Publications related to Validation of short-pulse reflectometry turbulence measurements with a synthetic diagnostic

Experiments and gyrokinetic simulations of TCV plasmas with negative triangularity in view of DTT operations

Olivier Sauter, Stefano Coda, Alberto Mariani, Justin Richard Ball, Filippo Bagnato, Matteo Vallar

Negative triangularity (NT) scenarios in TCV have been compared to positive triangularity (PT) scenarios using the same plasma shapes foreseen for divertor tokamak test tokamak operations. The experiments provided a NT/PT L-mode pair and a PT H-mode with d ...

Iop Publishing Ltd2024

Physical insights from the aspect ratio dependence of turbulence in negative triangularity plasmas

Stefano Coda, Justin Richard Ball

In this work, we study the impact of aspect ratio A = R 0 / r (the ratio of major radius R 0 to minor radius r) on the confinement benefits of negative triangularity (NT) plasma shaping. We use high-fidelity flux tube gyrokinetic GENE simulations and consi ...

Iop Publishing Ltd2024

NBI optimization on SMART and implications for scenario development

Mario Ludovico Podesta, Francesca Maria Poli

The SMall Aspect Ratio Tokamak (SMART) under commissioning at the University of Seville, Spain, aims to explore confinement properties and possible advantages in confinement for compact/spherical tokamaks operating at negative vs. positive triangularity. T ...

Iop Publishing Ltd2024

Quantitative characterization of the inorganic phosphate gene regulatory networks in S. cerevisiae and bottom up engineering an orthogonal gene network

Shiyu Cheng

Gene regulatory networks (GRNs) play a crucial role in an organism's response to changing environmental conditions. Cellular behaviors typically result from the integration of multiple gene outputs, and their regulation often demands precise control of num ...

EPFL2024

SPEEDING UP KRYLOV SUBSPACE METHODS FOR COMPUTING f(A)b VIA RANDOMIZATION

Daniel Kressner, Alice Cortinovis

This work is concerned with the computation of the action of a matrix function f(A), such as the matrix exponential or the matrix square root, on a vector b. For a general matrix A, this can be done by computing the compression of A onto a suitable Krylov ...

Siam Publications2024

Statistical learning quantifies transposable element-mediated cis-regulation

Didier Trono, Julien Léonard Duc, Alexandre Coudray, Cyril David Son-Tuyên Pulver, Shaoline Sheppard, Evaristo Jose Planet Letschert, Raphaël Gérard Théodore Michel Marie de Deloÿe et Fourcade de Fondeville, Julien Paul André Pontis, Delphine Yvette L Grun

Background: Transposable elements (TEs) have colonized the genomes of most metazoans, and many TE-embedded sequences function as cis-regulatory elements (CREs) for genes involved in a wide range of biological processes from early embryo- genesis to innate ...

2023

Modeling, analysis, and design of complex biological networks

Mohammadomid Oftadeh

Automating experimental procedures has resulted in an unprecedented increase in the volume of generated data, which, in turn, has caused an accumulation of unprocessed data. As a result, the need to develop tools to analyze data systematically has been ris ...

EPFL2023

Wide-scale identification of novel/eliminated genes responsible for evolutionary transformations

Daria Korotkova

BackgroundIt is generally accepted that most evolutionary transformations at the phenotype level are associated either with rearrangements of genomic regulatory elements, which control the activity of gene networks, or with changes in the amino acid conten ...

2023

Environment-dependent epistasis increases phenotypic diversity in gene regulatory networks

Florence Gauye, Florian Baier

Mutations to gene regulatory networks can be maladaptive or a source of evolutionary novelty. Epistasis con-founds our understanding of how mutations affect the expression patterns of gene regulatory networks, a chal-lenge exacerbated by the dependence of ...

AMER ASSOC ADVANCEMENT SCIENCE2023

cgNA+: A sequence-dependent coarse-grain model of double-stranded nucleic acids

Rahul Sharma

DNA mechanics plays a crucial role in many biological processes, including nucleosome positioning and protein-DNA interactions. It is believed that nature employs epigenetic modifications in DNA to further regulate gene expression. Moreover, double-strande ...

EPFL2023

Effect of triangularity on plasma turbulence and the SOL-width scaling in L-mode diverted tokamak configurations

Paolo Ricci, Louis Nicolas Stenger, Maurizio Giacomin, Davide Mancini

The effect of triangularity on tokamak boundary plasma turbulence is investigated using global, flux-driven, three-dimensional, two-fluid simulations. The simulations show that negative triangularity (NT) stabilizes boundary plasma turbulence, and linear i ...

IOP Publishing Ltd2023

Development of algorithms for the end-end system simulation and performance analysis for a high-frequency magnetic diagnostic system: Application to ITER, JET and TCV

Duccio Testa

An innovative and very detailed end-to-end system modelling tool has been developed and applied to test on simulated data the actual measurement capabilities of any generic high frequency (HF) magnetic diagnostic systems. The main goal of this rather compl ...

2022

Modelling of sawtooth-induced fast ion transport in positive and negative triangularity in TCV

Basil Duval, Olivier Sauter, Alexander Karpushov, Mario Ludovico Podesta, Duccio Testa, Antoine Pierre Emmanuel Alexis Merle, Marcelo Baquero Ruiz, Lorenzo Stipani, Matteo Vallar, Dmytry Mykytchuk

Internal kinks are a common magneto hydro-dynamic (MHD) instability observed in tokamak operation when the q profile in the plasma core is close to unity. This MHD instability impacts both the transport of the bulk plasma (current, particle and energy tran ...

IOP Publishing Ltd2022

IMPROVED VARIANTS OF THE HUTCH plus plus ALGORITHM FOR TRACE ESTIMATION

Daniel Kressner, Alice Cortinovis, Ulf David Persson

This paper is concerned with two improved variants of the Hutch++ algorithm for estimating the trace of a square matrix, implicitly given through matrix-vector products. Hutch++ combines randomized low-rank approximation in a first phase with stochastic tr ...

SIAM PUBLICATIONS2022

Enhanced confinement in diverted negative-triangularity L-mode plasmas in TCV

Olivier Sauter, Stefano Coda, Laurie Porte, Benoît Labit, Alessandro Marinoni, Antoine Pierre Emmanuel Alexis Merle, Leonardo Pigatto, Cedric Kar-Wai Tsui, Umar Sheikh, Filippo Bagnato, Alessandro Pau, Matteo Vallar

The favorable confinement properties of negative-triangularity (NT) tokamak configurations were discovered in the TCV tokamak in the late 1990s and were documented over the two following decades, through investigations of predominantly electron-heated plas ...

2022

Iterative refinement of Schur decompositions

Daniel Kressner, Zvonimir Bujanovic

The Schur decomposition of a square matrix A is an important intermediate step of state-of-the-art numerical algorithms for addressing eigenvalue problems, matrix functions, and matrix equations. This work is concerned with the following task: Compute a (m ...

SPRINGER2023

Minkowski's Loop Fractal Antenna Dedicated to Sixth Generation (6G) Communication

Maria-Alexandra Paun

In this study, we will discuss the engineering construction of a special sixth generation (6G) antenna, based on the fractal called Minkowski's loop. The antenna has the shape of this known fractal, set at four iterations, to obtain maximum performance. Th ...

MDPI2022

Generation of a Gal4-dependent gene recombination and illuminating mouse

Freddy Radtke

Cell labeling technologies, including the Cre/loxP system, are powerful tools in developmental biology. Although the conventional Cre/loxP system has been extensively used to label the expression of specific genes, it is less frequently used for labeling p ...

INT PRESS EDITING CENTRE INC2022

KRAB zinc-finger proteins and their transposable element targets: between antagonism and cooperation

Jonas Caspar De Tribolet-Hardy

There are 377 Krüppel-associated box (KRAB) domain-containing zinc finger proteins (KZFPs) in the human genome, making them the largest family of transcription factors. KZFPs are defined by a N-terminal KRAB domain and several zinc-finger domains arranged ...

EPFL2022

H I constraints from the cross-correlation of eBOSS galaxies and Green Bank Telescope intensity maps

Jean-Paul Richard Kneib

We present the joint analysis of Neutral Hydrogen (H I) Intensity Mapping observations with three galaxy samples: the Luminous Red Galaxy (LRG) and Emission Line Galaxy (ELG) samples from the eBOSS survey, and the WiggleZ Dark Energy Survey sample. The H I ...

OXFORD UNIV PRESS2022