Search results for "molecular dynamics"
showing 10 items of 1075 documents
The Interaction of Small Molecules with Biomolecules
2014
The binding of small molecules with biological targets is associated to interesting chemical and biological properties of the resulting supramolecular systems. We have recently reported on the synthesis and characterization of cationic first row transition metal complexes and the study of their DNA binding properties, in aqueous solutions at neutral pH, essentially investigated by viscosimetry and spectroscopic techniques such as circular dichroism, absorption and fluorescence in the UV-visible wavelength range. Of course, such procedure cannot furnish atomic level details of the molecule-DNA interaction. Computational Chemistry may provide support for the interpretation of experimental dat…
Amorphous Silica at Surfaces and Interfaces: Simulation Studies
2003
The structure of surfaces and interfaces of silica (SiO2) is investigated by large scale molecular dynamics computer simulations. In the case of a free silica surface, the results of a classical molecular dynamics simulation are compared to those of an ab initio method, the Car—Parrinello molecular dynamics. This comparative study allows to check the accuracy of the model potential that underlies the classical simulation. By means of a pure classical MD, the interface between amorphous and crystalline SiO2 is investigated, and as a third example the structure of a silica melt between walls is studied in equilibrium and under shear. We show that in the latter three examples important structu…
Qualitative characterisation of effective interactions of charged spheres on different levels of organisation using Alexander’s renormalised charge a…
2005
Abstract Effective interactions are conveniently determined from experimental or numerical data by fitting a Debye–Huckel potential with an effective charge Z ∗ and an effective electrolyte concentration c ∗ as free parameters. In this contribution we numerically solved the Poisson–Boltzmann equation to obtain the so-called renormalised charge Z PBC ∗ . For sufficiently large bare charge Z one finds a saturation of Z ∗ which scales as Z ∗ = A a / λ B , where a is the particle radius, λ B the Bjerrum length and A a proportionality factor of order (8–10). The saturation value increases with increased total micro-ion concentration and shows a shallow minimum as a function of packing fraction. …
Peeling of multilayer graphene creates complex interlayer sliding patterns
2015
Peeling, shearing, and sliding are important mechanical phenomena in van der Waals solids. However, theoretically they have been studied mostly using minimal periodic cells and in the context of accurate quantum simulations. Here, we investigate the peeling of large-scale multilayer graphene stacks with varying thicknesses, stackings, and peeling directions by using classical molecular dynamics simulations with a registry-dependent interlayer potential. Simulations show that, while at large scale the peeling proceeds smoothly, at small scale the registry shifts and sliding patterns of the layers are unexpectedly intricate and depend both on the initial stacking and on the peeling direction.…
Effects of shear flow on the structure and dynamics of ionic liquids in a metallic nanoconfinement.
2021
It has been shown that a weak shear can induce crystallisation in a disordered, glassy state. In this study, we use molecular dynamics simulations in order to investigate the out-of-equilibrium properties of [BMIM][BF4] confined between metal slabs. In particular, we want to understand the extent to which the shear flow modifies the interfacial properties. In particular, the questions we address here are (i) is the shear able to promote the crystalline phase in [BMIM][BF4]? (ii) Can, as a consequence of shear flow, a solid-like layer develop at the interface with a metallic surface? (iii) What are the tribological properties of nanoconfined [BMIM][BF4]? We find that the system behaves quite…
Effects of quantum statistics of phonons on the thermal conductivity of silicon and germanium nanoribbons.
2012
: We present molecular dynamics simulation of phonon thermal conductivity of semiconductor nanoribbons with an account for phonon quantum statistics. In our semiquantum molecular dynamics simulation, dynamics of the system is described with the use of classical Newtonian equations of motion where the effect of phonon quantum statistics is introduced through random Langevin-like forces with a specific power spectral density (color noise). The color noise describes interaction of the molecular system with the thermostat. The thermal transport of silicon and germanium nanoribbons with atomically smooth (perfect) and rough (porous) edges are studied. We show that the existence of rough (porous)…
Structural and dynamical properties of sodium silicate melts: An investigation by molecular dynamics computer simulation
2001
We present the results of large scale computer simulations in which we investigate the static and dynamic properties of sodium disilicate and sodium trisilicate melts. We study in detail the static properties of these systems, namely the coordination numbers, the temperature dependence of the Q^(n) species and the static structure factor, and compare them with experiments. We show that the structure is described by a partially destroyed tetrahedral SiO_4 network and the homogeneously distributed sodium atoms which are surrounded on average by 16 silicon and other sodium atoms as nearest neighbors. We compare the diffusion of the ions in the sodium silicate systems with that in pure silica a…
Bimodal Acidity at the Amorphous Silica/Water Interface
2015
International audience; Understanding the microscopic origin of the acid base behavior of mineral surfaces in contact with water is still a challenging task, for both the experimental and the theoretical communities. Even for a relatively simple material, such as silica, the origin of the bimodal acidity behavior is still a debated topic. In this contribution we calculate the acidity of single sites on the humid silica surface represented by a model for the hydroxylated amorphous surface. Using a thermodynamic integration approach based on ab initio molecular dynamics, we identify two different acidity values. In particular, some convex geminals and some type of vicinals are very acidic (pK…
Structure, stability, and fragmentation of sodium bis(2-ethylhexyl)sulfosuccinate negatively charged aggregates in vacuo by MD simulations.
2014
Negatively charged supramolecular aggregates formed in vacuo by n bis(2-ethylhexyl)sulfosuccinate (AOT(-)) anions and n + n(c) sodium counterions (i.e., [AOT(n) Na(n+nc)](nc)) have been investigated by molecular dynamics (MD) simulations for n = 1 to 20 and n(c) = -1 to -5. By comparing the maximum excess charge values of negatively and positively charged AOTNa aggregates, it is found that the charge storage capability is higher for the latter systems, the difference decreasing as the aggregation number increases. Statistical analysis of physical properties like gyration radii and moment of inertia tensors of aggregates provides detailed information on their structural properties. Even for …
Gas confinement in compartmentalized coordination polymers for highly selective sorption
2016
Discrimination between different gases is an essential aspect for industrial and environmental applications involving sensing and separation. Several classes of porous materials have been used in this context, including zeolites and more recently MOFs. However, to reach high selectivities for the separation of gas mixtures is a challenging task that often requires the understanding of the specific interactions established between the porous framework and the gases. Here we propose an approach to obtain an enhanced selectivity based on the use of compartmentalized coordination polymers, named CCP-1 and CCP-2, which are crystalline materials comprising isolated discrete cavities. These compar…