AiiDA: automated interactive infrastructure and database for computational science

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Publications associées (28)

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Motif Cut Sparsifiers

Mikhail Kapralov, Jakab Tardos, Mikhail Makarov

A motif is a frequently occurring subgraph of a given directed or undirected graph G (Milo et al.). Motifs capture higher order organizational structure of G beyond edge relationships, and, therefore, have found wide applications such as in graph clusterin ...

IEEE COMPUTER SOC2022

Computational tools and resources for designing new pathways to small molecules

Vassily Hatzimanikatis, Anastasia Sveshnikova

The metabolic engineering community relies on computational methods for pathway design to produce important small molecules in microbial hosts. Metabolic network databases are continuously curated and updated with known and novel reactions that expand the ...

CURRENT BIOLOGY LTD2022

Collapse-invariant properties of spaces equipped with signals or directions

Stefania Ebli

Collapsing cell complexes was first introduced in the 1930's as a way to deform a space into a topological-equivalent subspace with a sequence of elementary moves. Recently, discrete Morse theory techniques provided an efficient way to construct deformatio ...

EPFL2022

Electrical control of glass-like dynamics in vanadium dioxide for data storage and processing

Andras Kis, Andreas Schueler, Elison de Nazareth Matioli, Anna Krammer, Mohammad Samizadeh Nikooytabalvandani, Philip Johannes Walter Moll, Reza Soleiman Zadeh Ardebili, Guilherme Migliato Marega

Metal–oxide–semiconductor junctions are the building blocks of modern electronics and can provide a variety of functionalities, from memory to computing. The technology, however, faces constraints in terms of further miniaturization and compatibility with ...

Nature Research2022

Computational design of vaccine immunogens

Shuhao Xiao, Bruno Emanuel Ferreira De Sousa Correia, Andreas Scheck, Karla Montserrat Castro Gilabert

Computational protein engineering has enabled the rational design of customized proteins, which has propelled both sequence-based and structure-based immunogen engineering and delivery. By discerning antigenic determinants of viral pathogens, computational ...

CURRENT BIOLOGY LTD2022

Reconstruction of the Hippocampus

Henry Markram, Felix Schürmann, Armando Romani

The hippocampus is a widely studied brain region thought to play an important role in higher cognitive functions such as learning, memory, and navigation. The amount of data on this region increases every day and delineates a complex and fragmented picture ...

Springer2022

Computational design of novel protein–protein interactions – An overview on methodological approaches and applications

Bruno Emanuel Ferreira De Sousa Correia, Anthony Marchand, Alexandra Krina Van Hall-Beauvais

Protein–protein interactions (PPIs) govern numerous cellular functions in terms of signaling, transport, defense and many others. Designing novel PPIs poses a fundamental challenge to our understanding of molecular interactions. The capability to robustly ...

2022

Computed Three-Dimensional Atomic Force Microscopy Images of Biopolymers Using the Jarzynski Equality

Marcos Penedo Garcia

Three-dimensional atomic force microscopy (3D-AFM) has resolved three-dimensional distributions of solvent molecules at solid-liquid interfaces at the subnanometer scale. This method is now being extended to the imaging of biopolymer assemblies such as chr ...

2022