Accurate modeling of image formation in cryo-electron microscopy is an important requirement for quantitative image interpretation and optimization of the data acquisition strategy. Here we present a ...forward model that accounts for the specimen’s scattering properties, microscope optics, and detector response. The specimen interaction potential is calculated with the isolated atom superposition approximation (IASA) and extended with the influences of solvent’s dielectric and ionic properties as well as the molecular electrostatic distribution. We account for an effective charge redistribution via the Poisson–Boltzmann approach and find that the IASA-based potential forms the dominant part of the interaction potential, as the contribution of the redistribution is less than 10%. The electron wave is propagated through the specimen by a multislice approach and the influence of the optics is included via the contrast transfer function. We incorporate the detective quantum efficiency of the camera due to the difference between signal and noise transfer characteristics, instead of using only the modulation transfer function. The full model was validated against experimental images of 20S proteasome, hemoglobin, and GroEL. The simulations adequately predict the effects of phase contrast, changes due to the integrated electron flux, thickness, inelastic scattering, detective quantum efficiency and acceleration voltage. We suggest that beam-induced specimen movements are relevant in the experiments whereas the influence of the solvent amorphousness can be neglected. All simulation parameters are based on physical principles and, when necessary, experimentally determined.
► New, improved potential for the Al–O system. ► Charge transfer. ► Fits to a large database of Al
x
O
y
structures.
Molecular dynamics (MD) simulations of aluminum oxide material and the aluminum ...oxidation process require a sufficiently sophisticated and well-calibrated potential, one that takes into account locally varying Al/O ratios and adaptive charge transfer between Al and O atoms. In this work we show that the Charge Transfer Ionic Potential (CTIP) by Zhou et al. X.W. Zhou, H.N.G. Wadley, J.-S. Filhol, M.N. Neurock, Phys. Rev. B 69 (2004) 035402 in combination with a new, “Reference Free” version of the Modified Embedded Atom Method (RFMEAM) potential performs well for this purpose. This new potential has been parameterized by systematically fitting it to a large database of different Al
x
O
y
crystal energies, over a range of lattice constants and elastic deformations, using a recent method which separates the electrostatic and non-electrostatic fitting steps. The resulting potential yields more realistic atomic charges, crystal energies and lattice constants than earlier potentials. In particular, we show that the angular forces in the MEAM part are essential for α-Al
2O
3 to be the lowest-energy aluminum oxide. We compare the performance of our potential with the potential of Zhou et al., which lacks angular forces and was parameterized using a less involved fitting procedure, and show the results of a few molecular dynamics simulations. The two-step fitting method is generally applicable and can be adopted for constructing potentials for other metal–oxide systems.
We investigated SEM imaging of nanoparticle biomarkers suspended below a thin membrane, with the ultimate goal of integrating functional fluorescence and structural SEM measurements of samples kept ...at ambient or hydrated conditions. In particular, we investigated how resolving power in liquid SEM is affected by the interaction of the electron beam with the membrane. Simulations with the Geant4-based Monte Carlo scheme developed by Kieft and Bosch (2008) 1 are compared to experimental results with suspended nanoparticles. For 20nm and 50nm thin membranes, we found a beam broadening of 1.5nm and 3nm, respectively, with an excellent agreement between simulations and experiments. 15nm Au nanoparticles and bio-functionalized core-shell quantum dots can be individually resolved in denser clusters. We demonstrated the imaging of single EGF-conjugated quantum dots docked at filopodia during cellular uptake with both fluorescence microscopy and SEM simultaneously. These results open novel opportunities for correlating live fluorescence microscopy with structural electron microscopy.
•We investigate the achievable resolution in liquid scanning electron microscopy (SEM).•We demonstrate liquid SEM imaging of individual fluorescent nanoparticle bio-markers•We show imaging of cellular QDot uptake with simultaneous fluorescence microscopy and SEM.•The positions of individual QDots can be resolved with details on cellular structure.
Apnea and other breathing-related disorders have been linked to the development of hypertension or impairments of the cardiovascular, cognitive or metabolic systems. The combined assessment of ...multiple physiological signals acquired during sleep is of fundamental importance for providing additional insights about breathing disorder events and the associated impairments. In this work, we apply information-theoretic measures to describe the joint dynamics of cardiorespiratory physiological processes in a large group of patients reporting repeated episodes of hypopneas, apneas (central, obstructive, mixed) and respiratory effort related arousals (RERAs). We analyze the heart period as the target process and the airflow amplitude as the driver, computing the predictive information, the information storage, the information transfer, the internal information and the cross information, using a fuzzy kernel entropy estimator. The analyses were performed comparing the information measures among segments during, immediately before and after the respiratory event and with control segments. Results highlight a general tendency to decrease of predictive information and information storage of heart period, as well as of cross information and information transfer from respiration to heart period, during the breathing disordered events. The information-theoretic measures also vary according to the breathing disorder, and significant changes of information transfer can be detected during RERAs, suggesting that the latter could represent a risk factor for developing cardiovascular diseases. These findings reflect the impact of different sleep breathing disorders on respiratory sinus arrhythmia, suggesting overall higher complexity of the cardiac dynamics and weaker cardiorespiratory interactions which may have physiological and clinical relevance.
Scanning transmission electron microscopy (STEM) techniques reveal atomic-resolution details of organic and inorganic materials. The application of STEM to biological vitrified specimens under ...low-dose cryogenic imaging conditions demonstrates that STEM also achieves near-atomic-resolution 3D structures of biological macromolecules.
The increasing availability of time series data depicting the evolution of physical system properties has prompted the development of methods focused on extracting insights into the system behavior ...over time, discerning whether it stems from deterministic or stochastic dynamical systems. Surrogate data testing plays a crucial role in this process by facilitating robust statistical assessments. This ensures that the observed results are not mere occurrences by chance, but genuinely reflect the inherent characteristics of the underlying system. The initial process involves formulating a null hypothesis, which is tested using surrogate data in cases where assumptions about the underlying distributions are absent. A discriminating statistic is then computed for both the original data and each surrogate data set. Significantly deviating values between the original data and the surrogate data ensemble lead to the rejection of the null hypothesis. In this work, we present various surrogate methods designed to assess specific statistical properties in random processes. Specifically, we introduce methods for evaluating the presence of autodependencies and nonlinear dynamics within individual processes, using Information Storage as a discriminating statistic. Additionally, methods are introduced for detecting coupling and nonlinearities in bivariate processes, employing the Mutual Information Rate for this purpose. The surrogate methods introduced are first tested through simulations involving univariate and bivariate processes exhibiting both linear and nonlinear dynamics. Then, they are applied to physiological time series of Heart Period (RR intervals) and respiratory flow (RESP) variability measured during spontaneous and paced breathing. Simulations demonstrated that the proposed methods effectively identify essential dynamical features of stochastic systems. The real data application showed that paced breathing, at low breathing rate, increases the predictability of the individual dynamics of RR and RESP and dampens nonlinearity in their coupled dynamics.
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