Note on the physical basis of spatially resolved thermodynamic functions

The spatial resolution of thermodynamic functions, exemplified by the entropy, is discussed. A physical definition of the spatial resolution based on a spatial analogy of the partial molar entropy is advocated. It is shown that neither the grid cell theory (Gerogiokas et al., J. Chem. Theory Comput., 10, 35 [2014]), nor the first-order grid inhomogeneous solvation theory (Nguyen et al. J. Chem. Phys., 137, 044101 [2012]), of spatially resolved hydration entropies satisfies the definition.Comment: Essentially 2 double-column pages, no figure

Modification of the Gay-Berne potential for improved accuracy and speed

A modification of the Gay-Berne potential is proposed which is about 10% to 20% more speed efficient (that is, the original potential runs 15% to 25% slower, depending on architecture) and statistically more accurate in reproducing the energy of interaction of two linear Lennard-Jones tetratomics when averaged over all orientations. For the special cases of end-to-end and side-by-side configurations, the new potential is equivalent to the Gay-Berne one.Comment: 5 pages (incl. title page), [preprint,aip,jcp]{RevTEX-4.1}, 1 figure, 1 table. Revised version fixes mathematical typos and adds short paragraph on a natural generalization to dissimilar particle

Natural selection reduced diversity on human Y chromosomes

The human Y chromosome exhibits surprisingly low levels of genetic diversity. This could result from neutral processes if the effective population size of males is reduced relative to females due to a higher variance in the number of offspring from males than from females. Alternatively, selection acting on new mutations, and affecting linked neutral sites, could reduce variability on the Y chromosome. Here, using genome-wide analyses of X, Y, autosomal and mitochondrial DNA, in combination with extensive population genetic simulations, we show that low observed Y chromosome variability is not consistent with a purely neutral model. Instead, we show that models of purifying selection are consistent with observed Y diversity. Further, the number of sites estimated to be under purifying selection greatly exceeds the number of Y-linked coding sites, suggesting the importance of the highly repetitive ampliconic regions. While we show that purifying selection removing deleterious mutations can explain the low diversity on the Y chromosome, we cannot exclude the possibility that positive selection acting on beneficial mutations could have also reduced diversity in linked neutral regions, and may have contributed to lowering human Y chromosome diversity. Because the functional significance of the ampliconic regions is poorly understood, our findings should motivate future research in this area.Comment: 43 pages, 11 figure

Edit Distance for Pushdown Automata

The edit distance between two words $w_1, w_2$ is the minimal number of word operations (letter insertions, deletions, and substitutions) necessary to transform $w_1$ to $w_2$. The edit distance generalizes to languages $\mathcal{L}_1, \mathcal{L}_2$, where the edit distance from $\mathcal{L}_1$ to $\mathcal{L}_2$ is the minimal number $k$ such that for every word from $\mathcal{L}_1$ there exists a word in $\mathcal{L}_2$ with edit distance at most $k$. We study the edit distance computation problem between pushdown automata and their subclasses. The problem of computing edit distance to a pushdown automaton is undecidable, and in practice, the interesting question is to compute the edit distance from a pushdown automaton (the implementation, a standard model for programs with recursion) to a regular language (the specification). In this work, we present a complete picture of decidability and complexity for the following problems: (1)~deciding whether, for a given threshold $k$, the edit distance from a pushdown automaton to a finite automaton is at most $k$, and (2)~deciding whether the edit distance from a pushdown automaton to a finite automaton is finite.Comment: An extended version of a paper accepted to ICALP 2015 with the same title. The paper has been accepted to the LMCS journa