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Solvation Free Energies from Machine Learning Molecular Dynamics

Nicola Marzari, Nicéphore Arthur François Bonnet

The present work proposes an extension to the approach of [Xi, C; et al. J. Chem. Theory Comput. 2022, 18, 6878] to calculate ion solvation free energies from first-principles (FP) molecular dynamics (MD) simulations of a hybrid solvation model. The approa ...

Amer Chemical Soc2024

Encoding quantum-chemical knowledge into machine-learning models of complex molecular properties

Ksenia Briling

Statistical (machine-learning, ML) models are more and more often used in computational chemistry as a substitute to more expensive ab initio and parametrizable methods. While the ML algorithms are capable of learning physical laws implicitly from data, ad ...

EPFL2024

Structure and dynamics of liquid water from ab initio simulations: adding Minnesota density functionals to Jacob's ladder

Ursula Röthlisberger, Justin Villard, Martin Peter Bircher

The accurate representation of the structural and dynamical properties of water is essential for simulating the unique behavior of this ubiquitous solvent. Here we assess the current status of describing liquid water using ab initio molecular dynamics, wit ...

Royal Soc Chemistry2024

Thermal conductivity of Li 3 PS 4 solid electrolytes with ab initio accuracy

Michele Ceriotti, Federico Grasselli

The vast amount of computational studies on electrical conduction in solid-state electrolytes is not mirrored by comparable efforts addressing thermal conduction, which has been scarcely investigated despite its relevance to thermal management and (over)he ...

Amer Physical Soc2024

Machine learning-aided generative molecular design

Philippe Schwaller, Jeff Guo

Machine learning has provided a means to accelerate early-stage drug discovery by combining molecule generation and filtering steps in a single architecture that leverages the experience and design preferences of medicinal chemists. However, designing mach ...

Nature Portfolio2024

Microsecond time-resolved cryo-electron microscopy

Ulrich Lorenz

Microsecond time-resolved cryo-electron microscopy has emerged as a novel approach for directly observing protein dynamics. By providing microsecond temporal and near-atomic spatial resolution, it has the potential to elucidate a wide range of dynamics tha ...

2024

Multiscale biomolecular simulations in the exascale era

Ursula Röthlisberger, Simone Meloni

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 ...

Current Biology Ltd2024

Oxidative Defect Detection Within Free and Packed DNA Systems: A Quantum Mechanical/Molecular Mechanics (QM/ MM) Approach

Ursula Röthlisberger

Base excision repair enzymes (BERs) detect and repair oxidative DNA damage with efficacy despite the small size of the defects and their often only minor structural impact. A charge transfer (CT) model for rapid scanning of DNA stretches has been evoked to ...

Swiss Chemical Soc2024

Roughness Evolution Induced by Third-Body Wear

Jean-François Molinari, Tobias Brink, Antonio Joaquin Garcia Suarez

Surface roughness is a key factor when it comes to friction and wear, as well as to other physical properties. These phenomena are controlled by mechanisms acting at small scales, in which the topography of apparently flat surfaces is revealed. Roughness i ...

2024

Efficient and insightful descriptors for representing molecular and material space

Alexander Jan Goscinski

Data-driven approaches have been applied to reduce the cost of accurate computational studies on materials, by using only a small number of expensive reference electronic structure calculations for a representative subset of the materials space, and using ...

EPFL2024

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Solvation Free Energies from Machine Learning Molecular Dynamics

Nicola Marzari, Nicéphore Arthur François Bonnet

Amer Chemical Soc2024

Encoding quantum-chemical knowledge into machine-learning models of complex molecular properties

Ksenia Briling

EPFL2024

Structure and dynamics of liquid water from ab initio simulations: adding Minnesota density functionals to Jacob's ladder

Ursula Röthlisberger, Justin Villard, Martin Peter Bircher

Royal Soc Chemistry2024

Oxidative Defect Detection Within Free and Packed DNA Systems: A Quantum Mechanical/Molecular Mechanics (QM/ MM) Approach

Ursula Röthlisberger

Swiss Chemical Soc2024