The analog of Koopmans’ theorem for virtual Kohn-Sham orbital energies

Gritsenko, Oleg,Baerends, Evert Jan Canadian Science Publishing 2009 Canadian journal of chemistry Vol.87 No.10

<P> An analog of Koopmans’ theorem is formulated for the energies, εa, of virtual Kohn-Sham (KS) molecular orbitals (MOs) from the requirement that the KS theory provides, in principle, not only the exact electron density, but also its exact response. The starting point is the Kohn-Sham analog of Koopmans’ theorem, relating the vertical ionization energies, Ii, to the energies, εi, of the occupied MOs ( Chong, D.P.; Gritsenko, O.V.; Baerends, E.J. J. Chem. Phys. 2002, 116, 1760 ). Combining this with the coupled-perturbed equations of time-dependent density functional theory (TDDFT), exact relations between the energies, εa, of virtual KS MOs and the excitation energies, ωia, and vertical ionization energies (VIPs), Ii, are obtained. In the small matrix approximation for the coupling matrix K of TDDFT, two limiting cases of these relations are considered. In the limit of a negligible matrix element, Kia,ia, the energy, εa, can be interpreted as (minus) the energy of ionization from the ?i → ?a excited state, εa ≈ -Ia, where -Ia is defined from the relation Ii = ωia + Ia. This relation breaks down in special cases, such as charge-transfer transitions and the HOMO-LUMO (highest occupied molecular orbital - lowest unoccupied molecular orbital) transition of a dissociating electron-pair bond (also of charge-transfer character). The present results highlight the important difference between virtual orbital energies in the Kohn-Sham model (εa ≈ -Ia) and in the Hartree-Fock model (εa ≈ -Aa). Kohn-Sham differences εa - εi approximate the excitation energy, ωia, while Hartree-Fock differences [Formula: see text] do not approximate excitation energies but approximate the difference of an ionization energy and an electron affinity, Ii - Aa. </P>

Double excitation effect in non-adiabatic time-dependent density functional theory with an analytic construction of the exchange–correlation kernel in the common energy denominator approximation

Gritsenko, Oleg V.,Jan Baerends, Evert Royal Society of Chemistry 2009 Physical chemistry chemical physics Vol.11 No.22

<P>Time-dependent density functional (response) theory (TDDF(R)T) is applied almost exclusively in its adiabatic approximation (ATDDFT), which is restricted to predominantly single electronic excitations and neglects additional roots of the TDDFT eigenvalue problem stemming from the interaction between single and double excitations. We incorporate the effect of the latter interaction into a non-adiabatic frequency-dependent and spatially non-local Hartree-exchange–correlation (Hxc) kernel <I>f</I> (<B>r</B><SUB>1</SUB>, <B>r</B><SUB>2</SUB>, <I>ω</I>), the explicit analytical expression of which is derived for interacting single and double excitations well separated from the other excitations, within the common energy denominator approximation (CEDA) for the Kohn–Sham (KS) and interacting density response functions, <I>χ</I><SUB>s</SUB> and <I>χ</I>, respectively. The kernel <I>f</I> (<B>r</B><SUB>1</SUB>, <B>r</B><SUB>2</SUB>, <I>ω</I>) obtained from the direct analytical inverse of <I>χ</I> and <I>χ</I><SUP>CEDA</SUP> is a sum of the delta-function and non-local orbital-dependent spatial terms with frequency-dependent factors, with which <I>f</I> acquires a modulated quadratic dependence on <I>ω</I>. The effective incorporation in <I>f</I> of the complete manifold of excited states (through the delta function term) represents an extension of the kernel reported by Maitra, Zhang, Cave, and Burke [<I>J. Chem. Phys.</I>, 2004, <B>120</B>, 5932]. In the TDDFT eigenvalue equations considered in the diagonal approximation, <I>f</I> generates two excitation energies <I>ω</I><SUB><I>q</I></SUB> and <I>ω</I><SUB><I>q</I>+1</SUB>, which both correspond to the same single KS excitation <I>ω</I>, thus producing the effect of the single–double excitation interaction.</P> <P>Graphic Abstract</P><P>Double excitations, not included in linear response TDDFT, can be captured with proper frequency dependence in the xc kernel. A common-energy-denominator based derivation of this frequency dependence is given. <IMG SRC='http://pubs.rsc.org/services/images/RSCpubs.ePlatform.Service.FreeContent.ImageService.svc/ImageService/image/GA?id=b903123e'> </P>

Development of a “deconstructed” vector based on the genome of grapevine virus A

D. A. Gritsenko,R. T. Kenzhebekova,N. D. Deryabina,N. N. Galiakparov 한국식물생명공학회 2019 Plant biotechnology reports Vol.13 No.2

The development of new vectors based on plant viruses creates more efficient vectors driving high expression levels of heterologous proteins. Currently, deconstructed vectors are more suitable for the expression of target genes. We attempted to develop a deconstructed vector based on the genome of grapevine virus A (GVA) by replacing the coat protein gene of GVA to the coat protein gene (aCP) of ACLSV (apple chlorotic leaf spot virus). This is the first work on creation of deconstructed vector based on GVA genome. The heterologous gene was placed under the control of the CP subgenomic promoter of GVA and fused with ORF5. The 2A self-cleaving sequence was inserted between the target protein and the protein encoded by ORF5 to enable the expression of separate proteins. The transient expression of coat protein of ACLSV from this vector was assessed in both transgenic plants carrying the CP of GVA and in non-transgenic plants. The level of aCP expression in transgenic plants was higher than the expression level in non-transgenic plants. Transgenic plants were developed in this study to increase target protein yield, because GVA cannot move between cells in its non-encapsidated form. The developed vector based on the grapevine virus A genome can be used in transient expression of different heterologous proteins utilizing magnifection method or via co-agroinfiltration with native genome of GVA.

Current-Voltage Characteristics and Charge Accumulation in the SiO2

Gadiyak , G. V,Gritsenko, V. A,Nasyrov, K. A,Perchilo, Yu. A 대한전자공학회 1993 ICVC : International Conference on VLSI and CAD Vol.3 No.1

The policrystalline silicon -oxide silicon - monocrystalline silicon structure (Si_(pol) SiO₂-Si_(mono)) has been investigated using C-V and I-V technic, thermally stimulated depolarization and the electron luminescence method. The experimental samples were fabricated as a MOS-capacitor, with policrystalline silicon contacts. The substrates were with orientation (001). They were treated in peroxide ammonia solution with subsequent cleaning in a hydrofluoric acid water solution. Oxide was thermally grown at temperature 1000 C in dry oxygen ambient. As the result of the different fabrication treatments we can obtain the positive charge build up in SiO₂ near the polysilicon oxide interface. To explain the asymmetry of electron capture on the traps for different sign of applied bias we suggest a model which takes into account dependence of cross section captures upon the electric field.

Counterpoise correction is not useful for short and Van der Waals distances but may be useful at long range

Sheng, Xiao Wei,Mentel, Lukasz,Gritsenko, Oleg V.,Baerends, Evert Jan Wiley Subscription Services, Inc., A Wiley Company 2011 Journal of computational chemistry Vol.32 No.13

<P><B>Abstract</B></P><P>This article investigates the errors in supermolecule calculations for the helium dimer. In a full CI calculation, there are two errors. One is the basis set superposition error (BSSE), the other is the basis set convergence error (BSCE). Both of the errors arise from the incompleteness of the basis set. These two errors make opposite contributions to the interaction energies. The BSCE is by far the largest error in the short range and larger than (but much closer to) BSSE around the Van der Waals minimum. Only at the long range, the BSSE becomes the larger error. The BSCE and BSSE largely cancel each other over the Van der Waals well. Accordingly, it may be recommended to not include the BSSE for the calculation of the potential energy curve from short distance till well beyond the Van der Waals minimum, but it may be recommended to include the BSSE correction if an accurate tail behavior is required. Only if the calculation has used a very large basis set, one can refrain from including the counterpoise correction in the full potential range. These results are based on full CI calculations with the aug‐cc‐pVXZ (<I>X</I> = D, T, Q, 5) basis sets. © 2011 Wiley Periodicals, Inc. J Comput Chem 32: 2896–2901, 2011</P>

Embedded spectral descriptors: learning the point-wise correspondence metric via Siamese neural networks

Zhiyu Sun,Yusen He,Andrey Gritsenko,Amaury Lendasse,Stephen Baek 한국CDE학회 2020 Journal of computational design and engineering Vol.7 No.1

A robust and informative local shape descriptor plays an important role in mesh registration. In this regard, spectral descriptors that are based on the spectrum of the Laplace–Beltrami operator have been a popular subject of research for the last decade due to their advantageous properties, such as isometry invariance. Despite such, however, spectral descriptors often fail to give a correct similarity measure for nonisometric cases where the metric distortion between the models is large. Hence, they are not reliable for correspondence matching problems when the models are not isometric. In this paper, it is proposed a method to improve the similarity metric of spectral descriptors for correspondence matching problems. We embed a spectral shape descriptor into a different metric space where the Euclidean distance between the elements directly indicates the geometric dissimilarity. We design and train a Siamese neural network to find such an embedding, where the embedded descriptors are promoted to rearrange based on the geometric similarity. We demonstrate our approach can significantly enhance the performance of the conventional spectral descriptors by the simple augmentation achieved via the Siamese neural network in comparison to other state-of-the-art methods.

Hydrogen radical enhanced atomic layer deposition of TaO_x: saturation studies and methods for oxygen deficiency control

Egorov, Konstantin V.,Kuzmichev, Dmitry S.,Sigarev, Andrey A.,Myakota, Denis I.,Zarubin, Sergey S.,Chizov, Pavel S.,Perevalov, Timofey V.,Gritsenko, Vladimir A.,Hwang, Cheol Seong,Markeev, Andrey M. The Royal Society of Chemistry 2018 Journal of Materials Chemistry C Vol.6 No.36

<P>The growth per cycle saturation behaviors depending on the precursor pulse duration, reactant pulse duration, and reactant concentration were examined for hydrogen radical enhanced atomic layer deposition (REALD) of TaOx using tantalum-ethoxide as the precursor and plasma-activated hydrogen as the reactant. The chemical state of the TaOx film was dependent on the active hydrogen pulse duration and hydrogen volume fraction in the H2/Ar plasma mixture. The density of the electronic states in the dielectric band gap increased with the increase in the plasma exposure time (6-50 s) and hydrogen volume fraction (7-70%) whereas Ta4f core-level X-ray photoelectron spectroscopy indicated that the observed defects in the TaOx band gap are related to the oxygen deficiency. The <I>ab initio</I> calculations of oxygen deficiency concentrations and the energy spectrum satisfactorily correlated with the experimental data. The demonstrated combination of the growth saturation availability with the precise control of oxygen deficiency concentrations in the PEALD process could be highly useful in fields in which oxide dielectrics with adjustable oxygen deficiencies are required.</P>