Mathematical and theoretical biology

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Predicting Transformation Products during Aqueous Oxidation Processes: Current State and Outlook

Water quality and its impacts on human and ecosystem health presents tremendous global challenges. While oxidative water treatment can solve many of these problems related to hygiene and micropollutants, identifying and predicting transformation products f ...

2023

Dynamics of CLIMP-63 S-acylation control ER morphology

Vassily Hatzimanikatis, Françoise Gisou van der Goot Grunberg, Graham Knott, Kathryn Hess Bellwald, Laurence Gouzi Abrami, Béatrice Kunz, Luciano Andres Abriata, Sylvia Ho, Catherine Maclachlan, Patrick Alain Sandoz

A key player in the formation of endoplasmic reticulum sheets is CLIMP-63, but mechanistic details remained elusive. Here authors combined cellular experiments and mathematical modelling to show that S-acylation of CLIMP-63 regulates its function by mediat ...

Nature Portfolio2023

Contextual Stochastic Bilevel Optimization

Daniel Kuhn, Yifan Hu, Andreas Krause, Jie Wang

We introduce contextual stochastic bilevel optimization (CSBO) -- a stochastic bilevel optimization framework with the lower-level problem minimizing an expectation conditioned on some contextual information and the upper-level decision variable. This fram ...

2023

Beyond undulation! Body morphology and sensing components of elongated animals and robots reveal skills to maintain competent locomotion

Laura Isabel Paez Coy

Locomotion is an essential evolutive innovation of living beings that allows them to colonize and dominate the planet. As diverse as animal morphologies are (living) and were (extinct), their locomotion modalities are also diverse. In particular, animal mo ...

EPFL2023

New ultrahigh-speed device concepts: from THz nanoplasma devices to glass-like electronics for neuromorphic computation

Mohammad Samizadeh Nikooytabalvandani

There is a never-ending push for electronic systems to provide faster operation speeds, higher energy efficiencies, and higher power capabilities at smaller scales. These requirements are apparent in different areas of electronics, from radiofrequency (RF) ...

EPFL2023

Symbolic kinetic models in python (SKiMpy): intuitive modeling of large-scale biological kinetic models

Vassily Hatzimanikatis, Georgios Fengos, Maria Masid Barcon, Daniel Robert Weilandt, Zhaleh Hosseini, Pierre Guy Rémy Salvy

Motivation: Large-scale kinetic models are an invaluable tool to understand the dynamic and adaptive responses of biological systems. The development and application of these models have been limited by the availability of computational tools to build and ...

OXFORD UNIV PRESS2022

A Comprehensive Timing Model for Accurate Frequency Tuning in Dataflow Circuits

Paolo Ienne, Andrea Guerrieri, Lana Josipovic, Carmine Rizzi

The ability of dataflow circuits to implement dynamic scheduling promises to overcome the conservatism of static scheduling techniques that high-level synthesis tools typically rely on. Yet, the same distributed control mechanism that allows dataflow circu ...

IEEE COMPUTER SOC2022

Finding a vocation for validation: taking proteomics beyond association and location

Yimon Aye, Jinmin Liu

First established in the seventies, proteomics, chemoproteomics, and most recently, spatial/proximity-proteomics technologies have empowered researchers with new capabilities to illuminate cellular communication networks that govern sophisticated decision- ...

ROYAL SOC CHEMISTRY2022

Disentangling Light- and Temperature-Induced Thermal Effects in Colloidal Au Nanoparticles

Majed Chergui, Lijie Wang, Davood Zare

We present temperature-dependent (from room temperature to 80 degrees C) absorption spectra of Au/SiO2 core-shell nanoparticles (NPs) (core diameter: similar to 25 nm) in water in the range from 1.5 to 4.5 eV, which spans the localized surface plasmon reso ...

AMER CHEMICAL SOC2022

Preconditioners for robust optimal control problems under uncertainty

Fabio Nobile, Tommaso Vanzan

The discretization of robust quadratic optimal control problems under uncertainty using the finite element method and the stochastic collocation method leads to large saddle-point systems, which are fully coupled across the random realizations. Despite its ...

2023

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Contextual Stochastic Bilevel Optimization

Daniel Kuhn, Yifan Hu, Andreas Krause, Jie Wang

2023

Predicting Transformation Products during Aqueous Oxidation Processes: Current State and Outlook

Urs von Gunten

2023

Beyond undulation! Body morphology and sensing components of elongated animals and robots reveal skills to maintain competent locomotion

Laura Isabel Paez Coy

EPFL2023