Length-scale dependent mechanical properties of Al-Cu eutectic alloy: Molecular dynamics based model and its experimental verification

This paper attempts to gain an understanding of the effect of lamellar length scale on the mechanical properties of two-phase metal-intermetallic eutectic structure. We first develop a molecular dynamics model for the in-situ grown eutectic interface followed by a model of deformation of Al-Al2Cu lamellar eutectic. Leveraging the insights obtained from the simulation on the behaviour of dislocations at different length scales of the eutectic, we present and explain the experimental results on Al-Al2Cu eutectic with various different lamellar spacing. The physics behind the mechanism is further quantified with help of atomic level energy model for different length scale as well as different strain. An atomic level energy partitioning of the lamellae and the interface regions reveals that the energy of the lamellae core are accumulated more due to dislocations irrespective of the length-scale. Whereas the energy of the interface is accumulated more due to dislocations when the length-scale is smaller, but the trend is reversed when the length-scale is large beyond a critical size of about 80 nm. (C) 2014 Author(s).

Two-Phase Thermodynamic Model for Efficient and Accurate Absolute Entropy of Water from Molecular Dynamics Simulations

Presented here is the two-phase thermodynamic (2PT) model for the calculation of energy and entropy of molecular fluids from the trajectory of molecular dynamics (MD) simulations. In this method, the density of state (DoS) functions (including the normal modes of translation, rotation, and intramolecular vibration motions) are determined from the Fourier transform of the corresponding velocity autocorrelation functions. A fluidicity parameter (f), extracted from the thermodynamic state of the system derived from the same MD, is used to partition the translation and rotation modes into a diffusive, gas-like component (with 3Nf degrees of freedom) and a nondiffusive, solid-like component. The thermodynamic properties, including the absolute value of entropy, are then obtained by applying quantum statistics to the solid component and applying hard sphere/rigid rotor thermodynamics to the gas component. The 2PT method produces exact thermodynamic properties of the system in two limiting states: the nondiffusive solid state (where the fluidicity is zero) and the ideal gas state (where the fluidicity becomes unity). We examine the 2PT entropy for various water models (F3C, SPC, SPC/E, TIP3P, and TIP4P-Ew) at ambient conditions and find good agreement with literature results obtained based on other simulation techniques. We also validate the entropy of water in the liquid and vapor phases along the vapor-liquid equilibrium curve from the triple point to the critical point. We show that this method produces converged liquid phase entropy in tens of picoseconds, making it an efficient means for extracting thermodynamic properties from MD simulations.

Molecular Dynamics Investigation of Structure and Transport in the K2O-2SiO2 System Using a Partial Charge Based Model Potential

Potassium disilicate glass and melt have been investigated by using a new partial charge based potential model in which nonbridging oxygens are differentiated from bridging oxygens by their charges. The model reproduces the structural data pertaining to the coordination polyhedra around potassium and the various bond angle distributions excellently. The dynamics of the glass has been studied by using space and time correlation functions. It is found that K ions migrate by a diffusive mechanism in the melt and by hops below the glass transition temperature. They are also found to migrate largely through nonbridging oxygenrich sites in the silicate matrix, thus providing support to the predictions of the modified random network model.

Molecular dynamics Investigation of structure and transport in the K2O-2SiO2 system using a partial charge based model potential

Potassium disilicate glass and melt have been investigated by using anew partial charge based potential model in which nonbridging oxygens are differentiated from bridging oxygens by their charges. The model reproduces the structural data pertaining to the coordination polyhedra around potassium and the various bond angle distributions excellently. The dynamics of the glass has been studied by using space and time correlation functions. It is found that K ions migrate by a diffusive mechanism in the melt and by hops below the glass transition temperature. They are also found to migrate largely through nonbridging oxygen-rich sites in the silicate matrix, thus providing support to the predictions of the modified random network model.

Chain folding and A:T pairing in human telomeric DNA: a model-building and molecular dynamics study

The various types of chain folding and possible intraloop as well as interloop base pairing in human telomeric DNA containing d(TTAG(3)) repeats have been investigated by model-building, molecular mechanics, and molecular dynamics techniques. Model-building and molecular mechanics studies indicate that it is possible to build a variety of energetically favorable folded-back structures with the two TTA loops on same side and the 5' end thymines in the two loops forming TATA tetrads involving a number of different intraloop as well as interloop A:T pairing schemes. In these folded-back structures, although both intraloop and interloop Watson-Crick pairing is feasible, no structure is possible with interloop Hoogsteen pairing. MD studies of representative structures indicate that the guanine-tetraplex stem is very rigid and, while the loop regions are relatively much more flexible, most of the hydrogen bonds remain intact throughout the 350-ps in vacuo simulation. The various possible TTA loop structures, although they are energetically similar, have characteristic inter proton distances, which could give rise to unique cross-peaks in two-dimensional nuclear Overhauser effect spectroscopy (NOESY) experiments. These folded-back structures with A:T pairings in the loop region help in rationalizing the data from chemical probing and other biochemical studies on human telomeric DNA.

Subquadratic quantum number dependence and other anomalies of vibrational dephasing in liquid nitrogen: Molecular dynamics simulation study from the triple point to the critical point and beyond

Vibrational phase relaxation near gas-liquid and liquid-solid phase coexistence has been studied by molecular dynamics simulations of N-N stretch in N-2. Experimentally observed pronounced insensitivity of phase relaxation from the triple point to beyond the boiling point is found to originate from a competition between density relaxation and resonant-energy transfer terms. The sharp rise in relaxation rate near the critical point (CP) can be attributed at least partly to the sharp, rise in vibration-rotation coupling contribution. Substantial subquadratic quantum number dependence of overtone dephasing rate is found near the CP and in supercritical fluids. [S0031-9007 (99)09318-7].

Docking, molecular dynamics and QM/MM studies to delineate the mode of binding of CucurbitacinE to F-actin

CucurbitacinE (CurE) has been known to bind covalently to F-actin and inhibit depolymerization. However, the mode of binding of CurE to F-actin and the consequent changes in the F-actin dynamics have not been studied. Through quantum mechanical/molecular mechanical (QM/MM) and density function theory (DFT) simulations after the molecular dynamics (MD) simulations of the docked complex of F-actin and CurE, a detailed transition state (TS) model for the Michael reaction is proposed. The TS model shows nucleophilic attack of the sulphur of Cys257 at the beta-carbon of Michael Acceptor of CurE producing an enol intermediate that forms a covalent bond with CurE. The MD results show a clear difference between the structure of the F-actin in free form and F-actin complexed with CurE. CurE affects the conformation of the nucleotide binding pocket increasing the binding affinity between F-actin and ADP, which in turn could affect the nucleotide exchange. CurE binding also limits the correlated displacement of the relatively flexible domain 1 of F-actin causing the protein to retain a flat structure and to transform into a stable ``tense'' state. This structural transition could inhibit depolymerization of F-actin. In conclusion, CurE allosterically modulates ADP and stabilizes F-actin structure, thereby affecting nucleotide exchange and depolymerization of F-actin. (C) 2015 Elsevier Inc. All rights reserved.

NMR studies of molecular dynamics in tetramethylammonium tetrabromo cadmate

Internal motions in a A2BX4 compound (tetramethylammonium tetrabromo cadmate) have been investigated using proton spin—lattice relaxation time (T1) and second moment (M2) measurements in the temperature range 77 to 400 K. T1 measurements at three Larmor frequencies (10, 20 and 30 MHz) show isotropic tumbling of the tetramethylammonium group, random reorientation of methyl groups and spin—rotation interaction, and the corresponding parameters have been computed. The cw spectrum is narrow throughout the temperature range and shows side bands at the lowest temperature. This observation, along with the free-induction-decay behavior at these temperatures, is interpreted as the onset of a coherent motion, e.g. methyl group quantum tunnelling.

Molecular Dynamics in [(CH8)aN]z Cd14 A Proton Magnetic Relaxation Study

second moment measurements are carried out on [(CH,),N], CdI, in the temperature range 77 to 400 K. The results are interpreted based on a molecular dynamical model of randomly reorienting methyl groups and isotropically tumbling tetramethyl ammonium group. The relaxation data show contributions from spin-rotation interaction at high temperatures and presence of inequivalent methyl groups. The correlation times and associated activation energies, connected with this model, are calculated from the data. The structure in the absorption line and in the free-induction decay signal at 77 K indicates the possibility of tunnelling motion of the methyl groups. Im Temperaturbereich 77 bis 400 K werden an [(CH,),N],CdI, Protonen-Spin-Gitter-Relaxationsexperimente (bei Larmorfrequenzen von 10,20 und 30 MHz) und Messungen des zweiten Moments durchgefiihrt. Die Ergebnisse werden an Hand eines molekularen dynamischen Modells sich statistisch umorientierender Methylgruppen und isotrop taumelnder Tetramethyl-Ammoniumgruppen interpretiert. Die Relaxationswerte zeigen Beitriige von Spin-Rotations-Wechselwirkung bei hohen Temperaturen und die Anwesenheit von inaquivalenten Methylgruppen. Die Korrelationszeiten und verknupften Aktivierungsenergien, die mit diesem Model1 verbunden sind, werden am den Werten berechnet. Die Struktur in der Absorptionslinie und im Abklingsignal der freien Induktion bei 77 K zeigt die Moglichkeit einer Tunnelbewegung der Methylgruppen.

A molecular dynamics investigation of the structure of PbO---PbF2 glasses*1

The structure of PbO---PbF2 glasses has been studied using molecular dynamics (MD). The existence of [OPb4] structural units is observed over the entire glass-forming range, in conformity with a model proposed earlier based on various structural investigations of this system. Various other features of the structural model are also supported by the MD calculations.

Coarse-Grained Molecular Dynamics Simulation of the Aggregation Properties of Multiheaded Cationic Surfactants in Water

The aggregation property of multiheaded surfactants has been investigated by constant pressure molecular dynamics (MD) simulation in aqueous medium. The model multiheaded surfactants contain more than one headgroup (x = 2, 3, and 4) for a single tail group. This increases the hydrophilic charge progressively over the hydrophobic tail which has dramatic consequences in the aggregation behavior. In particular, we have looked at the change in the aggregation property such as critical micellar concentration (cmc), aggregation number, and size of the micelles for the multiheaded surfactants in water. We find with increasing number of headgroups of the Multiheaded surfactants that the cmc values increase and the aggregation numbers as well as the size of the micelles decrease. These trends are in agreement with the experimental findings as reported earlier with x = 1, 2, and 3. We also predict the aggregation properties of multiheaded surfactant With four headgroups (x = 4) for which no experimental studies exist yet.

Structure, dynamics, and interactions of jacalin. Insights from molecular dynamics simulations examined in conjunction with results of X-ray studies

Molecular dynamics simulations have been carried out on all the jacalin-carbohydrate complexes of known structure, models of unliganded molecules derived from the complexes and also models of relevant complexes where X-ray structures are not available. Results of the simulations and the available crystal structures involving jacalin permit delineation of the relatively rigid and flexible regions of the molecule and the dynamical variability of the hydrogen bonds involved in stabilizing the structure. Local flexibility appears to be related to solvent accessibility. Hydrogen bonds involving side chains and water bridges involving buried water molecules appear to be important in the stabilization of loop structures. The lectin-carbohydrate interactions observed in crystal structures, the average parameters pertaining to them derived from simulations, energetic contribution of the stacking residue estimated from quantum mechanical calculations, and the scatter of the locations of carbohydrate and carbohydrate-binding residues are consistent with the known thermodynamic parameters of jacalin-carbohydrate interactions. The simulations, along with X-ray results, provide a fuller picture of carbohydrate binding by jacalin than provided by crystallographic analysis alone. The simulations confirm that in the unliganded structures water molecules tend to occupy the positions occupied by carbohydrate oxygens in the lectin-carbohydrate complexes. Population distributions in simulations of the free lectin, the ligands, and the complexes indicate a combination of conformational selection and induced fit. Proteins 2009; 77:760-777.

Diffusion of Pure CH4 and Its Binary Mixture with CO2 in Faujasite NaY: A Combination of Neutron Scattering Experiments and Molecular Dynamics Simulations

The self-diffusion properties of pure CH4 and its binary mixture with CO2 within MY zeolite have been investigated by combining an experimental quasi-elastic neutron scattering (QENS) technique and classical Molecular dynamics simulations. The QENS measurements carried out at 200 K led to an unexpected self-diffusivity profile for Pure CH4 with the presence of a maximum for a loading of 32 CH4/unit cell, which was never observed before for the diffusion of apolar species in azeolite system With large windows. Molecular dynamics simulations were performed using two distinct microscopic models for representing the CH4/NaY interactions. Depending on the model, we are able to fairly reproduce either the magnitude or the profile of the self-diffusivity.Further analysis allowed LIS to provide some molecular insight into the diffusion mechanism in play. The QENS measurements report only a slight decrease of the self-diffusivity of CH4 in the presence of CO2 when the CO2 loading increases. Molecular dynamics simulations successfully capture this experimental trend and suggest a plausible microscopic diffusion mechanism in the case of this binary mixture.

Effect of coordinated ions on structure and flexibility of parallel G-quadruplexes: A molecular dynamics study

ingle tract guanine residues can associate to form stable parallel quadruplex structures in the presence of certain cations. Nanosecond scale molecular dynamics simulations have been performed on fully solvated fibre model of parallel d(G(7)) quadruplex structures with Na+ or K+ ions coordinated in the cavity formed by the O6 atoms of the guanine bases. The AMBER 4.1 force field and Particle Mesh Ewald technique for electrostatic interactions have been used in all simulations. There quadruplex structures are stable during the simulation, with the middle four base tetrads showing root mean square deviation values between 0.5 to 0.8 Angstrom from the initial structure as well the high resolution crystal structure. Even in the absence of any coordinated ion in the initial structure, the G-quadruplex structure remains intact throughout the simulation. During the 1.1 ns MD simulation, one Nai counter ion from the solvent as well as several water molecules enter the central cavity to occupy the empty coordination sites within the parallel quadruplex and help stabilize the structure. Hydrogen bonding pattern depends on the nature of the coordinated ion, with the G-tetrad undergoing local structural variation to accommodate cations of different sizes. in the absence of any coordinated ion. due to strong mutual repulsion, O6 atoms within G-tetrad are forced farther apart from each other, which leads to a considerably different hydrogen bonding scheme within the G-tetrads and very favourable interaction energy between the guanine bases constituting a G-tetrad. However, a coordinated ion between G-tetrads provides extra stacking energy for the G-tetrads and makes the quadruplex structure more rigid. Na+ ions, within the quadruplex cavity, are more mobile than coordinated K+ ions. A number of hydrogen bonded water molecules are observed within the grooves of all quadruplex structures.

Effect of coordinated ions on structure and flexiblity of parallel G-quandruplexes: a molecular dynamics study

Single tract guanine residues can associate to form stable parallel quadruplex structures in the presence of certain cations. Nanosecond scale molecular dynamics simulations have been performed on fully solvated fibre model of parallel d(G7) quadruplex structures with Na+ or K+ ions coordinated in the cavity formed by the 06 atoms of the guanine bases. The AMBER 4.1 force field and Particle Mesh Ewald technique for electrostatic interactions have been used in all simulations. These quadruplex structures are stable during the simulation, with the middle four base tetrads showing root mean square deviation values between 0.5 to 0.8 A from the initial structure as well the high resolution crystal structure. Even in the absence of any coordinated ion in the initial structure, the G-quadruplex structure remains intact throughout the simulation. During the 1.1 ns MD simulation, one Na+ counter ion from the solvent as well as several water molecules enter the central cavity to occupy the empty coordination sites within the parallel quadruplex and help stabilize the structure. Hydrogen bonding pattern depends on the nature of the coordinated ion, with the G-tetrad undergoing local structural variation to accommodate cations of different sizes. In the absence of any coordinated ion, due to strong mutual repulsion, 06 atoms within G-tetrad are forced farther apart from each other, which leads to a considerably different hydrogen bonding scheme within the G-tetrads and very favourable interaction energy between the guanine bases constituting a G-tetrad. However, a coordinated ion between G-tetrads provides extra stacking energy for the G-tetrads and makes the quadruplex structure more rigid. Na+ ions, within the quadruplex cavity, are more mobile than coordinated K+ ions. A number of hydrogen bonded water molecules are observed within the grooves of all quadruplex structures