@article{1072,
abstract = {Given a finite set of points in Rn and a radius parameter, we study the Čech, Delaunay–Čech, Delaunay (or alpha), and Wrap complexes in the light of generalized discrete Morse theory. Establishing the Čech and Delaunay complexes as sublevel sets of generalized discrete Morse functions, we prove that the four complexes are simple-homotopy equivalent by a sequence of simplicial collapses, which are explicitly described by a single discrete gradient field.},
author = {Bauer, Ulrich and Edelsbrunner, Herbert},
journal = {Transactions of the American Mathematical Society},
number = {5},
pages = {3741 -- 3762},
publisher = {American Mathematical Society},
title = {{The Morse theory of Čech and delaunay complexes}},
volume = {369},
year = {2017},
}
@article{1073,
abstract = {Let X and Y be finite simplicial sets (e.g. finite simplicial complexes), both equipped with a free simplicial action of a finite group G. Assuming that Y is d-connected and dimX≤2d, for some d≥1, we provide an algorithm that computes the set of all equivariant homotopy classes of equivariant continuous maps |X|→|Y|; the existence of such a map can be decided even for dimX≤2d+1. This yields the first algorithm for deciding topological embeddability of a k-dimensional finite simplicial complex into Rn under the condition k≤23n−1. More generally, we present an algorithm that, given a lifting-extension problem satisfying an appropriate stability assumption, computes the set of all homotopy classes of solutions. This result is new even in the non-equivariant situation.},
author = {Čadek, Martin and Krcál, Marek and Vokřínek, Lukáš},
issn = {01795376},
journal = {Discrete & Computational Geometry},
number = {4},
pages = {915 -- 965},
publisher = {Springer},
title = {{Algorithmic solvability of the lifting extension problem}},
doi = {10.1007/s00454-016-9855-6},
volume = {54},
year = {2017},
}
@article{1074,
abstract = {Recently it has become feasible to detect long blocks of nearly identical sequence shared between pairs of genomes. These IBD blocks are direct traces of recent coalescence events and, as such, contain ample signal to infer recent demography. Here, we examine sharing of such blocks in two-dimensional populations with local migration. Using a diffusion approximation to trace genetic ancestry, we derive analytical formulae for patterns of isolation by distance of IBD blocks, which can also incorporate recent population density changes. We introduce an inference scheme that uses a composite likelihood approach to fit these formulae. We then extensively evaluate our theory and inference method on a range of scenarios using simulated data. We first validate the diffusion approximation by showing that the theoretical results closely match the simulated block sharing patterns. We then demonstrate that our inference scheme can accurately and robustly infer dispersal rate and effective density, as well as bounds on recent dynamics of population density. To demonstrate an application, we use our estimation scheme to explore the fit of a diffusion model to Eastern European samples in the POPRES data set. We show that ancestry diffusing with a rate of σ ≈ 50–100 km/√gen during the last centuries, combined with accelerating population growth, can explain the observed exponential decay of block sharing with increasing pairwise sample distance.},
author = {Ringbauer, Harald and Coop, Graham and Barton, Nicholas H},
issn = {00166731},
journal = {Genetics},
number = {3},
pages = {1335 -- 1351},
publisher = {Genetics Society of America},
title = {{Inferring recent demography from isolation by distance of long shared sequence blocks}},
doi = {10.1534/genetics.116.196220},
volume = {205},
year = {2017},
}
@article{1076,
abstract = {Signatures of the Coulomb corrections in the photoelectron momentum distribution during laser-induced ionization of atoms or ions in tunneling and multiphoton regimes are investigated analytically in the case of a one-dimensional problem. A high-order Coulomb-corrected strong-field approximation is applied, where the exact continuum state in the S matrix is approximated by the eikonal Coulomb-Volkov state including the second-order corrections to the eikonal. Although without high-order corrections our theory coincides with the known analytical R-matrix (ARM) theory, we propose a simplified procedure for the matrix element derivation. Rather than matching the eikonal Coulomb-Volkov wave function with the bound state as in the ARM theory to remove the Coulomb singularity, we calculate the matrix element via the saddle-point integration method by time as well as by coordinate, and in this way avoiding the Coulomb singularity. The momentum shift in the photoelectron momentum distribution with respect to the ARM theory due to high-order corrections is analyzed for tunneling and multiphoton regimes. The relation of the quantum corrections to the tunneling delay time is discussed.},
author = {Klaiber, Michael and Daněk, Jiří and Yakaboylu, Enderalp and Hatsagortsyan, Karen and Keitel, Christoph},
issn = {24699926},
journal = { Physical Review A - Atomic, Molecular, and Optical Physics},
number = {2},
publisher = {American Physical Society},
title = {{Strong-field ionization via a high-order Coulomb-corrected strong-field approximation}},
doi = {10.1103/PhysRevA.95.023403},
volume = {95},
year = {2017},
}
@article{1077,
abstract = {Viral capsids are structurally constrained by interactions among the amino acids (AAs) of their constituent proteins. Therefore, epistasis is expected to evolve among physically interacting sites and to influence the rates of substitution. To study the evolution of epistasis, we focused on the major structural protein of the fX174 phage family by first reconstructing the ancestral protein sequences of 18 species using a Bayesian statistical framework. The inferred ancestral reconstruction differed at eight AAs, for a total of 256 possible ancestral haplotypes. For each ancestral haplotype and the extant species, we estimated, in silico, the distribution of free energies and epistasis of the capsid structure. We found that free energy has not significantly increased but epistasis has. We decomposed epistasis up to fifth order and found that higher-order epistasis sometimes compensates pairwise interactions making the free energy seem additive. The dN/dS ratio is low, suggesting strong purifying selection, and that structure is under stabilizing selection. We synthesized phages carrying ancestral haplotypes of the coat protein gene and measured their fitness experimentally. Our findings indicate that stabilizing mutations can have higher fitness, and that fitness optima do not necessarily coincide with energy minima.},
author = {Fernandes Redondo, Rodrigo A and Vladar, Harold and Włodarski, Tomasz and Bollback, Jonathan P},
issn = {17425689},
journal = {Journal of the Royal Society Interface},
number = {126},
publisher = {Royal Society of London},
title = {{Evolutionary interplay between structure, energy and epistasis in the coat protein of the fX174 phage family}},
doi = {10.1098/rsif.2016.0139},
volume = {14},
year = {2017},
}