571 research outputs found
The role of reconstruction in self-assembly of alkylthiolate monolayers on coinage metal surfaces
Through a combination of standard laboratory-based surface science methods, together with synchrotron radiation-based normal incidence X-ray standing wave (NIXSW) experiments, the interface structure of simple alkylthiolate ‘self-assembled monolayers’ on Cu(1 1 1), Ag(1 1 1) and Au(1 1 1) has been investigated over the last not, vert, similar15 years. A key conclusion is that in all cases the adsorbate produces a substantial, density-lowering, reconstruction of the outermost metal layer, although the nature of these reconstructions is quite different on the three metals. The main results of these investigations are briefly reviewed and contrasted
Improvements to the APBS biomolecular solvation software suite
The Adaptive Poisson-Boltzmann Solver (APBS) software was developed to solve
the equations of continuum electrostatics for large biomolecular assemblages
that has provided impact in the study of a broad range of chemical, biological,
and biomedical applications. APBS addresses three key technology challenges for
understanding solvation and electrostatics in biomedical applications: accurate
and efficient models for biomolecular solvation and electrostatics, robust and
scalable software for applying those theories to biomolecular systems, and
mechanisms for sharing and analyzing biomolecular electrostatics data in the
scientific community. To address new research applications and advancing
computational capabilities, we have continually updated APBS and its suite of
accompanying software since its release in 2001. In this manuscript, we discuss
the models and capabilities that have recently been implemented within the APBS
software package including: a Poisson-Boltzmann analytical and a
semi-analytical solver, an optimized boundary element solver, a geometry-based
geometric flow solvation model, a graph theory based algorithm for determining
p values, and an improved web-based visualization tool for viewing
electrostatics
Geometric modeling, simulation, and visualization methods for plasmid DNA molecules
Plasmid DNA molecules are a special type of DNA molecules that are used, among other applications,
in DNA vaccination and gene therapy. These molecules are characterized by, when in
their natural state, presenting a closed-circular conformation and by being supercoiled. The
production of plasmid DNA using bacteria as hosts implies a purification step where the plasmid
DNA molecules are separated from the DNA of the host and other contaminants. This purification
process, and all the physical and chemical variations involved, such as temperature
changes, may affect the plasmid DNA molecules conformation by uncoiling or even by open
them, which makes them useless for therapeutic applications. Because of that, researchers
are always searching for new purification techniques that maximize the amount of supercoiled
plasmid DNA that is produced. Computer simulations and 3D visualization of plasmid DNA can
bring many advantages because they allow researchers to actually see what can happen to the
molecules under certain conditions. In this sense, it was necessary to develop reliable and accurate
geometric models specific for plasmid DNA simulations. This dissertation presents a new
assembling algorithm for B-DNA specifically developed for plasmid DNA assembling. This new
assembling algorithm is completely adaptive in the sense that it allows researchers to assemble
any plasmid DNA base-pair sequence along any arbitrary conformation that fits the length
of the plasmid DNA molecule. This is specially suitable for plasmid DNA simulations, where
conformations are generated by simulation procedures and there is the need to assemble the
given base-pair sequence over that conformation, what can not be done by conventional predictive
DNA assembling methods. Unlike traditional molecular visualization methods that are
based on the atomic structure, this new assembling algorithm uses color coded 3D molecular
surfaces of the nucleotides as the building blocks for DNA assembling. This new approach, not
only reduces the amount of graphical objects and, consequently, makes the rendering faster,
but also makes it easier to visually identify the nucleotides in the DNA strands. The algorithm
used to triangulate the molecular surfaces of the nucleotides building blocks is also a novelty
presented as part of this dissertation. This new triangulation algorithm for Gaussian molecular
surfaces introduces a new mechanism that divides the atomic structure of molecules into boxes
and spheres. This new space division method is faster because it confines the local calculation
of the molecular surface to a specific region of influence of the atomic structure, not taking into
account atoms that do not influence the triangulation of the molecular surface in that region.
This new method also guarantees the continuity of the molecular surface. Having in mind that
the aim of this dissertation is to present a complete set of methods for plasmid DNA visualization
and simulation, it is also proposed a new deformation algorithm to be used for plasmid
DNA Monte Carlo simulations. This new deformation algorithm uses a 3D polyline to represent
the plasmid DNA conformation and performs small deformations on that polyline, keeping the
segments length and connectivity. Experiments have been performed in order to compare this
new deformation method with deformation methods traditionally used by Monte Carlo plasmid
DNA simulations These experiments shown that the new method is more efficient in the sense
that its trial acceptance ratio is higher and it converges sooner and faster to the elastic energy
equilibrium state of the plasmid DNA molecule. In sum, this dissertation successfully presents
an end-to-end set of models and algorithms for plasmid DNA geometric modelling, visualization
and simulation
Non-Euclidean geometry in nature
I describe the manifestation of the non-Euclidean geometry in the behavior of
collective observables of some complex physical systems. Specifically, I
consider the formation of equilibrium shapes of plants and statistics of sparse
random graphs. For these systems I discuss the following interlinked questions:
(i) the optimal embedding of plants leaves in the three-dimensional space, (ii)
the spectral statistics of sparse random matrix ensembles.Comment: 52 pages, 21 figures, last section is rewritten, a reference to
chaotic Hamiltonian systems is adde
- …