Project description:RNA-binding proteins play a key role in the regulation of all aspects of RNA metabolism, from the synthesis of RNA to its decay. Protein-RNA interactions have been thought to be mostly mediated by canonical RNA-binding domains that form stable secondary and tertiary structures. However, a number of pioneering studies over the past decades, together with recent proteome-wide data, have challenged this view, revealing surprising roles for intrinsically disordered protein regions in RNA binding. Here, we discuss how disordered protein regions can mediate protein-RNA interactions, conceptually grouping these regions into RS-rich, RG-rich, and other basic sequences, that can mediate both specific and non-specific interactions with RNA. Disordered regions can also influence RNA metabolism through protein aggregation and hydrogel formation. Importantly, protein-RNA interactions mediated by disordered regions can influence nearly all aspects of co- and post-transcriptional RNA processes and, consequently, their disruption can cause disease. Despite growing interest in disordered protein regions and their roles in RNA biology, their mechanisms of binding, regulation, and physiological consequences remain poorly understood. In the coming years, the study of these unorthodox interactions will yield important insights into RNA regulation in cellular homeostasis and disease.
Project description:Partitioning space into cells with certain extreme geometrical properties is a central problem in many fields of science and technology. Here we investigate the Quantizer problem, defined as the optimisation of the moment of inertia of Voronoi cells, i.e., similarly-sized 'sphere-like' polyhedra that tile space are preferred. We employ Lloyd's centroidal Voronoi diagram algorithm to solve this problem and find that it converges to disordered states associated with deep local minima. These states are universal in the sense that their structure factors are characterised by a complete independence of a wide class of initial conditions they evolved from. They moreover exhibit an anomalous suppression of long-wavelength density fluctuations and quickly become effectively hyperuniform. Our findings warrant the search for novel amorphous hyperuniform phases and cellular materials with unique physical properties.
Project description:Relaxation processes are decisive for many physical properties of amorphous materials. For amorphous phase-change materials (PCMs) used in nonvolatile memories, relaxation processes are, however, difficult to characterize because of the lack of bulk samples. Here, instead of bulk samples, we use powder mechanical spectroscopy for powder samples to detect the prominent excess wings-a characteristic feature of ?-relaxations-in a series of amorphous PCMs at temperatures below glass transitions. By contrast, ?-relaxations are vanishingly small in amorphous chalcogenides of similar composition, which lack the characteristic features of PCMs. This conclusion is corroborated upon crossing the border from PCMs to non-PCMs, where ?-relaxations drop substantially. Such a distinction implies that amorphous PCMs belong to a special kind of covalent glasses whose locally fast atomic motions are preserved even below the glass transitions. These findings suggest a correlation between ?-relaxation and crystallization kinetics of PCMs, which have technological implications for phase-change memory functionalities.
Project description:The general and practical inversion of diffraction data-producing a computer model correctly representing the material explored-is an important unsolved problem for disordered materials. Such modeling should proceed by using our full knowledge base, both from experiment and theory. In this paper, we describe a robust method to jointly exploit the power of ab initio atomistic simulation along with the information carried by diffraction data. The method is applied to two very different systems: amorphous silicon and two compositions of a solid electrolyte memory material silver-doped GeSe3. The technique is easy to implement, is faster and yields results much improved over conventional simulation methods for the materials explored. By direct calculation, we show that the method works for both poor and excellent glass forming materials. It offers a means to add a priori information in first-principles modeling of materials, and represents a significant step toward the computational design of non-crystalline materials using accurate interatomic interactions and experimental information.
Project description:The structure of amorphous GeSe2 (a-GeSe2) has been studied by means of a combination of two-edges X-ray absorption spectroscopy (XAS) and angle-dispersive X-ray diffraction under pressures up to about 30 GPa. Multiple-edge XAS data-analysis of a-GeSe2 at ambient conditions allowed us to reconstruct and compare the first-neighbor distribution function with previous results obtained by neutron diffraction with isotopic substitution. GeSe2 is found to remain amorphous up to the highest pressures attained, and a reversible 1.5 eV red-shift of the Ge K-edge energy indicating metallization, occurs between 10 GPa and 15 GPa. Two compression stages are identified by XAS structure refinement. First, a decrease of the first-neighbor distances up to about 10 GPa, in the same pressure region of a previously observed breakdown of the intermediate-range order. Second, an increase of the Ge-Se distances, bond disorder, and of the coordination number. This stage is related to a reversible non-isostructural transition involving a gradual conversion from tetra- to octa-hedral geometry which is not yet fully completed at 30 GPa.
Project description:Recent developments in the field of high efficiency perovskite solar cells are based on stabilization of the perovskite crystal structure of FAPbI3 while preserving its excellent optoelectronic properties. Compositional engineering of, for example, MA or Br mixed into FAPbI3 results in the desired effects, but detailed knowledge of local structural features, such as local (dis)order or cation interactions of formamidinium (FA) and methylammonium (MA), is still limited. This knowledge is, however, crucial for their further development. Here, we shed light on the microscopic distribution of MA and FA in mixed perovskites MA1-x FA x PbI3 and MA0.15FA0.85PbI2.55Br0.45 by combining high-resolution double-quantum 1H solid-state nuclear magnetic resonance (NMR) spectroscopy with state-of-the-art near-first-principles accuracy molecular dynamics (MD) simulations using machine-learning force-fields (MLFFs). We show that on a small local scale, partial MA and FA clustering takes place over the whole MA/FA compositional range. A reasonable driving force for the clustering might be an increase of the dynamical freedom of FA cations in FA-rich regions. While MA0.15FA0.85PbI2.55Br0.45 displays similar MA and FA ordering as the MA1-x FA x PbI3 systems, the average cation-cation interaction strength increased significantly in this double mixed material, indicating a restriction of the space accessible to the cations or their partial immobilization upon Br- incorporation. Our results shed light on the heterogeneities in cation composition of mixed halide perovskites, helping to exploit their full optoelectronic potential.
Project description:High-performance solution-processed organic semiconductors maintain macroscopic functionality even in the presence of microscopic disorder. Here we show that the functional robustness of certain organic materials arises from the ability of molecules to create connected mesoscopic electrical networks, even in the absence of periodic order. The hierarchical network structures of two families of important organic photovoltaic acceptors, functionalized fullerenes and perylene diimides, are analyzed using a newly developed graph methodology. The results establish a connection between network robustness and molecular topology, and also demonstrate that solubilizing moieties play a large role in disrupting the molecular networks responsible for charge transport. A clear link is established between the success of mono and bis functionalized fullerene acceptors in organic photovoltaics and their ability to construct mesoscopically connected electrical networks over length scales of 10 nm.
Project description:Blue phases (BPs) have a frustrated structure stabilized by chirality-dependent defects. They are classified into three categories: blue phase I (BPI), blue phase II (BPII), and blue phase III (BPIII). Among them, BPIII has recently attracted much attention due to its elusive amorphous structure and high-contrast electro-optical response. However, its structure has remained unelucidated, and the molecular design for stabilizing BPIII is still unclear. We present the following findings in this review. (1) BPIII is a spaghetti-like tangled arrangement of double-twist cylinders with characteristic dynamics. (2) Molecular biaxiality and flexibility contribute to stabilize BPIII. (3) BPIII exhibits submillisecond response, high contrast, and wide-viewing angle at room temperature without surface treatment or an optical compensation film. It was free from both hysteresis and residual transmittance. The electro-optical effects are explained in relation to the revealed structure of BPIII. Finally, we discuss the memory effect of a polymer network derived from the defects of BPIII.
Project description:With the rapid development of high-throughput sequencing technology, approaches for assessing biological ingredients in Traditional Chinese Medicine (TCM) preparations have also advanced. Using a multi-barcode sequencing approach, all biological ingredients could be identified from TCM preparations in theory, as long as their DNA is present. The biological ingredients of several classical TCM preparations were analyzed successfully based on this approach in previous studies. However, the universality, sensitivity and reliability of this approach on a diverse set of TCM preparations remain unclear. In this study, we selected four representative TCM preparations, namely Bazhen Yimu Wan, Da Huoluo Wan, Niuhuang Jiangya Wan, and You Gui Wan, for concrete assessment of the multi-barcode sequencing approach. Based on ITS2 and trnL biomarkers, we have successfully detected the prescribed herbal materials (PHMs) in these representative TCM preparations (minimum sensitivity: 77.8%, maximum sensitivity: 100%). The results based on ITS2 have also shown higher reliability than trnL at species level, while their combination could provide higher sensitivity and reliability. The multi-barcode sequencing approach has shown good universality, sensitivity and reliability in decoding these four representative TCM preparations. In the omics big-data era, this work has undoubtedly made one step forward for applying multi-barcode sequencing approach in PHMs analysis of TCM preparation, towards better digitization and modernization of drug quality control.
Project description:The standard procedure to identify the hole- or electron-acceptor character of amorphous organic materials used in OLEDs is to look at the values of a pair of basic parameters, namely, the ionization potential (IP) and the electron affinity (EA). Recently, using published experimental data, the present authors showed that only IP matters, i.e., materials with IP > 5.7 (<5.7) showing electron (hole) acceptor character. Only three materials fail to obey this rule. This work reports ab initio calculations of IP and EA of those materials plus two materials that behave according to that rule, following a route which describes the organic material by means of a single molecule embedded in a polarizable continuum medium (PCM) characterized by a dielectric constant ε . PCM allows to approximately describe the extended character of the system. This "compound" system was treated within density functional theory (DFT) using several combinations of the functional/basis set. In the preset work ε was derived by assuming Koopmans' theorem to hold. Optimal ε values are in the range 4.4⁻5.0, close to what is expected for this material family. It was assumed that the optical gap corresponds to the excited state with a large oscillator strength among those with the lowest energies, calculated with time-dependent DFT. Calculated exciton energies were in the range 0.76⁻1.06 eV, and optical gaps varied from 3.37 up to 4.50 eV. The results are compared with experimental data.