Solvent Evaporation

Cathode catalyst layer (CL) is one of the principal components for polymer electrolyte fuel cells. CL is typically prepared by solution processing techniques where a catalyst ink consisting of Pt-C (platinum on a carbon powder support), ionomer, and solvents (water/alcohol mixtures) is exposed to evaporation. The structure and stability of ionomer aggregates in solutions are the key to the physical properties of ionomer thin films. Thus, understanding the ionomer aggregation behaviors in solutions is of great importance to gain a deep insight into fundamental morphological characteristics of ionomers. In our previous studies, we have observed ionomer formation into cylindrical bundle-like aggregates in solutions. The size of ionomer bundles decreases with increasing alcohol content, indicating that the ionomers tend to be more dispersed at higher alcohol content, which is in good agreement with the trend inferred from the scattering experiments. In this study, evolution of ionomer aggregate structure in water solutions have been investigated using solvent evaporation simulations based on the course-grained molecular dynamics method, as shown in FIgure 1. The balance between evaporation, sedimentation, and diffusion was controlled by the dimensionless Peclet number, providing a link between experiments and simulations. The effects of substrate wettability on the ionomer thin film structure will be discussed in the presentation. Figure 1

Surface of Half-Neutralized Diamine Triflate Ionic Liquids. A Molecular Dynamics Study of Structure, Thermodynamics, and Kinetics of Water Absorption and Evaporation.

Surface properties of room temperature ionic liquids (RTILs) consisting of half neutralized diamine cations (H2N-(CH2)n-NH3+, n = 2, 4) and triflate anions have been investigated by molecular dynamics simulations, based on an empirical atomistic force field. Planar slabs periodically repeated in 2D have been considered, and the temperature range 260 ≤ T ≤ 360 K has been covered, extending from below the melting and glass point to the equilibrium liquid range of the diamine compounds under investigation. Addition of water at 1% weight concentration allowed us to investigate the kinetics of water absorption through the RTIL surface, and to characterize the structural and dynamical properties of subsurface water. Animations of the simulation trajectory highlight the quick absorption of water molecules, progressing downhill in free energy and taking place without apparent intermediate kinetic stages. To verify and quantify these observations, a variant of the umbrella sampling algorithm has been applied to compute the variation of excess free energy upon displacing a water molecule along the normal to the surface, from the center of the slab to the vapor phase. The results provide a comprehensive picture of the thermodynamic properties underlying the kinetics of water absorption and evaporation through the surface, and they also provide the ratio of the equilibrium density of water in the vapor and liquid phase at the average concentration considered by simulations. A variety of properties such as the surface energy, the 90-10% width of the profile, the layering of different species at the interface, and the electrostatic double layer at the surface are computed and discussed, focusing on the effect of water contamination on all of them.

An ab initio molecular dynamics study of the solvation structure and ultrafast dynamics of lithium salts in organic carbonates: A comparison between linear and cyclic carbonates

Carbonate-based lithium-ion electrolytes are of great importance due to their close relationship with the resulting battery efficiency and safety. Modifying the organic electrolyte has been paramount for achieving more efficient and safer lithium-ion batteries. However, the molecular picture of the electrolyte is still under scrutiny. Lately, ultrafast infrared spectroscopic studies have investigated the solvation structure and dynamics of the lithium ion (Li+) in both linear and cyclic carbonates. However, theoretical studies describing the molecular arrangements and transformation occurring in such time scales are scarce. In this study, ab initio molecular dynamics simulations were used to obtain the molecular structure and dynamics of the Li+ solvation shell in cyclic and linear carbonates. The theoretical results showed that molecular arrangement of the carbonates directly coordinating Li+ is not significantly altered by the carbonate chemical nature. However, the cyclic and linear carbonates showed significant different pictures of the overall solvation shell due to the intercalation phenomenon observed for cyclic carbonates, which significantly alters the motions of coordinated solvent. In addition, the intercalation appears to affect the propensity of ion pair formation and/or solvent exchange. Finally, the dynamics of the geometrical changes of the carbonates solvating Li+ is found to occur with characteristic times of tenths of picoseconds, while ion pair and solvent chemical exchange appear to happen in time scales which are at least an order of magnitude larger. Our study provides a comprehensive picture of the structure and dynamics of the molecular components in different carbonate-based lithium-ion electrolytes occurring in picosecond time scales.

Molecular dynamics study of structure, folding, and aggregation of poly-glycine-alanine (Poly-GA).

Poly-glycine-alanine (poly-GA) proteins are widely believed to be one of the main toxic dipeptide repeat molecules associated with amyotrophic lateral sclerosis (ALS) and frontotemporal dementia diseases. Using discontinuous molecular dynamics simulation and an all-atom model of the proteins, we study folding, stability, and aggregation of poly-GA. The results demonstrate that poly-GA is an aggregation-prone protein that, after a long enough time, forms β-sheet-rich aggregates that match recent experiment data and that two unique helical structures are formed very frequently, namely, β-helix and double-helix. The details of the two structures are analyzed. The analysis indicates that such helical structures are stable and share the characteristics of both α-helices and β-sheets. Molecular simulations indicate that identical phenomena also occur in the aggregation of poly-glycine-arginine (poly-GR). Therefore, we hypothesize that proteins of type (GX)n in which X may be any non-glycine amino acid and n is the repeat length may share the same folding structures of β-helix and double-helix and that it is the glycine in the repeat that contributes the most to this characteristic. Molecular dynamics simulation with continuous interaction potentials and explicit water molecules as the solvent supports the hypothesis. To our knowledge, this is the first molecular dynamics simulation of the phenomena involving poly-GA and poly-GR proteins.

Molecular dynamics study of structure and vibrational spectra at zwitterionoic lipid/aqueous KCl, NaCl, and CaCl2 solution interfaces.

Molecular dynamics (MD) simulations of KCl, NaCl, and CaCl2 solution/dipalmytoylphosphatidylcholine lipid interfaces were performed to analyze heterodyne-detected vibrational sum frequency generation (HD-VSFG) spectra in relation to the interfacial water structure. The present MD simulation well reproduces the experimental spectra and elucidates a specific cation effect on the interfacial structure. The K+, Na+, and Ca2+ cation species penetrate in the lipid layer more than the anions in this order, due to the electrostatic interaction with negative polar groups of lipid, and the electric double layer between the cations and anions cancels the intrinsic orientation of water at the water/lipid interface. These mechanisms explain the HD-VSFG spectrum of the water/lipid interface and its spectral perturbation by adding the ions. The lipid monolayer reverses the order of surface preference of the cations at the solution/lipid interface from that at the solution/air interface.

A molecular dynamics study of the nucleus interface structure and orientation relationships during the austenite-to-ferrite transformation in pure Fe

ABSTRACTMolecular dynamics simulations using an embedded-atom method potential for pure iron (Fe) were performed to investigate the solid-state transformation of a body-centred-cubic phase from a polycrystalline face-centred-cubic matrix. A Kurdjumov–Sachs orientation relationship accompanied with a step-ledge disconnection structure was detected in high mobility phase boundaries of a full 3D classical and barrier-free nucleation specimen. The results imply that interface coherency is an important factor for both nucleation and growth processes, which may significantly affect the transition rate of the austenite–ferrite transformation.

A Molecular Dynamics Study of Interfacial Structure and Ion Transport of Mixed Carbonate/LiPF6 Electrolytes Near Graphite Electrode Surfaces

Electrolyte and electrode materials utilized within lithium ion batteries have been extensively studied as separate segments, however the structural and dynamical properties of the electrode/electrolyte interface remain relatively undefined their immense role in dictating cell performance. By utilizing molecular dynamics simulations, we examine the structural reorganization of solvent molecules (cyclic ethylene carbonate: linear dimethyl carbonate 1:1 and 1:3 molar ratio doped with 1M LiPF6) upon the immersion of a graphite anode at various charge states. The interfacial structure was found to be sensitive to the molecular geometry and polarity of each solvent molecule as well as the surface structure and charge distribution of the negative electrode. An in depth analysis of the rearrangement of molecules at the anode/electrolyte interface elucidates structural influence on ion transport of both Li+ and fully or partially decomposed solvent molecules in order to better understand transient electrochemical processes which occur at this interface during the early stages of the SEI formation. The coupling of enhanced sampling techniques, such as metadynamics, with equilibrium structural data provides a computational framework for studying these processes at their onse,t which may further assist in efforts to engineer the anode/electrolyte interface leading to an optimal SEI layer.

Molecular dynamics study of perovskite structures with modified interatomic interaction potentials

The structure of compounds with the perovskite structure ABX3 (A and B are cations, X are anions O2—, F—, Cl—, Br—, and I—), which are widely used in engineering due to unique electrical, optical, and photovoltaic properties, has been considered. Hybrid organic—inorganic halide perovskites important for photovoltaics of a new generation are worth mentioning; they contain cations of organic nitrogen bases as monovalent cations. A molecular dynamics (MD) study of the CaTiO3 base structure (Ca2+, Ti4+, and O2—) has been performed in order to develop the methodology of computer simulation and optimization of the shape and parameters of atomic potentials for perovskite systems.

Molecular dynamics study of atomic-level structure in monatomic metallic glass

Molecular dynamics simulations have been performed to study the vitrification process and the local atomic structures in Ni monatomic metallic glasses (MG). The interatomic interactions are described by embedded atom method (EAM) potentials. Short-range order (SRO) and medium range order (MRO) in nickel monatomic MG is studied using several structural techniques such as the Radial distribution function (RDF); the Common neighbor analysis method (CNA) and the Voronoi tessellation. As a result, we found that the atomic packing in metallic glasses can be described globally as a superposition of the spherical-periodic order (SPO) and the local translational symmetry (LTS). From CNA method, we found that the majority of icosahedral clusters in Ni monatomic MG are connected together by vertex-sharing (VS), edge-sharing (ES), face-sharing (FS) and intercross-sharing (IS) rather than isolated clusters. These typical cluster connections constitute to the partial RDF of icosahedral atoms except the edge sharing which is hidden between the second and the third subpeaks of RDF. Furthermore, the visualization technologies are applied to follow the formation of clusters during rapid quenching. It is found that the clusters ⟨0,1,10,2⟩ and ⟨0,2,8,4⟩ are more dominant than the full icosahedral polyhedron ⟨0,0,12,0⟩ in our monatomic system. Furthermore, the splitting of the second peak in RDF curve in Ni glass is not only caused by the icosahedral clusters, but also by the Voronoi polyhedrons ⟨0,1,10,2⟩ and ⟨0,2,8,4⟩.

Molecular dynamics study of structure and glass forming ability of Zr70Pd30 alloy

In this study, the temperature effects on the structural evolution of the Zr70Pd30 binary alloy in the glassy and liquid states were studied using the molecular dynamics simulations based on the many-body type tight-binding potential. We considered the following properties in detail: the temperature dependence of the volume, the partial and total pair distribution functions and the simulated glass transition temperature. The effects of the cooling rates on the glass transition temperature were examined. The Wendt-Abraham parameter was calculated to determine the glass transition temperature of Zr70Pd30 glassy alloy. The pair analysis technique of Honeycutt-Andersen was applied to define local atomic arrangements produced from molecular dynamics simulations. The results show that the icosahedral ordering in glassy state has been composed during quenching period, and the simulated glass transition temperature and the total pair distribution functions are in good agreement with the experimental data.

分子動力学計算による燃料電池用電解質膜の構造と物質透過性に関する研究

高効率の固体高分子形燃料電池(PEFC)開発においては，プロトン伝導性が高く，燃料である水素やメタノールをブロックするのに適した高分子電解質膜が求められる．本研究では，高プロトン伝導度と低メタノールクロスオーバー(MCO)の両立に適した電解質膜の設計指針を得るため，種々の含水率，スルホン化度に設定したSPPOおよびNafion®を対象として，分子動力学計算を実施し，ポリマー構造とポリマー中のプロトン，水，メタノールの拡散メカニズムを解析した．その結果，高スルホン化度のSPPOの含水率を抑制することにより，高伝導度と低MCOの両立が可能であることが示された．この設計コンセプト実現のため，エポキシ，シランなどの架橋成分をSPPOにブレンドしたコンポジット膜の検討を行ったところ，含水率抑制を実現するとともに，Nafion®と同等のプロトン伝導度を維持し，MCOを低減することに成功した．