Modeling the self-assembly of Peptide amphiphiles into fibers using coarse-grained molecular dynamics

We have studied the self-assembly of peptide amphiphiles (PAs) into a cylindrical micelle fiber starting from a homogeneous mixture of PAs in water using coarse-grained molecular dynamics simulations. Nine independent 16 μs runs all show spontaneous fiber formation in which the PA molecules first form spherical micelles, and then micelles form a three-dimensional network via van der Waals interactions. As the hydrophobic core belonging to the different micelles merge, the three-dimensional network disappears and a fiber having a diameter of ～80 ? appears. In agreement with atomistic simulation results, water molecules are excluded from the hydrophobic core and penetrate to ～15 ? away from the axis of fiber. About 66% of the surface of fiber is covered with the IKVAV epitope, and ～92% of the epitope is exposed to water molecules.     

Fracture analysis of the pullout test

Pullout tests are increasingly being used to determine thein situ strength of concrete. Several studies have shown that a close correlation exists between the maximum pullout load and compressive strength of concrete. However, the failure mechanism of the pullout test is yet not understood. Conflicting theories have been forwarded to analyze the pullout test. In this study, progressive internal microcracking was examined during the pullout testing. A commercially available equipment was modified to enable monitoring the pullout load vs. relative displacement relationship. Specimens were loaded and unloaded from predetermined fractions of the ultimate load. Acoustic activity was measured during testing. Unloaded specimens were sectioned and examined for microcracking. Results indicate a two-stage cracking process. An extensive stable cracking system dominates for loads up to than the peak load. A different cracking pattern develops near the peak load and governs the shape of the finally extracted core.     

Molecular dynamics and atomistic based continuum studies of the interfacial behavior of nanoreinforced epoxy

In this study, we investigate the interfacial mechanical characteristics of carbon nanotube (CNT) reinforced epoxy composite using molecular dynamics (MD) simulations. The second-generation polymer consistent force field (PCFF) is used in the MD simulations. In particular, we compare MD results with those obtained by atomistic-based continuum (ABC) multiscale modeling technique, which makes use of the appropriate constitutive relations derived solely from interatomic potentials. The results of our comparative investigation suggest that (i) the ABC multiscale model and MD simulation provides almost identical predictions for the interfacial properties of the nanocomposite for smaller diameter of CNTs, (ii) the ABC model slightly over predict the interfacial properties of the nanocomposite for larger diameter of CNTs, and (iii) the MD simulations represents the real nanocomposite structure with the minimum assumptions compared to that of the ABC multiscale model but with much greater computer requirements and limited length scale.     

Electromagnetic interference shielding effectiveness of nanoreinforced polymer composites deposited with conductive metallic thin films

The effect of using conductive metallic thin films deposited on high density polyethylene (HDPE) and styrene butadiene copolymer (SBC) in conjunction with carbon nanofiber (CNF) reinforcement of HDPE and SBC was investigated in order to improve the electromagnetic interference shielding effectiveness (EMI SE) of the structures. Thin films of copper, silver and aluminum were deposited by thermal evaporation onto the polymeric matrices and its composites (0-20 wt.% of CNFs). Results show a synergistic effect of the two approaches (metallic coating and CNF reinforcement) toward improving the EMI SE. The chemical composition, surface morphology, carbon nanofiber distribution, thickness and microstructure of metallic coated polymers are examined using X-Ray Diffraction and Scanning Electron Microscopy.     

Evaluation of concrete spall repairs by pullout test

Spalling concrete was simulated in the laboratory by utilizing pullout test methods generally used for the determination ofin situ concrete strength. The cracking patterns displayed by pullout test specimens typify the damage of concrete by spalling. All specimens were damaged by pullout testing, repaired with epoxy mortar and subjected to a second pullout test at a later time. The test programme showed that the overriding factor which governs successful repairs to concrete is the soundness of the repair plane.     

Vibrational study of a molecular device using molecular dynamics simulations

A Potential scenario for the implementation of molecular electronic systems is introduced by applying digital signal processing techniques to results from classical molecular dynamics simulations of a molecular system interconnected by nanosize gold clusters. Under this new scenario, signals can be introduced, processed, and read through interactions with the internal vibrational modes of the small molecular unit. We use modulation operations intrinsically inherent to any molecular system as a concept proof. As an example of this type of analysis, we focus on the individual oscillations between C-H and C-C bonds and cluster-cluster displacements.     

On the effect of different polymer matrix and fibre treatment on single fibre pullout test using betelnut fibres

This study is aimed at exploring the possibility of improving the interfacial adhesion strength of betelnut fibres using different chemical treatments namely 4% and 6% of HCl and NaOH respectively. The fibre specimens were partially embedded into different thermosetting polymer matrix (polyester and epoxy) as reinforcement blocks. Single fibre pullout tests were carried out for both the untreated (Ut) and treated betelnut fibres with different resins and tested under dry conditions. Scanning electron microscopy was used to examine the material failure morphology. The studies revealed the differences of interfacial adhesion strengths for the various test specimens of betelnut fibres treated with the polyester and epoxy matrix which followed in the order of: N6 ? N4 > H4 > Ut > H6. It was proven that fibres treated with 6% of NaOH exhibits excellent interfacial adhesion properties. The interfacial adhesion shear strength of these fibres using polyester and epoxy has improved by 141% and 115% correspondingly compared to untreated fibre under the same treatment.     

Dot pattern generation technique using molecular dynamics

We have developed a new technique for generating homogeneously distributed irregular dot patterns useful for optical devices and digital halftoning technologies. To introduce irregularity, we use elaborately designed sequences called low-discrepancy sequences instead of pseudorandom numbers. We also use a molecular-dynamics redistribution method to improve the distribution of dots. Our method can produce arbitrary density distributions in accordance with a given design. The generated patterns are free from visible roughness as well as any moiré patterns when superimposed on other regular patterns. We demonstrate that our method effectively improves luminance uniformity and eliminates moiré patterns when used for a backlight unit of a liquid-crystal display.     

Modeling the crystallization of spherical nucleic acid nanoparticle conjugates with molecular dynamics simulations

We use molecular dynamics simulations to study the crystallization of spherical nucleic-acid (SNA) gold nanoparticle conjugates, guided by sequence-specific DNA hybridization events. Binary mixtures of SNA gold nanoparticle conjugates (inorganic core diameter in the 8-15 nm range) are shown to assemble into BCC, CsCl, AlB(2), and Cr(3)Si crystalline structures, depending upon particle stoichiometry, number of immobilized strands of DNA per particle, DNA sequence length, and hydrodynamic size ratio of the conjugates involved in crystallization. These data have been used to construct phase diagrams that are in excellent agreement with experimental data from wet-laboratory studies.     

Effects of pores on shear bands in metallic glasses: A molecular dynamics study

The effects of nanoscale pores on the strength and ductility of porous Cu₄₆Zr₅₄ metallic glasses during nanoindentation and uniaxial compression tests are modelled and investigated using molecular dynamics (MD) simulations. In the MD simulations, atomistic amorphous samples were digitally prepared through fast quenching from the liquid states of copper and zirconium alloy. In both of the nanoindentation and uniaxial compression simulations, shear transformation zones and shear bands are observed through the local deviatoric shear strains in the samples. The results show that the existence of pores causes strain concentrations and greatly promotes the initialization and propagation of shear bands. Importantly, only pores reaching critical size can effectively facilitate the formation of multiple shear bands. It is also observed that hardening occurs through pore annihilation and the shear band stops in porous metallic glasses.     

Modeling and simulations of nanofluids using classical molecular dynamics: Particle size and temperature effects on thermal conductivity

We use molecular dynamics simulations to investigate the thermal conductivity of argon-based nanofluid with copper nanoparticles through the Green-Kubo formalism. To describe the interaction between argon-argon atoms, we used the well-known Lennard-Jones (L-J) potential, while the copper–copper interactions are modeled using the embedded atom method (EAM) potential that takes the metallic bonding into account. The thermal conductivity of the pure argon liquid obtained in the present simulation agreed with available experimental results. In the case of nanofluid, our simulation predicted thermal conductivity values larger than those found by the existing analytical models, but in a good accordance with experimental results. This implies that our simulation is more adequate, to describe the thermal conductivity of nanofluids than the previous analytical models. The efficiency of nanofluids is improved and the thermal conductivity enhancement is appeared when the particle size and temperature increase.     

Impact of hydrogen microalloying on the mechanical behavior of Zr-bearing metallic glasses: A molecular dynamics study

Comparative studies on Zr_(35)Cu_(65)and Zr_(65)Cu_(35)amorphous systems were performed using molecular dynamic simulations to explore whether their hydrogenated mechanical behavior depends on the content of hydride-forming elements.Although both of them present an increased strength and ductility after hydrogen microalloying,we observe the improved mechanical behavior for Zr_(35)Cu_(65)is more pronounced than that for Zr_(65)Cu_(35).In these two samples,the distribution of configurational potential energy and flexibility volume respectively follows a similar H-induced variation tendency;all of the hydrogenated alloys not just have more stable atoms with smaller flexibility volume,but possess a larger fraction of readily activated atoms.However,the atomic-scale details,based on the localgradient atomic packing structuremodel,indicate minor additions of hydrogen can promote moresoft spotsalong with more strengthenedbackbonesin the low-Zr alloy than that in the high-Zr sample,which endows the former with much higher strength and deformability after hydrogen microalloying.We regard this finding as a further step forward to distilling the tell-tale metrics of the H-dependent mechanical behavior observed in Zr-based metallic glasses.     

Study of InN/GaN interfaces using molecular dynamics

Epitaxial growth of thin films is, in general, based on specific interfacial structures defined by a minimum of interfacial energy and usually influenced by the structural mismatch. In the present study, the structures and energies of (0001) InN/GaN epitaxial interfaces are studied using the Tersoff interatomic potential. The potential describes the metallic and intermetallic interactions sufficiently well and is assembled in order to accurately reproduce the lattice and elastic parameters of wurtzite Ga(In)-Nitrides. Different configurations are examined for each interface depending on polarity and atomic stacking. It is shown that the interfacial structures of InN thin films grown with indium polarity interfaces exhibit lower self-energies than those of N-polarity. Although the substrate and the epilayer were assumed to exhibit the wurtzite crystal structure, both wurtzite and zinc-blende type atomic stackings are possible at the interfacial region since they were found energetically degenerate within the accuracy of our model. Finally, the spatial location of the epitaxial interface is also energetically defined. Epitaxial interfaces in this system can in principle be imagined to pass through so-called single or double atomic bonds, but the former case was energetically more favourable.     

Modeling of skutterudite CoSb3 with molecular dynamics method

Skutterudite materials have generated considerable interest as new thermoelectric materials over the past few years. For binary skutterudite compound CoSb₃ with complicated cubic crystal structure, Morse potential energy function is employed to describe atomic interactions to lay special emphasis on its mechanical properties. The parameters of Morse potential function between different species of atom pairs (Co–Co, Sb–Sb and Co–Sb) are individually determined based on known crystal structures and elastic properties from experiment or first principle calculation results. To test the accuracy of the obtained potential parameters, molecular dynamics simulation was first performed to inverse deduce and compare with preceding used values, and the results show excellent agreement. Moreover, the practicability and feasibility of the potential was verified. In terms of the obtained potential parameters, the virtual uniaxial tensile simulation was performed for single crystal CoSb₃ with bulk model using the conventional molecular dynamics algorithm. The mechanical response and deformation behavior are carefully analyzed. In contrast to conventional bulk CoSb₃, single crystal bulk CoSb₃ exhibits much better mechanical performances. It undergoes elastic deformation before 10% strain, and achieves ultimate stress 13.3 GPa at the strain of 10.2%, subsequently sudden fracture occurs near the middle of the model, demonstrating typical brittleness.     

Characterizing mechanical properties of graphite using molecular dynamics simulation

The mechanical properties of graphite in the forms of single graphene layer and graphite flakes (containing several graphene layers) were investigated using molecular dynamics (MD) simulation. The in-plane properties, Young’s modulus, Poisson’s ratio, and shear modulus, were measured, respectively, by applying axial tensile stress and in-plane shear stress on the simulation box through the modified NPT ensemble. In order to validate the results, the conventional NVT ensemble with the applied uniform strain filed in the simulation box was adopted in the MD simulation. Results indicated that the modified NPT ensemble is capable of characterizing the material properties of atomistic structures with accuracy. In addition, it was found the graphene layers exhibit higher moduli than the graphite flakes; thus, it was suggested that the graphite flakes have to be expanded and exfoliated into numbers of single graphene layers in order to provide better reinforcement effect in nanocomposites.     

Modeling the relaxed cohesive energy of metallic nanoclusters

A model is developed to calculate the cohesive energy of metallic nanoclusters with relaxed structure. It is found that the relaxed cohesive energy is higher than that of the un-relaxed one due to relaxation process decreasing the total energy. The relaxed nanoclusters in present model are more close to real ones, and the efficiency of the model is confirmed by molecular dynamics results on Cu nanoclusters.     

An investigation into the melting of silicon nanoclusters using molecular dynamics simulations

Using the Stillinger-Weber?(SW) potential model, we have performed molecular dynamics?(MD) simulations to investigate the melting of silicon nanoclusters comprising a maximum of 9041 atoms. This study investigates the size, surface energy and root mean square displacement?(RMSD) characteristics of the silicon nanoclusters as they undergo a heating process. The numerical results reveal that an intermediate nanocrystal regime exists for clusters with more than 357?atoms. Within this regime, a linear relationship exists between the cluster size and its melting temperature. It is found that melting of the silicon nanoclusters commences at the surface and that T(m,N) = T(m,Bulk)-αN(-1/3). Therefore, the extrapolated melting temperature of the bulk with a surface decreases from T(m,Bulk) = 1821?K to a value of T(m,357) = 1380?K at the lower limit of the intermediate nanocrystal regime.     

Effects of surface nanostructure on boundary lubrication using molecular dynamics

Molecular dynamics simulations are used to study the boundary lubrication behaviors of squalane lubricant between two iron wall struc-tures during shearing at d...