Complex Energies and Transition-Dipoles for the Uracil anion Shape-type Resonances from stabilization curves via Padé

Absorption of slow moving electrons by neutral ground state nucleobases have been known to produce resonance, metastable, states. There are indications that such metastable states may play a key-role in DNA/RNA damage. Therefore, herein, we present an ab-initio, non-Hermitian investigation of the resonance positions and decay rates of the low lying shape-type states of the uracil anion. In addition, we calculate the complex transition dipoles between these resonance states. We employ the resonance via Padé (RVP) method to calculate these complex properties from real stabilization curves by analytical dilation into the complex plane. This method has al-ready been successfully applied to many small molecular systems and herein we present the first application of RVP to a medium-size system. The presented resonance energies are converged with respect to the size of the basis set and compared with previous theoretical works and experimental findings. Complex transition dipoles between the shape-type resonances are computed using the energy-converged basis set. The ability to calculate ab-initio energies and lifetimes of biologically relevant systems opens the door for studying reactions of such systems in which autoionization takes place. While the ability to also calculate their complex transition dipoles open the door for studying photo induced dynamics of such biological molecules.

Free Energy Surfaces and Barriers for Vacancy Diffusion on Al(100), Al(110), Al(111) Reconstructed Surfaces

Metadynamics is a popular enhanced sampling method based on the recurrent application of a history-dependent adaptive bias potential that is a function of a selected number of appropriately chosen collective variables. In this work, using metadynamics simulations, we performed a computational study for the diffusion of vacancies on three different Al surfaces [reconstructed Al(100), Al(110), and Al(111) surfaces]. We explored the free energy landscape of diffusion and estimated the barriers associated with this process on each surface. It is found that the surfaces are unique regarding vacancy diffusion. More specically, the reconstructed Al(110) surface presents four metastable states on the free energy surface having sizable and connected passage-ways with an energy barrier of height 0.55 eV. On the other hand, the reconstructed Al(100)/Al(111) surfaces exhibit two/three metastable states, respectively, with an energy barrier of height 0.33 eV. The findings in this study can help to understand surface vacancy diffusion in technologically relevant Al surfaces.

Electron Impact Ionization of Metastable States of Diatomic Molecules

The Binary-Encounter Bethe approach was applied to the estimation of total ionization induced by electron impact in metastable states of diatomic molecules. The cross sections recently obtained for N2 and CO are reviewed and the new results for H2 are presented, discussing their reliability through the comparison with other theoretical methods.

CALCULATION OF SCATTERING WAVE FUNCTIONS FOR METASTABLE STATES OF A DIATOMIC BERYLLIUM MOLECULE

Trong bài báo này chúng tôi trình bày sơ đồ thuật toán và kết quả tính toán hàm sóng tán xạ đối với các trạng thái siêu bền của phân tử lưỡng nguyên tử Beryli trong quang phổ laser. Nghiệm của bài toán biên được tính toán bằng chương trình phần mềm được biên soạn bởi tác giả bài báo cùng các cộng sự khoa học ở Viện Liên hiệp Nghiên cứu Hạt nhân Dubna, Thành phố Dubna, Liên bang Nga. Các thuật toán của chương trình tính toán này dựa trên phương pháp phần tử hữu hạn với độ chính xác cao. Hàm thế năng được cho ở dạng bảng giá trị được nối với hàm thế năng tiệm cận Waals bằng cách sử dụng đa thức nội suy Hermite và đảm bảo tính liên tục của nghiệm hàm cùng đạo hàm của nó. Sự hiệu quả của chương trình tính toán này được thể hiện bằng việc tính toán các giá trị năng lượng cộng hưởng ở dạng phức của các trạng thái siêu bền trong phổ xung động quay của phân tử lưỡng nguyên tử Beryli. Với các trạng thái siêu bền này, các hàm sóng tán xạ tương ứng với năng lượng cộng hưởng mang giá trị thực được tính toán và biểu diễn dưới dạng đồ thị.

Enhancing the Inhomogeneonus Photodynamics of Canonical Bacteriophytochrome

The ability of phytochromes to act as photoswitches in plants and microorganisms depends on interactions between a bilin-like chromophore and a protein. The interconversion occurs between the spectrally distinct red (Pr) and far-red (Pfr) conformers. This conformational change is triggered by the photoisomerization of the chromophore D-ring pyrrole. In this study, as a representative example of a phytochrome-bilin system, we take biliverdin IXα (BV) bound to bacteriophytochrome (BphP) from Deinococcus radiodurans. In the absence of light, we use an enhanced sampling molecular dynamics (MD) method to overcome the photoisomerization energy barrier. We find that the calculated free energy (FE) barriers between essential metastable states agree with spectroscopic results. We show that the enhanced dynamics of the BV chromophore in BphP triggers nanometer-scale conformational movements that propagate by two experimentally determined signal transduction pathways. Most importantly, we describe how the metastable states enable a thermal transition known as the dark reversion between Pfr and Pr, through a previously unknown intermediate state of Pfr. Here, for the first time, the heterogeneity of temperature-dependent Pfr states is presented at the atomistic level. This work paves a way toward understanding the complete mechanism of the photoisomerization of a bilin-like chromophore in phytochromes.

Enhancing the Inhomogeneonus Photodynamics of Canonical Bacteriophytochrome

The ability of phytochromes to act as photoswitches in plants and microorganisms depends on interactions between a bilin-like chromophore and a protein. The interconversion occurs between the spectrally distinct red (Pr) and far-red (Pfr) conformers. This conformational change is triggered by the photoisomerization of the chromophore D-ring pyrrole. In this study, as a representative example of a phytochrome-bilin system, we take biliverdin IXα (BV) bound to bacteriophytochrome (BphP) from Deinococcus radiodurans. In the absence of light, we use an enhanced sampling molecular dynamics (MD) method to overcome the photoisomerization energy barrier. We find that the calculated free energy (FE) barriers between essential metastable states agree with spectroscopic results. We show that the enhanced dynamics of the BV chromophore in BphP triggers nanometer-scale conformational movements that propagate by two experimentally determined signal transduction pathways. Most importantly, we describe how the metastable states enable a thermal transition known as the dark reversion between Pfr and Pr, through a previously unknown intermediate state of Pfr. Here, for the first time, the heterogeneity of temperature-dependent Pfr states is presented at the atomistic level. This work paves a way toward understanding the complete mechanism of the photoisomerization of a bilin-like chromophore in phytochromes.

Complex Energies and Transition-Dipoles for the Uracil anion Shape-type Resonances from stabilization curves via Padé

Absorption of slow moving electrons by neutral ground state nucleobases have been known to produce resonance, metastable, states. There are indications that such metastable states may play a key-role in DNA/RNA damage. Therefore, herein, we present an ab-initio, non-Hermitian investigation of the resonance positions and decay rates of the low lying shape-type states of the uracil anion. In addition, we calculate the complex transition dipoles between these resonance states. We employ the resonance via Padé (RVP) method to calculate these complex properties from real stabilization curves by analytical dilation into the complex plane. This method has al-ready been successfully applied to many small molecular systems and herein we present the first application of RVP to a medium-size system. The presented resonance energies are converged with respect to the size of the basis set and compared with previous theoretical works and experimental findings. Complex transition dipoles between the shape-type resonances are computed using the energy-converged basis set. The ability to calculate ab-initio energies and lifetimes of biologically relevant systems opens the door for studying reactions of such systems in which autoionization takes place. While the ability to also calculate their complex transition dipoles open the door for studying photo induced dynamics of such biological molecules.

Complex Energies and Transition-Dipoles for the Uracil anion Shape-type Resonances from stabilization curves via Padé

Absorption of slow moving electrons by neutral ground state nucleobases have been known to produce resonance, metastable, states. There are indications that such metastable states may play a key-role in DNA/RNA damage. Therefore, herein, we present an ab-initio, non-Hermitian investigation of the resonance positions and decay rates of the low lying shape-type states of the uracil anion. In addition, we calculate the complex transition dipoles between these resonance states. We employ the resonance via Padé (RVP) method to calculate these complex properties from real stabilization curves by analytical dilation into the complex plane. This method has al-ready been successfully applied to many small molecular systems and herein we present the first application of RVP to a medium-size system. The presented resonance energies are converged with respect to the size of the basis set and compared with previous theoretical works and experimental findings. Complex transition dipoles between the shape-type resonances are computed using the energy-converged basis set. The ability to calculate ab-initio energies and lifetimes of biologically relevant systems opens the door for studying reactions of such systems in which autoionization takes place. While the ability to also calculate their complex transition dipoles open the door for studying photo induced dynamics of such biological molecules.