Publications related to Molecular model

Efficient and insightful descriptors for representing molecular and material space

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

2023 Roadmap on molecular modelling of electrochemical energy materials

Alfredo Pasquarello, Chunmin Zhang, Assil Bouzid

New materials for electrochemical energy storage and conversion are the key to the electrification and sustainable development of our modern societies. Molecular modelling based on the principles of quantum mechanics and statistical mechanics as well as em ...

Iop Publishing Ltd2023

A recipe for cracking the quantum scaling limit with machine learned electron densities

Mario Geiger

A long-standing goal of science is to accurately simulate large molecular systems using quantum mechanics. The poor scaling of current quantum chemistry algorithms on classical computers, however, imposes an effective limit of about a few dozen atoms on tr ...

IOP Publishing Ltd2023

Atomic-level structure determination of amorphous molecular solids by NMR

David Lyndon Emsley, Arthur César Pinon, Pinelopi Moutzouri, Manuel Cordova

Structure determination of amorphous materials remains challenging, owing to the disorder inherent to these materials. Nuclear magnetic resonance (NMR) powder crystallography is a powerful method to determine the structure of molecular solids, but disorder ...

Nature Portfolio2023

Visualization, Interactive Handling and Simulation of Molecules in Commodity Augmented Reality in Web Browsers Using moleculARweb's Virtual Modeling Kits

Matteo Dal Peraro, Luciano Andres Abriata, Fabio Jose Cortes Rodriguez, Lucien Fabrice Krapp

moleculARweb (https://molecularweb.epfl.ch) began as a website for education and outreach in chemistry and structural biology through augmented reality (AR) content that runs in the web browsers of regular devices like smartphones, tablets, and computers. ...

SWISS CHEMICAL SOC2022

Random conical tilt reconstruction without particle picking in cryo-electron microscopy

Nicolas Boumal

A method is proposed to reconstruct the 3D molecular structure from micrographs collected at just one sample tilt angle in the random conical tilt scheme in cryo-electron microscopy. The method uses autocorrelation analysis on the micrographs to estimate f ...

INT UNION CRYSTALLOGRAPHY2022

New methods for structure determination and speciation by NMR crystallography

Martins Balodis

NMR crystallography has been around for half a century, but with the advent of NMR crystal structure determination protocols in the last decade it has shown perspectives that were not seen before. Amalgamation of NMR and crystal structure determination has ...

EPFL2022

Investigation of the specificity and mechanism of action of the ULK1/AMPK inhibitor SBI-0206965

Kei Sakamoto, Katyayanee Neopane

SBI-0206965, originally identified as an inhibitor of the autophagy initiator kinase ULK1, has recently been reported as a more potent and selective AMP-activated protein kinase (AMPK) inhibitor relative to the widely used, but promiscuous inhibitor Compou ...

2021

Fluid flow-induced left-right asymmetric decay of Dand5 mRNA in the mouse embryo requires a Bicc1-Ccr4 RNA degradation complex

Daniel Constam, Benjamin Marcel Daniel Rothé

Molecular left-right (L-R) asymmetry is established at the node of the mouse embryo as a result of the sensing of a leftward fluid flow by immotile cilia of perinodal crown cells and the consequent degradation of Dand5 mRNA on the left side. We here examin ...

Nature Portfolio2021

Trametinib Induces the Stabilization of a Dual GNAQ p.Gly48Leu-and FGFR4 p.Cys172Gly-Mutated Uveal Melanoma. The Role of Molecular Modelling in Personalized Oncology

Olivier Michielin, Krisztian Homicsko, Alexandre Wicky

We report a case of an uveal melanoma patient with GNAQ p.Gly48Leu who responded to MEK inhibition. At the time of the molecular analysis, the pathogenicity of the mutation was unknown. A tridimensional structural analysis showed that G alpha(q) can adopt ...

2020

Salt enhances the thermostability of enteroviruses by stabilizing capsid protein interfaces

Tamar Kohn, Matteo Dal Peraro, Simon Meister, Alessio Prunotto

Enteroviruses are common agents of infectious disease that are spread by the fecal-oral route. They are readily inactivated by mild heat, which causes the viral capsid to disintegrate or undergo conformational change. While beneficial for the thermal treat ...

American Society for Microbiology2020

Correlation between Optical Activity and the Helical Molecular Orbitals of Allene and Cumulenes

Anne-Clémence Corminboeuf, Marc Hamilton Folkmann Garner

Helical frontier molecular orbitals (MOs) appear in disubstituted allenes and even-n cumulenes. Chiral molecules are optically active, but while these molecules are single-handed chiral, p-orbitals of both helicities are present. Here we computationally ex ...

AMER CHEMICAL SOC2020

Microscopic Detection Analysis of Single Molecules in MoS2 Membrane Nanopores

Aleksandra Radenovic, Michael Graf

A systematic microscopic analysis of the various resistive effects involved in the electronic detection of single biomolecules in a nanopore of a MoS2 nanoribbon is presented. The variations of the transverse electronic current along the two-dimensional (2 ...

2020

Building blocks for commodity augmented reality-based molecular visualization and modeling in web browsers

Luciano Andres Abriata

For years, immersive interfaces using virtual and augmented reality (AR) for molecular visualization and modeling have promised a revolution in the way how we teach, learn, communicate and work in chemistry, structural biology and related areas. However, m ...

2020

Characterization of Protein-Membrane Interfaces through a Synergistic Computational-Experimental Approach

Alessio Prunotto

The characterization of biological interfaces is widely recognized as one of the main challenges for modern biology. In particular, biological membranes are nowadays known to be an active environment that allows membrane proteins to perform their work and ...

EPFL2020

Spectro-electrochemical toolbox for monitoring and controlling quinone-mediated redox-driven molecular gripping

Jovana Milic, Thomas Schneeberger

The control of molecular systems by electrical charge or light is a prerequisite for their application in nanoelectronics. Such potential has been uniquely exploited in quinone-based resorcin[4]arene cavitands that can act as molecular grippers, reversibly ...

2019

Synergy of classical and quantum computational methods to investigate the properties of microporous materials

Daniele Ongari

The aim of this thesis is to explore the power and the limits of classical and quantum molecular modelling, for the investigation of the adsorption properties of microporous crystalline materials. The materials analyzed are metal organic frameworks (MOFs) ...

EPFL2019

The Quest for Molecular Grippers: Photo-Electric Control of Molecular Gripping Machinery

Jovana Milic

The quest for nanoscale molecular machines has inspired the search for their close relatives, molecular grippers. This path was paved by the development of resorcin[4]arene cavitands and their quinone-based redox-active congeners. In this Concept article, ...

2019

Unsupervised machine learning in atomistic simulations, between predictions and understanding

Michele Ceriotti

Automated analyses of the outcome of a simulation have been an important part of atomistic modeling since the early days, addressing the need of linking the behavior of individual atoms and the collective properties that are usually the final quantity of i ...

2019

Determination and evaluation of the nonadditivity in wetting of molecularly heterogeneous surfaces

Francesco Stellacci, Michele Ceriotti, Sylvie Roke, Quy Ong Khac, Halil Ibrahim Okur, David Mark Wilkins, Zhi Luo, Anna Murello, Filip Kovacik

The interface between water and folded proteins is very complex. Proteins have "patchy" solvent-accessible areas composed of domains of varying hydrophobicity. The textbook understanding is that these domains contribute additively to interfacial properties ...

National Academy of Sciences2019