CplexA: a Mathematica package to study macromolecular-assembly control of gene expression

Summary: Macromolecular assembly vertebrates essential cellular processes, such as gene regulation and signal transduction. A major challenge for conventional computational methods to study these processes is tackling the exponential increase of the number of configurational states with the number of components. CplexA is a Mathematica package that uses functional programming to efficiently compute probabilities and average properties over such exponentially large number of states from the energetics of the interactions. The package is particularly suited to study gene expression at complex promoters controlled by multiple, local and distal, DNA binding sites for transcription factors. Availability: CplexA is freely available together with documentation at http://sourceforge.net/projects/cplexa/.Comment: 28 pages. Includes Mathematica, Matlab, and Python implementation tutorials. Software can be downloaded at http://cplexa.sourceforge.net

Multiprotein DNA looping

DNA looping plays a fundamental role in a wide variety of biological processes, providing the backbone for long range interactions on DNA. Here we develop the first model for DNA looping by an arbitrarily large number of proteins and solve it analytically in the case of identical binding. We uncover a switch-like transition between looped and unlooped phases and identify the key parameters that control this transition. Our results establish the basis for the quantitative understanding of fundamental cellular processes like DNA recombination, gene silencing, and telomere maintenance.Comment: 11 pages, 4 figure

Estudio del Rhynchosauroides santanderiensis, n. sp., y otras nuevas huellas de pisadas en el Trias de Santander, con notas sobre el ambiente paleográfico

Procedentes del Trías del área de Puentenansa (Santander) se describen cuatro tipos de huellas de pisadas de reptiles de pequeño tamaño. Ninguno de los tipos se conocía anteriormente, pero sólo se ha dado nombre a uno de ellos (Rhynchosauroides santanderiensis, n.sp.).Se expone también, realizado a partir de datos petrológicos, un esbozo de las condiciones existentes en el área en la época en que vivieron los autores de las pistas. Este esbozo coincide con las conclusiones que pueden deducirse de la existencia y características de las huellas (zona marginal respecto al conjunto de la cuenca, sometida a inundaciones periódicas)

Dynamics-informed deconvolutional neural networks for super-resolution identification of regime changes in epidemiological time series

Inferring the timing and amplitude of perturbations in epidemiological systems from their stochastically spread low-resolution outcomes is as relevant as challenging. It is a requirement for current approaches to overcome the need to know the details of the perturbations to proceed with the analyses. However, the general problem of connecting epidemiological curves with the underlying incidence lacks the highly effective methodology present in other inverse problems, such as super-resolution and dehazing from computer vision. Here, we develop an unsupervised physics-informed convolutional neural network approach in reverse to connect death records with incidence that allows the identification of regime changes at single-day resolution. Applied to COVID-19 data with proper regularization and model-selection criteria, the approach can identify the implementation and removal of lockdowns and other nonpharmaceutical interventions with 0.93-day accuracy over the time span of a year.Comment: 18 pages, 5 figure

Conservation Laws in Smooth Particle Hydrodynamics: the DEVA Code

We describe DEVA, a multistep AP3M-like-SPH code particularly designed to study galaxy formation and evolution in connection with the global cosmological model. This code uses a formulation of SPH equations which ensures both energy and entropy conservation by including the so-called \bn h terms. Particular attention has also been paid to angular momentum conservation and to the accuracy of our code. We find that, in order to avoid unphysical solutions, our code requires that cooling processes must be implemented in a non-multistep way. We detail various cosmological simulations which have been performed to test our code and also to study the influence of the \bn h terms. Our results indicate that such correction terms have a non-negligible effect on some cosmological simulations, especially on high density regions associated either to shock fronts or central cores of collapsed objects. Moreover, they suggest that codes paying a particular attention to the implementation of conservation laws of physics at the scales of interest, can attain good accuracy levels in conservation laws with limited computational resources.Comment: 36 pages, 10 figures. Accepted for publication in The Astrophysical Journa