Deterministic walks in random networks: an application to thesaurus graphs

In a landscape composed of N randomly distributed sites in Euclidean space, a walker (``tourist'') goes to the nearest one that has not been visited in the last \tau steps. This procedure leads to trajectories composed of a transient part and a final cyclic attractor of period p. The tourist walk presents universal aspects with respect to \tau and can be done in a wide range of networks that can be viewed as ordinal neighborhood graphs. As an example, we show that graphs defined by thesaurus dictionaries share some of the statistical properties of low dimensional (d=2) Euclidean graphs and are easily distinguished from random graphs. This approach furnishes complementary information to the usual clustering coefficient and mean minimum separation length.Comment: 12 pages, 5 figures, revised version submited to Physica A, corrected references to figure

Towards updatable, multivalent Covid vaccines: A platform process to produce trimeric spike protein of SARS-COV-2 variants expressed in HEK293 stable cell clones

Within 2.5 years since SARS-COV-2 emergence, COVID-19 pandemic has caused more than 6.3 million registered deaths and 530 million registered cases. The quick development of safe and effective vaccines was very important to mitigate the sanitary crisis. However, the continuous emergence of virus variants with increasing transmissibility continues to cause periodic outbreaks worldwide. The original vaccines keep protecting from severe disease and death caused by variants, but not from transmission and mild disease. Thus, new and improved vaccines are necessary, and updatable, multivalent pan-variant vaccines might be one way to control SARS-COV-2. The spike (S) protein of SARS-COV-2, a highly glycosylated and very large protein (1380 amino acids), is a key target for diagnostics, therapeutics (e.g. monoclonal antibodies) and vaccines. Very early in the pandemic, Wrapp et al. (https://doi.org/10.1126/science.abb2507) produced the recombinant spike protein as a trimer stabilized in the prefusion conformation and determined its structure by cryoelectron microscopy, providing evidence that it binds to the ACE-2 receptor. The stabilized spike trimer forms the basis of most approved COVID vaccines, across vaccine platforms. In the present work, we studied the expression and purification of the trimeric prefusion-stabilized spike protein in HEK293 cell lines and developed a platform process applicable to SARS-COV-2 variants (current - and potentially future - ones). Parental HEK293 cells (NRC, Canada or Thermofisher, USA) were transfected by lipofection using Lipofectamine 3000 (Thermofisher Scientific, USA) with a plasmid containing the gene encoding the spike protein. At first, for the ancestral strain (Wuhan), we used a plasmid intended for transient expression kindly provided by VRC/NIAID/NIH (USA). However, for the variants, we ordered synthetic genes (Genscript, USA) that were subcloned in a plasmid intended for stable expression. After genetic modification, stably transfected cells were maintained in the presence of G418 sulfate selection agent. After 3-4 weeks, stable cell pools were obtained and submitted to single cell deposit (FACS Aria, BD Biosciences) in order to obtain clonally-derived cell lines. Documented research cell banks of selected clones were cryopreserved. Batch and fed-batch cultivations were investigated in shake flasks and bioreactors, using the chemically defined HEK TF culture medium and HEK FS feed solution (both Sartorius Xell, Germany). For protein purification, different chromatographic techniques were investigated using Akta Purifier and Akta Pilot systems. Detection of the spike protein secreted in cell culture supernatant was performed by immunoblot, whereas UV280 (Nanodrop, Thermofisher, USA) was used for protein quantitation in purified samples. After first expressing the spike protein in February 2020 by transient transfection, we developed a stable cell pool by co-transfecting the same transient expression plasmid and an empty stable expression plasmid. This stable cell pool allowed the generation of Wuhan protein that was used to develop serological tests and a hyperimmune equine serum (Cunha et al., doi: 10.1016/j.isci.2021.103315; Alvim et al., in press) and was donated so far to over 90 laboratories in Brazil for basic or applied research. Please click Download on the upper right corner to see the full abstract

Role of anisotropy, frequency, and interactions in magnetic hyperthermia applications: noninteracting nanoparticles and linear chain arrangements

Efforts by numerous research groups have provided a deeper insight into the physical mechanisms behind the power absorption of single-domain magnetic nanoparticles in magnetic-fluid-hyperthermia applications and theoretical models now account for the main experimental observations. However, the role of all parameters relevant to the magnetic relaxation remains a matter of debate. Here, we employ a nonlinear model for the magnetic relaxation of single-domain magnetic nanoparticles with uniaxial effective anisotropy and evaluate the influence of particle-intrinsic parameters as well as experimental conditions on the power absorption of both noninteracting and interacting systems (linear arrangements). These effects are assessed through the enclosed hysteresis area of the magnetization loops as a function of relative anisotropy hK (the anisotropy field with respect to the amplitude of the ac field), i.e., the "area curve"of the system. These curves can be divided into four regions with distinct magnetic responses and boundaries that depend on the particle size, frequency of the applied field and interactions. Interactions change the effective anisotropy of the system and shift the area curve towards lower hK values. For the low relative anisotropy range, dipolar interactions increase the area of the hysteresis loops [thus, the specific power absorption (SPA)], while they are detrimental or produce nonsignificant effects for the range of high relative anisotropy. Our study resolves seemingly contradictory results of interaction effects in linear arrangements recently reported in the literature. Simulations of randomly oriented particles and chains were contrasted with the oriented cases. An analytical approach and the thermal interpretation of its validity range are discussed, both aimed at the design of nanoparticles and the choice of the experimental conditions for optimal heating. We find that systems with low-thermal-fluctuation influence are better candidates for the application due to their high SPA values. © 2021 American Physical Society

In silico before in vivo: How to predict the heating efficiency of magnetic nanoparticles within the intracellular space

This work aims to demonstrate the need for in silico design via numerical simulation to produce optimal Fe 3 O 4 -based magnetic nanoparticles (MNPs) for magnetic hyperthermia by minimizing the impact of intracellular environments on heating efficiency. By including the relevant magnetic parameters, such as magnetic anisotropy and dipolar interactions, into a numerical model, the heating efficiency of as prepared colloids was preserved in the intracellular environment, providing the largest in vitro specific power absorption (SPA) values yet reported. Dipolar interactions due to intracellular agglomeration, which are included in the simulated SPA, were found to be the main cause of changes in the magnetic relaxation dynamics of MNPs under in vitro conditions. These results pave the way for the magnetism-based design of MNPs that can retain their heating efficiency in vivo, thereby improving the outcome of clinical hyperthermia experiments

Low-Dimensional Assemblies of Magnetic MnFe2O4 Nanoparticles and Direct In Vitro Measurements of Enhanced Heating Driven by Dipolar Interactions: Implications for Magnetic Hyperthermia

Magnetic fluid hyperthermia (MFH), the procedure of raising the temperature of tumor cells using magnetic nanoparticles (MNPs) as heating agents, has proven successful in treating some types of cancer. However, the low heating power generated under physiological conditions makes it necessary a high local concentration of MNPs at tumor sites. Here, we report how the in vitro heating power of magnetically soft MnFe2O4 nanoparticles can be enhanced by intracellular low-dimensional clusters through a strategy that includes: (a) the design of the MNPs to retain Neel magnetic relaxation in high-viscosity media, and (b) culturing MNP-loaded cells under magnetic fields to produce elongated intracellular agglomerates. Our direct in vitro measurements demonstrated that the specific loss power (SLP) of elongated agglomerates (SLP = 576 +/- 33 W/g) induced by culturing BV2 cells in situ under a dc magnetic field was increased by a factor of 2 compared to the SLP = 305 +/- 25 W/g measured in aggregates freely formed within cells. A numerical mean-field model that included dipolar interactions quantitatively reproduced the SLPs of these clusters both in phantoms and in vitro, suggesting that it captures the relevant mechanisms behind power losses under high-viscosity conditions. These results indicate that in situ assembling of MNPs into low-dimensional structures is a sound possible way to improve the heating performance in MFH

The relevance of Brownian relaxation as power absorption mechanism in Magnetic Hyperthermia

The Linear Response Theory (LRT) is a widely accepted framework to analyze the power absorption of magnetic nanoparticles for magnetic fluid hyperthermia. Its validity is restricted to low applied fields and/or to highly anisotropic magnetic nanoparticles. Here, we present a systematic experimental analysis and numerical calculations of the specific power absorption for highly anisotropic cobalt ferrite (CoFe 2 O 4 ) magnetic nanoparticles with different average sizes and in different viscous media. The predominance of Brownian relaxation as the origin of the magnetic losses in these particles is established, and the changes of the Specific Power Absorption (SPA) with the viscosity of the carrier liquid are consistent with the LRT approximation. The impact of viscosity on SPA is relevant for the design of MNPs to heat the intracellular medium during in vitro and in vivo experiments. The combined numerical and experimental analyses presented here shed light on the underlying mechanisms that make highly anisotropic MNPs unsuitable for magnetic hyperthermia

Contact angle measurement of free-standing square-millimeter single-layer graphene

Supramolecular & Biomaterials Chemistr

Graphene-stablized lipid monolayer heterostructures: a novel biomembrane superstructure

Supramolecular & Biomaterials Chemistr

Exploratory Behavior, Trap Models and Glass Transitions

A random walk is performed on a disordered landscape composed of $N$ sites randomly and uniformly distributed inside a $d$-dimensional hypercube. The walker hops from one site to another with probability proportional to $\exp [- \beta E(D)]$, where $\beta = 1/T$ is the inverse of a formal temperature and $E(D)$ is an arbitrary cost function which depends on the hop distance $D$. Analytic results indicate that, if $E(D) = D^{d}$ and $N \to \infty$, there exists a glass transition at $\beta_d = \pi^{d/2}/\Gamma(d/2 + 1)$. Below $T_d$, the average trapping time diverges and the system falls into an out-of-equilibrium regime with aging phenomena. A L\'evy flight scenario and applications to exploratory behavior are considered.Comment: 4 pages, 1 figure, new versio

Controlling the dominant magnetic relaxation mechanisms for magnetic hyperthermia in bimagnetic core-shell nanoparticles

We report a simple and effective way to control the heat generation of a magnetic colloid under alternate magnetic fields by changing the shell composition of bimagnetic core-shell Fe 3 O 4 /Zn x Co 1-x Fe 2 O 4 nanoparticles. The core-shell structure constitutes a magnetically-coupled biphase system, with an effective anisotropy that can be tuned by the substitution of Co 2+ by Zn 2+ ions in the shell. Magnetic hyperthermia experiments of nanoparticles dispersed in hexane and butter oil showed that the magnetic relaxation is dominated by Brown relaxation mechanism in samples with higher anisotropy (i.e., larger concentration of Co within the shell) yielding high specific power absorption values in low viscosity media as hexane. Increasing the Zn concentration of the shell, diminishes the magnetic anisotropy, which results in a change to a Néel relaxation that dominates the process when the nanoparticles are dispersed in a high-viscosity medium. We demonstrate that tuning the Zn contents at the shell of these exchange-coupled core/shell nanoparticles provides a way to control the magnetic anisotropy without loss of saturation magnetization. This ability is an essential prerequisite for most biomedical applications, where high viscosities and capturing mechanisms are present. This journal i