Search results for "molecular dynamics"
showing 10 items of 1075 documents
Atomistic simulations of the FeK-edge EXAFS in FeF3using molecular dynamics and reverse Monte Carlo methods
2016
Atomistic simulations of the experimental Fe K-edge extended x-ray absorption fine structure (EXAFS) of rhombohedral (space group ) FeF3 at T = 300 K were performed using classical molecular dynamics and reverse Monte Carlo (RMC) methods. The use of two complementary theoretical approaches allowed us to account accurately for thermal disorder effects in EXAFS and to validate the developed force-field model, which was constructed as a sum of two-body Buckingham-type (Fe–F and F–F), three-body harmonic (Fe–F–Fe) and Coulomb potentials. We found that the shape of the Fe K-edge EXAFS spectrum of FeF3 is a more sensitive probe for the determination of potential parameters than the values of stru…
Uniaxial Alignment of Polycyclic Aromatic Hydrocarbons by Solution Processing
2005
The self-organization of two polycyclic aromatic hydrocarbons with different aromatic core sizes, dodecylphenyl-substituted hexa-peri- hexabenzocoronene and an extended disk consisting of 96 carbon atoms 6-fold-alkyl-substituted, on the surface from solution has been investigated. Highly ordered surface layers of both materials could be obtained by the zone-casting technique, despite an apparently low self-organization in drop-cast films. The zone-cast films revealed high macroscopic uniaxial orientation of the columns with a molecular edge-on arrangement on the glass support as confirmed by polarized optical microscopy, UV-vis measurements in polarized light, high-resolution transmission e…
First principles simulation of amorphous InSb
2013
Ab initio molecular dynamics simulations based on density functional theory have been performed to generate a model of amorphous InSb by quenching from the melt. The resulting network is mostly tetrahedral with a minor fraction ($10%$) of atoms in a fivefold coordination. The structural properties are in good agreement with available x-ray diffraction and extended x-ray-absorption fine structure data and confirm the proposed presence of a sizable fraction of homopolar In-In and Sb-Sb bonds whose concentration in our model amounts to about $20%$ of the total number of bonds.
Liquid Structure of Trihexyltetradecylphosphonium Chloride at Ambient Temperature: An X-ray Scattering and Simulation Study
2009
We report on an experimental and simulation study done on a representative room temperature ionic liquid, namely tetradecyltrihexylphosphonium chloride, at ambient conditions. The study was conducted using small and wide angle X-ray scattering and molecular dynamics simulations. Both approaches converge in indicating that this material is characterized by the existence of strong P-Cl interactions (with characteristic distances between 3.5 and 5.0 Å) and by the occurrence of nanoscale segregation, despite the symmetric nature of the cation and similarly to other room temperature ionic liquids. A good agreement is found between the structure factor and pair correlation functions obtained from…
Liquid structure of dibutyl sulfoxide
2016
We present experimental (X-ray diffraction) data on the structure of liquid dibutyl sulfoxide at 320 K and rationalise the data by means of molecular dynamics simulations. Not unexpectedly, DBSO bearing a strong dipolar moiety and two medium length, apolar butyl chains, this compound was characterised by a distinct degree of polar vs. apolar structural differentiation at the nm spatial scale, which was fingerprinted by a low Q peak in its X-ray diffraction pattern. Similar to, but to a larger extent than its shorter chain family members (such as DMSO), DBSO was also characterised by an enhanced dipole-dipole correlation, which was responsible for a moderate Kirkwood correlation factor as we…
Thermal effects during adsorption of n-butane on a slilicalite-1 membrane. A non-equilibrium molecular dynamics study
2007
Abstract Non-equilibrium molecular dynamic (NEMD) simulations have been used to study the kinetics of adsorption of n-butane molecules in a silicalite membrane. We have chosen this simple well-known process to demonstrate that the process is characterized by two stages, both non-isothermal. In the first stage the large chemical driving force leads to a rapid uptake of n-butane in all the membrane and a simultaneous increase in the membrane temperature, explained by the large enthalpy of adsorption, Δ H = − 61.6 kJ / mol butane. A diffusion coefficient for transport across the external surface layer is calculated from the relaxation time; a value of 3.4 × 10 −9 m 2 / s is found. During the a…
The self-association equilibria of doxorubicin at high concentration and ionic strength characterized by fluorescence spectroscopy and molecular dyna…
2019
Abstract The self-association equilibria of doxorubicin hydrochloride (DX), at high drug and NaCl concentrations, are studied by temperature scan fluorescence spectroscopy, with the support of molecular dynamics (MD) calculations. Even though all anthracyclines show dimerization equilibria, DX only can further associate into long polymeric chains according to DXmon ⇄ DXdim ⇄ DXpol. This is reflected not only in the mechanical properties of DXpol solutions (behaving as thixotropic gels) but also in their spectroscopic behaviour. Fluorescence, in particular, is the technique of election to study this complex set of equilibria. Upon increasing the temperature, DXpol melts into DXdim, which in …
Room temperature crystal structure of the fast switching M159T mutant of the fluorescent protein dronpa
2015
The fluorescent protein Dronpa undergoes reversible photoswitching reactions between the bright ‘on’ and dark ‘off’ states via photoisomerisation and proton transfer reactions. We report the room temperature crystal structure of the fast switching Met159Thr mutant of Dronpa at 2.0 A resolution in the bright on state. Structural differences with the wild type include shifted backbone positions of strand β8 containing Thr159 as well as an altered A-C dimer interface involving strands β7, β8, β10, and β11. The Met159Thr mutation increases the cavity volume for the p-hydroxybenzylidene-imidazolinone chromophore as a result of both the side chain difference and the backbone positional difference…
Sodium bis(2-ethylhexyl)sulfosuccinate self-aggregation in vacuo: molecular dynamics simulation.
2010
Molecular dynamics (MD) simulations were conducted for systems in vacuo consisting of n AOT(-) anions (bis(2-ethylhexyl)sulfosuccinate ions) and n+/- 1 or n Na(+) ions up to n = 20. For n = 15, positively charged systems with Li(+), K(+), and Cs(+) cations were also considered. All systems were observed to form reverse micelle-like aggregates whose centre is occupied by cations and polar heads in a very compact solid-like way, while globally the aggregate has the form of an elongated and rather flat ellipsoid. Various types of statistical analyses were carried out on the systems to enlighten structural and dynamical properties including gyration radius, atomic pair correlation functions, at…
Molecular dynamics simulation of single DNA stretching reveals a novel structure
2005
Abstract MD simulation, to closely mimic a torsionally unconstrained single-molecule stretching experiment of dsDNA, uncovers three distinct force regimes, characterized by fast and slow elongation regions with a transition regime in between, where the α and γ backbone torsion angles of the elongated double-stranded DNA find rapidly new stationary values. In the slow elongation regime DNA gradually looses its twist, collectively breaks all base-pair H-bonds and develops a remarkable base-stacked structure with the bases strongly tilted, forming a zipper-like stack on the major groove side, stabilized by the narrowing distance between the elongated strands, and by specific water interactions.