Search results for " Simulation"

Oxaaza cyclophanes in the recognition of nucleotides. The role of oxygen and electron-rich aromatic rings

2007

Dioxapolyaza cyclophanes derived from resorcinol and different polyamine chains have been studied in aqueous solution as abiotic receptors for nucleotides. The presence of the additional ethyleneoxy subunits is reflected in a higher basicity and in a significant increase in the log K values for the interaction with nucleotides relative to that of related polyazacyclophanes.

Tuning molecular self-assembly on bulk insulator surfaces by anchoring of the organic building blocks.

2013

Molecular self-assembly constitutes a versatile strategy for creating functional structures on surfaces. Tuning the subtle balance between intermolecular and molecule-surface interactions allows structure formation to be tailored at the single-molecule level. While metal surfaces usually exhibit interaction strengths in an energy range that favors molecular self-assembly, dielectric surfaces having low surface energies often lack sufficient interactions with adsorbed molecules. As a consequence, application-relevant, bulk insulating materials pose significant challenges when considering them as supporting substrates for molecular self-assembly. Here, the current status of molecular self-ass…

Dynamic and electronic transport properties of DNA translocation through graphene nanopores

2013

Graphene layers have been targeted in the last years as excellent host materials for sensing a remarkable variety of gases and molecules. Such sensing abilities can also benefit other important scientific fields such as medicine and biology. This has automatically led scientists to probe graphene as a potential platform for sequencing DNA strands. In this work, we use robust numerical tools to model the dynamic and electronic properties of molecular sensor devices composed of a graphene nanopore through which DNA molecules are driven by external electric fields. We performed molecular dynamic simulations to determine the relation between the intensity of the electric field and the transloca…

Telechelic Star Polymers as Self-Assembling Units from the Molecular to the Macroscopic Scale

2012

By means of multiscale molecular simulations, we show that telechelic-star polymers are a simple, robust, and tunable system, which hierarchically self-assembles into soft-patchy particles and mechanically stabilizes selected, open crystalline structures. The self-aggregating patchy behavior can be fully controlled by the number of arms per star and by the fraction of attractive monomeric units at the free ends of the arms. Such self-assembled soft-patchy particles while forming, upon augmenting density, gel-like percolating networks, preserve properties as particle size, number, and arrangement of patches per particle. In particular, we demonstrate that the flexibility inherent in the soft…

Synthesis of SWCNT Rings Made by Two Y Junctions and Possible Applications in Electron Interferometry

2007

Mechanical Properties of Pore-Spanning Lipid Bilayers Probed by Atomic Force Microscopy

2006

AbstractWe measure the elastic response of a free-standing lipid membrane to a local indentation by using an atomic force microscope. Starting point is a planar gold-coated alumina substrate with a chemisorbed 3-mercaptopropionic acid monolayer displaying circular pores of very well defined and tunable size, over which bilayers composed of N,N,-dimethyl-N,N,-dioctadecylammonium bromide or 1,2-dioleoyl-3-trimethylammonium-propane chloride were spread. Centrally indenting these “nanodrums” with an atomic force microscope tip yields force-indentation curves, which we quantitatively analyze by solving the corresponding shape equations of continuum curvature elasticity. Since the measured respon…

Ion transport and selectivity in nanopores with spatially inhomogeneous fixed charge distributions

2007

Polymeric nanopores with fixed charges show ionic selectivity when immersed in aqueous electrolyte solutions. The understanding of the electrical interaction between these charges and the mobile ions confined in the inside nanopore solution is the key issue in the design of potential applications. The authors have theoretically described the effects that spatially inhomogeneous fixed charge distributions exert on the ionic transport and selectivity properties of the nanopore. A comprehensive set of one-dimensional distributions including the skin, core, cluster, and asymmetric cases are analyzed on the basis of the Nernst-Planck equations. Current-voltage curves, nanopore potentials, and tr…

Engineering thermal conductance using a two-dimensional phononic crystal

2014

Controlling thermal transport has become relevant in recent years. Traditionally, this control has been achieved by tuning the scattering of phonons by including various types of scattering centres in the material (nanoparticles, impurities, etc). Here we take another approach and demonstrate that one can also use coherent band structure effects to control phonon thermal conductance, with the help of periodically nanostructured phononic crystals. We perform the experiments at low temperatures below 1 K, which not only leads to negligible bulk phonon scattering, but also increases the wavelength of the dominant thermal phonons by more than two orders of magnitude compared to room temperature…

Measurement of elastic forces between iron colloidal particles in a nematic liquid crystal.

2006

The forces that arise between two iron particles in a nematic liquid crystal with a strong homeotropic anchoring were studied. For the first time, the short range repulsive force resulting from the presence of a hedgehog defect between two particles was precisely determined thanks to application of a small magnetic field and observation of the equilibrium position resulting from the balance between the elastic and magnetic forces. Above a given threshold force, the particles stuck together whereas the hedgehog defect was expelled and transformed into a Saturn ring located between the particles. The attractive part of the interparticle force was determined with the same method on the entire …

Field theoretic study of bilayer membrane fusion: I. Hemifusion mechanism

2003

Self-consistent field theory is used to determine structural and energetic properties of metastable intermediates and unstable transition states involved in the standard stalk mechanism of bilayer membrane fusion. A microscopic model of flexible amphiphilic chains dissolved in hydrophilic solvent is employed to describe these self-assembled structures. We find that the barrier to formation of the initial stalk is much smaller than previously estimated by phenomenological theories. Therefore its creation it is not the rate limiting process. The barrier which is relevant is associated with the rather limited radial expansion of the stalk into a hemifusion diaphragm. It is strongly affected by…