DNA groove preference shift upon phosphorylation of a protamine-like cationic peptide

Protamines, arginine-rich DNA-binding proteins, are responsible for chromatin compaction in sperm cells, but their DNA groove preference, major or minor, is not clearly identified. We herein study the DNA groove preference of a short protamine-like cationic peptide before and after phosphorylation, using all-atom molecular dynamics and umbrella sampling simulations. According to various thermodynamic and structural analyses, a peptide in its non-phosphorylated native state prefers the minor groove over the major groove, but phosphorylation of the peptide bound to the minor groove not only reduces its binding affinity but also brings a serious deformation of the minor groove, eliminating the minor-groove preference. As protamines are heavily phosphorylated before binding to DNA, we expect that the structurally disordered phosphorylated protamines would prefer major grooves to enter into DNA during spermatogenesis.

Corrosion-driven droplet wetting on iron nanolayers

The classical Evans' drop describes a drop of aqueous salt solution, placed on a bulk metal surface where it displays a corrosion pit that grows over time producing further oxide deposits from the metal dissolution. We focus here on the corrosion-induced droplet spreading using iron nanolayers whose semi-transparency allowed us to monitor both iron corrosion propagation and electrolyte droplet behavior by simple optical means. We thus observed that pits grow under the droplet and merge into a corrosion front. This front reached the triple contact line and drove a non radial spreading, until it propagated outside the immobile droplet. Such chemically-active wetting is only observed in the presence of a conductive substrate that provides strong adhesion of the iron nanofilm to the substrate. By revisiting the classic Evan's drop experiment on thick iron film, a weaker corrosion-driven droplet spreading is also identified. These results require further investigations, but they clearly open up new perspectives on substrate wetting by corrosion-like electrochemical reactions at the nanometer scale.

DNA-protamine condensates under low salt conditions: molecular dynamics simulation with a simple coarse-grained model focusing on electrostatic interactions

Protamine, a small, strongly positively-charged protein, plays a key role in achieving chromatin condensation inside sperm cells and is also involved in the formulation of nanoparticles for gene therapy and packaging of mRNA-based vaccines against viral infection and cancer. The detailed mechanisms of such condensations are still poorly understood especially under low salt conditions where electrostatic interaction predominates. Our previous study, with a refined coarse-grained model in full consideration of the long-range electrostatic interactions, has demonstrated the crucial role of electrostatic interaction in protamine-controlled reversible DNA condensation. Therefore, we herein pay our attention only to the electrostatic interaction and devise a coarser-grained bead-spring model representing the right linear charge density on protamine and DNA chains but treating other short-range interactions as simply as possible, which would be suitable for real-scale simulations. Effective pair potential calculations and large-scale molecular dynamics simulations using this extremely simple model reproduce the phase behaviour of DNA in a wide range of protamine concentrations under low salt conditions, again revealing the importance of the electrostatic interaction in this process and providing a detailed nanoscale picture of bundle formation mediated by a charge disproportionation mechanism. Our simulations also show that protamine length alters DNA overcharging and in turn redissolution thresholds of DNA condensates, revealing the important role played by entropies and correlated fluctuations of condensing agents and thus offering an additional opportunity to design tailored nanoparticles for gene therapy. The control mechanism of DNA-protamine condensates will also provide a better microscopic picture of biomolecular condensates, i.e., membraneless organelles arising from liquid-liquid phase separation, that are emerging as key principles of intracellular organization. Such condensates controlled by post-translational modification of protamine, in particular phosphorylation, or by variations in protamine length from species to species may also be responsible for the chromatin-nucleoplasm patterning observed during spermatogenesis in several vertebrate and invertebrate species.

Protic Ionic Liquids for Intrinsically Stretchable Conductive Polymers

Inspired by the classic hard-soft acid-base theory and intrigued by a theoretical prediction of spontaneous ion exchange between poly(3,4-ethylenedioxythiophene):poly(styrenesulfonate) (PEDOT:PSS) and hard-cation-soft-anion ionic liquid (IL), we treat PEDOT:PSS with a new IL composed of a protic (i.e., extremely hard) cation (3-methylimidazolium, p-MIM⁺) and an extremely soft anion (tetracyanoborate, TCB^-). In fact, this protic IL (p-MIM:TCB) accomplishes the same levels of ion-exchange-mediated PEDOT-PSS separation, PEDOT-rich nanofibril formation, and electrical conductivity enhancement (∼2500 S/cm) as its aprotic counterpart (EMIM:TCB with 1-ethyl-3-methylimidazolium), the best IL used for this purpose so far. Furthermore, p-MIM:TCB significantly outperforms EMIM:TCB in terms of improving the stretchability (i.e., the highest tensile strain) of the PEDOT:PSS thin film. This enhancement is a result of the aromatic and protic cation p-MIM⁺, which acts as a molecular adhesive holding the exchanged ion pairs (PEDOT⁺:TCB^----p-MIM⁺:PSS^-) via ionic intercalation (at the surface of TCB^--decorated PEDOT⁺ clusters) and hydrogen bonding (to PSS^-), in which washing p-MIM⁺ out of the film degrades the stretchability while keeping the morphology. Our results offer molecular-level insight into the morphological, electrical, and mechanical properties of PEDOT:PSS and a molecular-interaction-based enhancement strategy that can be used for intrinsically stretchable conductive polymers.

Effect of phosphorylation of protamine-like cationic peptide on the binding affinity to DNA

Protamines are more arginine-rich and more basic than histones and are responsible for providing a highly compacted shape to the sperm heads in the testis. Phosphorylation and dephosphorylation are two events that occur in the late phase of spermatogenesis before the maturation of sperms. In this work, we have studied the effect of phosphorylation of protamine-like cationic peptides using all-atom molecular dynamics simulations. Through thermodynamic analyses, we found that phosphorylation reduces the binding efficiency of such cationic peptides on DNA duplexes. Peptide phosphorylation leads to a less efficient DNA condensation, due to a competition between DNA-peptide and peptide-peptide interactions. We hypothesize that the decrease of peptide bonds between DNA together with peptide self-assembly might allow an optimal re-organization of chromatin and an efficient condensation through subsequent peptide dephosphorylation. Based on the globular and compact conformations of phosphorylated peptides mediated by arginine-phosphoserine H-bonding, we furthermore postulate that phosphorylated protamines could more easily intrude into chromatin and participate to histone release through disruption of histone-histone and histone-DNA binding during spermatogenesis.

A Molecular-Switch-Embedded Organic Photodiode for Capturing Images against Strong Backlight

When the intensity of the incident light increases, the photocurrents of organic photodiodes (OPDs) exhibit relatively early saturation, due to which OPDs cannot easily detect objects against strong backlights, such as sunlight. In this study, this problem is addressed by introducing a light-intensity-dependent transition of the operation mode, such that the operation mode of the OPD autonomously changes to overcome early photocurrent saturation as the incident light intensity passes the threshold intensity. The photoactive layer is doped with a strategically designed and synthesized molecular switch, 1,2-bis-(2-methyl-5-(4-cyanobiphenyl)-3-thienyl)tetrafluorobenzene (DAB). The proposed OPD exhibits a typical OPD performance with an external quantum efficiency (EQE) of <100% and a photomultiplication behavior with an EQE of >100% under low-intensity and high-intensity light illuminations, respectively, thereby resulting in an extension of the photoresponse linearity to a light intensity of 434 mW cm^-2 . This unique and reversible transition of the operation mode can be explained by the unbalanced quantum yield of photocyclization/photocycloreversion of the molecular switch. The details of the operation mechanism are discussed in conjunction with various photophysical analyses. Furthermore, they establish a prototype image sensor with an array of molecular-switch-embedded OPD pixels to demonstrate their extremely high sensitivity against strong light illumination.

Hard-Cation-Soft-Anion Ionic Liquids for PEDOT:PSS Treatment

A promising conducting polymer poly(3,4-ethylenedioxythiophene):poly(styrenesulfonate) (PEDOT:PSS) experiences significant conductivity enhancement when treated with proper ionic liquids (ILs). Based on the hard-soft-acid-base principle, we propose a combination of a hydrophilic hard cation A⁺ (instead of the commonly used 1-ethyl-3-methyl imidazolium, EMIM⁺) and a hydrophobic soft anion X^- (such as tetracyanoborate, TCB^-) as the best ILs for this purpose. Such ILs would decouple hydrophilic-but-insulating PSS^- from conducting-but-hydrophobic PEDOT⁺ most efficiently by strong interactions with hydrophilic A⁺ and hydrophobic X^-, respectively. Such a favorable ion exchange between PEDOT⁺:PSS^- and A⁺:X^- ILs would allow the growth of conducting PEDOT⁺ domains decorated by X^-, not disturbed by PSS^- or A⁺. Using density functional theory calculations and molecular dynamics simulations, we demonstrate that a protic cation- (aliphatic N-alkyl pyrrolidinium, in particular) combined with the hydrophobic anion TCB^- indeed outperforms EMIM⁺ by promptly leaving hydrophobic TCB^- and strongly binding to hydrophilic PSS^-.

Effect of Bulky Atom Substitution on Backbone Coplanarity and Electrical Properties of Cyclopentadithiophene-Based Semiconducting Polymers

The effect of atomic substitution on the optoelectronic properties of a coplanar donor-acceptor (D-A) semiconducting polymer (SPs), prepared using cyclopentadithiophene (CDT) and 2,1,3-benzothiadiazole (BT) moieties, is investigated. By substituting a carbon atom in the BT unit with CF or C-Cl, two random D-A SPs are prepared, and their optoelectronic properties are thoroughly investigated. Density functional theory calculations demonstrate that the fluorinated polymer has a slightly smaller dihedral angle (ϴ = 0.6°) than the pristine polymer (ϴ = 1.9°) in its lowest-energy conformation, implying efficient charge transport through the coplanar backbone of the fluorinated polymer. However, the chlorinated polymer shows the lowest energy at a relatively larger dihedral angle (ϴ = 139°) due to the steric hindrance induced by bulky chlorine atoms in the backbone, thereby leading to thin-film morphology, which is unfavorable for charge transport. Consequently, the fluorinated polymer yields the highest field-effect mobility (μ) of 0.57 cm² V^-1 s^-1 , slightly higher than that of the pristine polymer (μ = 0.33 cm² V^-1 s^-1 ), and the extended device lifetime of organic field-effect transistors over 12 d without any encapsulation layers. The results of this study provide design guidelines for air-stable D-A SPs.

DNA-assisted assembly of cationic gold nanoparticles: Monte Carlo simulation

DNA-assisted assembly of ligand-stabilized gold nanoparticles is studied using Monte Carlo simulations with coarse-grained models for DNA and AuNP. Their interaction in a periodic simulation box is described by a combination of electrostatic and pairwise hard core potentials. We first probe the self-assembly of AuNPs resulting in an ordered distribution on a single fixed DNA strand. Subsequently, the effective force calculated between a pair of parallel DNA in the presence of AuNPs shows the attraction between them at short distance associated to a stable equilibrium position. Finally, the osmotic pressure calculated in a compact DNA-AuNP lattice with various amounts of monovalent salt ions shows that an increasing amount of salt prevents aggregate formation.

Protamine-Controlled Reversible DNA Packaging: A Molecular Glue

Packaging paternal genome into tiny sperm nuclei during spermatogenesis requires 10⁶-fold compaction of DNA, corresponding to a 10-20 times higher compaction than in somatic cells. While such a high level of compaction involves protamine, a small arginine-rich basic protein, the precise mechanism at play is still unclear. Effective pair potential calculations and large-scale molecular dynamics simulations using a simple idealized model incorporating solely electrostatic and steric interactions clearly demonstrate a reversible control on DNA condensates formation by varying the protamine-to-DNA ratio. Microscopic states and condensate structures occurring in semidilute solutions of short DNA fragments are in good agreement with experimental phase diagram and cryoTEM observations. The reversible microscopic mechanisms induced by protamination modulation should provide valuable information to improve a mechanistic understanding of early and intermediate stages of spermatogenesis where an interplay between condensation and liquid-liquid phase separation triggered by protamine expression and post-translational regulation might occur. Moreover, recent vaccines to prevent virus infections and cancers using protamine as a packaging and depackaging agent might be fine-tuned for improved efficiency using a protamination control.

Molecular Dynamics of PEDOT:PSS Treated with Ionic Liquids. Origin of Anion Dependence Leading to Cation Design Principles

Conductivity enhancement of PEDOT:PSS via the morphological change of PEDOT-rich domains has been achieved by introducing a 1-ethyl-3-methylimidazolium (EMIM)-based ionic liquid (IL) into its aqueous solution, and the degree of such change varies drastically with the anion coupled to the EMIM cation constituting the IL. We carry out a series of molecular dynamics simulations on various simple model systems for the extremely complex mixtures of PEDOT:PSS and EMIM:X IL in water, varying the anion X, the IL concentration, the oligomer model of PEDOT:PSS, and the size of the model systems. The common characteristic found in all simulations is that although planar hydrophobic anions X are the most efficient for ion exchange between PEDOT:PSS and EMIM:X, they tend to bring together planar EMIM cations to PEDOT-rich domains, disrupting PEDOT π-stacks with PEDOT-X-EMIM intercalating layers. Nonplanar hydrophobic anions, which leave most of EMIM cations in water, are efficient for both ion exchange and the formation of extended PEDOT π-stacks, as observed in experiments. Based on such findings, we propose a design principle for new cations replacing EMIM; nonplanar hydrophilic cations combined with hydrophobic anions should improve IL efficiency for PEDOT:PSS treatment.

Heterostructured Titanium Oxynitride-Manganese Cobalt Oxide Nanorods as High-Performance Electrode Materials for Supercapacitor Devices

Metal oxynitrides have been considered recently as emerging electrode materials for supercapacitors. Herein, we converted titanate nanotubes into a series of titanium oxynitride (TiON) nanorods at nitridation temperatures of 800, 900, and 1000 °C in ammonia gas and tested them as supercapacitor electrodes. TiON-800, TiON-900, and TiON-1000 showed capacities of 60, 140, and 71 F g^-1, respectively, at a current density of 1 A g^-1. However, because of TiON's low capacity, a heterostructure (TiON-900/MnCo₂O₄) was designed based on the optimized TiON with MnCo₂O₄ (MCO). The heterostructure TiON-900-MCO and MCO electrode materials showed specific capacities of 515 and 381 F g^-1, respectively, at a current density of 1 A g^-1. The cycling stability retention of TiON-900 and MCO were 75 and 68%, respectively; moreover, the heterostructure of TiON-900-MCO reached 78% at a current density of 5 A g^-1 over 5000 cycles. The increased capacity and sustained cycling stability retention are attributable to the synergistic effect of TiON-900 and MCO. A coin cell (CC)-type symmetric supercapacitor prototype of TiON-900-MCO was fabricated and tested in the voltage range of 0.0-2.0 V in 1 M LiClO₄ in propylene carbonate/dimethyl carbonate electrolyte, and a 79% cycling retention capacity of TiON-900-MCO-CC was achieved over 10 000 cycles at a current density of 250 mA g^-1. We demonstrated a prototypical single cell of TiON-900-MCO-CC as a sustained energy output by powering a red-light emitting diode that indicated TiON-900-MCo electrode materials' potential application in commercial supercapacitor devices.

Clinical features of subungual melanoma according to the extent of Hutchinson's nail sign: a retrospective single-centre study

BACKGROUND

Hutchinson's nail sign (HS) is among the diagnostic criteria for subungual melanoma (SUM). However, there is minimal evidence supporting the overall clinical significance of HS in SUM.

OBJECTIVES

To identify clinicopathological features of SUM according to the extent of HS.

METHODS

Retrospective cohort study was performed with consecutive SUM patients at a single centre from January 2006 to December 2017. The extent of HS was defined by the number of affected nail folds (range 0-4). Comparison groups were organized as follows: patients with HS (affecting ≥1 nail folds) vs. without HS; patients with HS affecting ≥2 nail folds vs. HS affecting <2 nail folds; patients with HS affecting ≥3 nail folds vs. HS affecting <3 nail folds. Clinicopathological characteristics of SUM were compared between the groups.

RESULTS

Sixty-one SUM patients were included. Forty-six (75.4%) exhibited HS; 22 (47.8%) on a toe and 24 (52.2%) on a finger. In multivariate analysis, nail destruction [hazard ratio (HR), 10.00; 95% confidence interval (CI), 2.61-38.30; P = 0.001] was significantly associated with the presence of HS and amputation was significantly associated with HS affecting ≥2 nail folds (HR, 4.75; 95% CI, 1.36-16.61; P = 0.015). High T stage (HR, 1.85; 95% CI, 1.20-2.85; P = 0.005, Fig. 2) was significantly associated with HS appearing in ≥3 nail folds.

CONCLUSION

Besides its value of detecting SUM, HS provides useful clinical information. The number of nail folds exhibiting HS could be a useful clinical clue for planning therapeutic strategies for SUM.

Liquid crystal ordering of nucleic acids

Several analytical calculations and computer simulations propose that cylindrical monodispersive rods having an aspect ratio (ratio of length to diameter) greater than 4 can exhibit liquid crystal (LC) ordering. But, recent experiments demonstrated the signature of LC ordering in systems of 4- to 20-base pair (bp) long nucleic acids (NAs) that do not satisfy the shape anisotropy criterion. Mechanisms of end-to-end adhesion and stacking have been proposed to explain this phenomenon. In this study, using all-atom molecular dynamics (MD) simulation, we explicitly verify the end-to-end stacking of double-stranded RNA (dsRNA) and demonstrate the LC ordering at the microscopic level. Using umbrella sampling (US) calculation, we quantify the potential of mean force (PMF) between two dsRNAs for various reaction coordinates (RCs) and compare our results with previously reported PMFs for double-stranded DNA (dsDNA). The PMF profiles demonstrate the anisotropic nature of inter-NA interaction. We find that, like dsDNA, dsRNA also prefers to stack on top of each other while repelling sideways, leading to the formation of supra-molecular-columns that undergo LC ordering at high NA volume fraction (φ). We also demonstrate and quantify the nematic ordering of the RNAs using several hundred nanosecond-long MD simulations that remain almost invariant for different initial configurations and under different external physiological conditions.

Molecular Engineering of a Donor-Acceptor Polymer To Realize Single Band Absorption toward a Red-Selective Thin-Film Organic Photodiode

Herein, we explore the strategy of realizing a red-selective thin-film organic photodiode (OPD) by synthesizing a new copolymer with a highly selective red-absorption feature. PCZ-Th-DPP, with phenanthrocarbazole (PCZ) and diketopyrrolopyrrole (DPP) as donor and acceptor units, respectively, was strategically designed/synthesized based on a time-dependent density functional theory calculation, which predicted the significant suppression of the band II absorption of PCZ-Th-DPP due to the extremely efficient intramolecular charge transfer. We demonstrate that the synthesized PCZ-Th-DPP exhibits not only a high absorption coefficient within the red-selective band I region, as theoretically predicted, but also a preferential face-on intermolecular structure in the thin-film state, which is beneficial for vertical charge extraction as an outcome of a glancing incidence X-ray diffraction study. By employing PCZ-Th-DPP as a photoactive layer of Schottky OPD, to fully match its absorption characteristic to the spectral response of the red-selective OPD, we demonstrate a genuine red-selective specific detectivity in the order of 10¹² Jones while maintaining a thin active layer thickness of ∼300 nm. This work demonstrates the possibility of realizing a full color image sensor with a synthetic approach to the constituting active layers without optical manipulation.

Correlational Effects of the Molecular-Tilt Configuration and the Intermolecular van der Waals Interaction on the Charge Transport in the Molecular Junction

Molecular conformation, intermolecular interaction, and electrode-molecule contacts greatly affect charge transport in molecular junctions and interfacial properties of organic devices by controlling the molecular orbital alignment. Here, we statistically investigated the charge transport in molecular junctions containing self-assembled oligophenylene molecules sandwiched between an Au probe tip and graphene according to various tip-loading forces ( F_L) that can control the molecular-tilt configuration and the van der Waals (vdW) interactions. In particular, the molecular junctions exhibited two distinct transport regimes according to the F_L dependence (i.e., F_L-dependent and F_L-independent tunneling regimes). In addition, the charge-injection tunneling barriers at the junction interfaces are differently changed when the F_L ≤ 20 nN. These features are associated to the correlation effects between the asymmetry-coupling factor (η), the molecular-tilt angle (θ), and the repulsive intermolecular vdW force ( F_vdW) on the molecular-tunneling barriers. A more-comprehensive understanding of these charge transport properties was thoroughly developed based on the density functional theory calculations in consideration of the molecular-tilt configuration and the repulsive vdW force between molecules.

Epitaxial Synthesis of Molybdenum Carbide and Formation of a Mo2C/MoS2 Hybrid Structure via Chemical Conversion of Molybdenum Disulfide

The epitaxial synthesis of molybdenum carbide (Mo₂C, a 2D MXene material) via chemical conversion of molybdenum disulfide (MoS₂) with thermal annealing under CH₄ and H₂ is reported. The experimental results show that adjusting the thermal annealing period provides a fully converted metallic Mo₂C from MoS₂ and an atomically sharp metallic/semiconducting hybrid structure via partial conversion of the semiconducting 2D material. Mo₂C/MoS₂ hybrid junctions display a low contact resistance (1.2 kΩ·μm) and low Schottky barrier height (26 meV), indicating the material's potential utility as a critical hybrid structural building block in future device applications. Density functional theory calculations are used to model the mechanisms by which Mo₂C grows and forms a Mo₂C/MoS₂ hybrid structure. The results show that Mo₂C conversion is initiated at the MoS₂ edge and undergoes sequential hydrodesulfurization and carbide conversion steps, and an atomically sharp interface with MoS₂ forms through epitaxial growth of Mo₂C. This work provides the area-controllable synthesis of a manufacturable MXene from a transition metal dichalcogenide material and the formation of a metal/semiconductor junction structure. The present results will be of critical importance for future 2D heterojunction structures and functional device applications.

Sub-nanometer pore formation in single-molecule-thick polyurea molecular-sieving membrane: a computational study

The surprisingly narrow sub-nm-pore-size distribution and urea-versus-glucose selectivity of a single-molecule-thick polyurea membrane are explained by Monte Carlo simulations on simple molecular models.

Shuttlecock-Shaped Molecular Rectifier: Asymmetric Electron Transport Coupled with Controlled Molecular Motion

A fullerene derivative with five hydroxyphenyl groups attached around a pentagon, (4-HOC₆H₄)₅HC₆₀ (1), has shown an asymmetric current-voltage (I-V) curve in a conducting atomic force microscopy experiment on gold. Such molecular rectification has been ascribed to the asymmetric distribution of frontier molecular orbitals over its shuttlecock-shaped structure. Our nonequilibrium Green's function (NEGF) calculations based on density functional theory (DFT) indeed exhibit an asymmetric I-V curve for 1 standing up between two Au(111) electrodes, but the resulting rectification ratio (RR ∼ 3) is insufficient to explain the wide range of RR observed in experiments performed under a high bias voltage. Therefore, we formulate a hypothesis that high RR (>10) may come from molecular orientation switching induced by a strong electric field applied between two electrodes. Indeed, molecular dynamics simulations of a self-assembled monolayer of 1 on Au(111) show that the orientation of 1 can be switched between standing-up and lying-on-the-side configurations in a manner to align its molecular dipole moment with the direction of the applied electric field. The DFT-NEGF calculations taking into account such field-induced reorientation between up and side configurations indeed yield RR of ∼13, which agrees well with the experimental value obtained under a high bias voltage.

The Arabidopsis splicing factors, AtU2AF65, AtU2AF35, and AtSF1 shuttle between nuclei and cytoplasms

The Arabidopsis splicing factors, AtU2AF65, AtU2AF35, and AtSF1 shuttle between nuclei and cytoplasms. These proteins also move rapidly and continuously in the nuclei, and their movements are affected by ATP depletion. The U2AF65 proteins are splicing factors that interact with SF1 and U2AF35 proteins to promote U2snRNP for the recognition of the pre-mRNA 3' splice site during early spliceosome assembly. We have determined the subcellular localization and movement of these proteins' Arabidopsis homologs. It was found that Arabidopsis U2AF65 homologs, AtU2AF65a, and AtU2AF65b proteins interact with AtU2AF35a and AtU2AF35b, which are Arabidopsis U2AF35 homologs. We have examined the mobility of these proteins including AtSF1 using fluorescence recovery after photobleaching and fluorescence loss in photobleaching analyses. These proteins displayed dynamic movements in nuclei and their movements were affected by ATP depletion. We have also demonstrated that these proteins shuttle between nuclei and cytoplasms, suggesting that they may also function in cytoplasm. These results indicate that such splicing factors show very similar characteristics to their human counterparts, suggesting evolutionary conservation.

RRM domain of Arabidopsis splicing factor SF1 is important for pre-mRNA splicing of a specific set of genes

The RNA recognition motif of Arabidopsis splicing factor SF1 affects the alternative splicing of FLOWERING LOCUS M pre-mRNA and a heat shock transcription factor HsfA2 pre-mRNA. Splicing factor 1 (SF1) plays a crucial role in 3' splice site recognition by binding directly to the intron branch point. Although plant SF1 proteins possess an RNA recognition motif (RRM) domain that is absent in its fungal and metazoan counterparts, the role of the RRM domain in SF1 function has not been characterized. Here, we show that the RRM domain differentially affects the full function of the Arabidopsis thaliana AtSF1 protein under different experimental conditions. For example, the deletion of RRM domain influences AtSF1-mediated control of flowering time, but not the abscisic acid sensitivity response during seed germination. The alternative splicing of FLOWERING LOCUS M (FLM) pre-mRNA is involved in flowering time control. We found that the RRM domain of AtSF1 protein alters the production of alternatively spliced FLM-β transcripts. We also found that the RRM domain affects the alternative splicing of a heat shock transcription factor HsfA2 pre-mRNA, thereby mediating the heat stress response. Taken together, our results suggest the importance of RRM domain for AtSF1-mediated alternative splicing of a subset of genes involved in the regulation of flowering and adaptation to heat stress.

Unraveling the Magnesium-Ion Intercalation Mechanism in Vanadium Pentoxide in a Wet Organic Electrolyte by Structural Determination

Magnesium batteries have received attention as a type of post-lithium-ion battery because of their potential advantages in cost and capacity. Among the host candidates for magnesium batteries, orthorhombic α-V₂O₅ is one of the most studied materials, and it shows a reversible magnesium intercalation with a high capacity especially in a wet organic electrolyte. Studies by several groups during the last two decades have demonstrated that water plays some important roles in getting higher capacity. Very recently, proton intercalation was evidenced mainly using nuclear resonance spectroscopy. Nonetheless, the chemical species inserted into the host structure during the reduction reaction are still unclear (i.e., Mg(H₂O)_n²⁺, Mg(solvent, H₂O)_n²⁺, H⁺, H₃O⁺, H₂O, or any combination of these). To characterize the intercalated phase, the crystal structure of the magnesium-inserted phase of α-V₂O₅, electrochemically reduced in 0.5 M Mg(ClO₄)₂ + 2.0 M H₂O in acetonitrile, was solved for the first time by the ab initio method using powder synchrotron X-ray diffraction data. The structure was tripled along the b-axis from that of the pristine V₂O₅ structure. No appreciable densities of elements were observed other than vanadium and oxygen atoms in the electron density maps, suggesting that the inserted species have very low occupancies in the three large cavity sites of the structure. Examination of the interatomic distances around the cavity sites suggested that H₂O, H₃O⁺, or solvated magnesium ions are too big for the cavities, leading us to confirm that the intercalated species are single Mg²⁺ ions or protons. The general formula of magnesium-inserted V₂O₅ is Mg_0.17H_xV₂O₅, (0.66 ≤ x ≤ 1.16). Finally, density functional theory calculations were carried out to locate the most plausible atomic sites of the magnesium and protons, enabling us to complete the structure modeling. This work provides an explicit answer to the question about Mg intercalation into α-V₂O₅.

Understanding the origin of liquid crystal ordering of ultrashort double-stranded DNA

Recent experiments have shown that short double-stranded DNA (dsDNA) fragments having six- to 20-base pairs exhibit various liquid crystalline phases. This violates the condition of minimum molecular shape anisotropy that analytical theories demand for liquid crystalline ordering. It has been hypothesized that the liquid crystalline ordering is the result of end-to-end stacking of dsDNA to form long supramolecular columns which satisfy the shape anisotropy criterion necessary for ordering. To probe the thermodynamic feasibility of this process, we perform molecular dynamics simulations on ultrashort (four base pair long) dsDNA fragments, quantify the strong end-to-end attraction between them, and demonstrate that the nematic ordering of the self-assembled stacked columns is retained for a large range of temperature and salt concentration.

Controlling Molecular Ordering in Aqueous Conducting Polymers Using Ionic Liquids

The molecular ordering of aqueous conducting polymers is controlled using a rational method. By introducing various ionic liquids, which have designed electrostatic interactions to PEDOT:PSS solutions, the evolution of the molecular ordering of the PEDOT is manipulated. Consequently, highly ordered nanostructures are achieved with a reduced π-π stacking distance of ≈3.38 Å and, thus, a maximum σ_dc of ≈2100 S cm^-1 .

Size-tunable synthesis of monolayer MoS2 nanoparticles and their applications in non-volatile memory devices

We report the CVD synthesis of a monolayer of MoS₂ nanoparticles such that the nanoparticle size was controlled over the range 5-100 nm and the chemical potential of sulfur was modified, both by controlling the hydrogen flow rate during the CVD process. As the hydrogen flow rate was increased, the reaction process of sulfur changed from a "sulfiding" process to a "sulfo-reductive" process, resulting in the growth of smaller MoS₂ nanoparticles on the substrates. The size control, crystalline quality, chemical configuration, and distribution uniformity of the CVD-grown monolayer MoS₂ nanoparticles were confirmed. The growth of the MoS₂ nanoparticles at different edge states was studied using density functional theory calculations to clarify the size-tunable mechanism. A non-volatile memory device fabricated using the CVD-grown size-controlled 5 nm monolayer MoS₂ nanoparticles as a floating gate showed a good memory window of 5-8 V and an excellent retention period of a decade.

OsNF-YC2 and OsNF-YC4 proteins inhibit flowering under long-day conditions in rice

OsNF-YC2 and OsNF-YC4 proteins regulate the photoperiodic flowering response through the modulation of three flowering-time genes ( Ehd1, Hd3a , and RFT1 ) in rice. Plant NUCLEAR FACTOR Y (NF-Y) transcription factors control numerous developmental processes by forming heterotrimeric complexes, but little is known about their roles in flowering in rice. In this study, it is shown that some subunits of OsNF-YB and OsNF-YC interact with each other, and among them, OsNF-YC2 and OsNF-YC4 proteins regulate the photoperiodic flowering response of rice. Protein interaction studies showed that the physical interactions occurred between the three OsNF-YC proteins (OsNF-YC2, OsNF-YC4 and OsNF-YC6) and three OsNF-YB proteins (OsNF-YB8, OsNF-YB10 and OsNF-YB11). Repression and overexpression of the OsNF-YC2 and OsNF-YC4 genes revealed that they act as inhibitors of flowering only under long-day (LD) conditions. Overexpression of OsNF-YC6, however, promoted flowering only under LD conditions, suggesting it could function as a flowering promoter. These phenotypes correlated with the changes in the expression of three rice flowering-time genes [Early heading date 1 (Ehd1), Heading date 3a (Hd3a) and RICE FLOWERING LOCUS T1 (RFT1)]. The diurnal and tissue-specific expression patterns of the subsets of OsNF-YB and OsNF-YC genes were similar to those of CCT domain encoding genes such as OsCO3, Heading date 1 (Hd1) and Ghd7. We propose that OsNF-YC2 and OsNF-YC4 proteins regulate the photoperiodic flowering response by interacting directly with OsNF-YB8, OsNF-YB10 or OsNF-YB11 proteins in rice.

Extremely Low Contact Resistance on Graphene through n-Type Doping and Edge Contact Design

The effects of graphene n-doping on a metal-graphene contact are studied in combination with 1D edge contacts, presenting a record contact resistance of 23 Ω μm at room temperature (19 Ω μm at 100 K). This contact scheme is applied to a graphene-perovskite hybrid photodetector, significantly improving its performance (0.6 → 1.8 A W(-1) in photoresponsivity and 3.3 × 10(4) → 5.4 × 10(4) Jones in detectivity).

N-Alkylthienopyrroledione versus benzothiadiazole pulling units in push–pull copolymers used for photovoltaic applications: density functional theory study

Low-band-gap push–pull copolymers are promising donor materials for bulk heterojunction organic solar cells.

D–A–D-type narrow-bandgap small-molecule photovoltaic donors: pre-synthesis virtual screening using density functional theory

A new series of D–A–D-type small-molecule photovoltaic donors are designed and screened before synthesis using time-dependent density functional theory calculations.

Lithium ion solvation by ethylene carbonates in lithium-ion battery electrolytes, revisited by density functional theory with the hybrid solvation model and free energy correction in solution

Li⁺/Li⁰ solvation free energy in the ethylene carbonate (EC) electrolyte calculated by density functional theory combined with a hybrid solvation model.

Controllable nondegenerate p-type doping of tungsten diselenide by octadecyltrichlorosilane

Despite heightened interest in 2D transition-metal dichalcogenide (TMD) doping methods for future layered semiconductor devices, most doping research is currently limited to molybdenum disulfide (MoS2), which is generally used for n-channel 2D transistors. In addition, previously reported TMD doping techniques result in only high-level doping concentrations (degenerate) in which TMD materials behave as near-metallic layers. Here, we demonstrate a controllable nondegenerate p-type doping (p-doping) technique on tungsten diselenide (WSe2) for p-channel 2D transistors by adjusting the concentration of octadecyltrichlorosilane (OTS). This p-doping phenomenon originates from the methyl (-CH3) functional groups in OTS, which exhibit a positive pole and consequently reduce the electron carrier density in WSe2. The controlled p-doping levels are between 2.1 × 10(11) and 5.2 × 10(11) cm(-2) in the nondegenerate regime, where the performance parameters of WSe2-based electronic and optoelectronic devices can be properly designed or optimized (threshold voltage↑, on-/off-currents↑, field-effect mobility↑, photoresponsivity↓, and detectivity↓ as the doping level increases). The p-doping effect provided by OTS is sustained in ambient air for a long time showing small changes in the device performance (18-34% loss of ΔVTH initially achieved by OTS doping for 60 h). Furthermore, performance degradation is almost completely recovered by additional thermal annealing at 120 °C. Through Raman spectroscopy and electrical/optical measurements, we have also confirmed that the OTS doping phenomenon is independent of the thickness of the WSe2 films. We expect that our controllable p-doping method will make it possible to successfully integrate future layered semiconductor devices.

Layer-controlled CVD growth of large-area two-dimensional MoS2 films

In spite of the recent heightened interest in molybdenum disulfide (MoS2) as a two-dimensional material with substantial bandgaps and reasonably high carrier mobility, a method for the layer-controlled and large-scale synthesis of high quality MoS2 films has not previously been established. Here, we demonstrate that layer-controlled and large-area CVD MoS2 films can be achieved by treating the surfaces of their bottom SiO2 substrates with the oxygen plasma process. Raman mapping, UV-Vis, and PL mapping are performed to show that mono, bi, and trilayer MoS2 films grown on the plasma treated substrates fully cover the centimeter scale substrates with a uniform thickness. Our TEM images also present the single crystalline nature of the monolayer MoS2 film and the formation of the layer-controlled bi- and tri-layer MoS2 films. Back-gated transistors fabricated on these MoS2 films are found to exhibit the high current on/off ratio of ∼10(6) and high mobility values of 3.6 cm(2) V(-1) s(-1) (monolayer), 8.2 cm(2) V(-1) s(-1) (bilayer), and 15.6 cm(2) V(-1) s(-1) (trilayer). Our results are expected to have a significant impact on further studies of the MoS2 growth mechanism as well as on the scaled layer-controlled production of high quality MoS2 films for a wide range of applications.

Switching mechanism of Al/La1−xSrxMnO3 resistance random access memory. I. Oxygen vacancy formation in perovskites

The oxygen vacancy formation in half-metallic perovskite LSMO itself plays an interesting role in the resistive switching.

A homolog of splicing factor SF1 is essential for development and is involved in the alternative splicing of pre-mRNA in Arabidopsis thaliana

During initial spliceosome assembly, SF1 binds to intron branch points and interacts with U2 snRNP auxiliary factor 65 (U2AF65). Here, we present evidence indicating that AtSF1, the Arabidopsis SF1 homolog, interacts with AtU2AF65a and AtU2AF65b, the Arabidopsis U2AF65 homologs. A mutant allele of AtSF1 (At5g51300) that contains a T-DNA insertion conferred pleiotropic developmental defects, including early flowering and abnormal sensitivity to abscisic acid. An AtSF1 promoter-driven GUS reporter assay showed that AtSF1 promoter activity was temporally and spatially altered, and that full AtSF1 promoter activity required a significant proportion of the coding region. DNA chip analyses showed that only a small proportion of the transcriptome was altered by more than twofold in either direction in the AtSF1 mutant. Expression of the mRNAs of many heat shock proteins was more than fourfold higher in the mutant strain; these mRNAs were among those whose expression was increased most in the mutant strain. An RT-PCR assay revealed an altered alternative splicing pattern for heat shock transcription factor HsfA2 (At2g26150) in the mutant; this altered splicing is probably responsible for the increased expression of the target genes induced by HsfA2. Altered alternative splicing patterns were also detected for the transcripts of other genes in the mutant strain. These results suggest that AtSF1 has functional similarities to its yeast and metazoan counterparts.

Effect of molecular desorption on the electronic properties of self-assembled polarizable molecular monolayers

We investigated the interfacial electronic properties of self-assembled monolayers (SAM)-modified Au metal surface at elevated temperatures. We observed that the work functions of the Au metal surfaces modified with SAMs changed differently under elevated-temperature conditions based on the type of SAMs categorized by three different features based on chemical anchoring group, molecular backbone structure, and the direction of the dipole moment. The temperature-dependent work function of the SAM-modified Au metal could be explained in terms of the molecular binding energy and the thermal stability of the SAMs, which were investigated with thermal desorption spectroscopic measurements and were explained with molecular modeling. Our study will aid in understanding the electronic properties at the interface between SAMs and metals in organic electronic devices if an annealing treatment is applied.

Dual function of a living polymerization initiator through the formation of a chain-end-protecting cluster: density functional theory calculation

The origin of the living nature of isocyanate polymerization by sodium benzanilide (Na⁺BA⁻) initiator is understood from the relative stabilities of (NaBA)_n clusters in THF solution.

Charge inhomogeneity of graphene on SiO2: dispersion-corrected density functional theory study on the effect of reactive surface sites

Reactive surface species present on SiO₂ in a mixture with inert ones is one likely origin of charge puddles observed in supported graphenes.

The sequence variation responsible for the functional difference between the CONSTANS protein, and the CONSTANS-like (COL) 1 and COL2 proteins, resides mostly in the region encoded by their first exons

Although the protein CONSTANS (CO) and its close relatives CONSTANS-like (COL) 1 and COL2 exhibit high amino acid sequence similarities, only the CO protein regulates floral induction in Arabidopsis. To investigate the structural basis for the functional differences between CO, COL1, and COL2 in flowering, we performed domain-swapping between CO, COL1, and COL2, and site-directed mutagenesis on the first exon of CO. The results suggest that the lack of flowering promotion activity by COL1 and COL2 is mainly attributed to the differences between CO and the COL1 and COL2 proteins in the amino acid sequence encoded by their first exons.