High level synthesis of Smith-Waterman dataflow implementations

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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

Advanced Silicon and SWIR Single-Photon Avalanche Diodes: Design, Simulation, and Characterization

Ekin Kizilkan

Low-level light detection with high spatial and timing accuracy is a growing area of interest by virtue of applications such as light detection and ranging (LiDAR), biomedical imaging, time-resolved Raman spectroscopy, and quantum applications. Single-phot ...

EPFL2024

Opportunities and challenges in design and optimization of protein function

Bruno Emanuel Ferreira De Sousa Correia, Casper Alexander Goverde

The field of protein design has made remarkable progress over the past decade. Historically, the low reliability of purely structure-based design methods limited their application, but recent strategies that combine structure-based and sequence-based calcu ...

Nature Portfolio2024

Molecular hypergraph neural networks

Philippe Schwaller, Junwu Chen

Graph neural networks (GNNs) have demonstrated promising performance across various chemistry-related tasks. However, conventional graphs only model the pairwise connectivity in molecules, failing to adequately represent higher order connections, such as m ...

Aip Publishing2024

Reach For the Arcs: Reconstructing Surfaces from SDFs via Tangent Points

Yingying Ren

We introduce an algorithm to reconstruct a mesh from discrete samples of a shape's Signed Distance Function (SDF). A simple geometric reinterpretation of the SDF lets us formulate the problem through a point cloud, from which a surface can be extracted wit ...

Association for Computing Machinery2024

Generative power of a protein language model trained on multiple sequence alignments

Anne-Florence Raphaëlle Bitbol, Umberto Lupo, Damiano Sgarbossa

Computational models starting from large ensembles of evolutionarily related protein sequences capture a representation of protein families and learn constraints associated to protein structure and function. They thus open the possibility for generating no ...

eLIFE SCIENCES PUBL LTD2023

Impact of phylogeny on structural contact inference from protein sequence data

Anne-Florence Raphaëlle Bitbol, Umberto Lupo, Nicola Dietler

Local and global inference methods have been developed to infer structural contacts from multiple sequence alignments of homologous proteins. They rely on correlations in amino acid usage at contacting sites. Because homologous proteins share a common ance ...

ROYAL SOC2023

Automating the Design of Programmable Interconnect for Reconfigurable Architectures

Stefan Nikolic

With Moore's law coming to an end, increasingly more hope is being put in specialized hardware implemented on reconfigurable architectures such as Field-Programmable Gate Arrays (FPGAs). Yet, it is often neglected that these architectures themselves experi ...

EPFL2023

Evaluating, Exploiting, and Hiding Power Side-Channel Leakage of Remote FPGAs

Ognjen Glamocanin

The pervasive adoption of field-programmable gate arrays (FPGAs) in both cyber-physical systems and the cloud has raised many security issues. Being integrated circuits, FPGAs are susceptible to fault and power side-channel attacks, which require physical ...

EPFL2023

IIBLAST: Speeding Up Commercial FPGA Routing by Decoupling and Mitigating the Intra-CLB Bottleneck

Mirjana Stojilovic, Stefan Nikolic, Shashwat Shrivastava

We identified that in modern commercial FPGAs, routing signals from the general interconnect to the configurable logic blocks (CLBs) through a very sparse input interconnect block (IIB) represents a significant runtime bottleneck. This is despite academic ...

IEEE2023

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

Zhidian Zhang

EPFL2024