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- Aydemir, Esra, et al.
(författare)
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Impact of silencing eEF2K expression on the malignant properties of chordoma
- 2023
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Ingår i: Molecular Biology Reports. - : Springer Science and Business Media LLC. - 0301-4851 .- 1573-4978. ; 50:4, s. 3011-3022
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Tidskriftsartikel (refereegranskat)abstract
- Background: Eukaryotic elongation factor 2 kinase (eukaryotic elongation factor 2 kinase, eEF2K) is a calcium calmodulin dependent protein kinase that keeps the highest energy consuming cellular process of protein synthesis under check through negative regulation. eEF2K pauses global protein synthesis rates at the translational elongation step by phosphorylating its only kown substrate elongation factor 2 (eEF2), a unique translocase activity in ekaryotic cells enabling the polypeptide chain elongation. Therefore, eEF2K is thought to preserve cellular energy pools particularly upon acute development of cellular stress conditions such as nutrient deprivation, hypoxia, or infections. Recently, high expression of this enzyme has been associated with poor prognosis in an array of solid tumor types. Therefore, in a growing number of studies tremendous effort is being directed to the development of treatment methods aiming to suppress eEF2K as a novel therapeutic approach in the fight against cancer. Methods: In our study, we aimed to investigate the changes in the tumorigenicity of chordoma cells in presence of gene silencing for eEF2K. Taking a transient gene silencing approach using siRNA particles, eEF2K gene expression was suppressed in chordoma cells. Results: Silencing eEF2K expression was associated with a slight increase in cellular proliferation and a decrease in death rates. Furthermore, no alteration in the sensitivity of chordoma cells to chemotherapy was detected in response to the decrease in eEF2K expression which intriguingly promoted suppression of cell migratory and invasion related properties. Conclusion: Our findings indicate that the loss of eEF2K expression in chordoma cell lines results in the reduction of metastatic capacity.
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| 3. |
- Kovyrshin, Arseny, et al.
(författare)
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A quantum computing implementation of nuclearelectronic orbital (NEO) theory: Toward an exact pre-Born-Oppenheimer formulation of molecular quantum systems
- 2023
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Ingår i: Journal of Chemical Physics. - 1089-7690 .- 0021-9606. ; 158:21
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Tidskriftsartikel (refereegranskat)abstract
- Nuclear quantum phenomena beyond the Born-Oppenheimer approximation are known to play an important role in a growing number of chemical and biological processes. While there exists no unique consensus on a rigorous and efficient implementation of coupled electron-nuclear quantum dynamics, it is recognized that these problems scale exponentially with system size on classical processors and, therefore, may benefit from quantum computing implementations. Here, we introduce a methodology for the efficient quantum treatment of the electron-nuclear problem on near-term quantum computers, based upon the Nuclear-Electronic Orbital (NEO) approach. We generalize the electronic two-qubit tapering scheme to include nuclei by exploiting symmetries inherent in the NEO framework, thereby reducing the Hamiltonian dimension, number of qubits, gates, and measurements needed for calculations. We also develop parameter transfer and initialization techniques, which improve convergence behavior relative to conventional initialization. These techniques are applied to H2 and malonaldehyde for which results agree with NEO full configuration interaction and NEO complete active space configuration interaction benchmarks for ground state energy to within 10-6 hartree and entanglement entropy to within 10-4. These implementations therefore significantly reduce resource requirements for full quantum simulations of molecules on near-term quantum devices while maintaining high accuracy.
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| 4. |
- Kovyrshin, Arseny, et al.
(författare)
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Nonadiabatic Nuclear-Electron Dynamics: A Quantum Computing Approach
- 2023
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Ingår i: Journal of Physical Chemistry Letters. - 1948-7185. ; 14:31, s. 7065-7072
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Tidskriftsartikel (refereegranskat)abstract
- Coupled quantum electron-nuclear dynamics is oftenassociatedwith the Born-Huang expansion of the molecular wave functionand the appearance of nonadiabatic effects as a perturbation. On theother hand, native multicomponent representations of electrons andnuclei also exist, which do not rely on any a priori approximation.However, their implementation is hampered by prohibitive scaling.Consequently, quantum computers offer a unique opportunity for extendingtheir use to larger systems. Here, we propose a quantum algorithmfor simulating the time-evolution of molecular systems and apply itto proton transfer dynamics in malonaldehyde, described as a rigidscaffold. The proposed quantum algorithm can be easily generalizedto include the explicit dynamics of the classically described molecularscaffold. We show how entanglement between electronic and nucleardegrees of freedom can persist over long times if electrons do notfollow the nuclear displacement adiabatically. The proposed quantumalgorithm may become a valid candidate for the study of such phenomenawhen sufficiently powerful quantum computers become available.
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- Nykänen, Anton, et al.
(författare)
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Toward Accurate Post-Born-Oppenheimer Molecular Simulations on Quantum Computers: An Adaptive Variational Eigensolver with Nuclear-Electronic Frozen Natural Orbitals
- 2023
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Ingår i: Journal of Chemical Theory and Computation. - 1549-9626 .- 1549-9618. ; 19:24, s. 9269-9277
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Tidskriftsartikel (refereegranskat)abstract
- Nuclear quantum effects such as zero-point energy and hydrogen tunneling play a central role in many biological and chemical processes. The nuclear-electronic orbital (NEO) approach captures these effects by treating selected nuclei quantum mechanically on the same footing as electrons. On classical computers, the resources required for an exact solution of NEO-based models grow exponentially with system size. By contrast, quantum computers offer a means of solving this problem with polynomial scaling. However, due to the limitations of current quantum devices, NEO simulations are confined to the smallest systems described by minimal basis sets, whereas realistic simulations beyond the Born-Oppenheimer approximation require more sophisticated basis sets. For this purpose, we herein extend a hardware-efficient ADAPT-VQE method to the NEO framework in the frozen natural orbital (FNO) basis. We demonstrate on H2 and D2 molecules that the NEO-FNO-ADAPT-VQE method reduces the CNOT count by several orders of magnitude relative to the NEO unitary coupled cluster method with singles and doubles while maintaining the desired accuracy. This extreme reduction in the CNOT gate count is sufficient to permit practical computations employing the NEO method─an important step toward accurate simulations involving nonclassical nuclei and non-Born-Oppenheimer effects on near-term quantum devices. We further show that the method can capture isotope effects, and we demonstrate that inclusion of correlation energy systematically improves the prediction of difference in the zero-point energy (ΔZPE) between isotopes.
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