Publications by authors named "Ruiheng Song"

Complex conjugation symmetry breaking and restoration generates two nonorthogonal configurations at the Hartree-Fock level that can capture static correlation naturally. In conjunction with broken spin-symmetry coupled cluster theory, the symmetry-projected wave function shows good agreement with full configuration interaction in beryllium hydride insertion, lithium fluoride dissociation, and symmetric stretching of tetrahedral H. By adding spin flip projection, we can also recover time reversal symmetry in the same coupled cluster framework.

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Repeated administration of methylamphetamine (MA) induces MA addiction, which is featured by awfully unpleasant physical and emotional experiences after drug use is terminated. Neurophysiological studies show that the lateral hypothalamus (LH) is involved in reward development and addictive behaviors. Here, we show that repeated administration of MA activates the expression of c-Fos in LH neurons responding to conditioned place preference (CPP).

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Projected Hartree-Fock theory provides an accurate description of many kinds of strong correlations but does not properly describe weakly correlated systems. On the other hand, single-reference methods, such as configuration interaction or coupled cluster theory, can handle weakly correlated problems but cannot properly account for strong correlations. Ideally, we would like to combine these techniques in a symmetry-projected coupled cluster approach, but this is far from straightforward.

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Nicotinamide adenine dinucleotide (NADH) has been reported to regulate synaptic plasticity recently, while its role in this process remains unclear. To explore the contribution and the underlying mechanisms of NADH regulating synaptic plasticity, here, we examined NADH's effect on immediate-early response genes (IEGs) expressions, including C-Fos and Arc in primary cultured cortical neurons and the frontal cortex of mouse brain. Our results showed that NADH promoted IEGs expression and that the C-Fos and Arc levels are increased in primary cultured cortical neurons, which is almost completely blocked by N-methyl-D-aspartate receptor (NMDAR) inhibitor, MK-801.

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Conformational transitions of protein between different states are often associated with their biological functions. These dynamic processes, however, are usually not easy to be well characterized by experimental measurements, mainly because of inadequate temporal and spatial resolution. Meantime, sampling of configuration space with molecular dynamics (MD) simulations is still a challenge.

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Store-operated calcium release-activated calcium (CRAC) channels mediate a variety of cellular signaling functions. The CRAC channel pore-forming protein, Orai1, is a hexamer arranged with 3-fold symmetry. Despite its importance in moving Ca ions into cells, a detailed mechanistic understanding of Orai1 activation is lacking.

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Molecular self-assembly provides a chemical strategy for the synthesis of nanostructures by using the principles of nature, and peptides serve as the promising building blocks to construct adaptable molecular architectures. Recently, a series of heptapeptides with alternative hydrophobic and hydrophilic residues were reported to form amyloid-like structures, which are capable of catalyzing acyl ester hydrolysis with remarkable efficiency. However, information remains elusive about the atomic structures of the fibrils.

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The generalized energy-based fragmentation (GEBF) method is extended to allow calculations of nuclear magnetic resonance (NMR) chemical shifts of macromolecular and condensed-phase systems feasible at a low computational cost. In this approach, NMR shielding constants in a large system are evaluated as a linear combination of the corresponding quantities from a series of small "electrostatically embedded" subsystems. Comparison of NMR shielding constants from the GEBF-X method [where X is an electronic structure method, such as Hartree-Fock (HF), density functional theory (DFT), .

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