Search results for "Quantitative"
showing 10 items of 2409 documents
Force probe simulations using an adaptive resolution scheme
2021
Molecular simulations of the forced unfolding and refolding of biomolecules or molecular complexes allow to gain important kinetic, structural and thermodynamic information about the folding process and the underlying energy landscape. In force probe molecular dynamics (FPMD) simulations, one pulls one end of the molecule with a constant velocity in order to induce the relevant conformational transitions. Since the extended configuration of the system has to fit into the simulation box together with the solvent such simulations are very time consuming. Here, we apply a hybrid scheme in which the solute is treated with atomistic resolution and the solvent molecules far away from the solute a…
Quantitative analysis of localized surface plasmons based on molecular probing
2010
International audience; We report on the quantitative characterization of the plasmonic optical near-field of a single silver nanoparticle. Our approach relies on nanoscale molecular molding of the confined electromagnetic field by photoactivated molecules. We were able to directly image the dipolar profile of the near-field distribution with a resolution better than 10 nm and to quantify the near-field depth and its enhancement factor. A single nanoparticle spectral signature was also assessed. This quantitative characterization constitutes a prerequisite for developing nanophotonic applications.
3D multispectral light propagation model for subcutaneous veins imaging
2008
In this paper, we describe a new 3D light propagation model aimed at understanding the effects of various physiological properties on subcutaneous vein imaging. In particular, we build upon the well known MCML (Monte Carlo Multi Layer) code and present a tissue model that improves upon the current state-of-the-art by: incorporating physiological variation, such as melanin concentration, fat content, and layer thickness; including veins of varying depth and diameter; using curved surfaces from real arm shapes; and modeling the vessel wall interface. We describe our model, present results from the Monte Carlo modeling, and compare these results with those obtained with other Monte Carlo metho…
Influence of Fano resonance on SERS enhancement in Fano-plasmonic oligomers
2019
Plasmonic oligomers can provide profound Fano resonance in their scattering responses. The sub-radiant mode of Fano resonance can result in significant near-field enhancement due to its light trapping capability into the so-called hotspots. Appearance of these highly localized hotspots at the excitation and/or Stokes wavelengths of the analytes makes such oligomers promising SERS active substrates. In this work, we numerically and experimentally investigate optical properties of two disk-type gold oligomers, which have different strength and origin of Fano resonance. Raman analysis of rhodamine 6G and adenine with the presence of the fabricated oligomers clearly indicates that an increment …
Deconvolution of the Effects of Binary Associations and Collective Assemblies on the Rheological Properties of Entangled Side-Chain Supramolecular Po…
2019
The properties and function of supramolecular polymer networks are determined not only by pairwise interchain transient associations but also by chain entanglement and nanoscopic phase separation of the associative groups. To unravel the impact and interplay of these different factors, we devise a set of model supramolecular polymer networks in which the number of entanglements and the density of associative groups are systematically varied. Rheological data show that by increasing the density of associative groups, the plateau modulus grows to a steady level and extends over a distinct frequency range. This is credited to the presence of binary associations with unique partner exchange tim…
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…
Coupling of Nanoparticle Dynamics to Polymer Center-of-Mass Motion in Semidilute Polymer Solutions
2017
We investigate the dynamics of nanoparticles in semidilute polymer solutions when the nanoparticles are comparably sized to the polymer coils using explicit- and implicit-solvent simulation methods. The nanoparticle dynamics are subdiffusive on short time scales before transitioning to diffusive motion on long time scales. The long-time diffusivities scale according to theoretical predictions based on full dynamic coupling to the polymer segmental relaxations. In agreement with our recent experiments, however, we observe that the nanoparticle subdiffusive exponents are significantly larger than predicted by the coupling theory over a broad range of polymer concentrations. We attribute this …
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…
Thermal disorder and correlation effects in anti-perovskite-type copper nitride
2017
This work has been supported by the Latvian National Research Program IMIS2. The EXAFS experiment has been financed from the European Community's Seventh Framework Programme under grant agreement No. 226716 (Project I-20100098 EC). J.T. also gratefully acknowledges support from the National Science Foundation under the DMREF program Grant No. CHE-1534184.
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 …