Search results for "Diffusion"
showing 10 items of 1615 documents
Information Exchange in Mobile Encounter Network
2007
In this paper we analyze an information exchange method based on information diffusion in mobile encounter networks, a form of mobile peer-to-peer networks. We utilize dual mobility model which provides support for more realistic simulations compared to mobility models based only one method of movement. The distribution of the mobile device encounter intervals are discussed and analyzed via simulation runs. The logistic model is suggested to provide reasonably accurate estimates of the information diffusion process.
HEXIM1 Diffusion in the Nucleus Is Regulated by Its Interactions with Both 7SK and P-TEFb
2019
International audience; How nuclear proteins diffuse and find their targets remains a key question in the transcription field. Dynamic proteins in the nucleus are classically subdiffusive and undergo anomalous diffusion, yet the underlying physical mechanisms are still debated. In this study, we explore the contribution of interactions to the generation of anomalous diffusion by the means of fluorescence spectroscopy and simulation. Using interaction-deficient mutants, our study indicates that HEXIM1 interactions with both 7SK RNA and positive transcription elongation factor b are critical for HEXIM1 subdiffusion and thus provides evidence of the effects of protein-RNA interaction on molecu…
Reversibility and Diffusion in Mandelythiamin Decarboxylation. Searching Dynamical Effects in Decarboxylation Reactions
2012
Decarboxylation of mandelylthiamin in aqueous solution is analyzed by means of quantum mechanics/molecular mechanics simulations including solvent effects. The free energy profile for the decarboxylation reaction was traced, assuming equilibrium solvation, while reaction trajectories allowed us to incorporate nonequilibrium effects due to the solvent degrees of freedom as well as to evaluate the rate of the diffusion process in competition with the backward reaction. Our calculations that reproduce the experimental rate constant show that decarboxylation takes place with a non-negligible free energy barrier for the backward reaction and that diffusion of carbon dioxide is very fast compared…
Antimicrobial Peptides and Their Superior Fluorinated Analogues: Structure-Activity Relationships as Revealed by NMR Spectroscopy and MD Calculations
2010
9 pag., 6 fig, 3 tab.
Nondestructive Size Determination of Thiol-Stabilized Gold Nanoclusters in Solution by Diffusion Ordered NMR Spectroscopy
2013
Diffusion ordered NMR spectroscopy (DOSY) was used as an analytical tool to estimate the size of thiol-stabilized gold nanoclusters in solution, namely, phenylethanethiol (PET) stabilized Au25(PET)18, Au38(PET)24, and Au144(PET)60. This was achieved by determining the diffusion coefficient and hydrodynamic radius from solution samples that were confirmed to be monodispersed by electrospray ionization mass spectrometry. The average cluster diameters obtained by this technique were estimated to be 1.7, 2.2, and 3.1 nm for the Au25(PET)18, Au38(PET)24, and Au144(PET)60 nanoclusters, respectively, which were shown to agree well with the average diameters of the corresponding single crystal or t…
How molecular knots can pass through each other
2014
We propose a mechanism in which two molecular knots pass through each other and swap positions along a polymer strand. Associated free energy barriers in our simulations only amount to a few $k_{B}T$, which may enable the interchange of knots on a single DNA strand.
Motion, relaxation dynamics, and diffusion processes in two-dimensional colloidal crystals confined between walls
2012
The dynamical behavior of single-component two-dimensional colloidal crystals confined in a slit geometry is studied by Langevin dynamics simulation of a simple model. The colloids are modeled as pointlike particles, interacting with the repulsive part of the Lennard-Jones potential, and the fluid molecules in the colloidal suspension are not explicitly considered. Considering a crystalline strip of triangular lattice structure with n=30 rows, the (one-dimensional) walls confining the strip are chosen as two rigidly fixed crystalline rows at each side, commensurate with the lattice structure and, thus, stabilizing long-range order. The case when the spacing between the walls is incommensura…
Irreversible gelation of thermally unfolded proteins:structural and mechanical properties of lysozyme aggregates
2010
The formation of protein aggregates is important in many fields of life science and technology. The morphological and mechanical properties of protein solutions depend upon the molecular conformation and thermodynamic and environmental conditions. Non-native or unfolded proteins may be kinetically trapped into irreversible aggregates and undergo precipitation or gelation. Here, we study the thermal aggregation of lysozyme in neutral solutions. We characterise the irreversible unfolding of lysozyme by differential scanning calorimetry. The structural properties of aggregates and their mechanisms of formation with the eventual gelation are studied at high temperature by spectroscopic, rheolog…
Channel Formation and Intermediate Range Order in Sodium Silicate Melts and Glasses
2004
We use inelastic neutron scattering and molecular dynamics simulation to investigate the interplay between the structure and the fast sodium ion diffusion in various sodium silicates. With increasing temperature and decreasing density the structure factors exhibit an emerging prepeak around 0.9 A^-1. We show, that this prepeak has its origin in the formation of sodium rich channels in the static structure. The channels serve as preferential ion conducting pathways in the relative immobile Si-O matrix. On cooling below the glass transition this intermediate range order is frozen in.
Dynamical Properties of Self-Assembled Surfactant-Based Mixtures: Triggering of One-Dimensional Anomalous Diffusion in Bis(2-ethylhexyl)phosphoric Ac…
2013
The dynamic features of bis(2-ethylhexyl)phosphoric acid (HDEHP)/n-octylamine (NOA) mixtures have been investigated as a function of the NOA mole fraction and temperature by (1)H NMR spectroscopy and rheometry. All data consistently suggest a composition-induced glass-forming behavior. The microscopic factors responsible for this behavior have been highlighted and have been explained in terms of driving forces given by HDEHP-to-NOA proton transfer, the tendency of the resulting species to establish H bonds and to spatially segregate the alkyl chains. The study sheds light on the molecular mechanism responsible for the peculiar behavior of transport properties in such systems and furnishes b…