Collapse of Flexible Polyelectrolytes in Multivalent Salt Solutions

The collapse of flexible polyelectrolytes in a solution of multivalent counterions is studied by means of a two state model. The states correspond to rod-like and spherically collapsed conformations respectively. We focus on the very dilute monomer concentration regime where the collapse transition is found to occur when the charge of the multivalent salt is comparable (but smaller) to that of the monomers. The main contribution to the free energy of the collapsed conformation is linear in the number of monomers $N$, since the internal state of the collapsed polymer approaches that of an amorphous ionic solid. The free energy of the rod-like state grows as $N\ln N$, due to the electrostatic energy associated with that shape. We show that practically all multivalent counterions added to the system are condensed into the polymer chain, even before the collapse.Comment: LaTeX-revtex, psfig file, 4 figure

Complexity of qualitative timeline-based planning

The timeline-based approach to automated planning was originally developed in the context of space missions. In this approach, problem domains are expressed as systems consisting of independent but interacting components whose behaviors over time, the timelines, are governed by a set of temporal constraints, called synchronization rules. Although timeline-based system descriptions have been successfully used in practice for decades, the research on the theoretical aspects only started recently. In the last few years, some interesting results have been shown concerning both its expressive power and the computational complexity of the related planning problem. In particular, the general problem has been proved to be EXPSPACE-complete. Given the applicability of the approach in many practical scenarios, it is thus natural to ask whether computationally simpler but still expressive fragments can be identified. In this paper, we study the timeline-based planning problem with the restriction that only qualitative synchronization rules, i.e., rules without explicit time bounds in the constraints, are allowed. We show that the problem becomes PSPACE-complete

Formation and nucleolytic processing of Cas9-induced DNA breaks in human cells quantified by droplet digital PCR

Cas9 endonuclease from S. pyogenes is widely used to induce controlled double strand breaks (DSB) at desired genomic loci for gene editing. Here, we describe a droplet digital PCR (ddPCR) method to precisely quantify the kinetic of formation and 5\u2032-end nucleolytic processing of Cas9-induced DSB in different human cells lines. Notably, DSB processing is a finely regulated process, which dictates the choice between non-homologous end joining (NHEJ) and homology directed repair (HDR). This step of DSB repair is also a relevant point to be taken into consideration to improve Cas9-mediated technology. Indeed, by this protocol, we show that processing of Cas9-induced DSB is impaired by CTIP or BRCA1 depletion, while it is accelerated after down-regulation of DNAPKcs and 53BP1, two DSB repair key factors. In conclusion, the method we describe here can be used to study DSB repair mechanisms, with direct utility for molecularly optimising the knock-out/in outcomes in genome manipulation

Non-monotonic swelling of surface grafted hydrogels induced by pH and/or salt concentration

We use a molecular theory to study the thermodynamics of a weak-polyacid hydrogel film that is chemically grafted to a solid surface. We investigate the response of the material to changes in the pH and salt concentration of the buffer solution. Our results show that the pH-triggered swelling of the hydrogel film has a non-monotonic dependence on the acidity of the bath solution. At most salt concentrations, the thickness of the hydrogel film presents a maximum when the pH of the solution is increased from acidic values. The quantitative details of such swelling behavior, which is not observed when the film is physically deposited on the surface, depend on the molecular architecture of the polymer network. This swelling-deswelling transition is the consequence of the complex interplay between the chemical free energy (acid-base equilibrium), the electrostatic repulsions between charged monomers, which are both modulated by the absorption of ions, and the ability of the polymer network to regulate charge and control its volume (molecular organization). In the absence of such competition, for example, for high salt concentrations, the film swells monotonically with increasing pH. A deswelling-swelling transition is similarly predicted as a function of the salt concentration at intermediate pH values. This reentrant behavior, which is due to the coupling between charge regulation and the two opposing effects triggered by salt concentration (screening electrostatic interactions and charging/discharging the acid groups), is similar to that found in end-grafted weak polyelectrolyte layers. Understanding how to control the response of the material to different stimuli, in terms of its molecular structure and local chemical composition, can help the targeted design of applications with extended functionality. We describe the response of the material to an applied pressure and an electric potential. We present profiles that outline the local chemical composition of the hydrogel, which can be useful information when designing applications that pursue or require the absorption of biomolecules or pH-sensitive molecules within different regions of the film.Fil: Longo, Gabriel Sebastian. Consejo Nacional de Investigaciones Científicas y Técnicas. Centro Científico Tecnológico la Plata. Instituto de Investigaciones Fisicoquímicas Teóricas y Aplicadas; Argentina. Northwestern University. Department of Biomedical Engineering; Estados Unidos. Northwestern University. Chemistry of Life Processes Institute; Estados UnidosFil: Olvera de la Cruz, Monica. Northwestern University; Estados UnidosFil: Szleifer, Igal. Northwestern University; Estados Unido

An Optimal Decision Procedure for MPNL over the Integers

Interval temporal logics provide a natural framework for qualitative and quantitative temporal reason- ing over interval structures, where the truth of formulae is defined over intervals rather than points. In this paper, we study the complexity of the satisfiability problem for Metric Propositional Neigh- borhood Logic (MPNL). MPNL features two modalities to access intervals "to the left" and "to the right" of the current one, respectively, plus an infinite set of length constraints. MPNL, interpreted over the naturals, has been recently shown to be decidable by a doubly exponential procedure. We improve such a result by proving that MPNL is actually EXPSPACE-complete (even when length constraints are encoded in binary), when interpreted over finite structures, the naturals, and the in- tegers, by developing an EXPSPACE decision procedure for MPNL over the integers, which can be easily tailored to finite linear orders and the naturals (EXPSPACE-hardness was already known).Comment: In Proceedings GandALF 2011, arXiv:1106.081

PyMembrane: A flexible framework for efficient simulations of elastic and liquid membranes

PyMembrane is a software package for simulating liquid and elastic membranes using a discretisation of the continuum description based on unstructured triangulated two-dimensional meshes embedded in three-dimensional space. The package is written in C++, with a flexible and intuitive Python interface, allowing for a quick setup, execution and analysis of complex simulations. PyMembrane follows modern software engineering principles and features a modular design that allows for straightforward implementation of custom extensions while ensuring consistency and enabling inexpensive maintenance. A hallmark feature of this design is the use of a standardized C++ interface which streamlines adding new functionalities. Furthermore, PyMembrane uses data structures optimised for unstructured meshes, ensuring efficient mesh operations and force calculations. By providing several templates for typical simulations supplemented by extensive documentation, the users can seamlessly set up and run research-level simulations and extend the package to integrate additional features, underscoring PyMembrane's commitment to user-centric design.Comment: 7 Figure

Thesaurus: un database per il patrimonio culturale sommerso

Thesaurus Project aims at promoting the knowledge of the underwater cultural heritage, ancient and modern, through the application of several typologies of tools: underwater autonomous vehicles, which will be able to explore the sea bottom in teams communicating with each other; a database, which will be useful to store and manage all the information referring to archaeological or historical objects, shipwrecks and sites. This paper aims to explain the logic structure of the database indicating the particular needs of the research, the different typologies of items which have to be managed (archaeological and historical objects; ancient, medieval or modern shipwrecks; underwater sites; written or figurative sources, etc.), the relation with other similar databases and projects. The main task of this part of Thesaurus is to plan and organize an IT system, which will allow archaeologists to describe information in detail, in order to make an efficient managing and retrieving data system available

Multiscale understanding of tricalcium silicate hydration reactions

Tricalcium silicate, the main constituent of Portland cement, hydrates to produce crystalline calcium hydroxide and calcium-silicate-hydrates (C-S-H) nanocrystalline gel. This hydration reaction is poorly understood at the nanoscale. The understanding of atomic arrangement in nanocrystalline phases is intrinsically complicated and this challenge is exacerbated by the presence of additional crystalline phase(s). Here, we use calorimetry and synchrotron X-ray powder diffraction to quantitatively follow tricalcium silicate hydration process: i) its dissolution, ii) portlandite crystallization and iii) C-S-H gel precipitation. Chiefly, synchrotron pair distribution function (PDF) allows to identify a defective clinotobermorite, Ca11Si9O28(OH)2.8.5H2O, as the nanocrystalline component of C-S-H. Furthermore, PDF analysis also indicates that C-S-H gel contains monolayer calcium hydroxide which is stretched as recently predicted by first principles calculations. These outcomes, plus additional laboratory characterization, yielded a multiscale picture for C-S-H nanocomposite gel which explains the observed densities and Ca/Si atomic ratios at the nano- and meso- scales.This work has been supported by Spanish MINECO through BIA2014-57658-C2-2-R, which is co-funded by FEDER, BIA2014-57658-C2-1-R and I3 (IEDI-2016-0079) grants. We also thank CELLS-ALBA (Barcelona, Spain) for providing synchrotron beam time at BL04-MSPD beamline

Antiproliferative Activity Predictor: A New Reliable In Silico Tool for Drug Response Prediction against NCI60 Panel

In vitro antiproliferative assays still represent one of the most important tools in the anticancer drug discovery field, especially to gain insights into the mechanisms of action of anticancer small molecules. The NCI-DTP (National Cancer Institute Developmental Therapeutics Program) undoubtedly represents the most famous project aimed at rapidly testing thousands of compounds against multiple tumor cell lines (NCI60). The large amount of biological data stored in the National Cancer Institute (NCI) database and many other databases has led researchers in the fields of computational biology and medicinal chemistry to develop tools to predict the anticancer properties of new agents in advance. In this work, based on the available antiproliferative data collected by the NCI and the manipulation of molecular descriptors, we propose the new in silico Antiproliferative Activity Predictor (AAP) tool to calculate the GI50 values of input structures against the NCI60 panel. This ligand-based protocol, validated by both internal and external sets of structures, has proven to be highly reliable and robust. The obtained GI50 values of a test set of 99 structures present an error of less than ±1 unit. The AAP is more powerful for GI50 calculation in the range of 4–6, showing that the results strictly correlate with the experimental data. The encouraging results were further supported by the examination of an in-house database of curcumin analogues that have already been studied as antiproliferative agents. The AAP tool identified several potentially active compounds, and a subsequent evaluation of a set of molecules selected by the NCI for the one-dose/five-dose antiproliferative assays confirmed the great potential of our protocol for the development of new anticancer small molecules. The integration of the AAP tool in the free web service DRUDIT provides an interesting device for the discovery and/or optimization of anticancer drugs to the medicinal chemistry community. The training set will be updated with new NCI-tested compounds to cover more chemical spaces, activities, and cell lines. Currently, the same protocol is being developed for predicting the TGI (total growth inhibition) and LC50 (median lethal concentration) parameters to estimate toxicity profiles of small molecules

Cumulus Cell DNA damage as an index of human oocyte competence

The determination of oocyte quality is crucial for achieving effective syngamy post-sperm injection and embryonic development. Cumulus cells (CCs) have been proposed as biomarkers of oocyte quality because of their close bio-dynamic relationship with the oocyte. To determine the quality of the oocyte, CCs were sampled during oocyte preparation for ICSI to determine a CC DNA fragmentation index (CCDFI) of each individual oocyte using a variant of the chromatin dispersion test. One hundred and thirty oocytes were selected and studied from two Spanish fertility clinics, 90 of which were fertilized and developed to embryos. Significant differences were found between the CCDFI of unfertilized and fertilized oocytes (p <.001) and between the CCDFI of embryos that were discarded and those that developed suitable for transfer or cryopreservation (p <.001). Oocyte quality was negatively correlated with CCDFI (Spearman’s rho = − 0.45; p <.001). Receiver operator characteristics curves (ROC) suggested that a cut-off value of 24% CCDFI was able to discriminate the capacity of the gametes to result in syngamy with a sensitivity and specificity of 75.6% and 65%, respectively. This cut-off supports the application of CCDFI as potential index for the evaluation of the reproductive potential of oocytes prior to fertilizatio