Spontaneous synchronization of two bistable pyridine-furan nanosprings connected by an oligomeric bridge

The intensive development of nanodevices acting as two-state systems has motivated the search for nanoscale molecular structures whose long-term conformational dynamics are similar to the dynamics of bistable mechanical systems such as Euler arches and Duffing oscillators. Collective synchrony in bistable dynamics of molecular-sized systems has attracted immense attention as a potential pathway to amplify the output signals of molecular nanodevices. Recently, pyridin-furan oligomers of helical shape that are a few nanometers in size and exhibit bistable dynamics similar to a Duffing oscillator have been identified through molecular dynamics simulations. In this article, we present the case of dynamical synchronization of these bistable systems. We show that two pyridine-furan springs connected by a rigid oligomeric bridge spontaneously synchronize vibrations and stochastic resonance enhances the synchronization effect

Spontaneous Vibrations and Stochastic Resonance of Short Oligomeric Springs

There is growing interest in molecular structures that exhibit dynamics similar to bistable mechanical systems. These structures have the potential to be used as nanodevices with two distinct states. Particularly intriguing are structures that display spontaneous vibrations and stochastic resonance. Previously, through molecular dynamics simulations, it was discovered that short pyridine-furan springs, when subjected to force loading, exhibit the bistable dynamics of a Duffing oscillator. In this study, we extend these simulations to include short pyridine-pyrrole and pyridine-furan springs in a hydrophobic solvent. Our findings demonstrate that these systems also display the bistable dynamics of a Duffing oscillator, accompanied by spontaneous vibrations and stochastic resonance activated by thermal noise.Comment: arXiv admin note: substantial text overlap with arXiv:2110.0409

Degradation versus self-assembly of block copolymer micelles

The stability of micelles self-assembled from block copolymers can be altered by the degradation of the blocks. Slow degradation shifts the equilibrium size distribution of block copolymer micelles and change their properties. Quasi-equilibrium scaling theory shows that the degradation of hydrophobic blocks in the core of micelles destabilize the micelles reducing their size, while the degradation of hydrophilic blocks forming coronas of micelles favors larger micelles and may, at certain conditions, induce the formation of micelles from individual chains.Comment: Published in Langmuir http://pubs.acs.org/doi/pdf/10.1021/la204625

Study on cosmogenic activation above ground for the DarkSide-20k project

The activation of materials due to the exposure to cosmic rays may become an important background source for experiments investigating rare event phenomena. DarkSide-20k is a direct detection experiment for galactic dark matter particles, using a two-phase liquid argon time projection chamber filled with 49.7 tonnes (active mass) of Underground Argon (UAr) depleted in 39Ar. Here, the cosmogenic activity of relevant long-lived radioisotopes induced in the argon and other massive components of the set-up has been estimated; production of 120 t of radiopure UAr is foreseen. The expected exposure above ground and production rates, either measured or calculated, have been considered. From the simulated counting rates in the detector due to cosmogenic isotopes, it is concluded that activation in copper and stainless steel is not problematic. Activation of titanium, considered in early designs but not used in the final design, is discussed. The activity of 39Ar induced during extraction, purification and transport on surface, in baseline conditions, is evaluated to be 2.8% of the activity measured in UAr from the same source, and thus considered acceptable. Other products in the UAr such as 37Ar and 3H are shown to not be relevant due to short half-life and assumed purification methods

Short Pyridine-Furan Springs Exhibit Bistable Dynamics of Duffing Oscillators

The intensive development of nanodevices acting as two-state systems has motivated the search for nanoscale molecular structures whose dynamics are similar to those of bistable mechanical systems, such as Euler arches and Duffing oscillators. Of particular interest are the molecular structures capable of spontaneous vibrations and stochastic resonance. Recently, oligomeric molecules that were a few nanometers in size and exhibited the bistable dynamics of an Euler arch were identified through molecular dynamics simulations of short fragments of thermo-responsive polymers subject to force loading. In this article, we present molecular dynamics simulations of short pyridine-furan springs a few nanometers in size and demonstrate the bistable dynamics of a Duffing oscillator with thermally-activated spontaneous vibrations and stochastic resonance

Short Pyridine-Furan Springs Exhibit Bistable Dynamics of Duffing Oscillators

The intensive development of nanodevices acting as two-state systems has motivated the search for nanoscale molecular structures whose dynamics are similar to those of bistable mechanical systems, such as Euler arches and Duffing oscillators. Of particular interest are the molecular structures capable of spontaneous vibrations and stochastic resonance. Recently, oligomeric molecules that were a few nanometers in size and exhibited the bistable dynamics of an Euler arch were identified through molecular dynamics simulations of short fragments of thermo-responsive polymers subject to force loading. In this article, we present molecular dynamics simulations of short pyridine-furan springs a few nanometers in size and demonstrate the bistable dynamics of a Duffing oscillator with thermally-activated spontaneous vibrations and stochastic resonance

Data Set Modelability by QSAR

We introduce a simple MODelability Index (MODI) that estimates the feasibility of obtaining predictive QSAR models (Correct Classification Rate above 0.7) for a binary dataset of bioactive compounds. MODI is defined as an activity class-weighted ratio of the number of the nearest neighbor pairs of compounds with the same activity class versus the total number of pairs. The MODI values were calculated for more than 100 datasets and the threshold of 0.65 was found to separate non-modelable from the modelable datasets

Predicting Binding Affinity of CSAR Ligands Using Both Structure-Based and Ligand-Based Approaches

We report on the prediction accuracy of ligand-based (2D QSAR) and structure-based (MedusaDock) methods used both independently and in consensus for ranking the congeneric series of ligands binding to three protein targets (UK, ERK2, and CHK1) from the CSAR 2011 benchmark exercise. An ensemble of predictive QSAR models was developed using known binders of these three targets extracted from the publicly-available ChEMBL database. Selected models were used to predict the binding affinity of CSAR compounds towards the corresponding targets and rank them accordingly; the overall ranking accuracy evaluated by Spearman correlation was as high as 0.78 for UK, 0.60 for ERK2, and 0.56 for CHK1, placing our predictions in top-10% among all the participants. In parallel, MedusaDock designed to predict reliable docking poses was also used for ranking the CSAR ligands according to their docking scores; the resulting accuracy (Spearman correlation) for UK, ERK2, and CHK1 were 0.76, 0.31, and 0.26, respectively. In addition, performance of several consensus approaches combining MedusaDock and QSAR predicted ranks altogether has been explored; the best approach yielded Spearman correlation coefficients for UK, ERK2, and CHK1 of 0.82, 0.50, and 0.45, respectively. This study shows that (i) externally validated 2D QSAR models were capable of ranking CSAR ligands at least as accurately as more computationally intensive structure-based approaches used both by us and by other groups and (ii) ligand-based QSAR models can complement structure-based approaches by boosting the prediction performances when used in consensus