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    <description>recent bookmarks from Vaguery</description>
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  </channel><item rdf:about="https://hal.science/tel-05570783v1">
    <title>Combinatorial Contemplations - Archive ouverte HAL</title>
    <dc:date>2026-05-24T17:22:15+00:00</dc:date>
    <link>https://hal.science/tel-05570783v1</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[The monograph contains three Chapters. The first chapter is an introduction, outlining my philosophical views on the nature of counting, combinatorial enumeration, things and their names. It also contains a description of the classical Goulden-Jackson method which is used in the second Chapter. The second Chapter, together with the third, present my contributions as well as some recent findings of the literature. More precisely, the second Chapter is focused on the combinatorics of certain types of patterns in the molecular structure of ribonucleic acids (RNAs, one of the most important elements of biological organisms). It examines the distribution of these patterns in the real-world RNA structures and their theoretical models. The third Chapter essentially addresses two things: a new Motzkin-counted restriction of Dyck paths and a new class of Fibonacci-counted words. Not only does it provide purely scientific results, it also gives some autobiographical context. The third section of the Chapter 3 concludes the monograph by presenting a description of related works and possible directions for further research, as well as several short poems about the mesmerising process of translating thoughts into the language of words and numbers.

]]></description>
<dc:subject>mathematical-recreations combinatorics book rather-interesting RNA-folding philosophy-of-science looking-to-see</dc:subject>
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<dc:identifier>https://pinboard.in/u:Vaguery/b:9c46af2bec6a/</dc:identifier>
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<item rdf:about="https://arxiv.org/abs/1806.03333">
    <title>[1806.03333] The rainbow-spectrum of RNA secondary structures</title>
    <dc:date>2020-01-10T21:01:53+00:00</dc:date>
    <link>https://arxiv.org/abs/1806.03333</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[In this paper we analyze the length-spectrum of rainbows in RNA secondary structures. A rainbow in a secondary structure is a maximal arc with respect to the partial order induced by nesting. We show that there is a significant gap in this length-spectrum. We shall prove that there asymptotically almost surely exists a unique longest rainbow of length at least n−O(n1/2) and that with high probability any other rainbow has finite length. We show that the distribution of the length of the longest rainbow converges to a discrete limit law and that, for finite k, the distribution of rainbows of length k, becomes for large n a negative binomial distribution. We then put the results of this paper into context, comparing the analytical results with those observed in RNA minimum free energy structures, biological RNA structures and relate our findings to the sparsification of folding algorithms.
]]></description>
<dc:subject>structural-biology RNA-folding hey-I-know-this-guy molecular-design simulation rather-interesting feature-construction to-write-about to-simulate consider:extreme-cases consider:feature-discovery</dc:subject>
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<dc:identifier>https://pinboard.in/u:Vaguery/b:a438e8d14c51/</dc:identifier>
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<item rdf:about="http://arxiv.org/abs/1312.0075">
    <title>[1312.0075] Sequence-dependent folding landscapes of adenine riboswitch aptamers</title>
    <dc:date>2014-03-30T11:36:24+00:00</dc:date>
    <link>http://arxiv.org/abs/1312.0075</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA[Prediction of the functions of riboswitches requires a quantitative description of the folding landscape so that the barriers and time scales for the conformational change in the switching region in the aptamer can be estimated. Using a combination of all atom molecular dynamics and coarse-grained model simulations we studied the response of adenine (A) binding add and pbuE A-riboswitches to mechanical force. The two riboswitches contain a structurally similar three-way junction formed by three paired helices, P1, P2, and P3, but carry out different functions. Using pulling simulations, with structures generated in MD simulations, we show that after P1 rips the dominant unfolding pathway in add A-riboswitch is the rupture of P2 followed by unraveling of P3. In the pbuE A-riboswitch, after P1 unfolds P3 ruptures ahead of P2. The order of unfolding of the helices, which is in accord with single molecule pulling experiments, is determined by the relative stabilities of the individual helices. Our results show that the stability of isolated helices determines the order of assembly and response to force in these non-coding regions. We use the simulated free energy profile for pbuE A-riboswitch to estimate the time scale for allosteric switching, which shows that this riboswitch is under kinetic control lending additional support to the conclusion based on single molecule pulling experiments. A consequence of the stability hypothesis is that a single point mutation (U28C) in the P2 helix of the add A-riboswitch, which increases the stability of P2, would make the folding landscapes of the two riboswitches similar. This prediction can be tested in single molecule pulling experiments.
]]></description>
<dc:subject>RNA-folding biophysics simulation contingency energy-landscapes molecular-design interesting nudge-targets consider:explanatory-model-refinement note:self-organizing-polymer-model</dc:subject>
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<item rdf:about="http://arxiv.org/abs/1003.3987">
    <title>[1003.3987] RNA-RNA interaction prediction based on multiple sequence alignments</title>
    <dc:date>2010-07-26T13:13:45+00:00</dc:date>
    <link>http://arxiv.org/abs/1003.3987</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA["Many computerized methods for RNA-RNA interaction structure prediction have been developed. Recently, $O(N^6)$ time and $O(N^4)$ space dynamic programming algorithms have become available that compute the partition function of RNA-RNA interaction complexes. However, few of these methods incorporate the knowledge concerning related sequences, thus relevant evolutionary information is often neglected from the structure determination. Therefore, it is of considerable practical interest to introduce a method taking into consideration both thermodynamic stability and sequence covariation. We present the \emph{a priori} folding algorithm \texttt{ripalign}, whose input consists of two (given) multiple sequence alignments (MSA). \texttt{ripalign} outputs (1) the partition function, (2) base-pairing probabilities, (3) hybrid probabilities and (4) a set of Boltzmann-sampled suboptimal structures consisting of canonical joint structures that are compatible to the alignments.…"
]]></description>
<dc:subject>RNA-folding algorithms numerical-methods bioinformatics nudge-targets</dc:subject>
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<item rdf:about="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0011308">
    <title>PLoS ONE: Is Thermosensing Property of RNA Thermometers Unique?</title>
    <dc:date>2010-07-03T12:09:33+00:00</dc:date>
    <link>http://www.plosone.org/article/info:doi/10.1371/journal.pone.0011308</link>
    <dc:creator>Vaguery</dc:creator><description><![CDATA["… We have developed a novel method of studying the melting of RNAs with temperature by computationally sampling the distribution of the RNA structures at various temperatures using the RNA folding software Vienna. In this study, we compared the thermosensing property of 100 randomly selected mRNAs and three well known thermometers…"
]]></description>
<dc:subject>molecular-design simulation computational-methods RNA-folding biomolecules nudge-targets via:twitter</dc:subject>
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