6,221 research outputs found
Analysis and minimization of bending losses in discrete quantum networks
We study theoretically the transfer of quantum information along bends in
two-dimensional discrete lattices. Our analysis shows that the fidelity of the
transfer decreases considerably, as a result of interactions in the
neighbourhood of the bend. It is also demonstrated that such losses can be
controlled efficiently by the inclusion of a defect. The present results are of
relevance to various physical implementations of quantum networks, where
geometric imperfections with finite spatial extent may arise as a result of
bending, residual stress, etc
Nanoscale Structure and Elasticity of Pillared DNA Nanotubes
We present an atomistic model of pillared DNA nanotubes (DNTs) and their
elastic properties which will facilitate further studies of these nanotubes in
several important nanotechnological and biological applications. In particular,
we introduce a computational design to create an atomistic model of a 6-helix
DNT (6HB) along with its two variants, 6HB flanked symmetrically by two double
helical DNA pillars (6HB+2) and 6HB flanked symmetrically by three double
helical DNA pillars (6HB+3). Analysis of 200 ns all-atom simulation
trajectories in the presence of explicit water and ions shows that these
structures are stable and well behaved in all three geometries. Hydrogen
bonding is well maintained for all variants of 6HB DNTs. We calculate the
persistence length of these nanotubes from their equilibrium bend angle
distributions. The values of persistence length are ~10 {\mu}m, which is 2
orders of magnitude larger than that of dsDNA. We also find a gradual increase
of persistence length with an increasing number of pillars, in quantitative
agreement with previous experimental findings. To have a quantitative
understanding of the stretch modulus of these tubes we carried out
nonequilibrium Steered Molecular Dynamics (SMD). The linear part of the force
extension plot gives stretch modulus in the range of 6500 pN for 6HB without
pillars which increases to 11,000 pN for tubes with three pillars. The values
of the stretch modulus calculated from contour length distributions obtained
from equilibrium MD simulations are similar to those obtained from
nonequilibrium SMD simulations. The addition of pillars makes these DNTs very
rigid.Comment: Published in ACS Nan
Effect of flow pattern at pipe bends on corrosion behaviour of low carbon steek and its challenges
Recent design work regarding seawater flow lines has emphasized the need to identify, develop, and verify critical relationships between corrosion prediction and flow regime mechanisms at pipe bend. In practice this often reduces to an pragmatic interpretation of the effects of corrosion mechanisms at pipe bends. Most importantly the identification of positions or sites, within the internal surface contact areas where the maximum corrosion stimulus may be expected to occur, thereby allowing better understanding, mitigation, monitoring and corrosion control over the life cycle. Some case histories have been reviewed in this context, and the interaction between corrosion mechanisms and flow patterns closely determined, and in some cases correlated. Since the actual relationships are complex, it was determined that a risk based decision making process using selected āwhatā if corrosion analyses linked to āwhat ifā flow assurance analyses was the best way forward. Using this in methodology, and pertinent field data exchange, it is postulated that significant improvements in corrosion prediction can be made. This paper outlines the approach used and shows how related corrosion modelling software data such as that available from corrosion models Norsok M5006, and Cassandra to parallel computational flow modelling in a targeted manner can generate very noteworthy results, and considerably more viable trends for corrosion control guidance. It is postulated that the normally associated lack of agreement between corrosion modelling and field experience, is more likely due to inadequate consideration of corrosion stimulating flow regime data, rather than limitations of the corrosion modelling. Applications of flow visualization studies as well as computations with the k-Īµ model of turbulence have identified flow features and regions where metal loss is a maximu
Molecular structure refinement by direct fitting of atomic coordinates to experimental ESR spectra
An attempt is made to bypass spectral analysis and fit internal coordinates
of radicals directly to experimental liquid- and solid-state electron spin
resonance (ESR) spectra. We take advantage of the recently introduced
large-scale spin dynamics simulation algorithms and of the fact that the
accuracy of quantum mechanical calculations of ESR parameters has improved to
the point of quantitative correctness. Partial solutions are offered to the
local minimum problem in spectral fitting and to the problem of spin
interaction parameters (hyperfine couplings, chemical shifts, etc.) being very
sensitive to distortions in molecular geometry.Comment: Submitted for publicatio
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Complex macrocycle exploration: parallel, heuristic, and constraint-based conformer generation using ForceGen.
ForceGen is a template-free, non-stochastic approach for 2D to 3D structure generation and conformational elaboration for small molecules, including both non-macrocycles and macrocycles. For conformational search of non-macrocycles, ForceGen is both faster and more accurate than the best of all tested methods on a very large, independently curated benchmark of 2859 PDB ligands. In this study, the primary results are on macrocycles, including results for 431 unique examples from four separate benchmarks. These include complex peptide and peptide-like cases that can form networks of internal hydrogen bonds. By making use of new physical movements ("flips" of near-linear sub-cycles and explicit formation of hydrogen bonds), ForceGen exhibited statistically significantly better performance for overall RMS deviation from experimental coordinates than all other approaches. The algorithmic approach offers natural parallelization across multiple computing-cores. On a modest multi-core workstation, for all but the most complex macrocycles, median wall-clock times were generally under a minute in fast search mode and under 2 min using thorough search. On the most complex cases (roughly cyclic decapeptides and larger) explicit exploration of likely hydrogen bonding networks yielded marked improvements, but with calculation times increasing to several minutes and in some cases to roughly an hour for fast search. In complex cases, utilization of NMR data to constrain conformational search produces accurate conformational ensembles representative of solution state macrocycle behavior. On macrocycles of typical complexity (up to 21 rotatable macrocyclic and exocyclic bonds), design-focused macrocycle optimization can be practically supported by computational chemistry at interactive time-scales, with conformational ensemble accuracy equaling what is seen with non-macrocyclic ligands. For more complex macrocycles, inclusion of sparse biophysical data is a helpful adjunct to computation
Predicting Transcription Factor Specificity with All-Atom Models
The binding of a transcription factor (TF) to a DNA operator site can
initiate or repress the expression of a gene. Computational prediction of sites
recognized by a TF has traditionally relied upon knowledge of several cognate
sites, rather than an ab initio approach. Here, we examine the possibility of
using structure-based energy calculations that require no knowledge of bound
sites but rather start with the structure of a protein-DNA complex. We study
the PurR E. coli TF, and explore to which extent atomistic models of
protein-DNA complexes can be used to distinguish between cognate and
non-cognate DNA sites. Particular emphasis is placed on systematic evaluation
of this approach by comparing its performance with bioinformatic methods, by
testing it against random decoys and sites of homologous TFs. We also examine a
set of experimental mutations in both DNA and the protein. Using our explicit
estimates of energy, we show that the specificity for PurR is dominated by
direct protein-DNA interactions, and weakly influenced by bending of DNA.Comment: 26 pages, 3 figure
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