326 research outputs found
Theory of internal relaxation in chemical kinetics
Master equation derived and applied to problems of internal vibrational relaxation and intramolecular rearrangement reaction
Analytical description of finite size effects for RNA secondary structures
The ensemble of RNA secondary structures of uniform sequences is studied
analytically. We calculate the partition function for very long sequences and
discuss how the cross-over length, beyond which asymptotic scaling laws apply,
depends on thermodynamic parameters. For realistic choices of parameters this
length can be much longer than natural RNA molecules. This has to be taken into
account when applying asymptotic theory to interpret experiments or numerical
results.Comment: 10 pages, 13 figures, published in Phys. Rev.
RNA denaturation: excluded volume, pseudoknots and transition scenarios
A lattice model of RNA denaturation which fully accounts for the excluded
volume effects among nucleotides is proposed. A numerical study shows that
interactions forming pseudoknots must be included in order to get a sharp
continuous transition. Otherwise a smooth crossover occurs from the swollen
linear polymer behavior to highly ramified, almost compact conformations with
secondary structures. In the latter scenario, which is appropriate when these
structures are much more stable than pseudoknot links, probability
distributions for the lengths of both loops and main branches obey scaling with
nonclassical exponents.Comment: 4 pages 3 figure
Zero Temperature Properties of RNA Secondary Structures
We analyze different microscopic RNA models at zero temperature. We discuss
both the most simple model, that suffers a large degeneracy of the ground
state, and models in which the degeneracy has been remove, in a more or less
severe manner. We calculate low-energy density of states using a coupling
perturbing method, where the ground state of a modified Hamiltonian, that
repels the original ground state, is determined. We evaluate scaling exponents
starting from measurements of overlaps and energy differences. In the case of
models without accidental degeneracy of the ground state we are able to clearly
establish the existence of a glassy phase with .Comment: 20 pages including 9 eps figure
Statistical mechanics of secondary structures formed by random RNA sequences
The formation of secondary structures by a random RNA sequence is studied as
a model system for the sequence-structure problem omnipresent in biopolymers.
Several toy energy models are introduced to allow detailed analytical and
numerical studies. First, a two-replica calculation is performed. By mapping
the two-replica problem to the denaturation of a single homogeneous RNA in
6-dimensional embedding space, we show that sequence disorder is perturbatively
irrelevant, i.e., an RNA molecule with weak sequence disorder is in a molten
phase where many secondary structures with comparable total energy coexist. A
numerical study of various models at high temperature reproduces behaviors
characteristic of the molten phase. On the other hand, a scaling argument based
on the extremal statistics of rare regions can be constructed to show that the
low temperature phase is unstable to sequence disorder. We performed a detailed
numerical study of the low temperature phase using the droplet theory as a
guide, and characterized the statistics of large-scale, low-energy excitations
of the secondary structures from the ground state structure. We find the
excitation energy to grow very slowly (i.e., logarithmically) with the length
scale of the excitation, suggesting the existence of a marginal glass phase.
The transition between the low temperature glass phase and the high temperature
molten phase is also characterized numerically. It is revealed by a change in
the coefficient of the logarithmic excitation energy, from being disorder
dominated to entropy dominated.Comment: 24 pages, 16 figure
Model-based probe set optimization for high-performance microarrays
A major challenge in microarray design is the selection of highly specific oligonucleotide probes for all targeted genes of interest, while maintaining thermodynamic uniformity at the hybridization temperature. We introduce a novel microarray design framework (Thermodynamic Model-based Oligo Design Optimizer, TherMODO) that for the first time incorporates a number of advanced modelling features: (i) A model of position-dependent labelling effects that is quantitatively derived from experiment. (ii) Multi-state thermodynamic hybridization models of probe binding behaviour, including potential cross-hybridization reactions. (iii) A fast calibrated sequence-similarity-based heuristic for cross-hybridization prediction supporting large-scale designs. (iv) A novel compound score formulation for the integrated assessment of multiple probe design objectives. In contrast to a greedy search for probes meeting parameter thresholds, this approach permits an optimization at the probe set level and facilitates the selection of highly specific probe candidates while maintaining probe set uniformity. (v) Lastly, a flexible target grouping structure allows easy adaptation of the pipeline to a variety of microarray application scenarios. The algorithm and features are discussed and demonstrated on actual design runs. Source code is available on request
Reduced stability of mRNA secondary structure near the translation-initiation site in dsDNA viruses
<p>Abstract</p> <p>Background</p> <p>Recent studies have demonstrated a selection pressure for reduced mRNA secondary-structure stability near the start codon of coding sequences. This selection pressure can be observed in bacteria, archaea, and eukaryotes, and is likely caused by the requirement of efficient translation initiation in cellular organism.</p> <p>Results</p> <p>Here, we surveyed the complete genomes of 650 dsDNA virus strains for signals of reduced stability of mRNA secondary structure near the start codon. Our analysis included viruses infecting eukaryotic, prokaryotic, and archaeic hosts. We found that many viruses showed evidence for reduced mRNA secondary-structure stability near the start codon. The effect was most pronounced in viruses infecting prokaryotes, but was also observed in viruses infecting eukaryotes and archaea. The reduction in stability generally increased with increasing genomic GC content. For bacteriophage, the reduction was correlated with a corresponding reduction of stability in the phage hosts.</p> <p>Conclusions</p> <p>We conclude that reduced stability of the mRNA secondary structure near the start codon is a common feature for dsDNA viruses, likely driven by the same selective pressures that cause it in cellular organisms.</p
Invertebrate 7SK snRNAs
7SK RNA is a highly abundant noncoding RNA in mammalian cells whose function in transcriptional regulation has only recently been elucidated. Despite its highly conserved sequence throughout vertebrates, all attempts to discover 7SK RNA homologues in invertebrate species have failed so far. Here we report on a combined experimental and computational survey that succeeded in discovering 7SK RNAs in most of the major deuterostome clades and in two protostome phyla: mollusks and annelids. Despite major efforts, no candidates were found in any of the many available ecdysozoan genomes, however. The additional sequence data confirm the evolutionary conservation and hence functional importance of the previously described 3′ and 5′ stem-loop motifs, and provide evidence for a third, structurally well-conserved domain
Midday measurements of leaf water potential and stomatal conductance are highly correlated with daily water use of Thompson Seedless grapevines
A study was conducted to determine the relationship between midday measurements of vine water status and daily water use of grapevines measured with a weighing lysimeter. Water applications to the vines were terminated on August 24th for 9 days and again on September 14th for 22 days. Daily water use of the vines in the lysimeter (ETLYS) was approximately 40 L vine−1 (5.3 mm) prior to turning the pump off, and it decreased to 22.3 L vine−1 by September 2nd. Pre-dawn leaf water potential (ΨPD) and midday Ψl on August 24th were −0.075 and −0.76 MPa, respectively, with midday Ψl decreasing to −1.28 MPa on September 2nd. Leaf g s decreased from ~500 to ~200 mmol m−2 s−1 during the two dry-down periods. Midday measurements of g s and Ψl were significantly correlated with one another (r = 0.96) and both with ETLYS/ETo (r = ~0.9). The decreases in Ψl, g s, and ETLYS/ETo in this study were also a linear function of the decrease in volumetric soil water content. The results indicate that even modest water stress can greatly reduce grapevine water use and that short-term measures of vine water status taken at midday are a reflection of daily grapevine water us
Ab initio Quantum and ab initio Molecular Dynamics of the Dissociative Adsorption of Hydrogen on Pd(100)
The dissociative adsorption of hydrogen on Pd(100) has been studied by ab
initio quantum dynamics and ab initio molecular dynamics calculations. Treating
all hydrogen degrees of freedom as dynamical coordinates implies a high
dimensionality and requires statistical averages over thousands of
trajectories. An efficient and accurate treatment of such extensive statistics
is achieved in two steps: In a first step we evaluate the ab initio potential
energy surface (PES) and determine an analytical representation. Then, in an
independent second step dynamical calculations are performed on the analytical
representation of the PES. Thus the dissociation dynamics is investigated
without any crucial assumption except for the Born-Oppenheimer approximation
which is anyhow employed when density-functional theory calculations are
performed. The ab initio molecular dynamics is compared to detailed quantum
dynamical calculations on exactly the same ab initio PES. The occurence of
quantum oscillations in the sticking probability as a function of kinetic
energy is addressed. They turn out to be very sensitive to the symmetry of the
initial conditions. At low kinetic energies sticking is dominated by the
steering effect which is illustrated using classical trajectories. The steering
effects depends on the kinetic energy, but not on the mass of the molecules.
Zero-point effects lead to strong differences between quantum and classical
calculations of the sticking probability. The dependence of the sticking
probability on the angle of incidence is analysed; it is found to be in good
agreement with experimental data. The results show that the determination of
the potential energy surface combined with high-dimensional dynamical
calculations, in which all relevant degrees of freedon are taken into account,
leads to a detailed understanding of the dissociation dynamics of hydrogen at a
transition metal surface.Comment: 15 pages, 9 figures, subm. to Phys. Rev.
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