364 research outputs found
An Object-Oriented Approach to Knowledge Representation in a Biomedical Domain
An object-oriented approach has been applied to the different stages involved in developing a knowledge base about insulin metabolism. At an early stage the separation of terminological and assertional knowledge was made. The terminological component was developed by medical experts and represented in CORE. An object-oriented knowledge acquisition process was applied to the assertional knowledge. A frame description is proposed which includes features like states and events, inheritance and collaboration. States and events are formalized with qualitative calculus. The terminological knowledge was very useful in the development of the assertional component. It assisteed in understanding the problem domain, and in the implementation stage, it assisted in building good inheritance hierarchies
On the origin of the extremely different solubilities of polyethers in water
The solubilities of polyethers are surprisingly counter-intuitive. The best-known example is the difference between polyethylene glycol ([âCH2âCH2âOâ]n) which is infinitely soluble, and polyoxymethylene ([âCH2âOâ]n) which is completely insoluble in water, exactly the opposite of what one expects from the C/O ratios of these molecules. Similar anomalies exist for oligomeric and cyclic polyethers. To solve this apparent mystery, we use femtosecond vibrational and GHz dielectric spectroscopy with complementary ab initio calculations and molecular dynamics simulations. We find that the dynamics of water molecules solvating polyethers is fundamentally different depending on their C/O composition. The ab initio calculations and simulations show that this is not because of steric effects (as is commonly believed), but because the partial charge on the O atoms depends on the number of C atoms by which they are separated. Our results thus show that inductive effects can have a major impact on aqueous solubilities
Colored-noise thermostats \`a la carte
Recently, we have shown how a colored-noise Langevin equation can be used in
the context of molecular dynamics as a tool to obtain dynamical trajectories
whose properties are tailored to display desired sampling features. In the
present paper, after having reviewed some analytical results for the stochastic
differential equations forming the basis of our approach, we describe in detail
the implementation of the generalized Langevin equation thermostat and the
fitting procedure used to obtain optimal parameters. We discuss in detail the
simulation of nuclear quantum effects, and demonstrate that, by carefully
choosing parameters, one can successfully model strongly anharmonic solids such
as neon. For the reader's convenience, a library of thermostat parameters and
some demonstrative code can be downloaded from an on-line repository
Double helical conformation and extreme rigidity in a rodlike polyelectrolyte
The ubiquitous biomacromolecule DNA has an axial rigidity persistence length
of ~50 nm, driven by its elegant double helical structure. While double and
multiple helix structures appear widely in nature, only rarely are these found
in synthetic non-chiral macromolecules. Here we describe a double helical
conformation in the densely charged aromatic polyamide
poly(2,2'-disulfonyl-4,4'-benzidine terephthalamide) or PBDT. This double helix
macromolecule represents one of the most rigid simple molecular structures
known, exhibiting an extremely high axial persistence length (~1 micrometer).
We present X-ray diffraction, NMR spectroscopy, and molecular dynamics (MD)
simulations that reveal and confirm the double helical conformation. The
discovery of this extreme rigidity in combination with high charge density
gives insight into the self-assembly of molecular ionic composites with high
mechanical modulus (~1 GPa) yet with liquid-like ion motions inside, and
provides fodder for formation of new 1D-reinforced composites.Comment: Accepted for publication by Nature Communication
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