Project description:Here we present a detailed ab initio study of two experimentally synthesized bismuth niobate BiNbO4 (BNO) polymorphs within the framework of density functional theory (DFT). We synthesized orthorhombic α-BNO and triclinic β-BNO using a solid-state reaction technique. The underlying Pnna and P1̄ crystal symmetries along with their respective phase purity have been confirmed from Rietveld refinement of the powdered X-ray diffraction measurements in combination with generalized gradient approximation of Perdew-Burke-Ernzerhof (GGA-PBE) based DFT simulations. The scanning electron micrographs revealed average grain sizes to be 500 nm and 1 μm for α-BNO and β-BNO respectively. The energy-dispersive X-ray spectroscopy identified the Bi, Nb, and O with proper stoichiometry. The phase purity of the as-synthesized samples was further confirmed by comparing the local density approximation (LDA) norm-conserving pseudo-potential based DFT-simulated Raman peaks with that of experimentally measured ones. The relevant bond vibrations detected in Fourier transform infrared spectroscopy were matched with GGA-PBE derived phonon density of states simulation for both polymorphs. The structural stability and the charge dynamics of the polymorphs were verified from elastic stress and born charge tensor simulations respectively. The dynamical stability of the α-BNO was confirmed from phonon band structure simulation using density functional perturbation theory with Heyd-Scuseria-Ernzerhof (HSE06) hybrid functional. The electronic band gaps of 3.08 and 3.36 eV for α-BNO and β-BNO measured from UV-Vis diffuse reflectance measurements were matched with the sophisticated HSE06 band structure simulation by adjusting the Hartree-Fock exchange parameter. Both GGA-PBE and HSE06 functional were used to simulate complex dielectric function and its derivatives with the help of Fermi's golden rule to define the optical properties in the linear regime. All these may have provided a rigorous theoretical analysis for the experimentally synthesized α-BNO and β-BNO polymorphs.
Project description:The paper introduces a novel computational approach to brain dynamics modeling that integrates dynamic gene-protein regulatory networks with a neural network model. Interaction of genes and proteins in neurons affects the dynamics of the whole neural network. Through tuning the gene-protein interaction network and the initial gene/protein expression values, different states of the neural network dynamics can be achieved. A generic computational neurogenetic model is introduced that implements this approach. It is illustrated by means of a simple neurogenetic model of a spiking neural network of the generation of local field potential. Our approach allows for investigation of how deleted or mutated genes can alter the dynamics of a model neural network. We conclude with the proposal how to extend this approach to model cognitive neurodynamics.
Project description:Finite-temperature lattice free energy differences between polymorphs of molecular crystals are fundamental to understanding and predicting the relative stability relationships underpinning polymorphism, yet are computationally expensive to obtain. Here, we implement and critically assess machine-learning-enabled targeted free energy calculations derived from flow-based generative models to compute the free energy difference between two ice crystal polymorphs (Ice XI and Ic), modeled with a fully flexible empirical classical force field. We demonstrate that even when remapping from an analytical reference distribution, such methods enable a cost-effective and accurate calculation of free energy differences between disconnected metastable ensembles when trained on locally ergodic data sampled exclusively from the ensembles of interest. Unlike classical free energy perturbation methods, such as the Einstein crystal method, the targeted approach analyzed in this work requires no additional sampling of intermediate perturbed Hamiltonians, offering significant computational savings. To systematically assess the accuracy of the method, we monitored the convergence of free energy estimates during training by implementing an overfitting-aware weighted averaging strategy. By comparing our results with ground-truth free energy differences computed with the Einstein crystal method, we assess the accuracy and efficiency of two different model architectures, employing two different representations of the supercell degrees of freedom (Cartesian vs quaternion-based). We conduct our assessment by comparing free energy differences between crystal supercells of different sizes and temperatures and assessing the accuracy in extrapolating lattice free energies to the thermodynamic limit. While at low temperatures and in small system sizes, the models perform with similar accuracy. We note that for larger systems and high temperatures, the choice of representation is key to obtaining generalizable results of quality comparable to that obtained from the Einstein crystal method. We believe this work to be a stepping stone toward efficient free energy calculations in larger, more complex molecular crystals.
Project description:The integration of a range of technologies including microfluidics, surface-enhanced Raman scattering and confocal microspectroscopy has been successfully used to characterize in situ single living CHO (Chinese hamster ovary) cells with a high degree of spatial (in three dimensions) and temporal (1 s per spectrum) resolution. Following the introduction of a continuous flow of ionomycin, the real time spectral response from the cell was monitored during the agonist-evoked Ca(2+) flux process. The methodology described has the potential to be used for the study of the cellular dynamics of a range of signalling processes.
Project description:Most currently marketed pharmaceuticals are manufactured in the solid state, where the bioavailability of the active pharmaceutical ingredient (API) can be optimized through different polymorphs, cocrystals, solvates, or salts. Efficient techniques are needed to monitor the structure of pharmaceuticals during production. Here, we explore the potential of linearly and circularly polarized Raman microscopy for distinguishing three polymorphs of sofosbuvir, an antiviral drug used to treat hepatitis C. Raman spectra were recorded on a Raman microscope for a polycrystalline API diluted in a KBr matrix. To understand spectral features including the low-frequency region, we simulated band frequencies and intensities using quantum-chemical computational strategies based on cluster and transfer approaches. Very good agreement was achieved between simulated and experimental intensities. The 20 to 200 cm-1 wavenumber region appeared particularly useful for polymorph discrimination already based on unpolarized measurements. The depolarization ratios obtained from linearly polarized Raman spectra made the distinction even more reliable. Moreover, circularly polarized Raman spectra and normalized degrees of circularity provided useful additional information and revealed several tentative markers of the different polymorphs of sofosbuvir. Although in some spectral regions the differences were less obvious, the results indicate that polarized Raman microscopy is a handy tool for discriminating between polymorphs of APIs and other compounds.
Project description:Strain engineering as one of the most powerful techniques for tuning optical and electronic properties of Ill-nitrides requires reliable methods for strain investigation. In this work, we reveal, that the linear model based on the experimental data limited to within a small range of biaxial strains (< 0.2%), which is widely used for the non-destructive Raman study of strain with nanometer-scale spatial resolution is not valid for the binary wurtzite-structure group-III nitrides GaN and AlN. Importantly, we found that the discrepancy between the experimental values of strain and those calculated via Raman spectroscopy increases as the strain in both GaN and AlN increases. Herein, a new model has been developed to describe the strain-induced Raman frequency shift in GaN and AlN for a wide range of biaxial strains (up to 2.5%). Finally, we proposed a new approach to correlate the Raman frequency shift and strain, which is based on the lattice coherency in the epitaxial layers of superlattice structures and can be used for a wide range of materials.Electronic supplementary materialSupplementary material (Table S1: Values of bulk phonon deformation potentials and elastic constants for GaN and AlN from each reference used in Table 1, Fig. S1: Lattice parameters of SL layers using Eq. (8), and Fig. S2: Raman mapping using Eq. (7)) is available in the online version of this article at 10.1007/s12274-021-3855-4.
Project description:Synucleinopathies are a heterogenous group of neurodegenerative diseases characterized by the progressive accumulation of pathological α-synuclein (α-Syn). The importance of structural polymorphism of α-Syn assemblies for distinct synucleinopathies and their progression is increasingly recognized. However, the underlying mechanisms are poorly understood. Here we use fluorescence lifetime imaging microscopy (FLIM) to investigate seeded aggregation of α-Syn in a biosensor cell line. We show that conformationally distinct α-Syn polymorphs exhibit characteristic fluorescence lifetimes. FLIM further revealed that α-Syn polymorphs were differentially processed by cellular clearance pathways, yielding fibrillar species with increased seeding capacity. Thus, FLIM is not only a powerful tool to distinguish different amyloid structures, but also to monitor the dynamic process of amyloid remodeling by the cellular environment. Our data suggest that the accumulation of highly seeding competent degradation products for particular polymorphs may account for accelerated disease progression in some patients.
Project description:Multi-excitation Raman Spectroscopy Complements Whole Genome Sequencing for Rapid Detection of Bacterial Infection and Resistance in WHO Priority Pathogens
Project description:A combined experimental and theoretical approach, consisting of lattice phonon Raman spectroscopy and density functional theory (DFT) calculations, is proposed as a tool for lattice dynamics characterization and polymorph phase identification. To illustrate the reliability of the method, the lattice phonon Raman spectra of two polymorphs of the molecule 2,7-dioctyloxy[1]benzothieno[3,2-b]benzothiophene are investigated. We show that DFT calculations of the lattice vibrations based on the known crystal structures, including many-body dispersion van der Waals (MBD-vdW) corrections, predict experimental data within an accuracy of ≪5 cm-1 (≪0.6 meV). Due to the high accuracy of the simulations, they can be used to unambiguously identify different polymorphs and to characterize the nature of the lattice vibrations and their relationship to the structural properties. More generally, this work implies that DFT-MBD-vdW is a promising method to describe also other physical properties that depend on lattice dynamics like charge transport.