Transcription factor (TF) binding to DNA is fundamental for gene regulation. However, it remains unknown how the dynamics of TF-DNA interactions change during cell-fate determination in vivo. Here, we use photo-activatable FCS to quantify TF-DNA binding in single cells of developing mouse embryos. In blastocysts, the TFs Oct4 and Sox2, which control pluripotency, bind DNA more stably in pluripotent than in extraembryonic cells. By contrast, in the four-cell embryo, Sox2 engages in more long-lived interactions than does Oct4. Sox2 long-lived binding varies between blastomeres and is regulated by H3R26 methylation. Live-cell tracking demonstrates that those blastomeres with more long-lived binding contribute more pluripotent progeny, and reducing H3R26 methylation decreases long-lived binding, Sox2 target expression, and pluripotent cell numbers. Therefore, Sox2-DNA binding predicts mammalian cell fate as early as the four-cell stage. More generally, we reveal the dynamic repartitioning of TFs between DNA sites driven by physiological epigenetic changes. VIDEO ABSTRACT.

The hybrid simulation tools (QM/MM) evolved into a fundamental methodology for studying chemical reactivity in complex environments. This paper presents an implementation of electronic structure calculations based on density functional theory. This development is optimized for performing hybrid molecular dynamics simulations by making use of graphic processors (GPU) for the most computationally demanding parts (exchange-correlation terms). The proposed implementation is able to take advantage of modern GPUs achieving acceleration in relevant portions between 20 to 30 times faster than the CPU version. The presented code was extensively tested, both in terms of numerical quality and performance over systems of different size and composition.

Mesoporous oxide films are attractive frameworks in technological areas such as catalysis, sensing, environmental protection, and photovoltaics. Herein, we used fluorescence correlation spectroscopy to explore how the pore dimensions of hydrated TiO mesoporous calcined films modulate the molecular diffusion. Rhodamine B molecules in mesoporous films follow a Fickian process 2-3 orders slower compared to the probe in water. The mobility increases with the pore and neck radii reaching an approximately constant value for a neck radius >2.8 nm. However, the pore size does not control the dye diffusion at low ionic strength emphasizing the relevance of the probe interactions with the pore walls on dye mobility. In conclusion, our results show that the thermal conditioning of TiO mesoporous films provides an exceptional tool for controlling the pore and neck radii on the nanometer scale and has a major impact on molecular diffusion within the mesoporous network.

This paper presents a new model for polymersomes developed using a poly(ethylene oxide)-poly(butadiene) diblock copolymer bilayer. The model is based on a coarse-grained approach using the MARTINI force field. Since no MARTINI parameters exist for poly(butadiene), we have refined these parameters using quantum mechanical calculations and molecular dynamics simulations. The model has been validated using extensive molecular dynamics simulations in systems with several hundred polymer units and reaching up to 6 μs. These simulations show that the copolymer coarse grain model self-assemble into bilayers and that NPT and NPT ensemble runs reproduce key structural and mechanical experimental properties for different copolymer length chains with a similar hydrophilic weight fraction.

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Fluorescence correlation spectroscopy (FCS) methods are powerful tools for unveiling the dynamical organization of cells. For simple cases, such as molecules passively moving in a homogeneous media, FCS analysis yields analytical functions that can be fitted to the experimental data to recover the phenomenological rate parameters. Unfortunately, many dynamical processes in cells do not follow these simple models, and in many instances it is not possible to obtain an analytical function through a theoretical analysis of a more complex model. In such cases, experimental analysis can be combined with Monte Carlo simulations to aid in interpretation of the data. In response to this need, we developed a method called FERNET (Fluorescence Emission Recipes and Numerical routines Toolkit) based on Monte Carlo simulations and the MCell-Blender platform, which was designed to treat the reaction-diffusion problem under realistic scenarios. This method enables us to set complex geometries of the simulation space, distribute molecules among different compartments, and define interspecies reactions with selected kinetic constants, diffusion coefficients, and species brightness. We apply this method to simulate single- and multiple-point FCS, photon-counting histogram analysis, raster image correlation spectroscopy, and two-color fluorescence cross-correlation spectroscopy. We believe that this new program could be very useful for predicting and understanding the output of fluorescence microscopy experiments.

The problem of skill acquisition is ubiquitous and fundamental to life. Most tasks in modern society involve the cooperation with other subjects. Notwithstanding its fundamental importance, teammate selection is commonly overlooked when studying learning. We exploit the virtually infinite repository of human behavior available in Internet to study a relevant topic in anthropological science: how grouping strategies may affect learning. We analyze the impact of team play strategies in skill acquisition using a turn-based game where players can participate individually or in teams. We unveil a subtle but strong effect in skill acquisition based on the way teams are formed and maintained during time. “Faithfulness-boost effect” provides a skill boost during the first games that would only be acquired after thousands of games. The tendency to play games in teams is associated with a long-run skill improvement while playing loyally with the same teammate significantly accelerates short-run skill acquisition.