Binding Density Research Articles

ChromatinHD connects single-cell DNA accessibility and conformation to gene expression through scale-adaptive machine learning

Gene regulation is inherently multiscale, but scale-adaptive machine learning methods that fully exploit this property in single-nucleus accessibility data are still lacking. Here, we develop ChromatinHD, a pair of scale-adaptive models that uses the raw accessibility data, without peak-calling or windows, to link regions to gene expression and determine differentially accessible chromatin. We show how ChromatinHD consistently outperforms existing peak and window-based approaches and find that this is due to a large number of uniquely captured, functional accessibility changes within and outside of putative cis-regulatory regions. Furthermore, ChromatinHD can delineate collaborating regulatory regions, including their preferential genomic conformations, that drive gene expression. Finally, our models also use changes in ATAC-seq fragment lengths to identify dense binding of transcription factors, a feature not captured by footprinting methods. Altogether, ChromatinHD, available at https://chromatinhd.org, is a suite of computational tools that enables a data-driven understanding of chromatin accessibility at various scales and how it relates to gene expression.

Behavioural and electrophysiological features of WAG/Rij rats with different forms of genetic epilepsy

WAG/Rij rats are widely used as a genetic model of absence epilepsy. Approximately 15–50% rats of the strain are susceptible to audiogenic seizures. WAG/Rij rats demonstrate depressive-like behavior. After preliminary sound provocation an increased level of anxiety was found in audiogenic susceptible WAG/Rij subgroup. Electrophysiological and behavioral studies suggest the involvement of the dopaminergic system in both absence and audiogenic epilepsy. An increased binding density to dopamine receptors was found in the dorsal striatum subregions in audiogenic prone rats compared to non-audiogenic. The study aims were (1) to determine whether behavioral changes in WAG/Rij rats were genetically determined or induced by prior sound stimulation; (2) how regions of the dorsal striatum with different density of dopamine receptors in subpopulations of WAG/Rij rats are involved in the absence epilepsy control. The study was conducted using two rat groups: WAG/Rij-nonAGS (absence epilepsy) and WAG/Rij-AGS (mixed epilepsy). The study was performed using tests: “Elevated plus maze”, “Forced swimming” and “Three chamber sociability test”. High-frequency deep brain stimulation was performed for evaluation of dorsal striatum involvement in the absence seizure control. After experiments animals were tested for the susceptibility to audiogenic seizures. It demonstrated that the increased level of anxiety in WAG/Rij-AGS rats is genetically determined, while depressive-like behavior in WAG/Rij rats is not dependent on a predisposition to audiogenic seizures. Deviations in social behavior were observed in WAG/Rij-AGS rats. Stimulation of the dorsal striatum indicates differences in the control of absence and mixed forms of epilepsy in the

Self-Assembled Bolaamphiphile-Based Organic Nanotubes as Efficient Cu(II) Ion Adsorbents.

Self-assembled organic nanotubes (ONTs) have been actively examined for various applications such as chemical separations and catalysis owing to their well-defined tubular nanostructures with distinct chemical environments at the wall and internal/external surfaces. Adsorption of heavy metal ions onto ONTs plays an essential role in many of these applications but has rarely been assessed quantitatively. Herein, we investigated interactions between Cu2+ and single-/quadruple-wall bolaamphiphile-based ONTs having inner carboxyl groups with different inner diameters, COOH-ONT10nm and COOH-ONT20nm. We first examined the effects of Cu2+ on their nanotubular structures using SAXS, STEM, and AFM. COOH-ONT10nm was stable in aqueous Cu2+ solution in contrast to COOH-ONT20nm owing to the presence of polyglycine-II-type hydrogen bonding networks within its wall. Subsequently, we studied the Cu2+ adsorption behavior of COOH-ONT10nm by monitoring the concentration of unbound Cu2+ using linear sweep anodic stripping voltammetry. The Cu2+ adsorption was quick, attributable to efficient Cu2+ partitioning through the open ends of the ONT, followed by fast Cu2+ diffusion in the uniform, relatively large nanochannel. More importantly, the Cu2+ adsorption capacity and affinity of COOH-ONT10nm were measured under different pH conditions using the Langmuir adsorption model. The adsorption capacity was similar at the pH range examined, showing the participation of approximately 25% of the inner carboxyl groups in the adsorption. The adsorption affinity increased with pH, indicating the essential role of the deprotonated carboxyl groups in Cu2+ adsorption. Most interestingly, the Langmuir adsorption constant was significantly higher than those of previously reported synthetic adsorbents and planar monolayer based on carboxyl binding sites. The high Cu2+ affinity of the ONT was attributable to the highly dense binding sites on the well-defined nanoscale concave structure of the inner channel. These results provide a valuable guideline for designing self-assembled nanomaterials for efficient chemical separations, detection, and catalysis.

A Mixture Transition Distribution Modeling for Higher‐Order Circular Markov Processes

ABSTRACTThis study considers the stationary higher‐order Markov process for circular data by employing the mixture transition distribution modeling. The underlying circular transition distribution is based on Wehrly and Johnson's bivariate joint circular models. The structures of the circular autocorrelation function, together with the circular partial autocorrelation function, are investigated. They are found to be similar to those of the autocorrelation and partial autocorrelation functions of the real‐valued autoregressive process when the underlying binding density has zero sine moments. The validity of the model is assessed by applying it to some Monte Carlo simulations and real directional data.

Self‐adaptive Coordination Evolution Mediated Pore‐Space‐Partition in Metal–Organic Frameworks for Boosting SF6/N2 Separation

AbstractThe controllable and precise structural regulation of metal–organic frameworks (MOFs) based on isoreticular chemistry is an effective strategy for creating functional material platforms, such as efficient porous adsorbents. Herein, for the first time, mediated by an unprecedented self‐adaptive coordination evolution (SACE) on pseudo‐D2h‐symmetric [M4(μ3‐O)2(COO)6] (M=Mn/Fe) clusters, two pore space partitioned MOFs (CTGU‐47‐Mn/Fe, CTGU=China Three Gorges University) have been successfully constructed. Owing to the more confined adsorption space and dense binding sites produced by pore space partitioning (PSP), the CTGU‐47‐Mn/Fe exhibit significantly enhanced performance in the capture or recovery SF6 (greenhouse/electronic specialty gas) from SF6/N2 mixture compared to their non‐partitioned homologous structures (CTGU‐46‐Mn/Fe) with adsorption selectivity increased from 37/72 to 634/157 (v/v, 10/90, 100 kPa). The theoretical calculations also elucidated that the implementation of PSP within CTGU‐47‐Mn/Fe leads to dramatically strengthened binding affinity for SF6 over N2 through extra multiple F⋅⋅⋅H interactions. This study represents a valuable advance in crystal engineering field: the SACE of polynuclear metal clusters is expected to be useful in the structural regulation of MOFs and the fabrication of advanced porous adsorbents.

Self-adaptive Coordination Evolution Mediated Pore-Space-Partition in Metal-Organic Frameworks for Boosting SF6/N2 Separation.

The controllable and precise structural regulation of metal-organic frameworks (MOFs) based on isoreticular chemistry is an effective strategy for creating functional material platforms, such as efficient porous adsorbents. Herein, for the first time, mediated by an unprecedented self-adaptive coordination evolution (SACE) on pseudo-D2h-symmetric [M4(μ3-O)2(COO)6] (M=Mn/Fe) clusters, two pore space partitioned MOFs (CTGU-47-Mn/Fe, CTGU=China Three Gorges University) have been successfully constructed. Owing to the more confined adsorption space and dense binding sites produced by pore space partitioning (PSP), the CTGU-47-Mn/Fe exhibit significantly enhanced performance in the capture or recovery SF6 (greenhouse/electronic specialty gas) from SF6/N2 mixture compared to their non-partitioned homologous structures (CTGU-46-Mn/Fe) with adsorption selectivity increased from 37/72 to 634/157 (v/v, 10/90, 100 kPa). The theoretical calculations also elucidated that the implementation of PSP within CTGU-47-Mn/Fe leads to dramatically strengthened binding affinity for SF6 over N2 through extra multiple F⋅⋅⋅H interactions. This study represents a valuable advance in crystal engineering field: the SACE of polynuclear metal clusters is expected to be useful in the structural regulation of MOFs and the fabrication of advanced porous adsorbents.

Non-adiabatic Couplings in Surface Hopping with Tight Binding Density Functional Theory: The Case of Molecular Motors.

Nonadiabatic molecular dynamics (NAMD) has become an essential computational technique for studying the photophysical relaxation of molecular systems after light absorption. These phenomena require approximations that go beyond the Born-Oppenheimer approximation, and the accuracy of the results heavily depends on the electronic structure theory employed. Sophisticated electronic methods, however, make these techniques computationally expensive, even for medium size systems. Consequently, simulations are often performed on simplified models to interpret the experimental results. In this context, a variety of techniques have been developed to perform NAMD using approximate methods, particularly density functional tight binding (DFTB). Despite the use of these techniques on large systems, where ab initio methods are computationally prohibitive, a comprehensive validation has been lacking. In this work, we present a new implementation of trajectory surface hopping combined with DFTB, utilizing nonadiabatic coupling vectors. We selected the methaniminium cation and furan systems for validation, providing an exhaustive comparison with the higher-level electronic structure methods. As a case study, we simulated a system from the class of molecular motors, which has been extensively studied experimentally but remains challenging to simulate with ab initio methods due to its inherent complexity. Our approach effectively captures the key photophysical mechanism of dihedral rotation after the absorption of light. Additionally, we successfully reproduced the transition from the bright to dark states observed in the time-dependent fluorescence experiments, providing valuable insights into this critical part of the photophysical behavior in molecular motors.

Optimizing Cu 3d Bands with Nanotubular SnO2 to Boost Their Catalytic Transfer Hydrogenation Activity.

Catalytic transfer hydrogenation (CTH) using Cu nanocatalysts offers significant advantages over direct high-pressure hydrogenation. However, the active hydrogen (H*) in this process exhibits poor adsorption and tends to release H2 readily due to the fully occupied 3d states of Cu. To address this issue, a tubular SnO2 support with electron-accepting ability was selected to host Cu nanoparticles, aiming to optimize the Cu 3d bands. The Cu/SnO2 nanohybrids were prepared through an electrospinning technique, followed by hydrothermal synthesis. As evidenced by X-ray photoelectron spectroscopy (XPS) binding energy shifts and density functional theory (DFT) simulations, some electrons from Cu transferred to SnO2 in the Cu/SnO2 nanohybrids due to their different work functions. Such electron transfer enables the Cu 3d orbitals to lose electrons and alters its valence configuration from 3d10 to 3d10-x, which enhances the adsorption of active H* atoms and thereby inhibits undesirable H2 release. The 15 wt % Cu/SnO2 exhibits improved catalytic hydrogenation of 4-nitrophenol with NaBH4, with an optimal normalized rate constant of 56.98 mg-1 min-1 and a turnover frequency of 4.82 min-1, surpassing most reported catalysts. The enhanced activity is attributed to the optimized electronic states, improved hydrogen adsorption, and the tubular structure of the support. This work might shed light on developing more non-noble metal nanocatalysts for CTH by tuning their d bands with appropriate oxide supports.

Superheavy magic nuclei: Ground-state properties, bubble structure and α-decay chains

Superheavy magic nuclei: Ground-state properties, bubble structure and α-decay chains

Adsorption of Guanine on Oxygen-Deficient TiO2 Surface: A Combined MD-DFTB/DFT Strategy.

Metal oxides (MOs) are key materials in many fields, including technological, industrial, and biomedical applications. In most of these implementations, surface reactivity and reducibility properties are critical considerations. In their nanosized form, MOs exhibit enhanced reactivity that is connected to toxicity. Besides the fact that the biological molecule and the surface of the corresponding material interact chemically, little is known about the toxicological mechanisms involved on the atomic scale. The goal of this study is to investigate the role of TiO2 surfaces in interaction with one genetic base, namely guanine. Using a combination of the quasi-electronic density functional-tight binding molecular dynamics simulations and density functional theory calculations, we explored the adsorption modes of guanine with a stoichiometric and oxygen-deficient anatase TiO2 (101) surface. With such an approach, we have characterized new adsorption modes not previously found, and we have highlighted the relevance of defective surfaces in the adsorption of genetic basis, as a model for explaining possible toxicology mechanisms induced by the adsorption process.

Hybrid Polystyrene-Plasmonic Systems as High Binding Density Biosensing Platforms.

Sensitive, accurate, and early detection of biomarkers is essential for prompt response to medical decisions for saving lives. Some infectious diseases are deadly even in small quantities and require early detection for patients and public health. The scarcity of these biomarkers necessitates signal amplification before diagnosis. Recently, we demonstrated single-molecule-level detection of tuberculosis biomarker, lipoarabinomannan, from patient urine using silver plasmonic gratings with thin plasma-activated alumina. While powerful, biomarker binding density was limited by the surface density of plasma-activated carbonyl groups, that degraded quickly, resulting in immediate use requirement after plasma activation. Therefore, development of stable high density binding surfaces such as high binding polystyrene is essential to improving shelf-life, reducing binding protocol complexity, and expanding to a wider range of applications. However, any layers topping the plasmonic grating must be ultra-thin (<10 nm) for the plasmonic enhancement of adjacent signals. Furthermore, fabricating thin polystyrene layers over alumina is nontrivial because of poor adhesion between polystyrene and alumina. Herein, we present the development of a stable, ultra-thin polystyrene layer on the gratings, which demonstrated 63.8 times brighter fluorescence compared to commercial polystyrene wellplates. Spike protein was examined for COVID-19 demonstrating the single-molecule counting capability of the hybrid polystyrene-plasmonic gratings.

Computational modeling of CH4 and CO2 adsorption on monolayer graphenylene: Implications for optoelectronic properties and hydrogen production

Computational modeling of CH4 and CO2 adsorption on monolayer graphenylene: Implications for optoelectronic properties and hydrogen production

Modeling the electroluminescence of atomic wires from quantum dynamics simulations.

Static and time-dependent quantum-mechanical approaches have been employed in the literature to characterize the physics of light-emitting molecules and nanostructures. However, the electromagnetic emission induced by an input current has remained beyond the realm of molecular simulations. This is the challenge addressed here with the help of an equation of motion for the density matrix coupled to a photon bath based on a Redfield formulation. This equation is evolved within the framework of the driven-Liouville von Neumann approach, which incorporates open boundaries by introducing an applied bias and a circulating current. The dissipated electromagnetic power can be computed in this context from the time derivative of the energy. This scheme is applied in combination with a self-consistent tight-binding Hamiltonian to investigate the effects of bias and molecular size on the electroluminescence of metallic and semiconducting chains. For the latter, a complex interplay between bias and molecular length is observed: there is an optimal number of atoms that maximizes the emitted power at high voltages but not at low ones. This unanticipated behavior can be understood in terms of the band bending produced along the semiconducting chain, a phenomenon that is captured by the self-consistency of the method. A simple analytical model is proposed that explains the main features revealed by the simulations. The methodology, applied here at a self-consistent tight-binding level but extendable to more sophisticated Hamiltonians such as density functional tight binding and time dependent density functional theory, promises to be helpful for quantifying the power and quantum efficiency of nanoscale electroluminescent devices.

Exploring the potential of Mbenes in energy storage

Exploring the potential of Mbenes in energy storage

Characterization of oxytocin and vasopressin receptors in the Southern giant pouched rat and comparison to other rodents.

Vasopressin and oxytocin are well known and evolutionarily ancient modulators of social behavior. The distribution and relative densities of vasopressin and oxytocin receptors are known to modulate the sensitivity to these signaling molecules. Comparative work is needed to determine which neural networks have been conserved and modified over evolutionary time, and which social behaviors are commonly modulated by nonapeptide signaling. To this end, we used receptor autoradiography to determine the distribution of vasopressin 1a and oxytocin receptors in the Southern giant pouched rat (Cricetomys ansorgei) brain, and to assess the relative densities of these receptors in specific brain regions. We then compared the relative receptor pattern to 23 other species of rodents using a multivariate ANOVA. Pouched rat receptor patterns were strikingly similar to hamsters and voles overall, despite the variation in social organization among species. Uniquely, the pouched rat had dense vasopressin 1a receptor binding in the caudate-putamen (i.e., striatum), an area that might impact affiliative behavior in this species. In contrast, the pouched rat had relatively little oxytocin receptor binding in much of the anterior forebrain. Notably, however, oxytocin receptor binding demonstrated extremely dense binding in the bed nucleus of the stria terminalis, which is associated with the modulation of several social behaviors and a central hub of the social decision-making network. Examination of the nonapeptide system has the potential to reveal insights into species-specific behaviors and general themes in the modulation of social behavior.

Computational method on highly efficient D-π-A-π-D-based different molecular acceptors for organic solar cells applications and non-linear optical behaviour

Eight molecular structures (BT-A1 to BT-A8) with high-performance non-fullerene acceptor (NFA) were selected for organic solar cells (OSCs) and non-linear optical (NLO) applications. Their electronic, photovoltaic (PV) and optoelectronic properties were tuned by adding powerful electron-withdrawing groups to the acceptor (A) of the D-π-A-π-D structure. Using time-dependent density functional theory (TD-DFT) techniques, based on the laws of quantum chemical calculations, the absorption spectra, stability of the highest and lowest-energy molecular orbitals (HOMO/LUMOs), electron density, intramolecular charge transfer (ICT), transition density matrix (TDM), were examined. The binding energy (Eb) and density of states (DOS) were probed to realize the optoelectronic analysis of the structures BT-A1 to BT-A8. Noncovalent interactions (NCIs) based on a reduced density gradient (RDG) were used to describe the nature and strength of D-A interactions in the molecules BT-A1 to BT-A8. The new refined molecules BT-A1 to BT-A8 exhibited strong absorbance bands between 408-721nm and high electron transfer contribution (ETC) ranges between 87-96%, along with the smallest excitation energies (Ex) between 1.71-3.55eV in the solvent dichloromethane. Dipolar moment strengths ranging from 0.38 to 4.72 Debye in both the excited and ground states have determined with good solubility properties of BT-A1 to BT-A8 in polar solvent. Highly effective charge mobilities and prevention of charge recombination have been demonstrated by the electron (0.18-0.41eV) and hole RE values (0.13-0.89eV) for the new compounds. Power conversion efficiencies (PCE) of BT-A1 to BT-A8 were nearly the same because of better outcomes compared to the molecules in the BT. Compared to poly[4.8-bis(5-(2-ethylhexyl)thiophen-2-yl)benzo[1,2-b: 4,5-b']dithiophene-2,6- diyl-alt-(4-2-ethylhexyl)-3-fluorothieno[3,4-b]thiophene-)-2-carboxylate-2-6-diyl)] (PTB7-Th), the open circuit voltages (Voc) of compounds BT-A1 to BT-A8 were ranged from 1.52 to 2.13eV. The polarizability (α) and hyperpolarizability (β) of the molecules BT-A1 to BT-A8 were used to determine the non-linear optical (NLO) properties. The results showed that BT-A2, BT-A6 and BT-A7 have good NLO activity. This computational analysis demonstrates the superiority of the molecules with NFA. Hence the compounds are advised for the use in production of high-performance OSCs and NLO activity.

Effects of Au doping on the adsorption of xanthate on pyrite surface in presence of H2O: A DFT study

Effects of Au doping on the adsorption of xanthate on pyrite surface in presence of H2O: A DFT study

D1-Like and D2-Like Dopamine Receptors in the Rat Prefrontal Cortex: Impacts of Genetic Generalized Epilepsies and Social Behavioral Deficits

The involvement of the prefrontal cortical dopaminergic system in the psychopathology of epilepsies and comorbid conditions such as autism spectrum disorder (ASD) still needs to be explored. We used autoradiography to study the D1-like (D1DR) and D2-like (D2DR) receptor binding density in the prefrontal cortex of normal Wistar rats and Wistar-derived strains with generalized convulsive and/or non-convulsive epilepsy. WAG/Rij rats served as a model for non-convulsive absence epilepsy, WAG/Rij-AGS as a model of mixed convulsive/non-convulsive form, and KM strain was a model for convulsive epilepsy comorbid with an ASD-like behavioral phenotype. The prefrontal cortex of rats with any epileptic pathology studied demonstrated profound decreases in binding densities to both D1DR and D2DR; the effects were localized in the primary and secondary anterior cingulate cortices, and adjacent regions. The local decreased D1DR and D2DR binding densities were independent of (not correlated with) each other. The particular group of epileptic rats with an ASD-like phenotype (KM strain) displayed changes in the lateral prefrontal cortex: D1DR were lowered, whereas D2DR were elevated, in the dysgranular insular cortex and adjacent regions. Thus, epilepsy-related changes in the dopaminergic system of the rat archeocortex were localized in the medial prefrontal regions, whereas ASD-related changes were seen in the lateral prefrontal aspects. The findings point to putative local dopaminergic dysfunctions, associated with generalized epilepsies and/or ASD.

Large-scale column-free purification of bovine F-ATP synthase

Mammalian F-ATP synthase is central to mitochondrial bioenergetics and is present in the inner mitochondrial membrane in a dynamic oligomeric state of higher oligomers, tetramers, dimers, and monomers. Invitro investigations of mammalian F-ATP synthase are often limited by the ability to purify the oligomeric forms present invivo at a quantity, stability, and purity that meets the demand of the planned experiment. We developed a purification approach for the isolation of bovine F-ATP synthase from heart muscle mitochondria that uses a combination of buffer conditions favoring inhibitor factor 1 binding and sucrose density gradient ultracentrifugation to yield stable complexes at high purity in the milligram range. By tuning the glyco-diosgenin to lauryl maltose neopentyl glycol ratio in a final gradient, fractions that are either enriched in tetrameric or monomeric F-ATP synthase can be obtained. It is expected that this large-scale column-free purification strategy broadens the spectrum of invitro investigation on mammalian F-ATP synthase.

Performance analysis of Fe2O3/CNT humidity sensor based on adsorption kinetics and DFT computations

Performance analysis of Fe2O3/CNT humidity sensor based on adsorption kinetics and DFT computations