@article{3435,
abstract = {We develop a new method for estimating effective population sizes, Ne, and selection coefficients, s, from time-series data of allele frequencies sampled from a single diallelic locus. The method is based on calculating transition probabilities, using a numerical solution of the diffusion process, and assuming independent binomial sampling from this diffusion process at each time point. We apply the method in two example applications. First, we estimate selection coefficients acting on the CCR5-Δ32 mutation on the basis of published samples of contemporary and ancient human DNA. We show that the data are compatible with the assumption of s = 0, although moderate amounts of selection acting on this mutation cannot be excluded. In our second example, we estimate the selection coefficient acting on a mutation segregating in an experimental phage population. We show that the selection coefficient acting on this mutation is ~0.43.},
author = {Jonathan Bollback and York, Thomas L and Nielsen, Rasmus},
journal = {Genetics},
number = {1},
pages = {497 -- 502},
publisher = {Genetics Society of America},
title = {{Estimation of 2Nes From Temporal Allele Frequency Data}},
doi = {10.1534/genetics.107.085019},
volume = {179},
year = {2008},
}
@inproceedings{3504,
abstract = {Simulation and bisimulation metrics for stochastic systems provide a quantitative gen- eralization of the classical simulation and bisimulation relations. These metrics capture the similarity of states with respect to quantitative specifications written in the quantitative μ-calculus and related probabilistic logics.
We present algorithms for computing the metrics on Markov decision processes (MDPs), turn- based stochastic games, and concurrent games. For turn-based games and MDPs, we provide a polynomial-time algorithm based on linear programming for the computation of the one-step metric distance between states. The algorithm improves on the previously known exponential-time algo- rithm based on a reduction to the theory of reals. We then present PSPACE algorithms for both the decision problem and the problem of approximating the metric distance between two states, matching the best known bound for Markov chains. For the bisimulation kernel of the metric, which corresponds to probabilistic bisimulation, our algorithm works in time O(n4) for both turn-based games and MDPs; improving the previously best known O(n9 · log(n)) time algorithm for MDPs. For a concurrent game G, we show that computing the exact distance between states is at least as hard as computing the value of concurrent reachability games and the square-root-sum problem in computational geometry. We show that checking whether the metric distance is bounded by a rational r, can be accomplished via a reduction to the theory of real closed fields, involving a
formula with three quantifier alternations, yielding O(|G|O(|G|5)) time complexity, improving the previously known reduction with O(|G|O(|G|7)) time complexity. These algorithms can be iterated
to approximate the metrics using binary search.},
author = {Chatterjee, Krishnendu and De Alfaro, Luca and Majumdar, Ritankar and Raman, Vishwanath},
pages = {107 -- 118},
publisher = {Schloss Dagstuhl - Leibniz-Zentrum für Informatik},
title = {{Algorithms for game metrics}},
doi = {10.4230/LIPIcs.FSTTCS.2008.1745},
volume = {2},
year = {2008},
}
@article{9457,
abstract = {Eukaryotic chromatin is separated into functional domains differentiated by posttranslational histone modifications, histone variants, and DNA methylation1–6. Methylation is associated with repression of transcriptional initiation in plants and animals, and is frequently found in transposable elements. Proper methylation patterns are critical for eukaryotic development4,5, and aberrant methylation-induced silencing of tumor suppressor genes is a common feature of human cancer7. In contrast to methylation, the histone variant H2A.Z is preferentially deposited by the Swr1 ATPase complex near 5′ ends of genes where it promotes transcriptional competence8–20. How DNA methylation and H2A.Z influence transcription remains largely unknown. Here we show that in the plant Arabidopsis thaliana, regions of DNA methylation are quantitatively deficient in H2A.Z. Exclusion of H2A.Z is seen at sites of DNA methylation in the bodies of actively transcribed genes and in methylated transposons. Mutation of the MET1 DNA methyltransferase, which causes both losses and gains of DNA methylation4,5, engenders opposite changes in H2A.Z deposition, while mutation of the PIE1 subunit of the Swr1 complex that deposits H2A.Z17 leads to genome-wide hypermethylation. Our findings indicate that DNA methylation can influence chromatin structure and effect gene silencing by excluding H2A.Z, and that H2A.Z protects genes from DNA methylation.},
author = {ZILBERMAN, Daniel and Coleman-Derr, Devin and Ballinger, Tracy and Henikoff, Steven},
issn = {1476-4687},
journal = {Nature},
keywords = {Multidisciplinary},
number = {7218},
pages = {125--129},
publisher = {Springer Nature},
title = {{Histone H2A.Z and DNA methylation are mutually antagonistic chromatin marks}},
doi = {10.1038/nature07324},
volume = {456},
year = {2008},
}
@article{2367,
abstract = {It was recently shown by Hansen that the Wigner-Yanase entropy is, for general states of quantum systems, not subadditive with respect to decomposition into two subsystems, although this property is known to hold for pure states. We investigate the question whether the weaker property of subadditivity for pure states with respect to decomposition into more than two subsystems holds. This property would have interesting applications in quantum chemistry. We show, however, that it does not hold in general, and provide a counterexample.},
author = {Robert Seiringer},
journal = {Letters in Mathematical Physics},
number = {3},
pages = {285 -- 288},
publisher = {Springer},
title = {{On the failure of subadditivity of the Wigner-Yanase entropy}},
doi = {10.1007/s11005-007-0159-x},
volume = {80},
year = {2007},
}
@article{2370,
abstract = {After recalling briefly the connection between spontaneous symmetry breaking and off-diagonal long-range order for models of magnets a general proof of spontaneous breaking of gauge symmetry as a consequence of Bose-Einstein condensation is presented. The proof is based on a rigorous validation of Bogoliubov's c-number substitution for the k = 0 mode operator α0.},
author = {Lieb, Élliott H and Robert Seiringer and Yngvason, Jakob},
journal = {Reports on Mathematical Physics},
number = {3},
pages = {389 -- 399},
publisher = {Elsevier},
title = {{Bose-Einstein condensation and spontaneous symmetry breaking}},
doi = {10.1016/S0034-4877(07)80074-7},
volume = {59},
year = {2007},
}
@article{2371,
abstract = {We give a proof of stability of relativistic matter with magnetic fields all the way up to the critical value of the nuclear charge Zα = 2/π.},
author = {Frank, Rupert L and Lieb, Élliott H and Robert Seiringer},
journal = {Communications in Mathematical Physics},
number = {2},
pages = {479 -- 489},
publisher = {Springer},
title = {{Stability of relativistic matter with magnetic fields for nuclear charges up to the critical value}},
doi = {10.1007/s00220-007-0307-2},
volume = {275},
year = {2007},
}
@article{2372,
abstract = {The increasing interest in the Müller density-matrix-functional theory has led us to a systematic mathematical investigation of its properties. This functional is similar to the Hartree-Fock (HF) functional, but with a modified exchange term in which the square of the density matrix γ(x, x′) is replaced by the square of γ1 2 (x, x′). After an extensive introductory discussion of density-matrix-functional theory we show, among other things, that this functional is convex (unlike the HF functional) and that energy minimizing γ 's have unique densities ρ(r), which is a physically desirable property often absent in HF theory. We show that minimizers exist if N≤Z, and derive various properties of the minimal energy and the corresponding minimizers. We also give a precise statement about the equation for the orbitals of γ, which is more complex than for HF theory. We state some open mathematical questions about the theory together with conjectured solutions.},
author = {Frank, Rupert L and Lieb, Élliott H and Robert Seiringer and Siedentop, Heinz K},
journal = {Physical Review A - Atomic, Molecular, and Optical Physics},
number = {5},
publisher = {American Physical Society},
title = {{Müller's exchange-correlation energy in density-matrix-functional theory}},
doi = {10.1103/PhysRevA.76.052517},
volume = {76},
year = {2007},
}
@article{2373,
abstract = {For the BCS equation with local two-body interaction λV(x), we give a rigorous analysis of the asymptotic behavior of the critical temperature as γ"0. We derive necessary and sufficient conditions onV(x) for the existence of a nontrivial solution for all values of γ>0.},
author = {Frank, Rupert L and Hainzl, Christian and Naboko, Serguei N and Robert Seiringer},
journal = {Journal of Geometric Analysis},
number = {4},
pages = {559 -- 567},
publisher = {Springer},
title = {{The critical temperature for the BCS equation at weak coupling}},
doi = {10.1007/BF02937429},
volume = {17},
year = {2007},
}
@article{2375,
abstract = {We give a Cwikel-Lieb-Rozenblum type bound on the number of bound states of Schrödinger operators with matrix-valued potentials using the functional integral method of Lieb. This significantly improves the constant in this inequality obtained earlier by Hundertmark.},
author = {Frank, Rupert L and Lieb, Élliott H and Robert Seiringer},
journal = {Letters in Mathematical Physics},
number = {2-3},
pages = {107 -- 116},
publisher = {Springer},
title = {{Number of bound states of Schrödinger operators with matrix-valued potentials}},
doi = {10.1007/s11005-007-0211-x},
volume = {82},
year = {2007},
}
@inbook{2705,
author = {László Erdös},
booktitle = {Spectral Theory and Mathematical Physics: a Festschrift in Honor of Barry Simon's 60th Birthday },
editor = {Gesztesy, Fritz and Deift, Percy and Galvez, Percy and Perry, Peter and Schlag, Wilhelm},
pages = {401 -- 428},
publisher = {American Mathematical Society},
title = {{Recent developments in quantum mechanics with magnetic fields}},
volume = {76},
year = {2007},
}