Publications related to Systematic model reduction captures the dynamics of extrinsic noise in biochemical subnetworks

Related publications (36)

Capturing behavioral and neural variability in multi-area spiking neuronal network models

How does the brain generate behavioral responses from sensory stimuli? This sensor-to-motor transformation is a fundamental question in systems neuroscience. While recent experiments have highlighted the complexity of neural representations across the cere ...

EPFL2025

Long-lived particle reconstruction downstream of the LHCb magnet

Olivier Schneider, Aurelio Bay, Guido Haefeli, Tatsuya Nakada, Frédéric Blanc, Lesya Shchutska, Elena Graverini, Sebastian Schulte, Donal Patrick Hill, Marie Theres Christin Bachmayer, Serhii Cholak, Ettore Zaffaroni, Aravindhan Venkateswaran, Luis Miguel Garcia Martin, Vitalii Lisovskyi, Elisabeth Maria Niel, Federico Ronchetti, Radoslav Marchevski, Anni Matilda Kauniskangas, Dimitrios Kaminaris, Raphaël van Laak, Pierre Paul Louis Mayencourt, Brianna Leililani Thielen, Arnaud Merlin Gauthey, Gianluca Zunica, Abdul-Kerim Guseinov, Esteban Curras Rivera, Yifei Song, Roberto Ribatti, Alexandre Brea Rodriguez, Rita De Sousa Ataíde Da Silva

Charged-particle trajectories are usually reconstructed with the LHCb detector using combined information from the tracking devices placed upstream and downstream of the 4 T m dipole magnet. Trajectories reconstructed using only information from the tracke ...

2025

Altruism, reciprocity, and tokens to reward forwarding data: Is that fair?

Verónica del Carmen Estrada Galiñanes

Decentralized storage networks offer services with intriguing possibilities to reduce inequalities in an extremely centralized market. Fair distribution of rewards, however, is still a persistent problem in the current generation of decentralized applicati ...

2024

Optimality principles for the analysis of biological processes across scales: From enzyme kinetics to microbiome dynamics

Asli Sahin

Microorganisms are essential for life on Earth, performing key roles in numerous biological processes. Their influence extends across a wide spectrum, from human health and ecological balance to advancements in biotechnology and industrial applications. Th ...

EPFL2024

Mechanisms and functions of protein S-acylation

Françoise Gisou van der Goot Grunberg, Laurence Gouzi Abrami, Francisco De Magalhães Sarmento Ribeiro De Mesquita

Over the past two decades, protein S-acylation (often referred to as S-palmitoylation) has emerged as an important regulator of vital signalling pathways. S-Acylation is a reversible post-translational modification that involves the attachment of a fatty a ...

Nature Portfolio2024

From Sequence to Dynamics to Function: Computational Design of Allostery and Ligand Selectivity in G-Protein Coupled Receptors

Mahdi Hijazi

The phenomenon of allostery, a general property in proteins that has been heralded as "the second secret of life" remains elusive to our understanding and even more challenging to incorporate into protein design. One example of allosteric proteins with gre ...

EPFL2024

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

Fast and Future: Towards Efficient Forecasting in Video Semantic Segmentation

Evann Pierre Guy Courdier

Deep learning has revolutionized the field of computer vision, a success largely attributable to the growing size of models, datasets, and computational power. Simultaneously, a critical pain point arises as several computer vision applications are deploye ...

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

Global, Passive Detection of Connection Tampering

Louis-Henri Manuel Jakob Merino

In-network devices around the world monitor and tamper with connections for many reasons, including intrusion prevention, combating spam or phishing, and country-level censorship. Connection tampering seeks to block access to specific domain names or keywo ...

Assoc Computing Machinery2023

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

Expanding computational biochemistry towards complex and non-natural compounds

Anastasia Sveshnikova

In the beginning was the metabolism. The biochemical processes that make life possible transformed the soup of chemicals into the life on Earth we know today. Since then, living organisms have evolved, and life on Earth has become more complex. Living orga ...

EPFL2023

Equilibria in Network Constrained Energy Markets

Leonardo Massai

We study an energy market composed of producers who compete to supply energy to different markets and want to maximize their profits. The energy market is modeled by a graph representing a constrained power network where nodes represent the markets and lin ...

Elsevier2023

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

Dataset for "First self-consistent simulations of trapped electron clouds in a gyrotron gun and comparison with experiments" - Physics of Plasmas 30, 030702 (2023)

Pierrick Paul Louis Giroud-Garampon

Dataset for the publication "First self-consistent simulations of trapped electron clouds in a gyrotron gun and comparison with experiments" - Physics of Plasmas 30, 030702 (2023) - https://doi.org/10.1063/5.0136340 Authors: G. Le Bars*,J. Loizu*, J.-Ph. ...

Zenodo2023

Artificial Neural Network Training on an Optical Processor via Direct Feedback Alignment

Florent Gérard Krzakala

Artificial Neural Networks (ANN) are habitually trained via the back-propagation (BP) algorithm. This approach has been extremely successful: Current models like GPT-3 have O(10 11 ) parameters, are trained on O(10 11 ) words and produce awe-inspiring resu ...

IEEE2023

Gas/Surface reactions probed by reflection absorption infrared spectroscopy

Harmina Vejayan

In my thesis, I present an investigation of the dissociation reactions of gas phase molecules on single crystal metal surfaces studied by a molecular beam in combination with Reflection Absorption Infrared Spectroscopy (RAIRS). Two gas/surface systems were ...

EPFL2023

Estimating pollution spread in water networks as a Schrödinger bridge problem with partial information

Isabel Haasler

Incidents where water networks are contaminated with microorganisms or pollutants can result in a large number of infected or ill persons, and it is therefore important to quickly detect, localize and estimate the spread and source of the contamination. In ...

Elsevier2023

Network Alignment With Holistic Embeddings

Quoc Viet Hung Nguyen, Thành Tâm Nguyên, Chi Thang Duong, Thanh Trung Huynh

Network alignment is the task of identifying topologically and semantically similar nodes across (two) different networks. It plays an important role in various applications ranging from social network analysis to bioinformatic network interactions. Howeve ...

IEEE COMPUTER SOC2023

Short-term dynamics of drainage density based on a combination of channel flow state surveys and water level measurements

Andrea Rinaldo, Jana Freiin von Freyberg, Izabela Bujak-Ozga

Headwater streams often experience intermittent flow. Consequently, the flowing drainage network expands and contracts and the flowing drainage density (DD) varies over time. Monitoring the DD dynamics is essential to understand the processes controlling i ...

Wiley2023