Publications related to Living systems

Structure and dynamics of liquid water from ab initio simulations: adding Minnesota density functionals to Jacob's ladder

Ursula Röthlisberger, Justin Villard, Martin Peter Bircher

The accurate representation of the structural and dynamical properties of water is essential for simulating the unique behavior of this ubiquitous solvent. Here we assess the current status of describing liquid water using ab initio molecular dynamics, wit ...

Royal Soc Chemistry2024

Learning the intrinsic dynamics of spatio-temporal processes through Latent Dynamics Networks

Alfio Quarteroni, Francesco Regazzoni, Stefano Pagani

Predicting the evolution of systems with spatio-temporal dynamics in response to external stimuli is essential for scientific progress. Traditional equations-based approaches leverage first principles through the numerical approximation of differential equ ...

Nature Portfolio2024

Learning Physics-Consistent Particle Interactions

Olga Fink, David Simon Kammer, Zhichao Han

Interacting particle systems play a key role in science and engineering. Access to the governing particle interaction law is fundamental for a complete understanding of such systems. However, the inherent system complexity keeps the particle interaction hi ...

Oxford University Press2023

Principles of checkpoint override

Ahmad Sadeghi

Why biological quality-control systems fail is often mysterious. Specifically, checkpoints such as the DNA damage checkpoint or the spindle assembly checkpoint are overriden after prolonged arrests allowing cells to continue dividing despite the continued ...

EPFL2022

Misplaced Trust and Distrust: How Not to Engage with Medical Artificial Intelligence

Marcello Ienca

Artificial intelligence (AI) plays a rapidly increasing role in clinical care. Many of these systems, for instance, deep learning-based applications using multilayered Artificial Neural Nets, exhibit epistemic opacity in the sense that they preclude compre ...

CAMBRIDGE UNIV PRESS2022

Robotic manipulation to investigate the physical principles of biological self-organization

Fazil Emre Uslu

Self-organization is the spontaneous formation of ordered patterns and networks from a population of comparatively simple elements or individuals with no prior information on neither the formation process nor the final organization. While the construction ...

EPFL2022

Modeling biochemical reaction networks in complex intracellular environments

Daniel Robert Weilandt

Whether one aims to design treatments for diseases such as cancer or diabetes, engineer cells to produce valuable biochemicals sustainably, or to grasp the behavior of living organisms, it is essential to understand how cells react to genetic, environmenta ...

EPFL2020

The emergence and promise of single-cell temporal-omics approaches

Gioele La Manno, Alex Russell Lederer

Single-cell transcriptomics enables the measurement of gene expression in complex biological systems at the resolution of individual cells. Multivariate analysis of single-cell data helps describe the variation in expression accompanying cellular processes ...

CURRENT BIOLOGY LTD2020

A Large Range of Motion 3D MEMS Scanner With Five Degrees of Freedom

Matthias Imboden

Here, we discuss a novel, mixed mode 3D XYZ scanner built within a single foundry process. The device has a large range of motion in X, Y, and Z (14.1 mu m in X and Y and 97.9 mu m in Z) and can also rotate about two axes (7.4 degrees), making it a 5 degre ...

Institute of Electrical and Electronics Engineers2019

Design of Surface-Supported Bio-inspired Networks for CO2 and O2 Activation at Room Temperature

Daniel Eduardo Hurtado Salinas

The structure of a biological system defines its function. Therefore, nature has developed sophisticated systems that catalyze chemical reactions that are vital for life on earth. For instance, the photosynthesis is a biological process that is partially r ...

EPFL2018

Profiling of Single-Cell Transcriptomes

Bart Deplancke, Vincent Roland Julien Gardeux, Antonio Carlos Alves Meireles Filho, Wanze Chen

Complex biological systems are composed of multiple cell types whose transcriptional activity can vary due to differences in cell state, environmental stimulation or intrinsic programs. Conventional bulk analysis methods capture the average transcriptional ...

2017

Caged luciferin probes for the bioluminescence imaging of nitroreductase and hydrogen sulfide in living animals

Anzhelika Vorobyeva

Molecular imaging advances our understanding of cellular and molecular functions within complex biological systems. The development of novel imaging probes that can be applied to answer fundamental biological questions, diagnose and monitor disease progres ...

EPFL2016

Environomic multi-objective optimization of an eco-industrial park

François Maréchal, Maziar Kermani, Lindsay Dianne Lessard

A circular economy refers to an industrial economy with a cradle to cradle vision, shifting from the use of fossil fuels towards renewable energy, minimizing the use of toxic chemicals and reducing waste by recycling through careful system design. The conc ...

2015

Advancing catchment hydrology to deal with predictions under change

Steven Vincent Weijs

Throughout its historical development, hydrology as an earth science, but especially as a problem-centred engineering discipline has largely relied (quite successfully) on the assumption of stationarity. This includes assuming time invariance of boundary c ...

Copernicus Gesellschaft Mbh2014

Mathematical models and computational methods for the analysis of genome-scale protein synthesis

Julien Racle

Proteins are a ubiquitous and indispensable element for every living organism, from simple bacteria to mammals. Already in the simplest organisms, there exist some thousands of different protein species that take up a great variety of structures, and thus ...

EPFL2014

Soft Cells for Programmable Self-Assembly of Robotic Modules

Dario Floreano, Ramon Pericet Camara, Andrea Maesani, Jürg Markus Germann

Programmable self-assembly of chained robotic systems holds potential for the automatic construction of complex robots from a minimal set of building blocks. However, current robotic platforms are limited to modules of uniform rigidity, which results in a ...

2014

Interfacial Self-Assembly as Catalytic Platform for Multielectron Redox Reactions

Astrid Johana Olaya Avendano

In Nature, many vital biological processes take place across the interface formed between two dielectric media. For instance, photosynthesis and aerobic respiration involve a series of redox reactions occurring across energy-transducing membranes, in charg ...

EPFL2013

Design, Modeling and Optimization of Stochastic Reactive Distributed Robotic Systems

Grégory Mermoud

This dissertation describes a complete methodological framework for designing, modeling and optimizing a specific class of distributed systems whose dynamics result from the multiple, stochastic interactions of their constitutive components. These componen ...

EPFL2012

Ultrafast (Bio)physical and (Bio)chemical Dynamics

Majed Chergui, Frank van Mourik, Andrea Cannizzo, Amal El Nahhas, Renske Marjan van der Veen, Cristina Consani, Ahmad Ajdar Zadeh Oskouei, Gerald Auböck, Olivier Christian Bräm

We give an overview of our recent work on ultrafast dynamics of chemical (organic dyes, metal-complexes, colloidal quantum dots), and biological (retinal and haem proteins) systems in the liquid phase, studied with a variety of ultrafast optical techniques ...

2011

Self-Assembled Nanometer-Scale Magnetic Networks on Surfaces: Fundamental Interactions and Functional Properties

Klaus Kern, Harald Brune, Stefano Rusponi, Pietro Gambardella, Anne Lehnert, Sergio Vlaic, Sebastian Stepanow

Nanomagnets of controlled size, organized into regular patterns open new perspectives in the fields of nanoelectronics, spintronics, and quantum computation. Self-assembling processes on various types of substrates allow designing fine-structured architect ...

Wiley-Blackwell2011