Publications related to Mathematical and theoretical biology

CONTROL OF HYPERBOLIC AND PARABOLIC EQUATIONS ON NETWORKS AND SINGULAR LIMITS

vanishing viscosity, networks. This work has received funding from the Alexander von Humboldt-Professorship program, the Transregio 154 Project "Mathematical Modelling, Simulation and Optimization Using the Example of Gas Networks" of the DFG, the grant PI ...

Amer Inst Mathematical Sciences-Aims2024

Thermal transport of glasses via machine learning driven simulations

Federico Grasselli

Accessing the thermal transport properties of glasses is a major issue for the design of production strategies of glass industry, as well as for the plethora of applications and devices where glasses are employed. From the computational standpoint, the che ...

Frontiers Media Sa2024

Dynamical system approach to navigation around obstacles

Aude Billard, Aradhana Nayak

In this article, we propose a dynamical system to avoid obstacles which are star shaped and simultaneously converge to a goal. The convergence is almost-global in a domain and the stationary points are identified explicitly. Our approach is based on the id ...

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

On distributional autoregression and iterated transportation

Victor Panaretos, Laya Ghodrati

We consider the problem of defining and fitting models of autoregressive time series of probability distributions on a compact interval of Double-struck capital R. An order-1 autoregressive model in this context is to be understood as a Markov chain, where ...

Wiley2024

Decoding Chromatin Ubiquitylation: A Chemical Biology Perspective

Beat Fierz, Pauline Franz

Since Strahl and Allis proposed the "language of covalent histone modifications", a host of experimental studies have shed light on the different facets of chromatin regulation by epigenetic mechanisms. Initially proposed as a concept for controlling gene ...

Academic Press Ltd- Elsevier Science Ltd2024

Physics-Informed Machine Learning for Modeling and Control of Dynamical Systems

Colin Neil Jones, Roland Schwan, Melanie Nicole Zeilinger, Xuan Truong Nghiem

Physics-informed machine learning (PIML) is a set of methods and tools that systematically integrate machine learning (ML) algorithms with physical constraints and abstract mathematical models developed in scientific and engineering domains. As opposed to ...

IEEE2023

On the similarity between aortic and carotid pressure diastolic decay: a mathematical modelling study

Nikolaos Stergiopoulos, Georgios Rovas, Sokratis Anagnostopoulos, Vasiliki Bikia

Aortic diastolic pressure decay (DPD) has been shown to have considerable pathophysiological relevance in the assessment of vascular health, as it is significantly affected by arterial stiffening. Nonetheless, the aortic pressure waveform is rarely availab ...

Nature Portfolio2023

Optimized numerical solutions of SIRDVW multiage model controlling SARS-CoV-2 vaccine roll out: An application to the Italian scenario

Alfio Quarteroni, Luca Dede', Nicola Parolini

In the context of SARS-CoV-2 pandemic, mathematical modelling has played a funda-mental role for making forecasts, simulating scenarios and evaluating the impact of pre-ventive political, social and pharmaceutical measures. Optimal control theory represent ...

KEAI PUBLISHING LTD2023

lifex-ep: a robust and efficient software for cardiac electrophysiology simulations

Alfio Quarteroni, Francesco Regazzoni, Stefano Pagani, Marco Fedele

Background: Simulating the cardiac function requires the numerical solution of multi-physics and multi-scale mathematical models. This underscores the need for streamlined, accurate, and high-performance computational tools. Despite the dedicated endeavors ...

BMC2023

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

Urs von Gunten

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, Gard Spreemann, Robin Alexander Denhardt-Eriksson

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