Search results for "molecular dynamics"
showing 10 items of 1075 documents
Molecular Dynamics Simulations
2003
A tutorial introduction to the technique of Molecular Dynamics (MD) is given, and some characteristic examples of applications are described. The purpose and scope of these simulations and the relation to other simulation methods is discussed, and the basic MD algorithms are described. The sampling of intensive variables (temperature T, pressure p) in runs carried out in the microcanonical (NVE) ensemble (N= particle number, V = volume, E = energy) is discussed, as well as the realization of other ensembles (e.g. the NVT ensemble). For a typical application example, molten SiO2, the estimation of various transport coefficients (self-diffusion constants, viscosity, thermal conductivity) is d…
From Gold Nanoseeds to Nanorods: The Microscopic Origin of the Anisotropic Growth
2016
Directly manipulating and controlling the size and shape of metal nanoparticles is a key step for their tailored applications. In this work, molecular dynamics simulations were applied to understand the microscopic origin of the asymmetric growth mechanism in gold nanorods. Different factors influencing the growth were selectively included in the models to unravel the role of the surfactants and ions. In the early stage of the growth, when the seed is only a few nanometers large, a dramatic symmetry breaking occurs as the surfactant layer preferentially covers the (100) and (110) facets, leaving the (111) facets unprotected. This anisotropic surfactant layer in turn promotes anisotropic gro…
Capillary Nematization of Semiflexible Polymers
2016
emiflexible polymers under good solvent conditions confined by two planar parallel repulsive walls are investigated for a wide range of monomer concentrations and distances between the walls, for a case where persistence length and contour length of the macromolecules are almost equal. Chain conformations and local nematic ordering near the walls are studied by both molecular dynamics methods and density functional theory, putting it in perspective with the recent work where the isotropic phase of semiflexible polymer solutions in the vicinity of a single repulsive wall in semi-infinite geometry is considered. Profiles of the total density of monomers as well as densities of end- and middle…
Temperature dependence of the local structure and lattice dynamics of wurtzite-type ZnO
2014
Temperature-dependent (10–300 K) Zn K-edge extended X-ray absorption fine structure (EXAFS) spectra of polycrystalline wurtzitetype ZnO were analyzed using ab initio multiple-scattering theory and taking into account anisotropy of the crystallographic structure and thermal disorder. We employed two different simulation approaches: classical molecular dynamics (MD) and reverse Monte Carlo coupled with an evolutionary algorithm (RMC/EA method). The accuracy of several force-field models, which are commonly used in the MD simulations of bulk and nanostructured ZnO, was tested based on a comparison between the experimental and simulated Zn K-edge EXAFS spectra. It was found that available force…
Semiflexible Polymers in the Bulk and Confined by Planar Walls
2016
Semiflexible polymers in solution under good solvent conditions can undergo an isotropic-nematic transition. This transition is reminiscent of the well-known entropically-driven transition of hard rods described by Onsager’s theory, but the flexibility of the macromolecules causes specific differences in behavior, such as anomalous long wavelength fluctuations in the ordered phase, which can be understood by the concept of the deflection length. A brief review of the recent progress in the understanding of these problems is given, summarizing results obtained by large-scale molecular dynamics simulations and density functional theory. These results include also the interaction of semiflexib…
Monitoring molecular dynamics of bacterial cellulose composites reinforced with graphene oxide by carboxymethyl cellulose addition
2017
[EN] Broadband Dielectric Relaxation Spectroscopy was performed to study the molecular dynamics of dried Bacterial Cellulose/Carboxymethyl Cellulose-Graphene Oxide (BC/CMC-GO) composites as a function of the concentration of CMC in the culture media. At low temperature the dielectric spectra are dominated by a dipolar process labelled as a beta -relaxation, whereas electrode polarization and the contribution of dc-conductivity dominate the spectra at high temperatures and low frequency. The CMC concentration affects the morphological structure of cellulose and subsequently alters its physical properties. X-ray diffractometry measurements show that increasing the concentration of CMC promote…
Equilibrium Dynamics and Shear Rheology of Semiflexible Polymers in Solution
2017
We study the structure and dynamics of semidilute solutions of semiflexible polymers at rest and under shear using hybrid molecular dynamics simulations that take hydrodynamic interactions into account. We show that the polymer center-of-mass diffusion coefficient significantly decreases with increasing chain stiffness at fixed monomer density. The zero-shear viscosity shows a corresponding increase due to the intermolecular interactions of stiffer chains. We apply steady shear flow to the polymer solutions and show that at high shear rates the flow properties become almost independent of polymer stiffness. We characterize the polymer conformations under shear and find that in this regime p…
PET/PEN Blends of Industrial Interest as Barrier Materials. Part I. Many-Scale Molecular Modeling of PET/PEN Blends
2006
Mesoscale molecular simulations, based on parameters obtained through atomistic molecular dynamics and Monte Carlo calculations, have been used for modeling and predicting the behavior of PET/PEN blends. Different simulations have been performed in order to study and compare pure homopolymer blends with blends characterized by the presence of PET/PEN block copolymers acting as compatibilizer. A many-scale molecular modeling strategy was devised to evaluate PET/PEN blend characteristics, simulate phase segregation in pure PET/PEN blends, and demonstrate the improvement of miscibility due to the presence of the transesterification reaction products. The behavior of distribution densities and …
Shear-Thinning in Oligomer Melts—Molecular Origins and Applications
2021
We investigate the molecular origin of shear-thinning in melts of flexible, semiflexible and rigid oligomers with coarse-grained simulations of a sheared melt. Entanglements, alignment, stretching and tumbling modes or suppression of the latter all contribute to understanding how macroscopic flow properties emerge from the molecular level. In particular, we identify the rise and decline of entanglements with increasing chain stiffness as the major cause for the non-monotonic behaviour of the viscosity in equilibrium and at low shear rates, even for rather small oligomeric systems. At higher shear rates, chains align and disentangle, contributing to shear-thinning. By performing simulations …
Exploiting Reaction-Diffusion Conditions to Trigger Pathway Complexity in the Growth of a MOF.
2021
Coordination polymers (CPs), including metal–organic frameworks (MOFs), are crystalline materials with promising applications in electronics, magnetism, catalysis, and gas storage/separation. However, the mechanisms and pathways underlying their formation remain largely undisclosed. Herein, we demonstrate that diffusion-controlled mixing of reagents at the very early stages of the crystallization process (i.e., within ≈40 ms), achieved by using continuous-flow microfluidic devices, can be used to enable novel crystallization pathways of a prototypical spin-crossover MOF towards its thermodynamic product. In particular, two distinct and unprecedented nucleation-growth pathways were experimen…