Search results for "molecular dynamics"
showing 10 items of 1075 documents
Spectral broadening of the Soret band in myoglobin: an interpretation by the full spectrum of low-frequency modes from a normal modes analysis.
2005
In this work the temperature dependence of the Soret band line shape in carbon-monoxy myoglobin is re-analyzed by using both the full correlator approach in the time domain and the frequency domain approach. The new analyses exploit the full density of vibrational states of carbon-monoxy myoglobin available from normal modes analysis, and avoid the artificial division of the entire set of vibrational modes coupled to the Soret transition into "high-frequency" and "low-frequency" subsets; the frequency domain analysis, however, makes use of the so-called short-times approximation, while the time domain one avoids it. Time domain and frequency domain analyses give very similar results, thus s…
Electromechanics of graphene spirals
2014
Among the most fascinating nanostructure morphologies are spirals, hybrids of somewhat obscure topology and dimensionality with technologically attractive properties. Here, we investigate mechanical and electromechanical properties of graphene spirals upon elongation by using density-functional tight-binding, continuum elasticity theory, and classical force field molecular dynamics. It turns out that electronic properties are governed by interlayer interactions as opposed to strain effects. The structural behavior is governed by van der Waals interaction: in its absence spirals unfold with equidistant layer spacings, ripple formation at spiral perimeter, and steadily increasing axial force;…
Molecular dynamics simulations of capillary rise experiments in nanotubes coated with polymer brushes.
2007
The capillary filling of a nanotube coated with a polymer brush is studied by molecular dynamics simulations of a coarse-grained model, assuming various conditions for the fluid-wall and fluid-brush interactions. Whereas the fluid is modeled by simple point particles interacting with Lennard-Jones forces, the (end-grafted, fully flexible) polymers that form the brush coating are described by a standard bead-spring model. Our experiments reveal that capillary filling is observed even for walls that would not be wetted by the fluid, provided the polymer brush coating itself wets. Generally, it is found that the capillary rise always proceeds through a t1/2 law with time t while the underlying…
Capillary Rise in Nanopores: Molecular Dynamics Evidence for the Lucas-Washburn Equation
2007
When a capillary is inserted into a liquid, the liquid will rapidly flow into it. This phenomenon, well studied and understood on the macroscale, is investigated by Molecular Dynamics simulations for coarse-grained models of nanotubes. Both a simple Lennard-Jones fluid and a model for a polymer melt are considered. In both cases after a transient period (of a few nanoseconds) the meniscus rises according to a $\sqrt{\textrm{time}}$-law. For the polymer melt, however, we find that the capillary flow exhibits a slip length $\delta$, comparable in size with the nanotube radius $R$. We show that a consistent description of the imbibition process in nanotubes is only possible upon modification o…
Anomalous Slowdown of Polymer Detachment Dynamics on Carbon Nanotubes
2019
The "wrapping" of polymer chains on the surface of carbon nanotubes allows one to obtain multifunctional hybrid materials with unique properties for a wide range of applications in biomedicine, electronics, nanocomposites, biosensors, and solar cell technologies. We study by means of molecular dynamics simulations the force-assisted desorption kinetics of a polymer from the surface of a carbon nanotube. We find that, due to the geometric coupling between the adsorbing surface and the conformation of the macromolecule, the process of desorption slows down dramatically upon increasing the windings around the nanotube. This behavior can be rationalized in terms of an overdamped dynamics with a…
Theoretical demonstration of the potentiality of boron nitride nanotubes to encapsulate anticancer molecule.
2015
Anticancer drug transport is now becoming an important scientific challenge since it would allow localizing the drug release near the tumor cell, avoiding secondary medical effects. We present theoretical results, based on density functional theory and molecular dynamics simulations, which demonstrate the stability of functionalized single (10,10) boron nitride nanotubes (BNNTs) filled with anticancer molecule such as carboplatin (CPT). For this functionalized system we determine the dependence of the adsorption energy on the molecule displacement near the inner BNNTs surface, together with their local morphological and electrical changes and compare the values to the adsorption energy obta…
Validation of a constrained 2D slab model for water adsorption simulation on 1D periodic TiO2 nanotubes
2018
Abstract Solar light driven hydrogen evolution is one focus of modern materials research. Among the different emerging technologies, particular interest is devoted towards metal oxide photocatalysts in the form of various 1D nanostructures. Presently, the mismatch between regular structures that can be synthesized and the largest structures that are feasible for computer simulation is still very large. For example, an in-depth study of water adsorption on nanotube (NT) surfaces requires, in addition to DFT calculations, molecular dynamics simulations to take into account the disordered nature of the aqueous phase. To completely immerse even a very thin nanotube into an aqueous system requir…
Microstructure development during NiAl intermetallic synthesis in reactive Ni–Al nanolayers: Numerical investigations vs. TEM observations
2013
Abstract Heterogeneous reactions leading to the formation of intermetallic compounds in nanometric Ni–Al multilayer system are examined both numerically and experimentally. On the numerical side, the reactivity of a layered Ni–Al–Ni system is studied by means of molecular dynamics simulations, using an embedded-atom method (EAM) potential. The mechanism of nucleation and growth of the intermetallic phase is determined. Four main stages in the reactive process, which lead to the formation of rounded shape grains of intermetallic phase at the Ni–Al interface, are delineated. On the experimental side, TEM imaging of quenched samples revealed the behavior of the Ni–Al reactive foils and showed …
Conformational changes in acetylcholine binding protein investigated by temperature accelerated molecular dynamics.
2014
Despite the large number of studies available on nicotinic acetylcholine receptors, a complete account of the mechanistic aspects of their gating transition in response to ligand binding still remains elusive. As a first step toward dissecting the transition mechanism by accelerated sampling techniques, we study the ligand-induced conformational changes of the acetylcholine binding protein (AChBP), a widely accepted model for the full receptor extracellular domain. Using unbiased Molecular Dynamics (MD) and Temperature Accelerated Molecular Dynamics (TAMD) simulations we investigate the AChBP transition between the apo and the agonist-bound state. In long standard MD simulations, both confo…