Dynamic Transformations of Genome-wide Epigenetic Marking and Transcriptional Control Establish T Cell Identity

T cell development comprises a stepwise process of commitment from a multipotent precursor. To define molecular mechanisms controlling this progression, we probed five stages spanning the commitment process using RNA-seq and ChIP-seq to track genome-wide shifts in transcription, cohorts of active transcription factor genes, histone modifications at diverse classes of cis-regulatory elements, and binding repertoire of GATA-3 and PU.1, transcription factors with complementary roles in T cell development. The results highlight potential promoter-distal cis-regulatory elements in play and reveal both activation sites and diverse mechanisms of repression that silence genes used in alternative lineages. Histone marking is dynamic and reversible, and though permissive marks anticipate, repressive marks often lag behind changes in transcription. In vivo binding of PU.1 and GATA-3 relative to epigenetic marking reveals distinctive factor-specific rules for recruitment of these crucial transcription factors to different subsets of their potential sites, dependent on dose and developmental context

Atomistic modeling of the mechanical properties: the rise of machine learning interatomic potentials

Since the birth of the concept of machine learning interatomic potentials (MLIPs) in 2007, a growing interest has been developed in the replacement of empirical interatomic potentials (EIPs) with MLIPs, in order to conduct more accurate and reliable molecular dynamics calculations. As an exciting novel progress, in the last couple of years the applications of MLIPs have been extended towards the analysis of mechanical and failure responses, providing novel opportunities not heretofore efficiently achievable, neither by EIPs nor by density functional theory (DFT) calculations. In this minireview, we first briefly discuss the basic concepts of MLIPs and outline popular strategies for developing a MLIP. Next, by considering several examples of recent studies, the robustness of MLIPs in the analysis of the mechanical properties will be highlighted, and their advantages over EIP and DFT methods will be emphasized. MLIPs furthermore offer astonishing capabilities to combine the robustness of the DFT method with continuum mechanics, enabling the first-principles multiscale modeling of mechanical properties of nanostructures at the continuum level. Last but not least, the common challenges of MLIP-based molecular dynamics simulations of mechanical properties are outlined and suggestions for future investigations are proposed

Machine-Learning Interatomic Potentials Enable First-Principles Multiscale Modeling of Lattice Thermal Conductivity in Graphene/Borophene Heterostructures

One of the ultimate goals of computational modeling in condensed matter is to be able to accurately compute materials properties with minimal empirical information. First-principles approaches such as the density functional theory (DFT) provide the best possible accuracy on electronic properties but they are limited to systems up to a few hundreds, or at most thousands of atoms. On the other hand, classical molecular dynamics (CMD) simulations and finite element method (FEM) are extensively employed to study larger and more realistic systems, but conversely depend on empirical information. Here, we show that machine-learning interatomic potentials (MLIPs) trained over short ab-initio molecular dynamics trajectories enable first-principles multiscale modeling, in which DFT simulations can be hierarchically bridged to efficiently simulate macroscopic structures. As a case study, we analyze the lattice thermal conductivity of coplanar graphene/borophene heterostructures, recently synthesized experimentally (Sci. Adv. 2019; 5: eaax6444), for which no viable classical modeling alternative is presently available. Our MLIP-based approach can efficiently predict the lattice thermal conductivity of graphene and borophene pristine phases, the thermal conductance of complex graphene/borophene interfaces and subsequently enable the study of effective thermal transport along the heterostructures at continuum level. This work highlights that MLIPs can be effectively and conveniently employed to enable first-principles multiscale modeling via hierarchical employment of DFT/CMD/FEM simulations, thus expanding the capability for computational design of novel nanostructures

First-Principles Multiscale Modeling of Mechanical Properties in Graphene/Borophene Heterostructures Empowered by Machine-Learning Interatomic Potentials

Density functional theory calculations are robust tools to explore the mechanical properties of pristine structures at their ground state but become exceedingly expensive for large systems at finite temperatures. Classical molecular dynamics (CMD) simulations offer the possibility to study larger systems at elevated temperatures, but they require accurate interatomic potentials. Herein the authors propose the concept of first-principles multiscale modeling of mechanical properties, where ab initio level of accuracy is hierarchically bridged to explore the mechanical/failure response of macroscopic systems. It is demonstrated that machine-learning interatomic potentials (MLIPs) fitted to ab initio datasets play a pivotal role in achieving this goal. To practically illustrate this novel possibility, the mechanical/failure response of graphene/borophene coplanar heterostructures is examined. It is shown that MLIPs conveniently outperform popular CMD models for graphene and borophene and they can evaluate the mechanical properties of pristine and heterostructure phases at room temperature. Based on the information provided by the MLIP-based CMD, continuum models of heterostructures using the finite element method can be constructed. The study highlights that MLIPs were the missing block for conducting first-principles multiscale modeling, and their employment empowers a straightforward route to bridge ab initio level accuracy and flexibility to explore the mechanical/failure response of nanostructures at continuum scale

Highly anisotropic mechanical and optical properties of 2D NbOX2 (X = Cl, Br, I) revealed by first-principle

In the latest experimental success, NbOI2 two-dimensional (2D) crystals with anisotropic electronic and optical properties have been fabricated (Adv. Mater. 33 (2021), 2101505). In this work inspired by the aforementioned accomplishment, we conduct first-principles calculations to explore the mechanical, electronic, and optical properties of NbOX2 (X = Cl, Br, I) nanosheets. We show that individual layers in these systems are weakly bonded, with exfoliation energies of 0.22, 0.23, and 0.24 J m-2, for the isolation of the NbOCl2, NbOBr2, and NbOI2 monolayers, respectively, distinctly lower than those of the graphene. The optoelectronic properties of the single-layer, bilayer, and bulk NbOCl2, NbOBr2, and NbOI2 crystals are investigated via density functional theory calculations with the HSE06 approach. Our results indicate that the layered bulk NbOCl2, NbOBr2, and NbOI2 crystals are indirect gap semiconductors, with band gaps of 1.79, 1.69, and 1.60 eV, respectively. We found a slight increase in the electronic gap for the monolayer and bilayer systems due to electron confinement at the nanoscale. Our results show that the monolayer and bilayer of these novel 2D compounds show suitable valence and conduction band edge positions for visible-light-driven water splitting reactions. The first absorption peaks of these novel monolayers along the in-plane polarization are located in the visible range of light which can be a promising feature to design advanced nanoelectronics. We found that the studied 2D systems exhibit highly anisotropic mechanical and optical properties. The presented first-principles results provide a comprehensive vision about direction-dependent mechanical and optical properties of NbOX2 (X = Cl, Br, I) nanosheets

Electronic, Optical, Mechanical and Li-Ion Storage Properties of Novel Benzotrithiophene-Based Graphdiyne Monolayers Explored by First Principles and Machine Learning

Recently, benzotrithiophene graphdiyne (BTT-GDY), a novel two-dimensional (2D) carbon-based material, was grown via a bottom-up synthesis strategy. Using the BTT-GDY lattice and by replacing the S atoms with N, NH and O, we designed three novel GDY lattices, which we named BTHP-, BTP- and BTF-GDY, respectively. Next, we explored structural, electronic, mechanical, optical, photocatalytic and Li-ion storage properties, as well as carrier mobilities, of novel GDY monolayers. Phonon dispersion relations, mechanical and failure behavior were explored using the machine learning interatomic potentials (MLIPs). The obtained HSE06 results reveal that BTX-GDYs (X = P, F, T) are direct gap semiconductors with band gaps in the range of 2.49–2.65 eV, whereas the BTHP-GDY shows a narrow indirect band gap of 0.06 eV. With appropriate band offsets, good carrier mobilities and a strong capability for the absorption of visible and ultraviolet range of light, BTF- and BTT-GDYs were predicted to be promising candidates for overall photocatalytic water splitting. The BTHP-GDY nanosheet, noticeably, was found to yield an ultrahigh Li-ion storage capacity of over 2400 mAh/g. The obtained findings provide a comprehensive vision of the critical physical properties of the novel BTT-based GDY nanosheets and highlight their potential for applications in nanoelectronics and energy storage and conversion systems