101 research outputs found
DFT-based Conformational Analysis of a Phospholipid Molecule (DMPC)
The conformational space of the dimyristoyl phosphatidylcholine (DMPC)
molecule has been studied using Density Functional Theory (DFT), augmented with
a damped empirical dispersion energy term (DFT-D). Fourteen ground-state
isomers have been found with total energies within less than 1 kcal/mol.
Despite differences in combinations of their torsion angles, all these
conformers share a common geometric profile, which includes a balance of
attractive, repulsive and constraint forces between and within specific groups
of atoms. The definition of this profile fits with most of the structural
characteristics deduced from measured NMR properties of DMPC solutions. The
calculated vibrational spectrum of the molecule is in good agreement with
experimental data obtained for DMPC bilayers. These results support the idea
that DMPC molecules preserve their individual molecular structures in the
various assemblies.Comment: 31 pages, 6 Tables, 4 Figure
Effects of boundary conditions on magnetization switching in kinetic Ising models of nanoscale ferromagnets
Magnetization switching in highly anisotropic single-domain ferromagnets has
been previously shown to be qualitatively described by the droplet theory of
metastable decay and simulations of two-dimensional kinetic Ising systems with
periodic boundary conditions. In this article we consider the effects of
boundary conditions on the switching phenomena. A rich range of behaviors is
predicted by droplet theory: the specific mechanism by which switching occurs
depends on the structure of the boundary, the particle size, the temperature,
and the strength of the applied field. The theory predicts the existence of a
peak in the switching field as a function of system size in both systems with
periodic boundary conditions and in systems with boundaries. The size of the
peak is strongly dependent on the boundary effects. It is generally reduced by
open boundary conditions, and in some cases it disappears if the boundaries are
too favorable towards nucleation. However, we also demonstrate conditions under
which the peak remains discernible. This peak arises as a purely dynamic effect
and is not related to the possible existence of multiple domains. We illustrate
the predictions of droplet theory by Monte Carlo simulations of two-dimensional
Ising systems with various system shapes and boundary conditions.Comment: RevTex, 48 pages, 13 figure
First-principles study of TMNan (TM= Cr, Mn, Fe, Co, Ni; n = 4-7) clusters
Geometry, electronic structure, and magnetic properties of TMNan (TM=Cr-Ni; n
= 4-7) clusters are studied within a gradient corrected density functional
theory (DFT) framework. Two complementary approaches, the first adapted to
all-electron calculations on free clusters, and the second been on plane wave
projector augmented wave (PAW) method within a supercell approach are used.
Except for NiNan, the clusters in this series are found to retain the atomic
moments of the TM atoms, and the magnetic moment presented an odd-even
oscillation with respect to the number of Na atoms. The origin of these
odd-even oscillations is explained from the nature of chemical bonding in these
clusters. Differences and similarities between the chemical bonding and the
magnetic properties of these clusters and the TMNan (TM = Sc, V and Ti; n =
4-6) clusters on one hand, and TM-doped Au and Ag clusters on the other hand,
are discussed
Cloning whole bacterial genomes in yeast
Most microbes have not been cultured, and many of those that are cultivatable are difficult, dangerous or expensive to propagate or are genetically intractable. Routine cloning of large genome fractions or whole genomes from these organisms would significantly enhance their discovery and genetic and functional characterization. Here we report the cloning of whole bacterial genomes in the yeast Saccharomyces cerevisiae as single-DNA molecules. We cloned the genomes of Mycoplasma genitalium (0.6 Mb), M. pneumoniae (0.8 Mb) and M. mycoides subspecies capri (1.1 Mb) as yeast circular centromeric plasmids. These genomes appear to be stably maintained in a host that has efficient, well-established methods for DNA manipulation
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