Ursula Röthlisberger

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A series of ca. 20-ns molecular dynamics simulation runs of the N-terminal H4 histone tail in its un- and tetraacetylated forms were performed using three different long-range electrostatic treatments namely, spherical-cutoff, reaction field, and particle ...

Microbial production of desired compounds provides an efficient framework for the development of renewable energy resources. To be competitive to traditional chemistry, one requirement is to utilize the full capacity of the microorganism to produce target ...

MiMiC is a framework for performing multiscale simulations in which loosely coupled external programs describe individual subsystems at different resolutions and levels of theory. To make it highly efficient and flexible, we adopt an interoperable approach ...

Two D−π−A dyes based on the dithieno[3,2-b:2′,3′-d]pyrrole π-bridge (DTP) were synthesized, characterized using UV−vis absorption spectroscopy and electrochemistry, modeled using quantum chemical calculations, and used as sensitizers in dye-sensitized sola ...

Nuclear quantum dynamics beyond the Born-Oppenheimer approximation is performed using quantum trajectories. Within the adiabatic representation of the electronic states, NABDY (NonAdiabatic Bohmian DYnamics) is used in combination with DFT and LR-TDDFT to ...

The structure and dynamics of the retinal chromophore of rhodopsin are investigated systematically in different environments (vacuum, methanol soln., and protein binding pocket) and with different computational approaches (classical, quantum, and hybrid qu ...

Mixtures of cations or halides with FAPbI(3) (where FA is formamidinium) lead to high efficiency in perovskite solar cells (PSCs) but also to blue-shifted absorption and long-term stability issues caused by loss of volatile methylammonium (MA) and phase se ...

A simple scheme for the evaluation of the core spin-polarization contribution within pseudopotential electronic structure methods is proposed. The method uses a reconstruction of the all-electron wave functions and the frozen valence spin-d. approxn. to so ...

We perform a replica exchange molecular dynamics simulation corresponding to a 2.8 mu s total time for the extensive enhanced sampling of the conformational space of the C-terminal part (residues 124-226) of the mouse prion protein (PrP); 1.3% of the confo ...

The non-relativistic quantum dynamics of nuclei and electrons is solved within the framework of quantum hydrodynamics using the adiabatic representation of the electronic states. An on-the-fly trajectory-based nonadiabatic molecular dynamics algorithm is d ...

The complexity of biological systems and processes, spanning molecular to macroscopic scales, necessitates the use of multiscale simulations to get a comprehensive understanding. lar dynamics (MD) simulations are crucial for capturing processes beyond the ...

A thorough theoretical description of ultrafast phenomena that occur in complex systems constitutes a formidable challenge. It not only necessitates the use of quantum mechanical methods that can describe ground and possibly even electronically excited sta ...

Zinc is an essential metal for many proteins. Here, the authors propose a model based on 3D convolutional networks to predict the location of zinc in experimental and computationally predicted structures within a framework readily extensible to other metal ...

Metal halide perovskites have shown exceptional potential in converting solar energy to electric power in photovoltaics, yet their application is hampered by limited operational stability. This stimulated the development of hybrid layered (two-dimensional, ...

In this paper, we extend the implementation of nonadiabatic molecular dynamics within the framework of time-dependent density-functional theory in an external field described in Tavernelli et al. [Phys. Rev. A 81, 052508 (2010)] by calculating on-the-fly p ...

Ursula Röthlisberger

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Influence of Long-range Electrostatic Treatments on the Folding of the N-terminal H4 Histone Tail Peptide

Integrating computational methods to retrofit enzymes to synthetic pathways

MiMiC: A high-performance framework for multiscale molecular dynamics simulations

Cold Ion Spectroscopy Reveals the Intrinsic Structure of a Decapeptide

Unravelling the Potential for Dithienopyrrole Sensitizers in Dye-Sensitized Solar Cells

Excited State Dynamics with Quantum Trajectories

Solvent and protein effects on the structure and dynamics of the rhodopsin chromophore

Vapor-assisted deposition of highly efficient, stable black-phase FAPbI(3) perovskite solar cells

Core spin-polarization correction in pseudopotential-based electronic structure calculations

Enhanced Sampling Molecular Dynamics Identifies PrPSc Structures Harboring a C-Terminal beta-Core

A Simple Approach to Room Temperature Phosphorescent Allenylidene Complexes

Trajectory-based solution of the nonadiabatic quantum dynamics equations: an on-the-fly approach for molecular dynamics simulations

Multiscale biomolecular simulations in the exascale era

Mixed Quantum Mechanical/Molecular Mechanical (QM/MM) simulations of Adiabatic and Nonadiabatic Ultrafast Phenomena

Atom-centered potentials for describing dispersion forces in density functional theory

Metal3D: a general deep learning framework for accurate metal ion location prediction in proteins

Predicting noncovalent interactions between aromatic biomolecules with London-dispersion-corrected DFT

Aryl-Acetylene Layered Hybrid Perovskites in Photovoltaics

Local control theory in trajectory-based nonadiabatic dynamics

Role of protein frame and solvent for the redox properties of azurin from Pseudomonas Aeruginosa