Seeking Solvation: Exploring the Role of Protein Hydration in Silk Gelation

The mechanism by which arthropods (e.g., spiders and many insects) can produce silk fibres from an aqueous protein (fibroin) solution has remained elusive, despite much scientific investigation. In this work, we used several techniques to explore the role of a hydration shell bound to the fibroin in native silk feedstock (NSF) from Bombyx mori silkworms. Small angle X-ray and dynamic light scattering (SAXS and DLS) revealed a coil size (radius of gyration or hydrodynamic radius) around 12 nm, providing considerable scope for hydration. Aggregation in dilute aqueous solution was observed above 65 °C, matching the gelation temperature of more concentrated solutions and suggesting that the strength of interaction with the solvent (i.e., water) was the dominant factor. Infrared (IR) spectroscopy indicated decreasing hydration as the temperature was raised, with similar changes in hydration following gelation by freezing or heating. It was found that the solubility of fibroin in water or aqueous salt solutions could be described well by a relatively simple thermodynamic model for the stability of the protein hydration shell, which suggests that the affected water is enthalpically favoured but entropically penalised, due to its reduced (vibrational or translational) dynamics. Moreover, while the majority of this investigation used fibroin from B. mori, comparisons with published work on silk proteins from other silkworms and spiders, globular proteins and peptide model systems suggest that our findings may be of much wider significance.

The pitfalls of inferring virus–virus interactions from co-detection prevalence data: application to influenza and SARS-CoV-2

There is growing experimental evidence that many respiratory viruses—including influenza and SARS-CoV-2—can interact, such that their epidemiological dynamics may not be independent. To assess these interactions, standard statistical tests of independence suggest that the prevalence ratio—defined as the ratio of co-infection prevalence to the product of single-infection prevalences—should equal unity for non-interacting pathogens. As a result, earlier epidemiological studies aimed to estimate the prevalence ratio from co-detection prevalence data, under the assumption that deviations from unity implied interaction. To examine the validity of this assumption, we designed a simulation study that built on a broadly applicable epidemiological model of co-circulation of two emerging or seasonal respiratory viruses. By focusing on the pair influenza–SARS-CoV-2, we first demonstrate that the prevalence ratio systematically underestimates the strength of interaction, and can even misclassify antagonistic or synergistic interactions that persist after clearance of infection. In a global sensitivity analysis, we further identify properties of viral infection—such as a high reproduction number or a short infectious period—that blur the interaction inferred from the prevalence ratio. Altogether, our results suggest that ecological or epidemiological studies based on co-detection prevalence data provide a poor guide to assess interactions among respiratory viruses.

Finite State Graphon Games with Applications to Epidemics

We consider a game for a continuum of non-identical players evolving on a finite state space. Their heterogeneous interactions are represented with a graphon, which can be viewed as the limit of a dense random graph. A player’s transition rates between the states depend on their control and the strength of interaction with the other players. We develop a rigorous mathematical framework for the game and analyze Nash equilibria. We provide a sufficient condition for a Nash equilibrium and prove existence of solutions to a continuum of fully coupled forward-backward ordinary differential equations characterizing Nash equilibria. Moreover, we propose a numerical approach based on machine learning methods and we present experimental results on different applications to compartmental models in epidemiology.

Noninertial effects on a composite system

In this paper, we investigate the relativistic dynamics of a fermion–antifermion pair holding through Dirac oscillator interaction in the rotating frame of [Formula: see text]-dimensional topological defect-generated geometric background. We obtain an exact energy spectrum for the system in question by solving the corresponding form of a fully covariant two-body Dirac equation. This energy spectrum depends on the angular velocity [Formula: see text] of uniformly rotating frame and angular deficit [Formula: see text] in the geometric background. Our results show that the effects of [Formula: see text] on each energy level of the system are not same and the [Formula: see text] impacts on the strength of interaction between the particles. Furthermore, we observe that it seems to be possible to actively tune the dynamics of such a fermion–antifermion system, in principle.

DNA-Based Electrodes and Computational Approaches on the Intercalation Study of Antitumoral Drugs

The binding between anticancer drugs and double-stranded DNA (dsDNA) is a key issue to understand their mechanism of action, and many chemical methods have been explored on this task. Molecular docking techniques successfully predict the affinity of small molecules into the DNA binding sites. In turn, various DNA-targeted drugs are electroactive; in this regard, their electrochemical behavior may change according to the nature and strength of interaction with DNA. A carbon paste electrode (CPE) modified with calf thymus ds-DNA (CPDE) and computational methods were used to evaluate the drug–DNA intercalation of doxorubicin (DOX), daunorubicin (DAU), idarubicin (IDA), dacarbazine (DAR), mitoxantrone (MIT), and methotrexate (MTX), aiming to evaluate eventual correlations. CPE and CPDE were immersed in pH 7 0.1 mM solutions of each drug with different incubation times. As expected, the CPDE response for all DNA-targeted drugs was higher than that of CPE, evidencing the drug–DNA interaction. A peak current increase of up to 10-fold was observed; the lowest increase was seen for MTX, and the highest increase for MIT. Although this increase in the sensitivity is certainly tied to preconcentration effects of DNA, the data did not agree entirely with docking studies, evidencing the participation of other factors, such as viscosity, interfacial electrostatic interactions, and coefficient of diffusion.

THE RELATIONSHIP BETWEEN COGNITIVE-LINGUISTIC TASK DIFFICULTY AND L1-L2 INTERACTION FOR ACADEMIC LISTENING COMPREHENSION IN TURKISH–DUTCH EMERGENT BILINGUALS

This study investigated the relationship between the level of cognitive-linguistic difficulty of task input and the size of the cross-linguistic relationship for academic listening comprehension in emergent bilinguals. It was theoretically motivated by task-dependent cross-linguistic interaction frameworks. We hypothesized that task item sets that involve a higher level of cognitive-linguistic difficulty, drawing on a number of sources of item difficulty, would show a smaller strength of interaction than sets involving a lower level. Using a task-based assessment instrument, listening comprehension was measured in 75 Turkish–Dutch bilingual children at first-grade entry (Mage = 6;7). Partial L1-L2 correlations indicated that cognitively more demanding item sets tended to coincide with smaller L1-L2 correlations. This finding was, in part, consistent for cognitive difficulty, yet inconclusive for linguistic difficulty. An explanation is discussed that, in line with information-processing theory, highlights a trade-off between cognitive-linguistic task demands and cross-linguistic influence.

Impact of Magnesium Salt on the Mechanical and Thermal Properties of Poly(vinyl alcohol)

The effects of magnesium salts with various anion species on the structure and properties of a poly(vinyl alcohol) (PVA) film were studied. The glass transition temperature of the PVA film increased following the addition of a magnesium salt. Furthermore, the salt greatly enhanced the modulus and yield stress and reduced the crystallinity of the film. These effects were attributed to the strong ion–dipole interactions between the magnesium salts and the PVA chains. The strength of interaction, i.e., the reduction of segmental motions, depended on the anion species in the following order: Mg(ClO4)2, MgBr2, MgCl2, Mg(CH3COO)2, and MgSO4. The order corresponded to the Hofmeister series, which predicts the ability to break the structure of water.

Comparing Dimerization Free Energies and Binding Modes of Small Aromatic Molecules with Different Force Fields

Dimerization free energies are fundamental quantities that describe the strength of interaction of different molecules. Obtaining accurate experimental values for small molecules and disentangling the conformations that contribute most to the binding can be extremely difficult, due to the size of the systems and the small energy differences. In many cases, one has to resort to computational methods to calculate such properties. In this work, we used molecular dynamics simulations in conjunction with metadynamics to calculate the free energy of dimerization of small aromatic rings, and compared three models from popular online servers for atomistic force fields, namely G54a7, CHARMM36 and OPLS. We show that, regardless of the force field, the profiles for the dimerization free energy of these compounds are very similar. However, significant care needs to be taken when studying larger molecules, since the deviations from the trends increase with the size of the molecules, resulting in force field dependent preferred stacking modes; for example, in the cases of pyrene and tetracene. Our results provide a useful background study for using topology builders to model systems which rely on stacking of aromatic moieties, and are relevant in areas ranging from drug design to supramolecular assembly.

Evaluation of viscosity in binary mixtures of dimethyl sulphoxide at 298.15K

The viscosity of binary mixtures of dimethyl sulphoxide with different alcohols such as methanol, ethanol, 1-propanol, iso-propanol, 1-butanol, iso-butanol, tertiary butanol has been determined at 298.15K. The experimental values are compared with theoretical values evaluated by different theories. It is observed that for some theories, values are in agreement with the experimental values. Further, an attempt has been made to study the intermolecular interactions in studied solutions in terms of excess free energy of mixing, strength of interaction parameters and interaction energy. The viscosity data of pure liquids and their mixtures are needed to design various chemical processes where heat and mass transfer are important.

Theoretical study of the adsorption of BMSF-BENZ drug for osteoporosis disease treatment on Al-doped carbon nanotubes (Al-CNT) as a drug delivery vehicle

The adsorption energy of the BMSF-BENZ adsorbed complexes was investigated to understand the non-local dispersion interactions, with many other chemical parameters related to this subject like HOMO and LUMO, energy gap, and the time needed for the BMSF-BENZ to be desorbed from the nanotube (recovery time). Our study reveals that Al-CNT is a promising adsorbent for this drug as Eads of BMSF-BENZ/Al-CNT complexes are -22.09, -38.68, -12.89, -31.01, -27.31, -21.90, and -21.42 kcal/mol in the gas phase on the active atoms of the BMSF BENZ (Br, N8, N9, N58, O35, O41, and S), respectively. In addition, the spontaneous and favorable interaction between the BMSF BENZ and all nanoparticles was confirmed by investigating Gibbs free energy and quantum theory of atoms in molecule analysis (QTAIM) so that it can be used as an electrochemical sensor or biosensor. Furthermore, to more visualize the nature of intermolecular bonding and the strength of interaction between the BMSF-BENZ drug molecule and the nanotube, QTAIM has been widely studied in the case of drug delivery purposes. Al-CNT (4,0) can be extended as a drug delivery system and the work function type sensor.