抗原变异可使得多种致病微生物易于逃避宿主免疫应答。表达在感染红细胞表面的恶性疟原虫红细胞表面蛋白1（PfPMP1）与感染红细胞、内皮细胞、树突状细胞以及胎盘的单个或多个受体作用，在黏附及免疫逃避中起关键的作用。每个单倍体基因组var基因家族编码约60种成员，通过启动转录不同的var基因变异体为抗原变异提供了分子基础。

疟原虫var基因转换速率变化导致抗原变异[英]／Paul H, Robert P, Christodoulou Z, et al//Proc Natl Acad Sci U S A

[신간의 별자리x] 우리/미술, 그리고 ‘슬픔의 박물관’

Deposits of clastic carbonate-dominated (calciclastic) sedimentary slope systems in the rock record have been identified mostly as linearly-consistent carbonate apron deposits, even though most ancient clastic carbonate slope deposits fit the submarine fan systems better. Calciclastic submarine fans are consequently rarely described and are poorly understood. Subsequently, very little is known especially in mud-dominated calciclastic submarine fan systems. Presented in this study are a sedimentological core and petrographic characterisation of samples from eleven boreholes from the Lower Carboniferous of Bowland Basin (Northwest England) that reveals a >250 m thick calciturbidite complex deposited in a calciclastic submarine fan setting. Seven facies are recognised from core and thin section characterisation and are grouped into three carbonate turbidite sequences. They include: 1) Calciturbidites, comprising mostly of highto low-density, wavy-laminated bioclast-rich facies; 2) low-density densite mudstones which are characterised by planar laminated and unlaminated muddominated facies; and 3) Calcidebrites which are muddy or hyper-concentrated debrisflow deposits occurring as poorly-sorted, chaotic, mud-supported floatstones. These

Phd by thesis

: The unpolarized absorption and circular dichroism spectra of the fundamental vibrational transitions of the chiral molecule, 4-methyl-2-oxetanone, are calculated ab initio. Harmonic force fields are obtained using Density Functional Theory (DFT), MP2, and SCF methodologies and a 5S4P2D/3S2P (TZ2P) basis set. DFT calculations use the Local Spin Density Approximation (LSDA), BLYP, and Becke3LYP (B3LYP) density functionals. Mid-IR spectra predicted using LSDA, BLYP, and B3LYP force fields are of significantly different quality, the B3LYP force field yielding spectra in clearly superior, and overall excellent, agreement with experiment. The MP2 force field yields spectra in slightly worse agreement with experiment than the B3LYP force field. The SCF force field yields spectra in poor agreement with experiment.The basis set dependence of B3LYP force fields is also explored: the 6-31G* and TZ2P basis sets give very similar results while the 3-21G basis set yields spectra in substantially worse agreements with experiment. jg

Ab initio calculation of vibrational absorption and circular dichroism spectra using density functional force fields

With recent advances in electronic structure methods, first-principles calculations of electronic response properties, such as linear and nonlinear polarizabilities, have become possible for molecules with more than 100 atoms. Basis set incompleteness is typically the main source of error in such calculations since traditional diffuse augmented basis sets are too costly to use or suffer from near linear dependence. To address this problem, we construct the first comprehensive set of property-optimized augmented basis sets for elements H–Rn except lanthanides. The new basis sets build on the Karlsruhe segmented contracted basis sets of split-valence to quadruple-zeta valence quality and add a small number of moderately diffuse basis functions. The exponents are determined variationally by maximization of atomic Hartree–Fock polarizabilities using analytical derivative methods. The performance of the resulting basis sets is assessed using a set of 313 molecular static Hartree–Fock polarizabilities. The mean...

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Property-optimized gaussian basis sets for molecular response calculations.

A recently proposed local self-interaction correction (LSIC) method [Zope \textit{et al.} J. Chem. Phys., 2019,{\bf 151}, 214108] when applied to the simplest local density approximation provides significant improvement over standard Perdew-Zunger SIC (PZSIC) for both equilibrium properties such as total or atomization energies as well as properties involving stretched bond such as barrier heights. The method uses an iso-orbital indicator to identify the single-electron regions. To demonstrate the LSIC method, Zope \textit{et al.} used the ratio $z_\sigma$ of von Weizsacker $\tau_\sigma^W$ and total kinetic energy densities $\tau_\sigma$, ($z_\sigma = \tau_\sigma^W/\tau_\sigma$) as a scaling factor to scale the self-interaction correction. The present work further explores the LSIC method using a simpler scaling factor as a ratio of orbital and spin densities in place of the ratio of kinetic energy densities. We compute a wide array of both, equilibrium and non-equilibrium properties using the LSIC and orbital scaling methods using this simple scaling factor and compare them with previously reported results. Our study shows that the present results with simple scaling factor are comparable to those obtained by LSIC($z_\sigma$) for most properties but have slightly larger errors. We furthermore study the binding energies of small water clusters using both the scaling factors. Our results show that LSIC with $z_{\sigma}$ has limitation in predicting the binding energies of weakly bonded system due to the inability of $z_{\sigma}$ to distinguish weakly bonded region from slowly varying density region. LSIC when used with density ratio as a scaling factor, on the other hand, provides good description of water cluster binding energies, thus highlighting the appropriate choice of iso-orbital indicator.

Local self-interaction correction method with a simple scaling factor.

Most widely used density functional approximations suffer from self-interaction (SI) error, which can be corrected using the Perdew-Zunger (PZ) self-interaction correction (SIC). We implement the recently proposed size-extensive formulation of PZ-SIC using Fermi-Lowdin Orbitals (FLOs) in real space, which is amenable to systematic convergence and large-scale parallelization. We verify the new formulation within the generalized Slater scheme by computing atomization energies and ionization potentials of selected molecules and comparing to those obtained by existing FLOSIC implementations in Gaussian based codes. The results show good agreement between the two formulations, with new real-space results somewhat closer to experiment on average for the systems considered. We also obtain the ionization potentials and atomization energies by scaling down the Slater statistical average of SIC potentials. The results show that scaling down the average SIC potential improves both atomization energies and ionization potentials, bringing them closer to experiment. Finally, we verify the present formulation by calculating the barrier heights of chemical reactions in the BH6 dataset, where significant improvements are obtained relative to Gaussian based FLOSIC results.

Implementation of Perdew-Zunger self-interaction correction in real space using Fermi-L\"owdin orbitals

We study the electronic structure of C60 fullerenes functionalized with a thiophene-diketo-pyrrolopyrrole-thiophene based chromophore using density functional theory combined with large polarized basis sets. As the attached chromophore has electron donor character, the functionalization of the fullerene leads to a donor-acceptor (DA) system. We examine in detail the effect of the linker and the addition site on the electronic structure of the functionalized fullerenes. We further study the electronic structure of these DA complexes with a focus on the charge transfer excitations. Finally, we examine the interface of the functionalized fullerenes with the widely used poly(3-hexylthiophene-2,5-diyl) (P3HT) donor. Our results show that all functionalized fullerenes with an exception of the C60-pyrrolidine [6,6], where the pyrrolidine is attached at a [6,6] site, have larger electron affinities relative to the pristine C60 fullerene. We also estimate the quasi-particle gap, lowest charge transfer excitation energy, and the exciton binding energies of the functionalized fullerene-P3MT model systems. Results show that the exciton binding energies in these model complexes are slightly smaller compared to a similarly prepared phenyl-C61-butyric acid methyl ester (PCBM)-P3MT complex.

Density functional study of the electronic structure of dye-functionalized fullerenes and their model donor-acceptor complexes containing P3HT

We report a detailed investigation of structural, electronic, and spectroscopic properties of VSc2N@C68 endohedral fullerene. First, the candidate structures of the ground state are obtained using a systematic approach in which 900 isomers of endohedral fullerenes were screened for their energetic stability. The stability of some of the most promising isomers was studied using density functional theory at the all-electron level using large polarized Gaussian basis sets. Although the dopant vanadium atom is also in the same charge state as Sc, the doping changes the structure and the spin state from that of Sc3N@C68. The d-orbitals of the V atom lead to a spin state with spin moment of 2 μB for the endohedral fullerene. The spin–orbit coupling strength is, however, weak, leading to vanishingly small zero-field splitting of the spin levels. The ionization energy, electron affinity, and the quasi-particle gap of the most stable isomer are comparable to those of C60. The vibrational frequency analysis shows t...

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Electronic and Optical Properties of VSc2N@C68 Fullerene

We present a detailed study of charge transfer (CT) excited states for a large number of configurations in a light-harvesting Carotenoid-diaryl-Porphyrin-C60 (CPC60) molecular triad. The chain-like molecular triad undergoes photoinduced charge transfer process exhibiting a large excited state dipole moment, making it suitable for application to molecular-scale opto-electronic devices. An important consideration is that the structural flexibility of the CPC60 triad impacts its dynamics in solvents. Since experimentally measured dipole moments for the triad of ∼110 D and ∼160 D strongly indicate a range in structural variability in the excited state, studying the effect of structural changes on the CT excited state energetics furthers the understanding of its charge transfer states. We have calculated the variation in the lowest CT excited state energies by performing a scan of possible variation in the structure of the triad. Some of these configurations were generated by incrementally scanning a 360° torsional (dihedral) twist at the C60-porhyrin linkage and the porphyrin-carotenoid linkage. Additionally, five different CPC60 conformations were studied to determine the effect of pi-conjugation and particle-hole Coulombic attraction on the CT excitation energies. Our calculations show that configurational changes in the triad induces a variation of ∼0.6 eV in CT excited state energies in the gas-phase. The corresponding calculated excited state dipoles show a range of 47 D-188 D. The absorption spectra and density of states of these structures show little variation except for the structures where the porphyrin and aryl conjugation is changed.

Rajendra R. Zope

Papers

Local self-interaction correction method with a simple scaling factor.

Implementation of Perdew-Zunger self-interaction correction in real space using Fermi-L\"owdin orbitals

Density functional study of the electronic structure of dye-functionalized fullerenes and their model donor-acceptor complexes containing P3HT

Electronic and Optical Properties of VSc2N@C68 Fullerene

The effect of structural changes on charge transfer states in a light-harvesting carotenoid-diaryl-porphyrin-C60 molecular triad