Publications associées à cgNA plus web : A Visual Interface to the cgNA plus Sequence-dependent Statistical Mechanics Model of Double-stranded Nucleic Acids

On the use of Cramér-Rao Lower Bound for least-variance circuit parameters identification of Li-ion cells

Electrochemical Impedance Spectroscopy (EIS) and Equivalent Circuit Models (ECMs) are widely used to characterize the impedance and estimate parameters of electrochemical systems such as batteries. We use a generic ECM with ten parameters grouped to model ...

2024

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

cgNA+: A sequence-dependent coarse-grain model of double-stranded nucleic acids

Rahul Sharma

DNA mechanics plays a crucial role in many biological processes, including nucleosome positioning and protein-DNA interactions. It is believed that nature employs epigenetic modifications in DNA to further regulate gene expression. Moreover, double-strande ...

EPFL2023

Landscapes of DNA Mechanics and Genomes

Thomas Antonin Zwahlen

The local physical properties - such as shape and flexibility - of the DNA double-helix is today widely believed to be influenced by nucleic acid sequence in a non-trivial way. Furthermore, there is strong evidence that these properties play a role in many ...

EPFL2023

A fully-coupled highly-parallelized geomechanical simulator for assessing induced seismicity

Jean-François Molinari, Guillaume Anciaux, Nicolas Richart, Brice Tanguy Alphonse Lecampion, Emil Gallyamov

Induced seismicity caused by anthropogenic modification of the subsurface effective stress state has been observed in a number of industrial applications -- from hydrocarbon extraction (e.g., Groningen [1]), drilling waste-water disposal (e.g., [2]) to the ...

2023

Recycling of Polymerase Chain Reaction (PCR) Kits

Francesco Stellacci, Yong Zhu, Weina Liu

Polymerase chain reaction (PCR) kits have been used as common diagnosing tools during the outbreak of the severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) pandemic, with daily worldwide usage in the millions. It is well known that at the beginn ...

AMER CHEMICAL SOC2023

Adapting Haptic Feedback for Guided Meditation

Nicolas Henchoz, Cédric Duchene, Andreas Sonderegger, Romain Simon Collaud, Emily Clare Groves, Yoann Pierre Douillet

Technology supporting meditation is a multimillion-dollar market that continues to grow. There is also strong academic interest to understand and improve the impact technology can have for the user experience of practitioners. However, little work investig ...

2023

Prompting Large Language Models to Power Educational Chatbots

Denis Gillet, Sandy Ingram, Juan Carlos Farah, Fanny Kim-Lan Lasne

The recent rise in both popularity and performance of large language models has garnered considerable interest regarding their applicability to education. Technologies like ChatGPT, which can engage in human-like dialog, have already disrupted educational ...

Springer2023

Telomere protection against oxidative stress

Thu Trang Nguyen

Telomeres are nucleoprotein structures at the ends of linear chromosomes, being essential for the maintenance of genomic integrity. Telomeres have a unique structure which distinguishes chromosome termini from DNA damage sites. Shelterin complexes are the ...

EPFL2023

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

Dynamic Personalized Ranking

Jérémie Rappaz

Personalized ranking methods are at the core of many systems that learn to produce recommendations from user feedbacks. Their primary objective is to identify relevant items from very large vocabularies and to assist users in discovering new content. These ...

EPFL2022

m6A methylation potentiates cytosolic dsDNA recognition in a sequence-specific manner

Andrea Ablasser, Muhammet Fatih Gülen

Nucleic acid sensing through pattern recognition receptors is critical for immune recognition of microbial infections. Microbial DNA is frequently methylated at the N-6 position of adenines (m6A), a modification that is rare in mammalian host DNA. We show ...

ROYAL SOC2021

Electronic and structural dynamics in DNA single strands

Benjamin Bauer

The absorption, conversion and transport of electronic energy in molecular aggregates is at the heart of many important natural and artificial photochemical systems, including organic solar cell materials, photosynthetic light-harvesting complexes and DNA ...

EPFL2021

Sequence-dependent structural properties of B-DNA: what have we learned in 40 years?

John Maddocks, Daiva Petkeviciute, Paolo Carloni, Marco Pasi, Rahul Sharma

The structure of B-DNA, the physiological form of the DNA molecule, has been a central topic in biology, chemistry and physics. Far from uniform and rigid, the double helix was revealed as a flexible and structurally polymorphic molecule. Conformational ch ...

Springernature2021

How Florist Apprentices Explore Bouquet Designs: Supporting Design Space Exploration for Vocational Students

Pierre Dillenbourg, Kevin Gonyop Kim, Catharine Regina Monika Maria Oertel Genannt Bierbach

Context: Exploring the design space is an important process in a design task. In this study, we considered design space exploration for the learners in vocational education and training (VET). The goal of the study was to investigate how they explore the d ...

2021

Requirements for DNA bubble structure for efficient cleavage by helix-two-turn-helix DNA glycosylases

Kristina Makasheva

Oxidative DNA lesions, constantly generated by both endogenous and environmentally induced reactive oxygen species, are removed via the base excision repair pathway. In bacteria, Fpg and Nei DNA glycosylases, belonging to the helix-two-turn-helix (H2TH) st ...

2020

Structural and DNA binding properties of mycobacterial integration host factor mIHF

Giovanni Dietler, Stewart Cole, Aleksandre Japaridze, Rajkumar Singh, Luciano Andres Abriata, Nina Theres Odermatt, Jérémie Piton, David Lyndon Emsley, Moreno Lelli

In bacteria, nucleoid associated proteins (NAPs) take part in active chromosome organization by supercoil management, three-dimensional DNA looping and direct transcriptional control. Mycobacterial integration host factor (mIHF, rv1388) is a NAP restricted ...

Elsevier2020

Establishing a Ternary System for Optical Monitoring of DNA-Protein Interactions with Single-Walled Carbon Nanotubes

Shang-Jung Wu

DNA-protein interactions lie at the crux of life's essential processes. As such, various technologies have been developed to characterize these interactions. The distinct advantages of these technologies can be leveraged to study different facets of these ...

EPFL2020

Structural transitions and mechanochemical coupling in the nucleoprotein filament explain homology selectivity and Rad51 protein cooperativity in cellular DNA repair

Daniel Migliozzi

The nucleoprotein filament (NPF) is the fundamental element of homologous recombination (HR), a major mechanism for the repair of double-strand DNA breaks in the cell. The NPF is made of the damaged DNA strand surrounded by recombinase proteins, and its se ...

AMER PHYSICAL SOC2020

Macromolecular modeling and design in Rosetta: recent methods and frameworks

Bruno Emanuel Ferreira De Sousa Correia, Jaume Bonet Martinez, Thomas Huber, Lei Shi, Andreas Scheck, Patrick Daniel Barth, Hamed Khakzad, Alisa Khramushin

The Rosetta software for macromolecular modeling, docking and design is extensively used in laboratories worldwide. During two decades of development by a community of laboratories at more than 60 institutions, Rosetta has been continuously refactored and ...

NATURE PUBLISHING GROUP2020