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1. Locality-Sensitive Bucketing Functions for the Edit Distance

   Chen, Ke ; Shao, Mingfu ( August 2022 , 22nd International Workshop on Algorithms in Bioinformatics (WABI 2022))

   Boucher, Christina ; Rahmann, Sven (Ed.)

   Many bioinformatics applications involve bucketing a set of sequences where each sequence is allowed to be assigned into multiple buckets. To achieve both high sensitivity and precision, bucketing methods are desired to assign similar sequences into the same bucket while assigning dissimilar sequences into distinct buckets. Existing k-mer-based bucketing methods have been efficient in processing sequencing data with low error rate, but encounter much reduced sensitivity on data with high error rate. Locality-sensitive hashing (LSH) schemes are able to mitigate this issue through tolerating the edits in similar sequences, but state-of-the-art methods still have large gaps. Here we generalize the LSH function by allowing it to hash one sequence into multiple buckets. Formally, a bucketing function, which maps a sequence (of fixed length) into a subset of buckets, is defined to be (d₁, d₂)-sensitive if any two sequences within an edit distance of d₁ are mapped into at least one shared bucket, and any two sequences with distance at least d₂ are mapped into disjoint subsets of buckets. We construct locality-sensitive bucketing (LSB) functions with a variety of values of (d₁,d₂) and analyze their efficiency with respect to the total number of buckets needed as well as the number of buckets that a specific sequence is mapped to. We also prove lower bounds of these two parameters in different settings and show that some of our constructed LSB functions are optimal. These results provide theoretical foundations for their practical use in analyzing sequences with high error rate while also providing insights for the hardness of designing ungapped LSH functions. 

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2. Semileptonic form factors for $$B\rightarrow D^*\ell \nu $$ at nonzero recoil from $$2+1$$-flavor lattice QCD: Fermilab Lattice and MILC Collaborations

   https://doi.org/10.1140/epjc/s10052-022-10984-9  

   Bazavov, A. ; DeTar, C. E. ; Du, D. ; El-Khadra, A. X. ; Gámiz, E. ; Gelzer, Z. ; Gottlieb, S. ; Heller, U. M. ; Kronfeld, A. S. ; Laiho, J. ; et al ( December 2022 , The European Physical Journal C)

   We present the first unquenched lattice-QCD calculation of the form factors for the decay$$B\rightarrow D^*\ell \nu $$$B\to D^{\ast }\ell \nu$at nonzero recoil. Our analysis includes 15 MILC ensembles with$$N_f=2+1$$$N_f=2+1$flavors of asqtad sea quarks, with a strange quark mass close to its physical mass. The lattice spacings range from$$a\approx 0.15$$$a\approx 0.15$fm down to 0.045 fm, while the ratio between the light- and the strange-quark masses ranges from 0.05 to 0.4. The valencebandcquarks are treated using the Wilson-clover action with the Fermilab interpretation, whereas the light sector employs asqtad staggered fermions. We extrapolate our results to the physical point in the continuum limit using rooted staggered heavy-light meson chiral perturbation theory. Then we apply a model-independent parametrization to extend the form factors to the full kinematic range. With this parametrization we perform a joint lattice-QCD/experiment fit using several experimental datasets to determine the CKM matrix element$$|V_{cb}|$$$|V_{\mathrm{cb}}|$. We obtain$$\left| V_{cb}\right| = (38.40 \pm 0.68_{\text {th}} \pm 0.34_{\text {exp}} \pm 0.18_{\text {EM}})\times 10^{-3}$$$\left(V_{\mathrm{cb}}\right)=(38.40\pm 0.{68}_{\text{th}}\pm 0.{34}_{\text{exp}}\pm 0.{18}_{\text{EM}})\times {10}^{-3}$. The first error is theoretical, the second comes from experiment and the last one includes electromagnetic and electroweak uncertainties, with an overall$$\chi ^2\text {/dof} = 126/84$$${\chi }^2\text{/dof}=126/84$, which illustrates the tensions between the experimental data sets, and between theory and experiment. This result is in agreement with previous exclusive determinations, but the tension with the inclusive determination remains. Finally, we integrate the differential decay rate obtained solely from lattice data to predict$$R(D^*) = 0.265 \pm 0.013$$$R\left(D^{\ast }\right)=0.265\pm 0.013$, which confirms the current tension between theory and experiment.

    

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3. Charge transport in individual short base stacked single-stranded RNA molecules

   https://doi.org/10.1038/s41598-023-46263-0  

   Chandra, Subrata ; Williams, Ajoke ; Maksudov, Farkhad ; Kliuchnikov, Evgenii ; Pattiya Arachchillage, Keshani G. G. ; Piscitelli, Patrick ; Castillo, Aderlyn ; Marx, Kenneth A. ; Barsegov, Valeri ; Artes Vivancos, Juan M. ( November 2023 , Scientific Reports)

   Charge transport in biomolecules is crucial for many biological and technological applications, including biomolecular electronics devices and biosensors. RNA has become the focus of research because of its importance in biomedicine, but its charge transport properties are not well understood. Here, we use the Scanning Tunneling Microscopy-assisted molecular break junction method to measure the electrical conductance of particular 5-base and 10-base single-stranded (ss) RNA sequences capable of base stacking. These ssRNA sequences show single-molecule conductance values around$$10^{-3}G_0$$${10}^{-3}{G}_0$($$G_0= 2e^2/h$$$G_0=2e^2/h$), while equivalent-length ssDNAs result in featureless conductance histograms. Circular dichroism (CD) spectra and MD simulations reveal the existence of extended ssRNA conformations versus folded ssDNA conformations, consistent with their different electrical behaviors. Computational molecular modeling and Machine Learning-assisted interpretation of CD data helped us to disentangle the structural and electronic factors underlying CT, thus explaining the observed electrical behavior differences. RNA with a measurable conductance corresponds to sequences with overall extended base-stacking stabilized conformations characterized by lower HOMO energy levels delocalized over a base-stacking mediating CT pathway. In contrast, DNA and a control RNA sequence without significant base-stacking tend to form closed structures and thus are incapable of efficient CT.

    

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4. Evidence of a liquid–liquid phase transition in H$$_2$$O and D$$_2$$O from path-integral molecular dynamics simulations

   https://doi.org/10.1038/s41598-022-09525-x  

   Eltareb, Ali ; Lopez, Gustavo E. ; Giovambattista, Nicolas ( April 2022 , Scientific Reports)

   We perform path-integral molecular dynamics (PIMD), ring-polymer MD (RPMD), and classical MD simulations of H$$_2$$${}_2$O and D$$_2$$${}_2$O using the q-TIP4P/F water model over a wide range of temperatures and pressures. The density$$\rho (T)$$$\rho \left(T\right)$, isothermal compressibility$$\kappa _T(T)$$${\kappa }_T\left(T\right)$, and self-diffusion coefficientsD(T) of H$$_2$$${}_2$O and D$$_2$$${}_2$O are in excellent agreement with available experimental data; the isobaric heat capacity$$C_P(T)$$$C_P\left(T\right)$obtained from PIMD and MD simulations agree qualitatively well with the experiments. Some of these thermodynamic properties exhibit anomalous maxima upon isobaric cooling, consistent with recent experiments and with the possibility that H$$_2$$${}_2$O and D$$_2$$${}_2$O exhibit a liquid-liquid critical point (LLCP) at low temperatures and positive pressures. The data from PIMD/MD for H$$_2$$${}_2$O and D$$_2$$${}_2$O can be fitted remarkably well using the Two-State-Equation-of-State (TSEOS). Using the TSEOS, we estimate that the LLCP for q-TIP4P/F H$$_2$$${}_2$O, from PIMD simulations, is located at$$P_c = 167 \pm 9$$$P_c=167\pm 9$ MPa,$$T_c = 159 \pm 6$$$T_c=159\pm 6$ K, and$$\rho _c = 1.02 \pm 0.01$$${\rho }_c=1.02\pm 0.01$ g/cm$$^3$$${}^3$. Isotope substitution effects are important; the LLCP location in q-TIP4P/F D$$_2$$${}_2$O is estimated to be$$P_c = 176 \pm 4$$$P_c=176\pm 4$ MPa,$$T_c = 177 \pm 2$$$T_c=177\pm 2$ K, and$$\rho _c = 1.13 \pm 0.01$$${\rho }_c=1.13\pm 0.01$ g/cm$$^3$$${}^3$. Interestingly, for the water model studied, differences in the LLCP location from PIMD and MD simulations suggest that nuclear quantum effects (i.e., atoms delocalization) play an important role in the thermodynamics of water around the LLCP (from the MD simulations of q-TIP4P/F water,$$P_c = 203 \pm 4$$$P_c=203\pm 4$ MPa,$$T_c = 175 \pm 2$$$T_c=175\pm 2$ K, and$$\rho _c = 1.03 \pm 0.01$$${\rho }_c=1.03\pm 0.01$ g/cm$$^3$$${}^3$). Overall, our results strongly support the LLPT scenario to explain water anomalous behavior, independently of the fundamental differences between classical MD and PIMD techniques. The reported values of$$T_c$$$T_c$for D$$_2$$${}_2$O and, particularly, H$$_2$$${}_2$O suggest that improved water models are needed for the study of supercooled water.

    

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5. Green function estimates on complements of low-dimensional uniformly rectifiable sets

   https://doi.org/10.1007/s00208-022-02379-8  

   David, Guy ; Feneuil, Joseph ; Mayboroda, Svitlana ( March 2022 , Mathematische Annalen)

   It has been recently established in David and Mayboroda (Approximation of green functions and domains with uniformly rectifiable boundaries of all dimensions.arXiv:2010.09793) that on uniformly rectifiable sets the Green function is almost affine in the weak sense, and moreover, in some scenarios such Green function estimates are equivalent to the uniform rectifiability of a set. The present paper tackles a strong analogue of these results, starting with the “flagship degenerate operators on sets with lower dimensional boundaries. We consider the elliptic operators$$L_{\beta ,\gamma } =- {\text {div}}D^{d+1+\gamma -n} \nabla $$$L_{\beta ,\gamma }=-\text{div}{D}^{d+1+\gamma -n}\nabla$associated to a domain$$\Omega \subset {\mathbb {R}}^n$$$\Omega \subset R^n$with a uniformly rectifiable boundary$$\Gamma $$$\Gamma$of dimension$$d < n-1$$$d<n-1$, the now usual distance to the boundary$$D = D_\beta $$$D=D_{\beta }$given by$$D_\beta (X)^{-\beta } = \int _{\Gamma } |X-y|^{-d-\beta } d\sigma (y)$$$D_{\beta }{\left(X\right)}^{-\beta }={\int }_{\Gamma }{|X-y|}^{-d-\beta }d\sigma \left(y\right)$for$$X \in \Omega $$$X\in \Omega$, where$$\beta >0$$$\beta >0$and$$\gamma \in (-1,1)$$$\gamma \in (-1,1)$. In this paper we show that the Green functionGfor$$L_{\beta ,\gamma }$$$L_{\beta ,\gamma }$, with pole at infinity, is well approximated by multiples of$$D^{1-\gamma }$$$D^{1-\gamma }$, in the sense that the function$$\big | D\nabla \big (\ln \big ( \frac{G}{D^{1-\gamma }} \big )\big )\big |^2$$$|D\nabla (ln(\frac{G}{D^{1-\gamma }})){|}^2$satisfies a Carleson measure estimate on$$\Omega $$$\Omega$. We underline that the strong and the weak results are different in nature and, of course, at the level of the proofs: the latter extensively used compactness arguments, while the present paper relies on some intricate integration by parts and the properties of the “magical distance function from David et al. (Duke Math J, to appear).

    

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