To distinguish between chemical bonding and physical binding is usually simple. They differ, in the normal case, in both interaction strength (binding energy) and interaction length (structure). ...However, chemical bonding can be weak (e.g. in some metallic bonding) and physical binding can be strong (e.g. due to permanent electrostatic moments, hydrogen binding, etc) making differentiation non-trivial. But since these are shared-electron or unshared-electron interactions, respectively, it is in principle possible to distinguish the type of interaction by analyzing the electron density around the interaction point(s)/interface. After all, the former should be a contact while the latter should be a tunneling barrier. Here, we investigate within the framework of density functional theory typical molecules and crystals to show the behaviour of the electron localization function (ELF) in different shared-electron interactions, such as chemical (covalent) and metallic bonding and compare to unshared-electron interactions typical for physical binding, such as ionic, hydrogen and Keesom, dispersion (van der Waals) binding and attempt to categorise them only by the ELF and the electron population in the interaction region. It is found that the ELF method is not only useful for the characterization of covalent bonds but a lot of information can be extracted also for weaker types of binding. Furthermore, the charge integration over the interaction region(s) and tracing the ELF profile can reveal the strength of the bonding/binding ranging from the triple bonds to weak dispersion.
Large-scale sequencing of RNA from individual cells can reveal patterns of gene, isoform and allelic expression across cell types and states
. However, current short-read single-cell RNA-sequencing ...methods have limited ability to count RNAs at allele and isoform resolution, and long-read sequencing techniques lack the depth required for large-scale applications across cells
. Here we introduce Smart-seq3, which combines full-length transcriptome coverage with a 5' unique molecular identifier RNA counting strategy that enables in silico reconstruction of thousands of RNA molecules per cell. Of the counted and reconstructed molecules, 60% could be directly assigned to allelic origin and 30-50% to specific isoforms, and we identified substantial differences in isoform usage in different mouse strains and human cell types. Smart-seq3 greatly increased sensitivity compared to Smart-seq2, typically detecting thousands more transcripts per cell. We expect that Smart-seq3 will enable large-scale characterization of cell types and states across tissues and organisms.
Mammalian gene expression is inherently stochastic
, and results in discrete bursts of RNA molecules that are synthesized from each allele
. Although transcription is known to be regulated by ...promoters and enhancers, it is unclear how cis-regulatory sequences encode transcriptional burst kinetics. Characterization of transcriptional bursting, including the burst size and frequency, has mainly relied on live-cell
or single-molecule RNA fluorescence in situ hybridization
recordings of selected loci. Here we determine transcriptome-wide burst frequencies and sizes for endogenous mouse and human genes using allele-sensitive single-cell RNA sequencing. We show that core promoter elements affect burst size and uncover synergistic effects between TATA and initiator elements, which were masked at mean expression levels. Notably, we provide transcriptome-wide evidence that enhancers control burst frequencies, and demonstrate that cell-type-specific gene expression is primarily shaped by changes in burst frequencies. Together, our data show that burst frequency is primarily encoded in enhancers and burst size in core promoters, and that allelic single-cell RNA sequencing is a powerful model for investigating transcriptional kinetics.
Attention deficit hyperactivity disorder (ADHD) frequently persists into adulthood. Family and twin studies delineate a disorder with strong genetic influences among children and adolescents based on ...parent- and teacher-reported data but little is known about the genetic and environmental contribution to DSM-IV ADHD symptoms in adulthood. We therefore aimed to investigate the impact of genetic and environmental influences on the inattentive and hyperactive-impulsive symptoms of ADHD in adults.
Twin methods were applied to self-reported assessments of ADHD symptoms from a large population-based Swedish twin study that included data from 15 198 Swedish male and female twins aged 20 to 46 years.
The broad heritability i.e., A + D, where A is an additive genetic factor and D (dominance) a non-additive genetic factor was 37% (A = 11%, D = 26%) for inattention and 38% (A = 18%, D = 20%) for hyperactivity-impulsivity. The results also indicate that 52% of the phenotypic correlation between inattention and hyperactivity-impulsivity (r = 0.43) was explained by genetic influences whereas the remaining part of the covariance was explained by non-shared environmental influences. These results were replicated across age strata.
Our findings of moderate broad heritability estimates are consistent with previous literature on self-rated ADHD symptoms in older children, adolescents and adults and retrospective reports of self-rated childhood ADHD by adults but differ from studies of younger children with informant ratings. Future research needs to clarify whether our data indicate a true decrease in the heritability of ADHD in adults compared to children, or whether this relates to the use of self-ratings in contrast to informant data.
Gas-sensing properties of nitrogenated holey graphene (C2N), graphdiyne (GDY) and their van der Waals heterostructure (C2N…GDY) have been studied towards particular volatile organic compounds (VOCs) ...by means of spin-polarized, dispersion-corrected DFT calculations. We find that VOCs such as acetone, ethanol, propanal, and toluene interact weakly with the GDY monolayer; however, the bindings are significantly enhanced with the C2N monolayer and the hybrid C2N…GDY heterostructure in AB stacking. Electron localization function (ELF) analysis shows that all VOCs are van der Waals bound (physical binding) to the 2D materials, which result in significant changes of the charge density of C2N and GDY monolayers and the C2N…GDY heterostructure. These changes alter the electronic properties of C2N and GDY, and the C2N…GDY heterostructure, upon VOC adsorption, which are investigated by density-of-states plots. We further apply thermodynamic analysis to study the sensing characteristics of VOCs under varied conditions of pressure and temperature. Our findings clearly indicate that the C2N…GDY heterostructure is a promising material for sensing of certain VOCs.
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Density functional theory is used to show that the adhesion between single-walled carbon nanotubes (SWNTs) and the catalyst particles from which they grow needs to be strong to support nanotube ...growth. It is found that Fe, Co, and Ni, commonly used to catalyze SWNT growth, have larger adhesion strengths to SWNTs than Cu, Pd, and Au and are therefore likely to be more efficient for supporting growth. The calculations also show that to maintain an open end of the SWNT it is necessary that the SWNT adhesion strength to the metal particle is comparable to the cap formation energy of the SWNT end. This implies that the difference between continued and discontinued SWNT growth to a large extent depends on the carbon−metal binding strength, which we demonstrate by molecular dynamics (MD) simulations. The results highlight that first principles computations are vital for the understanding of the binding strength's role in the SWNT growth mechanism and are needed to get accurate force field parameters for MD.
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•The new types of 2D transition metal carbide and nitride electrode materials with high stability and capacity are needed.•Exhibits ultra-low energy barriers of 0.1 and 0.01 eV for Li ...and Na, respectively.•Demonstrate excellent cycle stability, restoring its initial state within a mere 2.5 picoseconds.•Exhibits storage capacity of 379.88 mAh.g−1 for both Li and Na, respectively.
We present first-principles insights into the electrical and electrochemical properties of Cu2N, a newly synthesized two-dimensional material that features a planar, checkerboard lattice structure Hu et al., Nano Lett. 2023, 23 (12), 5610–5616. We evaluate the suitability of monolayer Cu2N as an anode material for Li and Na-ion batteries by examining its storage capacity, diffusion barrier, open-circuit voltage (OCV), volume expansion, and the impact of defects on its electrochemical performance. The monolayer Cu2N demonstrates a storage capacity of 379.88 mAh.g−1 for both Li and Na, comparable to that of commercial graphite for Li (372 mAh.g−1) and significantly higher for Na (less than 35 mAh.g−1). The migration barriers for Li and Na are found to be 0.1 eV and 0.01 eV, respectively, substantially lower than those theoretically reported for commercial anodes TiO2 (0.4–1.0 eV) and graphite (∼0.4 eV), which imply that monolayer Cu2N demonstrates excellent charge/discharge capabilities. Moreover, the volume growth of monolayer Cu2N is 4.14 % with maximal Li adsorption, which is 2.4 times less than graphite. The analysis of vacancy defects reveals a significant enhancement in the binding energies of Li and Na atoms, accompanied by minimal changes in diffusion barriers. Since monolayer Cu2N has already been successfully synthesized, these findings would pave the way for large-scale experimental fabrication of monolayer Cu2N as a battery anode.
Ohno's hypothesis postulates that upregulation of X-linked genes rectifies their dosage imbalance relative to autosomal genes, which are present in two active copies per cell. Here we have dissected ...X-chromosome upregulation into the kinetics of transcription, inferred from allele-specific single-cell RNA sequencing data from somatic and embryonic mouse cells. We confirmed increased X-chromosome expression levels in female and male cells and found that the X chromosome achieved upregulation by elevated burst frequencies. By monitoring transcriptional kinetics in differentiating female mouse embryonic stem cells, we found that increased burst frequency was established on the active X chromosome when X inactivation took place on the other allele. Thus, our study provides mechanistic insights into X-chromosome upregulation.
We report first-principle calculations of the recently synthesized Pb-free double perovskite Cs2PtI6, which we found to have the potential to be an excellent thermoelectric material, through the ...investigation of its electronic and phonon transport properties. The Heyd–Scuseria–Ernzerhof functional results in an indirect band gap of 1.40 eV, perfectly matching the experiment. Our well-converged phonon dispersion displays positive frequencies in the entire Brillouin zone and hence confirms the dynamic stability of the material. Further, the low-lying optical modes mix significantly with the heat-carrying acoustic phonons and add to their scattering phase space. We have found strong phonon anharmonicity due to the nonsymmetric and nonspherical electron densities of the atoms derived from their bonding environment, which in combination with low group velocities and high phonon scattering rates results in ultralow lattice thermal conductivity in Cs2PtI6. For example, it is 0.15 W/mK at 300 K, which is 8-fold smaller than that reported for the typical thermoelectric material Bi2Te3. Our simulations show that it could be reduced by another factor of 2 by nanostructuring the material with features of around 8 nm. We have found a remarkably high p-type Seebeck coefficient of 139 μV/K at the maximum considered carrier concentration and temperature. Our calculations also find a high figure of merit of 1.03 for the p-type carriers at room temperature, attributed to the substantial thermoelectric coefficient S 2σ/τ, where S, σ, and τ are the Seebeck coefficient, the electrical conductivity, and the relaxation time, respectively.
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