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Complex network analysis of free-energy landscapes

Related publications (31)

Advancing first principle-based molecular dynamics of biological systems with machine learning

Molecular dynamics (MD) simulations have emerged as a transformative approach to analyse molecular systems at the atomic level, offering valuable insights into complex biological processes. Many biological phenomena can only accurately be described by inco ...

EPFL2023

Comparing transferability in neural network approaches and linear models for machine-learning interaction potentials

Kevin Rossi

Atomic simulations using machine learning interatomic potential (MLIP) have gained a lot of popularity owing to their accuracy in comparison to conventional empirical potentials. However, the transferability of MLIP to systems outside the training set pose ...

AMER PHYSICAL SOC2023

Aggregation and Exploration of High-Dimensional Data Using the Sudokube Data Cube Engine

Christoph Koch, Sachin Basil John, Peter Lindner, Zhekai Jiang

We present Sudokube, a novel system that supports interactive speed querying on high-dimensional data using partially materialized data cubes. Given a storage budget, it judiciously chooses what projections to precompute and materialize during cube constru ...

Association for Computing Machinery2023

Systems and methods for de novo design of protein interactions with learned surface fingerprints

Anthony Marchand, Zander Harteveld, Pablo Gainza Cirauqui, Freyr Sverrisson, Andreas Scheck, Sarah Wehrle, Alexandra Krina Van Hall-Beauvais, Michael Bronstein

The present application relates to a computer-implemented systems and methods for protein interaction design using surface fingerprints. The method comprises predicting at least one target interface site with high binding propensity, wherein, optionally, t ...

2023

Deposition freezing, pore condensation freezing and adsorption: three processes, one description?

Mária Lbadaoui-Darvas, Athanasios Nenes

Heterogeneous ice nucleation impacts the hydrological cycle and climate through affecting cloud microphysical state and radiative properties. Despite decades of research, a quantitative description and understanding of heterogeneous ice nucleation remains ...

Copernicus GmbH2023

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

Bruno Lemaitre, Luciano Andres Abriata, Kuan-Lin Wu, Samuel Rommelaere, Han Xiao

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

Emergent non-Hermitian localization phenomena in the synthetic space of zero-dimensional bosonic systems

Fabrizio Minganti

Phase transitions in non-Hermitian systems are at the focus of cutting edge theoretical and experimental research. On the one hand, parity-time- (PT-) and anti-PT-symmetric physics have gained ever-growing interest, due to the existence of non-Hermitian sp ...

AMER PHYSICAL SOC2023

Opinion Formation over Adaptive Networks

Virginia Bordignon

An adaptive network consists of multiple communicating agents, equipped with sensing and learning abilities that allow them to extract meaningful information from measurements. The objective of the network is to solve a global inference problem in a decent ...

EPFL2022

A generic framework for hierarchical de novo protein design

Bruno Emanuel Ferreira De Sousa Correia, Zander Harteveld, Jaume Bonet Martinez, Fabian Sesterhenn, Che Yang, Stéphane Rosset

De novo protein design enables the exploration of novel sequences and structures absent from the natural protein universe. De novo design also stands as a stringent test for our understanding of the underlying physical principles of protein folding and may ...

National Academy of Sciences2022

A machine learning approach to portfolio pricing and risk management for high-dimensional problems

Damir Filipovic

We present a general framework for portfolio risk management in discrete time, based on a replicating martingale. This martingale is learned from a finite sample in a supervised setting. Our method learns the features necessary for an effective low-dimensi ...

WILEY2022

Towards automating de novo protein design for novel functionalities: controlling protein folds and protein-protein interactions

Zander Harteveld

The sheer size of the protein sequence space is massive: a protein of 100 residues can have 20^100 possible sequence combinations; and knowing that this exceeds the number of atoms in the universe, the chance of randomly discovering a stable new sequence w ...

EPFL2022