Publications related to High robustness of correlation-based alignment with Penrose patterns to marker damage in electron beam lithography

Impact of phylogeny on structural contact inference from protein sequence data

Nicola Dietler, Umberto Lupo, Anne-Florence Raphaëlle Bitbol

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

Saliency prediction in 360° architectural scenes: Performance and impact of daylight variations

Marilyne Andersen, Sabine Süsstrunk, Kynthia Chamilothori, Bahar Aydemir, Caroline Karmann, Seungryong Kim

Saliency models are image-based prediction models that estimate human visual attention. Such models, when applied to architectural spaces, could pave the way for design decisions where visual attention is taken into account. In this study, we tested the pe ...

2023

A New Analytical Approximation of the Fluid Antenna System Channel

Malek Khammassi

Fluid antenna systems (FAS) are an emerging technology that promises a significant diversity gain even in the smallest spaces. It consists of a freely moving antenna in a small linear space to pick up the strongest received signal. Previous works in the li ...

Ieee-Inst Electrical Electronics Engineers Inc2023

The two-point correlation function covariance with fewer mocks

Cheng Zhao

We present FITCOV an approach for accurate estimation of the covariance of two-point correlation functions that requires fewer mocks than the standard mock-based covariance. This can be achieved by dividing a set of mocks into jackknife regions and fitting ...

Oxford Univ Press2023

Towards a multiscale point cloud structural similarity metric

Touradj Ebrahimi, Davi Nachtigall Lazzarotto

Point clouds are effective data structures for the rep- resentation of three-dimensional media and hence adopted in a wide range of practical applications. In many cases, the portrayed data is expected to be visualized by humans. After acquisition, point c ...

IEEE2023

Small-scale dynamo with finite correlation times

Jennifer Waltraud Schober

Fluctuation dynamos occur in most turbulent plasmas in astrophysics and are the prime candidates for amplifying and maintaining cosmic magnetic fields. A few analytical models exist to describe their behavior, but they are based on simplifying assumptions. ...

AMER PHYSICAL SOC2023

Correlation properties of a one-dimensional repulsive Bose gas at finite temperature

Riccardo Rota

We present a comprehensive study shedding light on how thermal fluctuations affect correlations in a Bose gas with contact repulsive interactions in one spatial dimension. The pair correlation function, the static structure factor, and the one-body density ...

IOP Publishing Ltd2023

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

Umberto Lupo, Anne-Florence Raphaëlle Bitbol, 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

Metal-Free Molecular Catalysts for the Oxygen Reduction Reaction: Electron Affinity as an Activity Descriptor

Ganna Gryn'ova, Juliette Veronique Schleicher

Heteroatom-doped polyaromatic hydrocarbons (or nanographenes) are promising molecular electrocatalysts for the oxygen reduction reaction (ORR). Here, we use density functional theory to investigate the first step of the ORR pathway (chemisorption) for a se ...

AMER CHEMICAL SOC2023

Deep excavation of the impact from endogenous and exogenous uncertainties on long-term energy planning

François Maréchal, Xiang Li

Endogenous and exogenous uncertainties exert significant influences on energy planning. In this study, we propose a systematic methodology to excavate the uncertainty space, by combining mix-integer linear programming (MILP), Monte Carlo simulation, and ma ...

ELSEVIER2023

Emergent U(1) symmetry in non-particle-conserving one-dimensional models

Frédéric Mila, Natalia Chepiga, Mohamed Zakaria Jouini, Loïc Jean Pierre Herviou

The properties of stable Luttinger liquid phases in models with a nonconserved number of particles are investigated. We study the Luttinger liquid phases in one-dimensional models of hard-core boson and spinless fermion chains where particles can be create ...

Amer Physical Soc2023

Combining phylogeny and coevolution improves the inference of interaction partners among paralogous proteins

Anne-Florence Raphaëlle Bitbol

Author summaryWhen two protein families interact, their sequences feature statistical dependencies. First, interacting proteins tend to share a common evolutionary history. Second, maintaining structure and interactions through the course of evolution yiel ...

PUBLIC LIBRARY SCIENCE2023

Characterization of transversely confined electron beam-generated plasma using two-dimensional particle-in-cell simulations

Guang-Yu Sun, Haomin Sun

Electron beam-generated plasmas (EBPs) have been used to modify the surface properties. In certain applications, EBPs are transversely confined and their properties are of value to the treatment. In this paper, the characteristics of an electron beam-gener ...

American Institute of Physics (AIP)2023

Daily Contributors of Tinnitus Loudness and Distress: An Ecological Momentary Assessment Study

Patrick Karl Alois Neff

BackgroundTinnitus is a heterogeneous condition which may be associated with moderate to severe disability, but the reasons why only a subset of individuals is burdened by the condition are not fully clear. Ecological momentary assessment (EMA) allows a be ...

FRONTIERS MEDIA SA2022

Protein language models trained on multiple sequence alignments learn phylogenetic relationships

Umberto Lupo, Anne-Florence Raphaëlle Bitbol, Damiano Sgarbossa

Self-supervised neural language models with attention have recently been applied to biological sequence data, advancing structure, function and mutational effect prediction. Some protein language models, including MSA Transformer and AlphaFold's EvoFormer, ...

Nature Portfolio2022

Statistical potentials from the Gaussian scaling behaviour of chain fragments buried within protein globules

Stefano Zamuner

Knowledge-based approaches use the statistics collected from protein data-bank structures to estimate effective interaction potentials between amino acid pairs. Empirical relations are typically employed that are based on the crucial choice of a reference ...

PUBLIC LIBRARY SCIENCE2022

Subhalo abundance matching through the lens of a hydrodynamical simulation

Ginevra Favole

We use the IllustrisTNG100 hydrodynamical simulation to study the dependence of the galaxy two-point correlation function on a broad range of secondary subhalo and galactic properties. We construct galaxy mock catalogues adopting a standard subhalo abundan ...

OXFORD UNIV PRESS2022

On the durability of surgical masks after simulated handling and wear

Véronique Michaud, Vincent Marc Varanges, Jian Wang, Baris Çaglar, Yann Albert Gérard Lebaupin, René M. Rossi

After the spread of COVID-19, surgical masks became highly recommended to the public. They tend to be handled and used multiple times, which may impact their performance. To evaluate this risk, surgical masks of Type IIR were submitted to four simulated tr ...

Nature Research2022

Influence of static correlation on the magnon dynamics of an itinerant ferromagnet with competing exchange interactions: First-principles study of MnBi

Henrik Moodysson Rønnow, Thorbjørn Skovhus

We present first-principles calculations of the dynamic susceptibility in strained and doped ferromagnetic MnBi using time-dependent density functional theory. In spite of being a metal, MnBi exhibits signatures of strong correlation and a proper descripti ...

AMER PHYSICAL SOC2022

Femtosecond laser-based optomechanical processes for permanent and high-precision fine alignment of optical systems

Saood Ibni Nazir

Miniaturization has been at the forefront of scientific research in the past decade covering diverse areas such as electronics, mechanics, and optics. While 'small is beautiful' may be a vast generalization, the true benefits of miniaturization are especia ...

EPFL2021