Cooperativity-Dependent Folding of Single-Stranded DNA

The folding of biological macromolecules is a fundamental process of which we lack a full comprehension. Mostly studied in proteins and RNA, single-stranded DNA (ssDNA) also folds, at physiological salt conditions, by forming nonspecific secondary structures that are difficult to characterize with biophysical techniques. Here, we present a helix-coil model for secondary-structure formation, where ssDNA bases are organized in two different types of domains (compact and free). The model contains two parameters: the energy gain per base in a compact domain, ε , and the cooperativity related to the interfacial energy between different domains, γ . We test the ability of the model to quantify the formation of secondary structure in ssDNA molecules mechanically stretched with optical tweezers. The model reproduces the experimental force-extension curves in ssDNA of different molecular lengths and varying sodium and magnesium concentrations. Salt-correction effects for the energy of compact domains and the interfacial energy are found to be compatible with those of DNA hybridization. The model also predicts the folding free energy and the average size of domains at zero force, finding good agreement with secondary-structure predictions by mfold. We envision the model could be further extended to investigate native folding in RNA and protein

Functionalization of fluorinated ionic liquids: A combined experimental-theoretical study

FCT/MCTES (Portugal), through: grant SFRH/BD/130965/2017 (M.LF.); Investigador FCT 2014 (IF/00190/2014 to A.B.P. and IF/00210/2014 to J.M.M.A.); projects PTDC/EQU-EQU/29737/2017, PTDC/QEQ-FTT/3289/2014 and IF/00210/2014/CP1244/CT0003. Associate Laboratory for Green Chemistry-LAQV, financed by national funds from FCT/MCTES (UID/QUI/50006/2019). projects 2018-LC-01 and 2019-URL-IR1rQ-011, from Obra Social "la Caixa" and by Khalifa University through project RCII-2018-0024.We present new experimental and modelling data concerning imidazolium based-FILs synthesized with a hydroxyl group in the end of the cationic hydrogenated side chain and compared them with the analogous non-functionalized FILs in order to verify their suitability in the biomedical field. The thermophysical and thermodynamic properties of the neat compounds and the self-aggregation behaviour of FILs in aqueous solutions were measured and compared with theoretical results from the soft-SAFT equation of state, in good agreement with each other. Results showed that the presence of the hydroxyl group increases the density and viscosity of pure compounds and aqueous mixtures, whereas the thermal stability, melting, free volume, ionicity and self-aggregation behaviour decrease. These properties are improved with respect to the conventional perfluorosurfactants for the desired application, due to the full miscibility in water and the promising improved biocompatibility.authorsversionpublishe

Direct detection of molecular intermediates from first-passage times

All natural phenomena are governed by energy landscapes. However, the direct measurement of this fundamen-tal quantity remains challenging, particularly in complex systems involving intermediate states. Here, we uncover key details of the energy landscapes that underpin a range of experimental systems through quantitative analysis of first-passage time distributions. By combined study of colloidal dynamics in confinement, transport through a biological pore, and the folding kinetics of DNA hairpins, we demonstrate conclusively how a short-time, power-law regime of the first-passage time distribution reflects the number of intermediate states associated with each of these processes, despite their differing length scales, time scales, and interactions. We thereby establish a powerful method for investigating the underlying mechanisms of complex molecular processes

Screening of Ionic Liquids and Deep Eutectic Solvents for Physical CO2Absorption by Soft-SAFT Using Key Performance Indicators

RC2-2019-007 PID2019108014RB-C21 SFRH/BD/130965/2017 UID/QUI/50006/2019The efficient screening of solvents for CO2 capture requires a reliable and robust equation of state to characterize and compare their thermophysical behavior for the desired application. In this work, the potentiality of 14 ionic liquids (ILs) and 7 deep eutectic solvents (DESs) for CO2 capture was examined using soft-SAFT as a modeling tool for the screening of these solvents based on key process indicators, namely, cyclic working capacity, enthalpy of desorption, and CO2 diffusion coefficient. Once the models were assessed versus experimental data, soft-SAFT was used as a predictive tool to calculate the thermophysical properties needed for evaluating their performance. Results demonstrate that under the same operating conditions, ILs have a far superior performance than DESs primarily in terms of amount of CO2 captured, being at least two-folds more than that captured using DESs. The screening tool revealed that among all the examined solvents and conditions, [C4 py][NTf2] is the most promising solvent for physical CO2 capture. The collection of the acquired results confirms the reliability of the soft-SAFT EoS as an attractive and valuable screening tool for CO2 capture and process modeling.publishersversionpublishe

Systematic study of the influence of the molecular structure of fluorinated ionic liquids on the solubilization of atmospheric gases using a soft-SAFT based approach

FCT/ MCTES (Portugal) through grant SFRH/BD/130965/2017 (M. L. Ferreira) and Investigador FCT 2014 ( IF/00190/2014 to A. B. Pereiro and IF/00210/2014 to J. M. M. Araújo), and projects PTDC/EQU-EQU/29737/2017, PTDC/QEQ-FTT/3289/2014 and IF/00210/2014/CP1244/CT0003. This work was also supported by the Associate Laboratory for Green Chemistry – LAQV, which is financed by national funds from FCT / MCTES ( UID/QUI/50006/2019 ). Additional financial support has been provided by Khalifa University of Science and Technology through projects RCII-2018-24 (CeCaS Center) and RCII-2019-007 (RICH Center), as well as projects 2018-LC-01 and 2019-URL-IR1rQ-011 from Obra Social “La Caixa” .This work focuses on the design and development of fluorinated ionic liquids (FILs) as alternatives to perfluorocarbons (PFCs), widely used in industrial applications. A combined theoretical-experimental approach has been used to characterize ionic liquids (ILs), considering their thermodynamic behaviour in the presence of atmospheric gases (oxygen (O2), nitrogen (N2) and carbon dioxide (CO2)). The selected ILs are based on perfluorobutanesulfonate ([C4F9SO3]−), perfluoropentanoate ([C4F9CO2]−), trifluoromethanesulfonate ([CF3SO3]−) and trifluoroacetate ([CF3CO2]−) anions, combined with imidazolium ([CnC1Im]+, n = 2 and 4) and pyridinium ([C2C1py]+) cations. The soft-SAFT (Statistical Associating Fluid Theory) molecular-based equation of state has been used to determine the solubility behaviour of atmospheric gases in the ILs. Models for three FILs not yet parametrized, [C2C1py][C4F9SO3], [C2C1Im][C4F9CO2] and [C2C1py][C4F9CO2], have been built from transferable molecular models. The solubility of O2, N2 and CO2 in the ILs has been determined, in excellent agreement with experimental data, indicating the robustness of the soft-SAFT approach. The highest solubilities have been obtained for the FILs based on the perfluorobutanesulfonate anion ([C4F9SO3]−) combined with 1-ethyl-3-methylpyridinium cation ([C2C1py]+) and 1-butyl-3-methylimidazolium cation ([C4C1Im]+). This approach grants to evolve highly predictive IL models inherently, regarding the process of parametrization from the molecular structure, which allows to describe the behaviour of these complex systems in a faster and more robust way.authorsversionpublishe

Voltage-based magnetization switching and reading in magnetoelectric spin-orbit nanodevices

Abstract As CMOS technologies face challenges in dimensional and voltage scaling, the demand for novel logic devices has never been greater, with spin-based devices offering scaling potential, at the cost of significantly high switching energies. Alternatively, magnetoelectric materials are predicted to enable low-power magnetization control, a solution with limited device-level results. Here, we demonstrate voltage-based magnetization switching and reading in nanodevices at room temperature, enabled by exchange coupling between multiferroic BiFeO3 and ferromagnetic CoFe, for writing, and spin-to-charge current conversion between CoFe and Pt, for reading. We show that, upon the electrical switching of the BiFeO3, the magnetization of the CoFe can be reversed, giving rise to different voltage outputs. Through additional microscopy techniques, magnetization reversal is linked with the polarization state and antiferromagnetic cycloid propagation direction in the BiFeO3. This study constitutes the building block for magnetoelectric spin-orbit logic, opening a new avenue for low-power beyond-CMOS technologies