1,330 research outputs found
How to mesh up Ewald sums (II): An accurate error estimate for the P3M algorithm
We construct an accurate estimate for the root mean square force error of the
particle-particle-particle-mesh (P3M) algorithm by extending a single particle
pair error measure which has been given by Hockney and Eastwood. We also derive
an easy-to-use analytic approximation to the error formula. This allows a
straightforward and precise determination of the optimal splitting parameter
(as a function of system specifications and P3M parameters) and hence knowledge
of the force accuracy prior to the actual simulation. The high quality of the
estimate is demonstrated in several examples.Comment: 9 pages, 7 figures included, revtex styl
Attraction and ionic correlations between charged stiff polyelectrolytes
We use Molecular Dynamics simulations to study attractive interactions and
the underlying ionic correlations between parallel like-charged rods in the
absence of additional salt. For a generic bulk system of rods we identify a
reduction of short range repulsions as the origin of a negative osmotic
coefficient. The counterions show signs of a weak three-dimensional order in
the attractive regime only once the rod-imposed charge-inhomogeneities are
divided out. We also treat the case of attraction between a single pair of rods
for a few selected line charge densities and rod radii. Measurements of the
individual contributions to the force between close rods are studied as a
function of Bjerrum length. We find that even though the total force is always
attractive at sufficiently high Bjerrum length, the electrostatic contribution
can ultimately become repulsive. We also measure azimuthal and longitudinal
correlation functions to answer the question how condensed ions are distributed
with respect to each other and to the neighboring rod. For instance, we show
that the prevalent image of mutually interlocked ions is qualitatively correct,
even though modifications due to thermal fluctuations are usually strong.Comment: 14 pages, 14 figures, REVTeX4 styl
Interplay between Secondary and Tertiary Structure Formation in Protein Folding Cooperativity
Protein folding cooperativity is defined by the nature of the finite-size
thermodynamic transition exhibited upon folding: two-state transitions show a
free energy barrier between the folded and unfolded ensembles, while downhill
folding is barrierless. A microcanonical analysis, where the energy is the
natural variable, has shown better suited to unambiguously characterize the
nature of the transition compared to its canonical counterpart. Replica
exchange molecular dynamics simulations of a high resolution coarse-grained
model allow for the accurate evaluation of the density of states, in order to
extract precise thermodynamic information, and measure its impact on structural
features. The method is applied to three helical peptides: a short helix shows
sharp features of a two-state folder, while a longer helix and a three-helix
bundle exhibit downhill and two-state transitions, respectively. Extending the
results of lattice simulations and theoretical models, we find that it is the
interplay between secondary structure and the loss of non-native tertiary
contacts which determines the nature of the transition.Comment: 3 pages, 3 figure
Twist-bend instability for toroidal DNA condensates
We propose that semiflexible polymers in poor solvent collapse in two stages.
The first stage is the well known formation of a dense toroidal aggregate.
However, if the solvent is sufficiently poor, the condensate will undergo a
second structural transition to a twisted entangled state, in which individual
filaments lower their bending energy by additionally orbiting around the mean
path along which they wind. This ``topological ripening'' is consistent with
known simulations and experimental results. It connects and rationalizes
various experimental observations ranging from strong DNA entanglement in viral
capsids to the unusually short pitch of the cholesteric phase of DNA in
sperm-heads. We propose that topological ripening of DNA toroids could improve
the efficiency and stability of gene delivery.Comment: 4 pages, 3 figures, RevTeX4 styl
How to mesh up Ewald sums (I): A theoretical and numerical comparison of various particle mesh routines
Standard Ewald sums, which calculate e.g. the electrostatic energy or the
force in periodically closed systems of charged particles, can be efficiently
speeded up by the use of the Fast Fourier Transformation (FFT). In this article
we investigate three algorithms for the FFT-accelerated Ewald sum, which
attracted a widespread attention, namely, the so-called
particle-particle-particle-mesh (P3M), particle mesh Ewald (PME) and smooth PME
method. We present a unified view of the underlying techniques and the various
ingredients which comprise those routines. Additionally, we offer detailed
accuracy measurements, which shed some light on the influence of several tuning
parameters and also show that the existing methods -- although similar in
spirit -- exhibit remarkable differences in accuracy. We propose combinations
of the individual components, mostly relying on the P3M approach, which we
regard as most flexible.Comment: 18 pages, 8 figures included, revtex styl
Efficient tunable generic model for fluid bilayer membranes
We present a model for the efficient simulation of generic bilayer membranes.
Individual lipids are represented by one head- and two tail-beads. By means of
simple pair potentials these robustly self-assemble to a fluid bilayer state
over a wide range of parameters, without the need for an explicit solvent. The
model shows the expected elastic behavior on large length scales, and its
physical properties (eg fluidity or bending stiffness) can be widely tuned via
a single parameter. In particular, bending rigidities in the experimentally
relevant range are obtained, at least within . The model is
naturally suited to study many physical topics, including self-assembly,
fusion, bilayer melting, lipid mixtures, rafts, and protein-bilayer
interactions.Comment: 4 Pages 4 Figure
Mesh-to-raster based non-rigid registration of multi-modal images
Region of interest (ROI) alignment in medical images plays a crucial role in
diagnostics, procedure planning, treatment, and follow-up. Frequently, a model
is represented as triangulated mesh while the patient data is provided from CAT
scanners as pixel or voxel data. Previously, we presented a 2D method for
curve-to-pixel registration. This paper contributes (i) a general
mesh-to-raster (M2R) framework to register ROIs in multi-modal images; (ii) a
3D surface-to-voxel application, and (iii) a comprehensive quantitative
evaluation in 2D using ground truth provided by the simultaneous truth and
performance level estimation (STAPLE) method. The registration is formulated as
a minimization problem where the objective consists of a data term, which
involves the signed distance function of the ROI from the reference image, and
a higher order elastic regularizer for the deformation. The evaluation is based
on quantitative light-induced fluoroscopy (QLF) and digital photography (DP) of
decalcified teeth. STAPLE is computed on 150 image pairs from 32 subjects, each
showing one corresponding tooth in both modalities. The ROI in each image is
manually marked by three experts (900 curves in total). In the QLF-DP setting,
our approach significantly outperforms the mutual information-based
registration algorithm implemented with the Insight Segmentation and
Registration Toolkit (ITK) and Elastix
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