Publications related to Exploring the Molecular Conformation Space by Soft Molecule- Surface Collision

Related publications (40)

Engineering Spin Interaction Channels of FePc on Au(111)

We demonstrate the reversible control of interactions between a local molecular spin, hosted within an iron phthalocyanine (FePc) molecule, and the conduction electrons of a supporting Au(111) surface. Using the tip of a scanning tunneling microscope, we d ...

American Chemical Society (ACS)2025

2D Metalorganic Ferromagnets

Diego Radillo Ochoa, Céline Hensky, Christian Wäckerlin, Quy Hien Le

Low-dimensional materials exhibiting stable magnetic ordering are interesting from a fundamental point of view as well as for future application in information technologies. Metalorganic magnets, created by linking metal atoms with specific organic molecul ...

WILEY2025

Boon and Bane of Local Solid State Chemistry on the Performance of LSM-Based Solid Oxide Electrolysis Cells

Hanna Christine Türk

Advanced Energy Materials published by Wiley-VCH GmbH.High-temperature solid oxide cells are highly efficient energy converters. However, their lifetime is limited by rapid deactivation. Little is known about the local, atomic scale transformation that dri ...

2025

Development of synthetic methods starting from cyclopropenes: taming cyclopropyl radical, cyclopropyl and cyclopropenium cations

Vladyslav Smyrnov

Due to the high ring strain and unique bonding, cyclopropenes represent important 3-carbon synthons in organic synthesis. Intrigued by the unique reactivity of cyclopropenes, we were interested in further exploration of their chemical properties. Trying to ...

EPFL2025

Dynamical features of smooth muscle actin pathological mutants: The arginine-257(258)-Cysteine cases

Andrea Cavalli

The R257(8)C mutation in smooth muscle actins, ACTG2 and ACTA2, is the most frequent cause of severe genetic diseases: namely, visceral myopathy, and familial thoracic aortic aneurysms and dissections, which respectively, stem from impairment of the viscer ...

ELSEVIER2025

Engineering novel protein interactions with therapeutic potential using deep learning-guided surface design

Anthony Marchand

Proteins are foundational biomolecules of life playing a crucial role in a myriad of biological processes. Their function often requires interplay with other biomolecules, including proteins themselves. Protein-protein interactions (PPIs) are essential for ...

EPFL2024

Inverse Design of Singlet-Fission Materials with Uncertainty-Controlled Genetic Optimization

Rubén Laplaza Solanas, Jacob Terence Blaskovits

Singlet fission has shown potential for boosting the efficiency of solar cells, but the scarcity of suitable molecular materials hinders its implementation. We introduce an uncertainty-controlled genetic algorithm (ucGA) based on ensemble machine learning ...

Wiley2024

Hydrophobic Interaction and its Small Molecule effect

Ting Mao

Protein stabilization has a crucial rule sustaining biological functionality, disease prevention, and pharmaceutical formulation stabilization, and yet its stabilization mechanism by small molecules such as amino acids is not fully understood. In this work ...

EPFL2024

Predicting protein interactions using geometric deep learning on protein surfaces

Freyr Sverrisson

In the domain of computational structural biology, predicting protein interactions based on molecular structure remains a pivotal challenge. This thesis delves into this challenge through a series of interconnected studies. The first chapter introduces th ...

EPFL2024

Bridging Native and Intrinsic Structures of Microhydrated Biomolecules by Cold Ion Spectroscopy

Andrei Zviagin

Solving native structures of such large molecules, like biomolecules, is often challenging, particularly due to the potentially infinite number of non-covalent interactions with water. In this thesis, we report the use of cold ion gas-phase action spectros ...

EPFL2023

Development of tools and methods for protein identification: From single molecules to in vivo applications

Salome Riccarda Püntener

As the fundamental machinery orchestrating cellular functions, proteins influence the state of every cell profoundly. As cells exhibit significant variations from one to another, analyzing the proteome on a single-cell level is imperative to unravel their ...

EPFL2024

A Geometric Transformer for Structural Biology: Development and Applications of the Protein Structure Transformer

Lucien Fabrice Krapp

Proteins, the central building blocks of life, play pivotal roles in nearly every biological function. To do so, these macromolecular structures interact with their surrounding environment in complex ways, leading to diverse functional behaviors. The predi ...

EPFL2023

Ion Spectroscopy Reveals Structural Difference for Proteins Microhydrated by Retention and Condensation of Water

Oleg Boyarkine, Andrei Zviagin

Protein ubiquitin in its +7 charge state microhydrated by 5 and 10 water molecules has been interrogated in the gas phase by cold ion UV/IR spectroscopy. The complexes were formed either by condensing water onto the unfolded bare proteins in a temperature- ...

Amer Chemical 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

Computational design of dynamic receptor—peptide signaling complexes applied to chemotaxis

Andreas Füglistaler, Ana Paola Rico Villarreal, Patrick Daniel Barth, Mahdi Hijazi, Aurélien Laurent Jean-Charles Oggier, Robert Everett Jefferson

Engineering protein biosensors that sensitively respond to specific biomolecules by triggering precise cellular responses is a major goal of diagnostics and synthetic cell biology. Previous biosensor designs have largely relied on binding structurally well ...

Nature Research2023

Protein target highlights in CASP15: Analysis of models by structure providers

Bruno Lemaitre, Luciano Andres Abriata, Samuel Rommelaere

We present an in-depth analysis of selected CASP15 targets, focusing on their biological and functional significance. The authors of the structures identify and discuss key protein features and evaluate how effectively these aspects were captured in the su ...

WILEY2023

Investigating the intra-molecular and inter-molecular effects of post-translational modifications on intrinsically disordered protein regions and structured protein regions

Zhidian Zhang

Post-translational modifications (PTMs) play a pivotal role in regulating protein structure, interaction, and function. Aberrant PTM patterns are associated with diseases. Moreover, individual PTMs have a complex interaction with each other, known as PTM c ...

EPFL2024

Microsecond Time-Resolved Cryo-Electron Microscopy

Oliver Florian Harder

Recently, single-particle cryo-electron microscopy emerged as a technique capable of determining protein structures at near-atomic resolution and resolving protein dynamics with a temporal resolution ranging from second to milliseconds. This thesis describ ...

EPFL2024

Fast viral dynamics revealed by microsecond time-resolved cryo-EM

Marcel Drabbels, Ulrich Lorenz, Oliver Florian Harder, Sarah Victoria Barrass

Observing proteins as they perform their tasks has largely remained elusive, which has left our understanding of protein function fundamentally incom- plete. To enable such observations, we have recently proposed a technique that improves the time resoluti ...

Nature Research2023

Structural heterogeneity of the ion and lipid channel TMEM16F

Horst Arthur Vogel

Transmembrane protein 16 F (TMEM16F) is a Ca2+-activated homodimer which functions as an ion channel and a phospholipid scramblase. Despite the availability of several TMEM16F cryogenic electron microscopy (cryo-EM) structures, the mechanism of activation ...

Nature Portfolio2024