Intranasal delivery of shRNA to knockdown the 5HT-2A receptor enhances memory and alleviates anxiety.

Short-hairpin RNAs (shRNA), targeting knockdown of specific genes, hold enormous promise for precision-based therapeutics to treat numerous neurodegenerative disorders. However, whether shRNA constructed molecules can modify neuronal circuits underlying certain behaviors has not been explored. We designed shRNA to knockdown the human HTR2A gene in vitro using iPSC-differentiated neurons. Multi-electrode array (MEA) results showed that the knockdown of the 5HT-2A mRNA and receptor protein led to a decrease in spontaneous electrical activity. In vivo, intranasal delivery of AAV9 vectors containing shRNA resulted in a decrease in anxiety-like behavior in mice and a significant improvement in memory in both mice (104%) and rats (92%) compared to vehicle-treated animals. Our demonstration of a non-invasive shRNA delivery platform that can bypass the blood-brain barrier has broad implications for treating numerous neurological mental disorders. Specifically, targeting the HTR2A gene presents a novel therapeutic approach for treating chronic anxiety and age-related cognitive decline.

Approximate inclusion of four-mode couplings in vibrational coupled-cluster theory.

The vibrational coupled cluster (VCC) equations are analyzed in terms of vibrational Mo̸ller-Plesset perturbation theory aiming specifically at the importance of four-mode couplings. Based on this analysis, new VCC methods are derived for the calculation of anharmonic vibrational energies and vibrational spectra using vibrational coupled cluster response theory. It is shown how the effect of four-mode coupling and excitations can be efficiently and accurately described using approximations for their inclusion. Two closely related approaches are suggested. The computational scaling of the so-called VCC[3pt4F] method is not higher than the fifth power in the number of vibrational degrees of freedom when up to four-mode coupling terms are present in the Hamiltonian and only fourth order when only up to three-mode couplings are present. With a further approximation, one obtains the VCC[3pt4] model which is shown to scale with at most the fourth power in the number of vibrational degrees of freedom for Hamiltonians with both three- and four-mode coupling levels, while sharing the most important characteristics with VCC[3pt4F]. Sample calculations reported for selected tetra-atomic molecules as well as the larger dioxirane and ethylene oxide molecules support that the new models are accurate and useful.

Vibrational absorption spectra from vibrational coupled cluster damped linear response functions calculated using an asymmetric Lanczos algorithm.

We report the theory and implementation of vibrational coupled cluster (VCC) damped response functions. From the imaginary part of the damped VCC response function the absorption as function of frequency can be obtained, requiring formally the solution of the now complex VCC response equations. The absorption spectrum can in this formulation be seen as a matrix function of the characteristic VCC Jacobian response matrix. The asymmetric matrix version of the Lanczos method is used to generate a tridiagonal representation of the VCC response Jacobian. Solving the complex response equations in the relevant Lanczos space provides a method for calculating the VCC damped response functions and thereby subsequently the absorption spectra. The convergence behaviour of the algorithm is discussed theoretically and tested for different levels of completeness of the VCC expansion. Comparison is made with results from the recently reported [P. Seidler, M. B. Hansen, W. Györffy, D. Toffoli, and O. Christiansen, J. Chem. Phys. 132, 164105 (2010)] vibrational configuration interaction damped response function calculated using a symmetric Lanczos algorithm. Calculations of IR spectra of oxazole, cyclopropene, and uracil illustrate the usefulness of the new VCC based method.

Computation of expectation values from vibrational coupled-cluster at the two-mode coupling level.

In this work we show how the vibrational coupled-cluster method at the two-mode coupling level can be used to calculate zero-point vibrational averages of properties. A technique is presented, where any expectation value can be calculated using a single set of Lagrangian multipliers computed solving iteratively a single linear set of equations. Sample calculations are presented which show that the resulting algorithm scales only with the third power of the number of modes, therefore making large systems accessible. Moreover, we present applications to water, pyrrole, and para-nitroaniline.

Vibrational coupled cluster response theory: a general implementation.

The calculation of vibrational contributions to molecular properties using vibrational coupled cluster (VCC) response theory is discussed. General expressions are given for expectation values, linear response functions, and transition moments. It is shown how these expressions can be evaluated for arbitrary levels of excitation in the wave function parameterization as well as for arbitrary coupling levels in the potential and property surfaces. The convergence of the method is assessed by benchmark calculations on formaldehyde. Furthermore, excitation energies and infrared intensities are calculated for the fundamental vibrations of furan using VCC limited to up to two-mode and up to three-mode excitations, VCC[2] and VCC[3], as well as VCC with full two-mode and approximate three-mode couplings, VCC[2pt3].

A Lanczos-chain driven approach for calculating damped vibrational configuration interaction response functions.

We present an approach based on the Lanczos method for calculating the vibrational configuration interaction response functions necessary for evaluating the pure vibrational contributions to the polarizabilities and first hyperpolarizabilities of molecules. The method iteratively builds a tridiagonal representation of the central response matrix, which is subsequently used for solving the response equations. From the same chain, the response functions can be evaluated approximately for any frequency as well as using any complex damping factor. Applications to formaldehyde, cyclopropene, and uracil illustrate the concepts presented.

Vibrational absorption spectra calculated from vibrational configuration interaction response theory using the Lanczos method.

The Lanczos method is used to efficiently obtain the linear vibrational response function for all frequencies in an arbitrary interval. The complex part of the response function gives the absorption spectrum which can subsequently be analyzed. The method provides a way to obtain global information on the absorption spectrum without explicitly converging all vibrational eigenstates of the system. The tridiagonal Lanczos matrix used to obtain the response functions needs only be constructed once for each operator. Example calculations on cyclopropene and uracil are presented.

New Formulation and Implementation of Vibrational Self-Consistent Field Theory.

A new implementation of the vibrational self-consistent field (VSCF) method is presented on the basis of a second quantization formulation. A so-called active terms algorithm is shown to be a significant improvement over a standard implementation reducing the computational effort by one order in the number of degrees of freedom. Various types of screening provide even further reductions in computational scaling and absolute CPU time. VSCF calculations on large polyaromatic hydrocarbon model systems are presented. Further, it is demonstrated that in cases where distant modes are not directly coupled in the Hamiltonian, down to linear scaling of the required CPU time with respect to the number of vibrational modes can be obtained. This is illustrated with calculations on simple model systems with up to 1 million degrees of freedom.

Automatic derivation and evaluation of vibrational coupled cluster theory equations.

A scheme for automatic derivation and evaluation of the expressions occurring in vibrational coupled cluster theory is introduced. The method is based on a Baker-Campbell-Hausdorff expansion of the similarity transformed Hamiltonian and is general both with respect to the excitation level in the parameter space and the mode coupling level in the Hamiltonian. In addition to deriving general expressions, intermediates that lower the computational scaling are automatically detected. The final equations are then evaluated. Due to the commutator based nature of the algorithm, it is also applicable to the evaluation of quantities needed for response theory. Different aspects of the theory and implementation are illustrated by calculations on model systems. Furthermore, all fundamental excitation energies of ethylene oxide are calculated.

Vibrational coupled cluster theory with full two-mode and approximate three-mode couplings: the VCC[2pt3] model.

Vibrational coupled cluster (VCC) calculations of molecular vibrational energy levels can be characterized by the number of modes coupled in the Hamiltonian operator and the number of modes simultaneously excited in the parameter space. We propose a VCC model which includes all two-mode couplings in the Hamiltonian and excitation space but only an approximate treatment of three-mode couplings. The approximation is based on a perturbational analysis and the introduced concepts can also be used for even more accurate treatments. The method is iterative and allows the use of VCC response theory to obtain excitation energies. Furthermore, the method is shown to scale with the number of vibrational modes to the third power which is no higher than the corresponding VCC model with only two-mode couplings. Encouraging benchmark calculations are given for a test set of three- and four-atomic molecules. The fundamentals of the larger ethylene oxide molecule have been calculated as well using a grid-based potential energy surface obtained from electronic coupled cluster theory with singles, doubles, and perturbative triples (CCSD(T)).

Towards fast computations of correlated vibrational wave functions: vibrational coupled cluster response excitation energies at the two-mode coupling level.

An efficient implementation of vibrational coupled cluster theory with two-mode excitations and a two-mode Hamiltonian is described. The algorithm is shown to scale cubically with respect to the number of modes which is identical to the scaling of the corresponding vibrational configuration interaction algorithm. This is achieved through the use of special intermediates. The same algorithm can also be used in vibrational Møller-Plesset calculations. To improve performance, screening techniques have been implemented as well. Test calculations on polyaromatic hydrocarbons with up to 264 coupled modes and model systems with up to 1140 modes are used to illustrate the various features of the algorithm.

Vibrational excitation energies from vibrational coupled cluster response theory.

Response theory in the context of vibrational coupled cluster (VCC) theory is introduced and used to obtain vibrational excitation energies. The relation to the vibrational configuration interaction (VCI) approach is described, and the increase in accuracy of VCC response energies relative to VCI energies is discussed theoretically in terms of a perturbational order expansion and demonstrated numerically. To illustrate the theory, a pilot implementation is used to obtain anharmonic vibrational frequencies for fundamental, first overtone and combination excitations of formaldehyde as well as for the fundamental transitions of ethylene.

Calculation of vibrational infrared intensities and Raman activities using explicit anharmonic wave functions.

Methods for automatic computation of IR intensities and Raman activities are described using vibrational self-consistent field (VSCF) and vibrational configuration interaction (VCI) wave functions. Inclusion of effects due to anharmonicity in the potential energy and property surfaces are found to improve the results substantially as compared to experimental data. Sample calculations employing water and formaldehyde are presented, allowing for comparison between different vibrational methods. The convergence with respect to excitation level in VCI and the extent of mode coupling in the potential and property expansions is investigated. In addition, different electronic methods used for generating the potential and property surfaces, namely CCSD, CCSD(T), DFT/B3LYP, and DFT/CAM-B3LYP have been compared. Details of the potential and property surfaces may have significant effects on the IR and Raman intensities.