Publications associées à C2CAplus: A One-Pot Isothermal Circle-to-Circle DNA Amplification System

Advancing Cell-Free Synthetic Biology: From sustained PURE protein synthesis to an isothermal one-pot DNA replication system

One of the goals of synthetic biology is the development of an artificial cell. Building an artificial cell from scratch will provide a deeper understanding of fundamental mechanisms and models in biology and promises to contribute towards building novel p ...

EPFL2024

Micropreparative Gel Electrophoresis for Purification of Nanoscale Bioconjugates

Vitalijs Zubkovs, Ardemis Anoush Boghossian, Sayyed Hashem Sajjadi, Shang-Jung Wu, Yahya Rabbani

Conventional techniques for purifying macromolecular conjugates often require complex and costly installments that are inaccessible to most laboratories. In this work, we develop a one-step micropreparative method based on a trilayered polyacrylamide gel e ...

2024

Chromosome organization shapes replisome dynamics in Caulobacter crescentus

Suliana Manley, Laurent Casini, Chen Zhang

DNA replication in bacteria takes place on highly compacted chromosomes, where segregation, transcription, and repair must occur simultaneously. Within this dynamic environment, colocalization of sister replisomes has been observed in many bacterial specie ...

Nature Portfolio2024

High-order geometric integrators for the variational Gaussian wavepacket dynamics and application to vibronic spectra at finite temperature

Roya Moghaddasi Fereidani

Molecular quantum dynamics simulations are essential for understanding many fundamental phenomena in physics and chemistry. They often require solving the time-dependent Schrödinger equation for molecular nuclei, which is challenging even for medium-sized ...

EPFL2024

SIMPLE HIERARCHICAL PLANNING WITH DIFFUSION

Chang Chen, Caglar Gulcehre

Diffusion-based generative methods have proven effective in modeling trajectories with offline datasets. However, they often face computational challenges and can falter in generalization, especially in capturing temporal abstractions for long- horizon tas ...

2024

Efficient Continual Finite-Sum Minimization

Volkan Cevher, Leello Tadesse Dadi, Efstratios Panteleimon Skoulakis

Given a sequence of functions

f_1,\ldots,f_n

with

f_i:\mathcal{D}\mapsto \mathbb{R}

, finite-sum minimization seeks a point

{x}^\star \in \mathcal{D}

minimizing

\sum_{j=1}^nf_j(x)/n

. In this work, we propose a key twist into the finite-sum minimizat ...

2024

A Reduced Order Model for Domain Decompositions with Non-conforming Interfaces

Alfio Quarteroni, Andrea Manzoni

In this paper, we propose a reduced-order modeling strategy for two-way Dirichlet-Neumann parametric coupled problems solved with domain-decomposition (DD) sub-structuring methods. We split the original coupled differential problem into two sub-problems wi ...

Springer/Plenum Publishers2024

Resolving bacterial cell biology: from replisome dynamics to cell wall synthesis

Chen Zhang

Bacteria are ubiquitous single cellular organisms. Compared to eukaryotic cells, bacteria have two unique characteristics: the membrane-less nucleoid and the cell wall built of peptidoglycan (PG). In most bacteria, a single circular chromosome is compacted ...

EPFL2024

Quantifying the Unknown: Data-Driven Approaches and Applications in Energy Systems

Paul Scharnhorst

In light of the challenges posed by climate change and the goals of the Paris Agreement, electricity generation is shifting to a more renewable and decentralized pattern, while the operation of systems like buildings is increasingly electrified. This calls ...

EPFL2024

Iterative removal of sources to model the turbulent electromotive force

Jennifer Waltraud Schober, Abhijit Bhausaheb Bendre

We describe a novel method to compute the components of dynamo tensors from direct magnetohydrodynamic (MHD) simulations. Our method relies upon an extension and generalization of the standard H & ouml;gbom CLEAN algorithm widely used in radio astronomy to ...

Oxford Univ Press2024

Residual-based attention in physics-informed neural networks

Nikolaos Stergiopoulos, Sokratis Anagnostopoulos

Driven by the need for more efficient and seamless integration of physical models and data, physics -informed neural networks (PINNs) have seen a surge of interest in recent years. However, ensuring the reliability of their convergence and accuracy remains ...

Elsevier Science Sa2024

Method of preparation of amyloidogenic protein aggregates and uses thereof

Hilal Lashuel, Galina Limorenko

The invention relates to methods for the preparation of method of preparation of Tau aggregates, including fibrils, fibrillar species, soluble and insoluble oligomeric species, new Tau aggregates and uses thereof. The invention further relates to the uses ...

2024

Microfluidic device for sample encapsulation and method for operation thereof

Philippe Renaud, Jiande Zhou

The invention relates to a microfluidic device (3) comprising: - an inlet channel (31) having an inlet configured to be operatively connected with a droplet source (2) wherein the inlet channel (31) has a width wi and height hi; and - an outlet channel wit ...

2023

Electronic readout of DNA amplification in nanoliter chambers. Strategies towards highly parallel semiconductor-based nucleic acid amplification testing

Saurabh Tomar

Polymerase chain reaction (PCR) has been the most significant driver in the field of nucleic acid testing (NAT) since its invention. Popularized as an abbreviation by the Covid-19 pandemic, PCR-based methods are the gold standard in the field of diagnostic ...

EPFL2023

On the fast assemblage of finite element matrices with application to nonlinear heat transfer problems

Yannis Dirk Voet

The finite element method is a well-established method for the numerical solution of partial differential equations (PDEs), both linear and nonlinear. However, the repeated re -assemblage of finite element matrices for nonlinear PDEs is frequently pointed ...

ELSEVIER SCIENCE INC2023

PROBING INTRACELLULAR ELASTICITY WITH MINIMAL-HESSIAN REGISTRATION

Michaël Unser

We propose an image-based elastography method to measure the heterogeneous stiffness inside a cell and its nucleus. It uses a widely accessible setup consisting of plate compression imaged with fluorescence microscopy. Our framework recovers a spatial map ...

IEEE2023

Efficient and Accurate Handling of Periodic Flows in Time-Sensitive Networks

Jean-Yves Le Boudec, Seyed Mohammadhossein Tabatabaee

Total Flow Analysis (TFA) is a method for the worst-case analysis of time-sensitive networks. It uses service curve characterizations of the network nodes and arrival curves of flows at their sources; for tractability, the latter are often taken to be line ...

2023

Regulation and impact of TERRA R-loops at human telomeres

Rita Valador Fernandes

Telomeres are the nucleoprotein structures found at the ends of linear chromosomes. They ensure that the termini of chromosomes are not inappropriately recognized as sites of DNA damage, and are therefore crucial for genome stability. In spite of the heter ...

EPFL2023

Diaryl ether compound and manufacturing method from lignin

Paul Joseph Dyson, Mingyang Liu

Herein described are diaryl ether compounds having the structure (I) as well as a method for their manufacture from lignin. ...

2023

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