Identifying statistical dependence in genomic sequences via mutual information estimates

Questions of understanding and quantifying the representation and amount of information in organisms have become a central part of biological research, as they potentially hold the key to fundamental advances. In this paper, we demonstrate the use of information-theoretic tools for the task of identifying segments of biomolecules (DNA or RNA) that are statistically correlated. We develop a precise and reliable methodology, based on the notion of mutual information, for finding and extracting statistical as well as structural dependencies. A simple threshold function is defined, and its use in quantifying the level of significance of dependencies between biological segments is explored. These tools are used in two specific applications. First, for the identification of correlations between different parts of the maize zmSRp32 gene. There, we find significant dependencies between the 5' untranslated region in zmSRp32 and its alternatively spliced exons. This observation may indicate the presence of as-yet unknown alternative splicing mechanisms or structural scaffolds. Second, using data from the FBI's Combined DNA Index System (CODIS), we demonstrate that our approach is particularly well suited for the problem of discovering short tandem repeats, an application of importance in genetic profiling.Comment: Preliminary version. Final version in EURASIP Journal on Bioinformatics and Systems Biology. See http://www.hindawi.com/journals/bsb

Küllî Aşkın Merkezinde Mecâzî A-şkın Simge Olması: Mevlânâ Örneği

Aşk tasavvuf edebiyatında ilâhi ve mecâzî olarak genişçe yer bulan bir kavramdır. Mevlânâ, aşkın farklı türevlerinden yola çıkarak mecâzî aşkı hakikî aşka vesile görmektedir. Mecâz, ilâhi sevginin aracı olduğundan Mecnun’da olduğu gibi ilâhi nur ve güzelliğe dönüşebilir. Dolayısıyla mecâz olarak zikredilen fani aşk; mâşûka ulaşınca gizemini kaybetse de hakiki aşka vasıtadır. Gönül kapısından aklı değerlendiren Mevlânâ için cüz’î akıl, aşkın sırları ve hakikatini açıklama hususunda yetersizdir. Gönüllerinde aşk derdi olanlar çeşitli arayışlarla hakîkate ulaşmaya çalışmaktadır. Mevlânâ, olgunlaşma merhalelerini açıklarken; çileyi olgunlaşma, cezbeyi yakınlaşma, muhabbeti ise kurtuluş kapısı olarak zikretmektedir. İlâhi sevgi hakîkat râyihası olmakla beraber insan bu kokuyu özellikle cüz’iyyatta arayıp durmaktadır. Bu arayış mâşukunda yok olan pervanenin ateşte yanarak ateş olması gibi vuslatı değil aşkın kendisini sevdirir. Mecâzî aşkın şehvet ve arzuların aracı olmasından öte yüksek değer ve gaye olduğunu ifade eden Mevlânâ, ilâhi aşkı beşeri aşkla iç içe betimlemektedir. Samimi ve mükemmel beşeri aşkla Hakk’a ermek ve ilâhi aşka ulaşmak, Bir’den başka bir şeyin görülmeyeceği kemâlattır. Mevlânâ’nın betimlemelerinde kemâle erdiren bu aşk tasavvuf edebiyatında önemli bir yere sahiptir. Allah’ın yarattığı güzellik kullarında tecelli etmektedir. Bundan dolayı Mevlânâ’nın “Aşk ister maddi varlıklara yönelik olsun, isterse ötekilerine, bil ki o seni O’na erdirecektir” sözü, âşığın Hakk’a ermesinin, mecâzî aşkın hakikatinin köprüsü olduğunun göstergesidir. Mevlana'ya göre aşk, ezelde olan ve ebediyette olacak olan bir metafiziksel bir tecrübe ve evrenin oluşumunu sağlayan tek hâldir. Ancak bu aşkın önündeki engel cüz’î aklın nefsin girdabına düşmesidir. Cüz’î akıl karışık ve taklitten ibaret olduğu için noksandır ve ilâhi aşkı anlamada problem teşkil etmektedir. Bu çalışma, âşıkların çile dolu hayatlarında karşılaştıkları her zorluğa rağmen maşukta yok olup gitmelerinin süreç ve imkânını Mevlânâ anlayışı açısından değerlendirmeyi amaçlamaktadır

Ab Initio No Core Shell Model with Leadership-Class Supercomputers

Nuclear structure and reaction theory is undergoing a major renaissance with advances in many-body methods, strong interactions with greatly improved links to Quantum Chromodynamics (QCD), the advent of high performance computing, and improved computational algorithms. Predictive power, with well-quantified uncertainty, is emerging from non-perturbative approaches along with the potential for guiding experiments to new discoveries. We present an overview of some of our recent developments and discuss challenges that lie ahead. Our foci include: (1) strong interactions derived from chiral effective field theory; (2) advances in solving the large sparse matrix eigenvalue problem on leadership-class supercomputers; (3) selected observables in light nuclei with the JISP16 interaction; (4) effective electroweak operators consistent with the Hamiltonian; and, (5) discussion of A=48 system as an opportunity for the no-core approach with the reintroduction of the core.Comment: 23 pages, 7 figures, Conference Proceedings online at http://ntse.khb.ru/files/uploads/2016/proceedings/Vary.pd

Analytic preconditioners for decoupled potential integral equations for wideband analysis of scattering from PEC objects

Many integral equations used to analyze scattering, such as the standard combined field integral equation (CFIE), are not well-conditioned for a wide range of frequencies and multi-scale geometries. There has been significant effort to alleviate this problem. A more recent one is using a set of decoupled potential integral equations (DPIE). These equations have been shown to be robust at low frequencies and immune to topology breakdown. But they mimic the behavior of CFIE at high frequencies. This paper addresses this deficiency. We do so by deriving new Calder\'{o}n-type identities through the Vector Potential Integral Equation (VPIE) and Scalar Potential Integral Equation (SPIE), and constructing novel analytic preconditioners for the vector potential integral equation (VPIE) and scalar potential integral equation (SPIE) constrained to perfect electric conductors (PEC). These new formulations are wide-band well-conditioned and converge rapidly for multi-scale geometries. This is demonstrated though a number of examples that use analytic and piecewise basis sets

The ReaxFF reactive force-field : development, applications and future directions

The reactive force-field (ReaxFF) interatomic potential is a powerful computational tool for exploring, developing and optimizing material properties. Methods based on the principles of quantum mechanics (QM), while offering valuable theoretical guidance at the electronic level, are often too computationally intense for simulations that consider the full dynamic evolution of a system. Alternatively, empirical interatomic potentials that are based on classical principles require significantly fewer computational resources, which enables simulations to better describe dynamic processes over longer timeframes and on larger scales. Such methods, however, typically require a predefined connectivity between atoms, precluding simulations that involve reactive events. The ReaxFF method was developed to help bridge this gap. Approaching the gap from the classical side, ReaxFF casts the empirical interatomic potential within a bond-order formalism, thus implicitly describing chemical bonding without expensive QM calculations. This article provides an overview of the development, application, and future directions of the ReaxFF method

Ab Initio No Core Shell Model - Recent Results and Further Prospects

There has been significant recent progress in solving the long-standing problems of how nuclear shell structure and collective motion emerge from underlying microscopic inter-nucleon interactions. We review a selection of recent significant results within the ab initio No Core Shell Model (NCSM) closely tied to three major factors enabling this progress: (1) improved nuclear interactions that accurately describe the experimental two-nucleon and three-nucleon interaction data; (2) advances in algorithms to simulate the quantum many-body problem with strong interactions; and (3) continued rapid development of high-performance computers now capable of performing $20 \times 10^{15}$ floating point operations per second. We also comment on prospects for further developments.Comment: Invited paper presented at NTSE-2014 and published online in the proceedings (see footnote on p.1