Edge effects control helical wrapping of carbon nanotubes by polysaccharides (original) (raw)
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Carbon nanotube structures: molecular dynamics simulation at realistic limit
Computer Physics Communications, 2002
Single walled carbon nanotubes as all-carbon molecules of tubular form exemplify modern nanometre scale material structures, where the number of atoms range from less than a million up to few millions. Such system are quite ideal for computational studies like Molecular Dynamics simulations because the studies can be done at the realistic limit, rendering them in a way predictive. This point of view we try to explore through simulations of novel ring-like carbon nanotubes, observed experimentally. Whether these structures are toroidal or coiled is under debate. To this question we seek insight by studying the structure, the minimum energy configuration, and the thermal stability of large toroidal nanotubes of (n, n)-and (n, 0)-helicity using large scale Molecular Dynamics simulations based on the interaction potential by Brenner. The system sizes of the studied tori range one and half orders of magnitude, in diameter from about 22 nm up to 700 nm, where the latter corresponds to the sizes of experimentally observed ring-like structures. Our simulations indicate that the toroidal form influences strongly the structure of the tubes for small tori while for the larger tori the structural changes are extremely small. We also find that there exists a critical tube radius dependent buckling radius at which the torus buckles. This was also found to be helicity dependent.
Monte Carlo Computer Simulation of Chain Formation from Nanoparticles
Spontaneous assembly of long chains of nanoparticles (NPs) has been experimentally observed for many different materials including nanocolloids of semiconductors, metal oxides, and metals. While the origin of dipole moment in various colloids can be different, a universal explanation of chain assembly can be provided by the hypothesis of dipole-dipole attraction of nanocolloids. In this paper, we describe the application of the Monte Carlo method for modeling of self-organization of large ensembles of NPs. As the first approximation, the Derjaguin-Landau-Verwey-Overbeek (DLVO) theory provides an adequate description of self-organization of several hundreds of NPs. Unlike microscale colloids that served as a classical model for DLVO, we used a distance-dependent media dielectric constant. The simulated chains are morphologically and geometrically similar to those observed experimentally. This establishes the fundamentally important ability of NPs to self-assemble due to their intrinsic anisotropy. Thermodynamic analysis of Monte Carlo results reveals the role of partial removal of the stabilizer shell in CdTe nanocolloids necessary for reduction of interparticle repulsion. Analysis of the field distribution around short chains demonstrates that the growth of linear agglomerates is kinetically controlled by a high activation barrier for NPs approaching from all of the directions except one end of the chain. The presented algorithm can be applied to other interparticle interactions, such as induced dipoles, which can stimulate chain formation in the absence of permanent dipole moment. It can also serve as a theoretical foundation for the understanding of the large complex superstructures forming from anisotropic and anisometric NPs. Monte Carlo simulation of nanoscale dipoles can also be extended to the interactions of NP with proteins, and related biological systems important for a variety of applications in medicine.
Molecular dynamics simulation of nanomaterials using an artificial neural net
Physical Review B, 2004
We report a method of conducting molecular dynamics (MD) simulations that uses an artificial neural net (ANN) to significantly increase computational speed. The technique enables dynamical simulation of hard objects with essentially arbitrarily complex geometry and is well suited to the simulation of granular matter over a wide range of densities. In hard systems, binary collisions are well defined and the ANN approach enables an efficient algorithm to determine the time to next collision with high accuracy. The method has been used to enable an MD study of an ensemble of 1800 hard, smooth, impenetrable equilateral triangles in a two-dimensional periodic space. At high packing fraction ͑0.6Ͻ Ͻ 0.9͒, the hard-triangle system exists as a liquid-crystalline-like phase (LCP) in which there is no long-range translational order but in which there is nearly perfect long-range orientational order. As the packing fraction decreases, the LCP undergoes a transition to a fluid state in which the long-range orientational correlation vanishes but short-range order is retained. Long-lived clusters, notably hexamers, are clearly apparent in the liquid phase and appear to be stabilized by a sort of internal "orientational" osmotic pressure. Insofar as can be inferred from our machine calculations, the transition between the LCP and the liquid occurs around ϳ 0.57 and appears to be second order. At low density, the hard-triangle system undergoes "chattering" collisions in which pairs of triangles collide and become associated, undergoing multiple collisions with each other before colliding with a third particle. The radial distribution function obtained from both molecular dynamics and Monte Carlo calculations shows a weak peak at low packing fraction.
2020
The properties of bio-molecules are explicitly influenced by their organization in bulk and vicinity of substrate. Organization of bio-molecules can be of various kinds such as folded, unfolded, helix, swollen, globule, and so forth. These organizations of bio-molecule also depend on the local surrounding environmental conditions like temperature, solvency, adsorption, and encapsulation. Variation in environmental conditions helps to manipulate and control the organizations for the desired applications. Adsorption and encapsulation of bio-molecule over substrate have many applications in the area of drug delivery, design and development of bio-sensors, advance bio-separation process, etc. Molecular dynamics simulation is a very powerful tool to investigate the molecular structures, synthesis process and optimum properties, etc. A large number of efficient force field parameters and molecular dynamics simulators are available for large-scale simulation.
The structural properties of a flexible and semiflexible circular chain confined in an array of parallel nanoposts with a square lattice cross-sectional projection were studied using coarse-grained molecular dynamics simulations. To address the effect of the circular topology, a comparison with linear analogs was also carried out. In the interpretation of the chain structural properties, the geometry of the post array is considered as a combination of a channel approximating the interstitial volume with the diameter d c and a slit approximating the passage aperture with the width w p . The number of interstitial volumes occupied by a chain monotonically increases with the decreasing ratio d c /w p regardless of the way the geometry of the post array is varied. However, depending on how the array geometry is modified, the chain span along the posts displays a monotonic (constant post separation) or a non-monotonic behavior (constant passage width) when plotted as a function of the post diameter. In the case of monotonic trend, the width of interstitial spaces increases with the increasing chain occupation number, while, in the case of non-monotonic trend, the width of interstitial spaces decreases with the increasing chain occupation number. In comparison with linear topology, for circular topology, the stiffness affects more significantly the relative chain extension along the posts and less significantly the occupation number. The geometrical parameters of the post arrays are stored in the single-chain structure factors. The characteristic humps are recognized in the structure factor which ensue from the local increase in the density of segments in the circular chains presented in an interstitial volume or from the correlation of parallel chain fragments separated by a row of posts. Although the orientation correlations provide qualitative information about the chain topology and the character of confinement within a single interstitial volume, information about the array periodicity is missing.
Cifra_et_al-1999-Macromolecular_Theory_and_Simulations.pdf
Using lattice simulations the effect of confinement on the size, orientation and elastic properties of athermal chains was investigated. For chains confined in a slit or in a "cylinder" with square profile a minimum was observed in the dependence of the mean-square end-to-end distance pR 2 P on the plate distance D. However, the components of the mean chain dimensions perpendicular and parallel to the walls, pR 2 k P and pR 2 00 P, steadily diverge with reduction of the pore size. In a slit the distribution functions of the chain vector perpendicular and parallel to the plates, WpR 2 k P and WpR 2 00 P, respectively, were computed. The marked difference between these distribution functions is interpreted as a sign of enhanced alignment of chains of the shape of elongated ellipsoids along the pore walls. A major part of the free energy of confinement DA cf stems from this mechanism of pore-induced macromolecular orientation. A striking anisotropy was observed in the elastic free energies A el k and A el 00 of chains deformed in the direction perpendicular and parallel to the walls and in the corresponding force-displacement functions. Finally, the relation between the elastic free energy A el and the free energy of confinement DA cf and between the forces f and f solv derived thereof is analysed.
MRS Proceedings, 2011
ABSTRACTIn this work we present preliminary results from molecular dynamics simulations for carbon nanotubes serpentine dynamics formation. These S-like nanostructures consist of a series of parallel and straight nanotube segments connected by alternating U-turn shaped curves. Nanotube serpentines were experimentally synthesized and reported in recent years, but up to now no atomistic simulations have been carried out to address the dynamics of formation of these structures. We have carried out fully atomistic molecular dynamics simulations in the framework of classical mechanics with a standard molecular force field. Multi-million atoms structures formed by stepped substrates with a carbon nanotube (about 1 micron in length) placed on top of them have been considered in our simulations. A force is applied to the upper part of the tube during a short period of time and then turned off and the system set free to evolve in time. Our results showed that these conditions are sufficient ...
Coarse-grained molecular dynamics simulations of a diblock copolymer consisting of a flexible and semi-flexible block in a dense array of parallel nanoposts with a square lattice packing were performed. The mutual interactions between the two blocks of the confined diblock chain were investigated through a comparison of their size, structure, and penetration among nanoposts with the corresponding separate chains. The geometry of a nanopost array was varied at constant post separation or at constant width of the passage between nanoposts. The size of a single interstitial volume was comparable to or smaller than the size of the diblock chain. A comparison of the blocks with their separate analogous chains revealed that the mutual interactions between the blocks were shielded by the nanoposts and, thus, the blocks behaved independently. At constant passage width, competitive effects of the axial chain extension in interstitial volumes and the lateral chain expansion among interstitial volumes led to a nonmonotonic behavior of the axial span. The position of the maximum in the span plotted against the filling fraction for a diblock chain was dictated by the semi-flexible block. The semi-flexible block penetrates among the nanoposts more readily and the expansion of the whole diblock copolymer is governed by the semiflexible block. The main findings were explained using the free energy arguments when an interstitial volume was approximated by a channel geometry and a passage aperture by a slit geometry. Detail knowledge of controlled conformational behavior in a compartmentalized environment can contribute to new processes in the storage and retrieval of information.