Characterizing Conical Intersections in DNA/RNA Nucleobases with Multiconfigurational Wave Functions of Varying Active Space Size

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Regulation of cGAS- and RLR-mediated immunity to nucleic acids

Andrea Ablasser

Pathogen-derived nucleic acids are crucial signals for innate immunity. Despite the structural similarity between those and host nucleic acids, mammalian cells have been able to evolve powerful innate immune signaling pathways that originate from the detec ...

NATURE PUBLISHING GROUP2020

Optical absorption properties of metal-organic frameworks: solid stateversusmolecular perspective

Berend Smit, Anne-Clémence Corminboeuf, Ivano Tavernelli, Maria Fumanal Quintana

The vast chemical space of metal and ligand combinations in Transition Metal Complexes (TMCs) gives rise to a rich variety of electronic excited states with local and non-local character such as intra-ligand (IL), metal-centered (MC), metal-to-ligand (MLCT ...

2020

Electronic and structural dynamics in DNA single strands

Benjamin Bauer

The absorption, conversion and transport of electronic energy in molecular aggregates is at the heart of many important natural and artificial photochemical systems, including organic solar cell materials, photosynthetic light-harvesting complexes and DNA ...

EPFL2021

Human shelterin protein POT1 prevents severe telomere instability induced by homology-directed DNA repair

Joachim Lingner, Galina Glousker, Anna-Sophia Briod

The evolutionarily conserved POT1 protein binds single-stranded G-rich telomeric DNA and has been implicated in contributing to telomeric DNA maintenance and the suppression of DNA damage checkpoint signaling. Here, we explore human POT1 function through g ...

WILEY2020

Optimal radial basis for density-based atomic representations

Michele Ceriotti, Félix Benedito Clément Musil, Jigyasa Nigam, Sergey Pozdnyakov, Alexander Jan Goscinski

The input of almost every machine learning algorithm targeting the properties of matter at the atomic scale involves a transformation of the list of Cartesian atomic coordinates into a more symmetric representation. Many of the most popular representations ...

2021

Electronic Relaxation Dynamics of UV-Photoexcited 2-Aminopurine-Thymine Base Pairs in Watson-Crick and Hoogsteen Conformations

Rebecca Ann Ingle, Hugo Jean Baptiste Marroux

The fluorescent analogue 2-aminopurine (2AP) of the canonical nucleobase adenine (6-aminopurine) base-pairs with thymine (T) without disrupting the helical structure of DNA. It therefore finds frequent use in molecular biology for probing DNA and RNA struc ...

AMER CHEMICAL SOC2019

Weakness of Correlation Effect Manifestation in BaNi2As2: An ARPES and LDA plus DMFT Study

Daniil Yevtushynsky

The electronic spectral function of BaNi2As2 is investigated using both angle-resolved photoemission spectroscopy (ARPES) and a combined computational scheme of local density approximation and dynamical mean-field theory (LDA + DMFT). In contrast to the we ...

AMER CHEMICAL SOC2021

Quantum mechanical static dipole polarizabilities in the QM7b and AlphaML showcase databases

Michele Ceriotti, David Mark Wilkins, Andrea Grisafi

While density functional theory (DFT) is often an accurate and efficient methodology for evaluating molecular properties such as energies and multipole moments, this approach often yields larger errors for response properties such as the dipole polarizabil ...

2019

Detecting topological variations of DNA at single-molecule level

Aleksandra Radenovic, Georg Fantner, Adrian Pascal Nievergelt, Ke Liu

In addition to their use in DNA sequencing, ultrathin nanopore membranes have potential applications in detecting topological variations in deoxyribonucleic acid (DNA). This is due to the fact that when topologically edited DNA molecules, driven by electro ...

Nature Research2019

m6A methylation potentiates cytosolic dsDNA recognition in a sequence-specific manner

Andrea Ablasser, Muhammet Fatih Gülen

Nucleic acid sensing through pattern recognition receptors is critical for immune recognition of microbial infections. Microbial DNA is frequently methylated at the N-6 position of adenines (m6A), a modification that is rare in mammalian host DNA. We show ...

ROYAL SOC2021

High-order geometric integrators for representation-free Ehrenfest dynamics

Jiri Vanicek, Seonghoon Choi

Ehrenfest dynamics is a useful approximation for ab initio mixed quantum-classical molecular dynamics that can treat electronically nonadiabatic effects. Although a severe approximation to the exact solution of the molecular time-dependent Schrödinger equa ...

2021

Shedding Light on the Basis Set Dependence of the Minnesota Functionals: Differences Between Plane Waves, Slater Functions, and Gaussians

Ursula Röthlisberger, Martin Peter Bircher, Pablo Lopez Tarifa

The Minnesota family of exchange-correlation (xc) functionals are among the most popular, accurate, and abundantly used functionals available to date. However, their use in plane-wave based first-principles MD has been limited by their sparse availability. ...

2019