pinecone/core-2020-05-10-deduplication huggingface dataset:
Extension of the QuickFF force field protocol for an improved accuracy of structural, vibrational, mechanical and thermal properties of metal-organic frameworks

QuickFF was originally launched in 2015 to derive accurate force fields for isolated and complex molecular systems in a quick and easy way. Apart from the general applicability, the functionality was especially tested for metal-organic frameworks (MOFs), a class of hybrid materials consisting of organic and inorganic building blocks. Herein, we launch a new release of the QuickFF protocol which includes new major features to predict structural, vibrational, mechanical and thermal properties with greater accuracy, without compromising its robustness and transparent workflow. First, the ab initio data necessary for the fitting procedure may now also be derived from periodic models for the molecular system, as opposed to the earlier cluster-based models. This is essential for an accurate description of MOFs with one-dimensional metal-oxide chains. Second, cross terms that couple internal coordinates (ICs) and anharmonic contributions for bond and bend terms are implemented. These features are essential for a proper description of vibrational and thermal properties. Third, the fitting scheme was modified to improve robustness and accuracy. The new features are tested on MIL-53(Al), MOF-5, CAU-13 and NOTT-300. As expected, periodic input data are proven to be essential for a correct description of structural, vibrational and thermodynamic properties of MIL-53(Al). Bulk moduli and thermal expansion coefficients of MOF-5 are very accurately reproduced by static and dynamic simulations using the newly derived force fields which include cross terms and anharmonic corrections. For the flexible materials CAU-13 and NOTT-300, the transition pressure is accurately predicted provided cross terms are taken into account
Calculating particle pair potentials from fluid-state pair correlations:
  Iterative Ornstein-Zernike Inversion

An iterative Monte Carlo inversion method for the calculation of particle
pair potentials from given particle pair correlations is proposed in this
paper. The new method, which is best referred to as Iterative Ornstein-Zernike
Inversion, represents a generalization and an improvement of the established
Iterative Boltzmann Inversion technique [Reith, P\"{u}tz \& M\"{u}ller-Plathe,
J. Comput. Chem. 24, 1624 (2003)]. Our modification of Iterative Boltzmann
Inversion consists of replacing the potential of mean force as an approximant
for the pair potential with another, generally more accurate approximant that
is based on a trial bridge function in the Ornstein-Zernike integral equation
formalism. As an input, the new method requires the particle pair correlations
both in real space and in the Fourier conjugate wavenumber space. An
accelerated iteration method is included in the discussion, by which the
required number of iterations can be greatly reduced below that of the simple
Picard iteration that underlies most common implementations of Iterative
Boltzmann Inversion. Comprehensive tests with various pair potentials show that
the new method generally surpasses the Iterative Boltzmann Inversion method in
terms of reliability of the numerical solution for the particle pair potential.Comment: Accepted for publication in J. Comput. Che
Performance Evaluation of the Zero-Multipole Summation Method in Modern
  Molecular Dynamics Software

We evaluate the practical performance of the zero-multiple summation method
(ZMM), a method for approximately calculating electrostatic interactions in
molecular dynamics simulations. The performance of the ZMM is compared with
that of the smooth particle mesh Ewald method (SPME). Even though the ZMM uses
a larger cutoff distance than the SPME does, the performance of the ZMM is
found to be comparable to or better than that of the SPME. In particular, the
ZMM with quadrupole or octupole cancellation and no damping factor is an
excellent candidate for the fast calculation of electrostatic potentials.Comment: Preprint submitted to Comput. Phys. Com
Synthesis, Characterization and Oxide Ionic Conductivity of Binary  -(Bi2o3)1-x(Lu2o3)x System

In this study, after doping Lu2O3 to  -Bi2O3 in the range of 11%   n   20% in a series of different mole ratios,\ud
heat treatment was performed by applying a cascade temperature rise in the range of 700-800 oC for\ud
72 hours and new phases were obtained in the (Bi2O3)1-x(Lu2O3)x system. After 72 hours of heat treatment\ud
at 800 oC, mixtures containing 14-16% Lu2O3 formed a face-centered cubic phase. Mixtures containing\ud
11– 13%, 17%, 18% mole Lu2O3 were subjected to a quenching process at 825 oC and face-centered cubic\ud
phases were obtained. With the help of XRD, the crystal systems and lattice parameters of the solid solutions\ud
were obtained and their characterization was carried out. Thermal measurements were made by using\ud
a simultaneous DTA/TG system. The total conductivity ( T) in the  -Bi2O3 doped with Lu2O3 system\ud
was measured using the four-probe DC method. Keywords: Bismuth oxide; lutesium oxide; oxygen ionic\ud
conductivity; X-ray techniques; thermal analysis
On DRC-covering of Kn by cycles

International audienceThis paper considers the cycle covering of complete graphs motivated by the design of survivable WDM networks, where the requests are routed on INF-networks which are protected independently from each other. The problem can be stated as follows: for a given graph G, find a cycle covering of the edge set of Kn, where V(Kn) = V(G), such that each cycle in the covering satisfies the disjoint routing constraint (DRC), relatively to G, which can be stated as follows: to each edge of Kn we associate in G a path and all the paths associated to the edges of a cycle of the covering must be vertex disjoint. Here we consider the case where G = Cn, a ring of size n and we want to minimize the number of cycles in the covering. We give optimal solutions for the problem as well as for variations of the problem, namely, its directed version and the case when the cycle length is fixed to 4
The geometry of sets of orthogonal frequency hypercubes

V.C. Mavron, T.P. McDonough, Gary L. Mullen, The geometry of sets of orthogonal frequency hypercubes. Journal of Combinatorial Designs, Volume 15, Issue 6, pages 449?459, November 2007.We extend the notion of a framed net, introduced by D. Jungnickel, V. C. Mavron, and T. P. McDonough, J Combinatorial Theory A, 96 (2001), 376?387, to that of a d-framed net of type ?, where d???2 and 1???????d-1, and we establish a correspondence between d-framed nets of type ? and sets of mutually orthogonal frequency hypercubes of dimension d. We provide a new proof of the maximal size of a set of mutually orthogonal frequency hypercubes of type ? and dimension d, originally established by C. F. Laywine, G. L. Mullen, and G. Whittle, Monatsh Math 119 (1995), 223?238, and we obtain a geometric characterization of the framed net when this bound is satisfied as a PBIBD based on a d-class association Hamming scheme H(d,n).Peer reviewe
Constructing Regular Self-complementary Uniform Hypergraphs

AMS Subject Classication Codes: 05C65, 05B05 05E20, 05C85.In this paper, we examine the possible orders of t-subset-regular self-complementary k-uniform hypergraphs, which form examples of large sets of two isomorphic t-designs. We reformulate Khosrovshahi and Tayfeh-Rezaie's necessary conditions on the order of these structures in terms of the binary representation of the rank k, and these conditions simplify to a more transparent relation between the order n and rank k in the case where k is a sum of consecutive powers of 2. Moreover, we present new constructions for 1-subset-regular self-complementary uniform hypergraphs, and prove that these necessary conditions are sufficient for all k, in the case where t = 1.https://onlinelibrary.wiley.com/doi/abs/10.1002/jcd.2028
Gerechte Designs with Rectangular Regions

A \emph{gerechte framework} is a partition of an $n \times n$ array into $n$
regions of $n$ cells each. A \emph{realization} of a gerechte framework is a
latin square of order $n$ with the property that when its cells are partitioned
by the framework, each region contains exactly one copy of each symbol. A
\emph{gerechte design} is a gerechte framework together with a realization.
  We investigate gerechte frameworks where each region is a rectangle. It seems
plausible that all such frameworks have realizations, and we present some
progress towards answering this question. In particular, we show that for all
positive integers $s$ and $t$, any gerechte framework where each region is
either an $s \times t$ rectangle or a $t\times s$ rectangle is realizable.Comment: 14 pages, 12 figure
Detachments of Amalgamated 3-uniform Hypergraphs : Factorization
  Consequences

A detachment of a hypergraph $\scr F$ is a hypergraph obtained from $\scr F$
by splitting some or all of its vertices into more than one vertex.
Amalgamating a hypergraph $\scr G$ can be thought of as taking $\scr G$,
partitioning its vertices, then for each element of the partition squashing the
vertices to form a single vertex in the amalgamated hypergraph $\scr F$. In
this paper we use Nash-Williams lemma on laminar families to prove a detachment
theorem for amalgamated 3-uniform hypergraphs, which yields a substantial
generalization of previous amalgamation theorems by Hilton, Rodger and
Nash-Williams.
  To demonstrate the power of our detachment theorem, we show that the complete
3-uniform $n$-partite multi-hypergraph $\lambda K_{m_1,\ldots,m_n}^{3}$ can be
expressed as the union $\scr G_1\cup \ldots \cup\scr G_k$ of $k$ edge-disjoint
factors, where for $i=1,\ldots, k$, $\scr G_i$ is $r_i$-regular, if and only if
(i) $m_i=m_j:=m$ for all $1\leq i,j\leq k$, (ii) $3$ divides $r_imn$ for each
$i$, $1\leq i\leq k$, and (iii) $\sum_{i=1}^{k} r_i=\lambda \binom{n-1}{2}m^2$.Comment: 20 pages, 4 figure
Turyn-type sequences: Classification, Enumeration and Construction

Turyn-type sequences, TT(n), are quadruples of {+,-1}-sequences (A;B;C;D),
with lengths n,n,n,n-1 respectively, where the sum of the nonperiodic
autocorrelation functions of A,B and twice that of C,D is a delta-function
(i.e., vanishes everywhere except at 0). Turyn-type sequences TT(n) are known
to exist for all even n not larger than 36. We introduce a definition of
equivalence to construct a canonical form for TT(n) in general. By using this
canonical form, we enumerate the equivalence classes of TT(n) for n up to and
including 32. We also construct the first example of Turyn-type sequences
TT(38).Comment: 14 pages, 3 table
The isotopism problem of a class of 6-dimensional rank 2 semifields and
  its solution

In [U. Dempwolff: \textit{More Translation Planes and Semifields from
Dembowski-Ostrom Polynomials}, Designs, Codes, Cryptogr. \textbf{68} (1-3)
(2013), 81--103] three classes of rank two presemifields of order $q^{2n}$,
with $q$ and $n$ odd, were exhibited, leaving as an open problem the isotopy
issue. In [M. Lavrauw, G. Marino, O. Polverino, R. Trombetti: \textit{Solution
to an isotopism question concerning rank 2 semifields}, J. Comb. Des., to
appear. DOI: 10.1002/jcd.21382], the authors faced with this problem answering
the question whether these presemifields are new for $n>3$. In this paper we
complete the study solving the case $n=3$
Constructing minimal blocking sets using field reduction

We present a construction for minimal blocking sets with respect to (k-1)-spaces in PG (n-1,qt), the (n-1)-dimensional projective space over the finite field Fqt of order qt. The construction relies on the use of blocking cones in the field reduced representation of PG (n-1,qt), extending the well-known construction of linear blocking sets. This construction is inspired by the construction for minimal blocking sets with respect to the hyperplanes by Mazzocca, Polverino, and Storme (the MPS-construction); we show that for a suitable choice of the blocking cone over a planar blocking set, we obtain larger blocking sets than the ones obtained from planar blocking sets in F. Mazzocca and O. Polverino, J Algebraic Combin 24(1) (2006), 61-81. Furthermore, we show that every minimal blocking set with respect to the hyperplanes in PG (n-1,qt) can be obtained by applying field reduction to a minimal blocking set with respect to (nt-t-1)-spaces in PG (nt-1,q). We end by relating these constructions to the linearity conjecture for small minimal blocking sets. We show that if a small minimal blocking set is constructed from the MPS-constructionthen it is of Redei-type, whereas a small minimal blocking set arises from our cone construction if and only if it is linear
Well Balanced Designs for Data Placement

International audienceThe problem we consider in this article is motivated by data placement, in particular data replication in distributed storage and retrieval systems. We are given a set V of v servers along with b files (data, documents). Each file is replicated on exactly k servers. A placement consists in finding a family of b subsets of V (representing the files) called blocks, each of size k. Each server has some probability to fail and we want to find a placement which minimizes the variance of the number of available files. It was conjectured that there always exists an optimal placement (with variance better than that of any other placement for any value of the probability of failure). We show that the conjecture is true, if there exists a well balanced design, that is a family of blocks, each of size k, such that each j-element subset of V , 1 ≤ j ≤ k, belongs to the same or almost the same number of blocks (difference at most one). The existence of well balanced designs is a difficult problem as it contains as a subproblem the existence of Steiner systems. We completely solve the case k = 2 and give bounds and constructions for k = 3 and some values of v and b
Dominating sets in projective planes

We describe small dominating sets of the incidence graphs of finite
projective planes by establishing a stability result which shows that
dominating sets are strongly related to blocking and covering sets. Our main
result states that if a dominating set in a projective plane of order $q>81$ is
smaller than $2q+2[\sqrt{q}]+2$ (i.e., twice the size of a Baer subplane), then
it contains either all but possibly one points of a line or all but possibly
one lines through a point. Furthermore, we completely characterize dominating
sets of size at most $2q+\sqrt{q}+1$. In Desarguesian planes, we could rely on
strong stability results on blocking sets to show that if a dominating set is
sufficiently smaller than 3q, then it consists of the union of a blocking set
and a covering set apart from a few points and lines.Comment: 19 page
Transversals in Latin arrays with many distinct symbols

An array is row-Latin if no symbol is repeated within any row. An array is
Latin if it and its transpose are both row-Latin. A transversal in an $n\times
n$ array is a selection of $n$ different symbols from different rows and
different columns. We prove that every $n \times n$ Latin array containing at
least $(2-\sqrt{2}) n^2$ distinct symbols has a transversal. Also, every $n
\times n$ row-Latin array containing at least $\frac14(5-\sqrt{5})n^2$ distinct
symbols has a transversal. Finally, we show by computation that every Latin
array of order $7$ has a transversal, and we describe all smaller Latin arrays
that have no transversal
Triple arrays from difference sets

This paper addresses the question whether triple arrays can be constructed from Youden squares developed from difference sets. We prove that if the difference set is abelian, then having −1 as multiplier is both a necessary and sufficient condition for the construction to work. Using this, we are able to give a new infinite family of triple arrays. We also give an alternative and more direct version of the construction, leaving out the intermediate step via Youden squares. This is used when we analyse the case of non-abelian difference sets, for which we prove a sufficient condition for giving triple arrays. We do a computer search for such non-abelian difference sets, but have not found any examples satisfying the given condition.PostprintPeer reviewe
Ramsey theory on Steiner triples

We call a partial Steiner triple system C (configuration) t-Ramsey if for large enough n (in terms of (Formula presented.)), in every t-coloring of the blocks of any Steiner triple system STS(n) there is a monochromatic copy of C. We prove that configuration C is t-Ramsey for every t in three cases: C is acyclic every block of C has a point of degree one C has a triangle with blocks 123, 345, 561 with some further blocks attached at points 1 and 4 This implies that we can decide for all but one configurations with at most four blocks whether they are t-Ramsey. The one in doubt is the sail with blocks 123, 345, 561, 147. © 2017 Wiley Periodicals, Inc
Enclosings of decompositions of complete multigraphs in 2-factorizations.

Let k, m, n, λ, and μ be positive integers. A decomposition of math formula into edge-disjoint subgraphs math formula is said to be enclosed by a decomposition of math formula into edge-disjoint subgraphs math formula if math formula and, after a suitable labeling of the vertices in both graphs, math formula is a subgraph of math formula and math formula is a subgraph of math formula for all math formula. In this paper, we continue the study of enclosings of given decompositions by decompositions that consist of spanning subgraphs. A decomposition of a graph is a 2-factorization if each subgraph is 2-regular and spanning, and is Hamiltonian if each subgraph is a Hamiltonian cycle. We give necessary and sufficient conditions for the existence of a 2-factorization of math formula that encloses a given decomposition of math formula whenever math formula and math formula. We also give necessary and sufficient conditions for the existence of a Hamiltonian decomposition of math formula that encloses a given decomposition of math formula whenever math formula and either math formula or math formula and math formula, or math formula, math formula, and math formula
On the number of SQSs, latin hypercubes and MDS codes

It is established that the logarithm of the number of latin $d$-cubes of
order $n$ is $\Theta(n^{d}\ln n)$ and the logarithm of the number of pairs of
orthogonal latin squares of order $n$ is $\Theta(n^2\ln n)$. Similar
estimations are obtained for systems of mutually strong orthogonal latin
$d$-cubes. As a consequence, it is constructed a set of Steiner quadruple
systems of order $n$ such that the logarithm of its cardinality is
$\Theta(n^3\ln n)$ as $n\rightarrow\infty$ and $n\ {\rm mod}\ 6= 2\ {\rm or}\
4$.Comment: 10 page
Carcinoembryonic Antigen Gene Family

The carcinoembryonic antigen (CEA) gene family belongs to the immunoglobulin supergene family and can be divided into two main subgroups based on sequence comparisons. In humans it is clustered on the long arm of chromosome 19 and consists of approximately 20 genes. The CEA subgroup genes code for CEA and its classical crossreacting antigens, which are mainly membrane-bound, whereas the other subgroup genes encode the pregnancy-specific glycoproteins (PSG), which are secreted. Splice variants of individual genes and differential post-translational modifications of the resulting proteins, e.g., by glycosylation, indicate a high complexity in the number of putative CEA-related molecules. So far, only a limited number of CEA-related antigens in humans have been unequivocally assigned to a specific gene. Rodent CEA-related genes reveal a high sequence divergence and, in part, a completely different domain organization than the human CEA gene family, making it difficult to determine individual gene counterparts. However, rodent CEA-related genes can be assigned to human subgroups based on similarity of expression patterns, which is characteristic for the subgroups. Various functions have been determined for members of the CEA subgroup in vitro, including cell adhesion, bacterial binding, an accessory role for collagen binding or ecto-ATPases activity. Based on all that is known so far on its biology, the clinical outlook for the CEA family has been reassessed.
Correlation between Etest®, disk diffusion, and microdilution methods for antifungal susceptibility testing of Candida species from infection and colonization

The correlation between the microdilution (MD), Etest® (ET), and disk diffusion (DD) methods was determined for amphotericin B, itraconazole and fluconazole. The minimal inhibitory concentration (MIC) of those antifungal agents was established for a total of 70 Candida spp. isolates from colonization and infection. The species distribution was: Candida albicans (n=27), C. tropicalis (n=17), C. glabrata (n=16), C. parapsilosis (n=8), and C. lusitaniae (n=2). Non-Candida albicans Candida species showed higher MICs for the three antifungal agents when compared with C. albicans isolates. The overall concordance (based on the MIC value obtainedwithin two dilutions) between the ET and the MD method was 83% for amphotericin B, 63% for itraconazole, and 64% for fluconazole. Considering the breakpoint, the agreement between the DD and MD methods was 71% for itraconazole and 67% for fluconazole. The DD zone diameters are highly reproducible and correlate well with the MD method, making agar-based methods a viable alternative to MD for susceptibility testing. However, data on agar-based tests for itraconazole and amphotericin B are yet scarce. Thus, further research must still be carried out to ensure the standardization to other antifungal agents.Coordenação de Aperfeiçoamento de Pessoal de Nível Superior (CAPES) - BEX 4642/06-
Intersubject variability of blood analysis reference values: assessment of age and locality influence by means of a linear discriminant analysis model

Glycemic and lipidic profiles might be influenced by several factors. The fact that the age group might alter the most extensively evaluated lipidic and glycemic parameters is a more or less well accepted fact. To verify this empirical notion, 996 human subjects aged between 21 and 90 years from different localities were characterized according to age. To assess lipid profile, total cholesterol and cholesterol associated with lipoprotein fractions (c-LDL and c-HDL) and triglycerides were determined. Regarding glycemic profile, glucose and glycated hemoglobin were measured. The majority of the population had values of lipidic parameters fit into the reference values, presenting low or moderate risk for developing cardiovascular disease. Blood glucose was often far above the desirable, but this can be devalued due to the HbA1c values, which were overwhelmingly located in the normal range. The categorization of data in different age groups did not allow defining statistically significant differences. Despite the discriminant linear model was presented, the results indicate that age group did not act as a strong discriminant factor. Somehow unexpectedly, the most significant differences were found among the different localities, which tended to show a similarity according with their latitude. Furthermore, there were no significant correlations in the parameters associated with lipidic profile, but there was a direct correlation between glucose levels and HbA1c (glycemic parameters)