A generalized exchange-correlation functional: the Neural-Networks approach

A Neural-Networks-based approach is proposed to construct a new type of exchange-correlation functional for density functional theory. It is applied to improve B3LYP functional by taking into account of high-order contributions to the exchange-correlation functional. The improved B3LYP functional is based on a neural network whose structure and synaptic weights are determined from 116 known experimental atomization energies, ionization potentials, proton affinities or total atomic energies which were used by Becke in his pioneer work on the hybrid functionals [J. Chem. Phys. ${\bf 98}$, 5648 (1993)]. It leads to better agreement between the first-principles calculation results and these 116 experimental data. The new B3LYP functional is further tested by applying it to calculate the ionization potentials of 24 molecules of the G2 test set. The 6-311+G(3{\it df},2{\it p}) basis set is employed in the calculation, and the resulting root-mean-square error is reduced to 2.2 kcal$\cdot$mol$^{-1}$ in comparison to 3.6 kcal$\cdot$mol$^{-1}$ of conventional B3LYP/6-311+G(3{\it df},2{\it p}) calculation.Comment: 10 pages, 1figur

Neurovascular Photoacoustic Tomography

Neurovascular coupling refers to the relationship between neuronal activities and downstream hemodynamic responses. Photoacoustic tomography (PAT), enabling comprehensive label-free imaging of hemodynamic activities with highly scalable penetration and spatial resolution, has great potential in the study of neurovascular coupling. In this review, we first introduce the technical basis of hemodynamic PAT – including label-free quantification of total hemoglobin concentration, blood oxygenation, and blood flow – as well as its applications in hemodynamic monitoring. Then, we demonstrate the potential application of PAT in neurovascular imaging by highlighting representative studies on cerebral vascular responses to whisker stimulation and Alzheimer's disease. Finally, potential research directions and associated technical challenges are discussed

Photoacoustic computed tomography guided microrobots for targeted navigation in intestines in vivo

Tremendous progress in synthetic micro/nanomotors has been made for potential biomedical applications. However, existing micro/nanomotor platforms are inefficient for deep tissue imaging and motion control in vivo. Here, we present a photoacoustic computed tomography (PACT) guided investigation of micromotors in intestines in vivo. The micromotors enveloped in microcapsules exhibit efficient propulsion in various biofluids once released. PACT has visualized the migration of micromotor capsules toward the targeted regions in real time in vivo. The integration of the developed microrobotic system and PACT enables deep imaging and precise control of the micromotors in vivo

Territorial barriers in interagency government data sharing

Interagency government data sharing (IDS) is an indispensable precondition for the development of citizen-centred smart government. Adopting a theory of territoriality, this paper reports on an on-going research investigation, which explores, identifies, and qualifies the barriers to the lack of IDS.Methods. The research adopts an inductive approach, which combines a critical literature review, and three case studies in Central China. 118 articles, and 45 government officials and data managers from three regional government agencies collected as interview data were included and analysed using a thematic approach. Interorganisational dynamism affects the formulation of individual agencies’ psychological ownership on data, which leads to territorial marking and defending behaviours against IDS. Territoriality theory offers a novel and useful perspective to interpret, understand and resolve IDS problems. Albeit this research is situated in China, the research findings offer valuable indications and insights that can be shared across international borders.Peer Reviewe

On the Convergence of QM/MM Energies

We have studied the convergence of QM/MM calculations with respect to the size of the QM system. We study a proton transfer between a first-sphere cysteine ligand and a second-sphere histidine group in [Ni,Fe] hydrogenase and use a 446-atom model of the protein, treated purely with QM methods as a reference. We have tested 12 different ways to redistribute charges close to the junctions (to avoid overpolarization of the QM system), but once the junctions are moved away from the active site, there is little need to redistribute the charges. We have tested 13 different variants of QM/MM approaches, including two schemes to correct errors caused by the truncation of the QM system. However, we see little gain from such correction schemes; on the contrary, they are sensitive to the charge-redistribution scheme and may cause large errors if charges are close to the junctions. In fact, the best results were obtained with a mechanical embedding approach that does not employ any correction scheme and ignores polarization. It gives a mean unsigned error for 40 QM systems of different sizes of 7 kJ/mol with a maximum error of 28 kJ/mol. The errors can be significantly decreased if bonds between the QM and MM system (junctions) are moved one residue away from all active-site residues. Then, most QM/MM variants give mean unsigned errors of 5-9 kJ/mol, maximum errors of 16-35 kJ/mol, and only five to seven residues give an error of over 5 kJ/mol. In general, QM/MM calculations converge faster with system size than pure QM calculations

Accurate reaction energies in proteins obtained by combining QM/MM and large QM calculations

We here suggest and test a new method to obtain stable energies in proteins for charge-neutral reactions by running large quantum mechanical (QM) calculations on structures obtained by combined QM and molecular mechanics (QM/MM) geometry optimisation on several snapshots from molecular dynamics simulations. As a test case, we use a proton transfer between a metal-bound cysteine residue and a second-sphere histidine residue in the active site of [Ni,Fe] hydrogenase, which has been shown to be very sensitive to the surroundings. We include in the QM calculations all residues within 4.5 Å of the active site, two capped residues on each side of the active-site residues, as well as all charged groups that are buried inside the protein, which for this enzyme includes three iron–sulphur clusters, in total 930 atoms. These calculations are performed at the BP86/def2-SV(P) level, but the energies are then extrapolated to the B3LYP/def2-TZVP level with a smaller QM system and zero-point energy, entropy, and thermal effects are added. We test three approaches to model the remaining atoms of the protein solvent, viz. by standard QM/MM approaches using either mechanical or electrostatic embedding, or by using a continuum solvation model for the large QM systems. Quite encouragingly, the three approaches give the same results within 13 kJ/mol and variations in the size of the QM system do not change the energies by more than 8 kJ/mol, provided that the QM/MM junctions are not moved closer to the QM system. The statistical precision for the average over ten snapshots is 1–3 kJ/mol