Publications related to Biophysics

Artificial intelligence for natural product drug discovery

Philippe Schwaller, Florian Huber, Albert Hofstetter, Michael Alexander Skinnider

Developments in computational omics technologies have provided new means to access the hidden diversity of natural products, unearthing new potential for drug discovery. In parallel, artificial intelligence approaches such as machine learning have led to e ...

Nature Portfolio2023

New insights into rodent brain microstructure and metabolism in hepatic encephalopathy

Jessie Julie Mosso

Type C hepatic encephalopathy (HE) is a severe neuropsychiatric complication of chronic liver disease, for which the prognosis is poor in the absence of liver transplantation. Cirrhosis in type C HE leads to a toxic accumulation of ammonia in the blood, wh ...

EPFL2023

Towards elucidating the structural and cellular determinants of a-synuclein seeding and toxicity

Somanath Jagannath

Although it has been nearly two and half decades since the discovery of alpha-synuclein (aSyn) as the major component of Lewy bodies (LBs), our understanding of the involvement of different aSyn species, their seeding, spreading and toxicity in Parkinson's ...

EPFL2022

Probing Surfactant Bilayer Interactions by Tracking Optically Trapped Single Nanoparticles

Olivier Martin, Jeonghyeon Kim

Single-particle tracking and optical tweezers are powerful techniques for studying diverse processes at the microscopic scale. The stochastic behavior of a microscopic particle contains information about its interaction with surrounding molecules, and an o ...

WILEY2022

Rapid Characterization and Quantification of Extracellular Vesicles by Fluorescence-Based Microfluidic Diffusion Sizing

Pablo Rivera Fuentes, Adam Miklos Eördögh

Extracellular vesicles (EVs) are emerging as promising diagnostic and therapeutic tools for a variety of diseases. The characterization of EVs requires a series of orthogonal techniques that are overall time- and material-consuming. Here, a microfluidic de ...

WILEY2021

Reviewing Challenges of Predicting Protein Melting Temperature Change Upon Mutation Through the Full Analysis of a Highly Detailed Dataset with High-Resolution Structures

Luciano Andres Abriata

Predicting the effects of mutations on protein stability is a key problem in fundamental and applied biology, still unsolved even for the relatively simple case of small, soluble, globular, monomeric, two-state-folder proteins. Many articles discuss the li ...

2021

Wetting of nanopores probed with pressure

Aleksandra Radenovic, Andrey Chernev, Sanjin Marion, Michal Daniel Macha, Sebastian James Davis

Nanopores are both a tool to study single-molecule biophysics and nanoscale ion transport, but also a promising material for desalination or osmotic power generation. Understanding the physics underlying ion transport through nano-sized pores allows better ...

ROYAL SOC CHEMISTRY2021

Persistence of bioconvection-induced mixed layers in a stratified lake

Alfred Johny Wüest, Damien Bouffard, Oscar Rodrigo Sepúlveda Steiner

In situ observations of biophysical interactions in natural waters typically focus on physical mechanisms influencing biological activity. Yet, biological activity can also drive physical processes in aquatic environments. A community of photoautotrophic, ...

American Society of Limnology and Oceanography2021

Visualizing intracellular nanostructures of living cells by nanoendoscopy-AFM

Marcos Penedo Garcia

Atomic force microscopy (AFM) is the only technique that allows label-free imaging of nanoscale biomolecular dynamics, playing a crucial role in solving biological questions that cannot be addressed by other major bioimaging tools (fluorescence or electron ...

AMER ASSOC ADVANCEMENT SCIENCE2021

Polymer Coatings to Minimize Protein Adsorption in Solid-State Nanopores

Aleksandra Radenovic, Sanjin Marion, Sebastian James Davis, Michael Mayer

Nanopore-based resistive-pulse recordings represent a promising approach for single-molecule biophysics with applications ranging from rapid DNA and RNA sequencing to "fingerprinting" proteins. Based on advances in fabrication methods, solid-state nanopore ...

WILEY-V C H VERLAG GMBH2020

Biomolecular Simulation: a Perspective from High Performance Computing

Ursula Röthlisberger, Viacheslav Bolnykh, Paolo Carloni

High-Performance Computing is impacting on all biomedical sciences, including molecular biophysics. Here, we describe general parallel computing strategies (multi-threading and distributed computing) used in all the natural sciences, including molecular bi ...

WILEY-V C H VERLAG GMBH2020

PEG/HA Hybrid Hydrogels for Biologically and Mechanically Tailorable Bone Marrow Organoids

Nicolas Antoine Vincent Broguiere, Martin Ehrbar, Queralt Vallmajó Martín

Bone marrow (BM) organoids provide powerful tools to study the vital interplay between the BM microenvironment and resident cells. Current biomaterials, however, are limited in terms of versatility for independently studying the biochemical and biophysical ...

WILEY-V C H VERLAG GMBH2020

The Diverse Nature of Ion Speciation at the Nanoscale Hydrophobic/Water Interface

Sylvie Roke, Halil Ibrahim Okur, Evangelia Zdrali

Many biological systems are composed of nanoscale structures having hydrophobic and hydrophilic groups adjacent to one another and in contact with aqueous electrolyte solution. The interaction of ions with such structures is of fundamental importance. Alth ...

AMER CHEMICAL SOC2019

Microbial life in porous systems

David Scheidweiler

Microbial life in porous systems dominates the functioning of numerous ecosystems, ranging from stream sediments to soils. While these environments are characterized by structures that vary spatially over orders of magnitude, the traditional research focus ...

EPFL2019

The physiological variability of channel density in hippocampal CA1 pyramidal cells and interneurons explored using a unified data-driven modeling workflow

Henry Markram, Eilif Benjamin Muller, Ying Shi, Armando Romani, Felix Schürmann, Jean-Denis Georges Emile Courcol, Werner Alfons Hilda Van Geit, Christian Andreas Rössert, Maurizio Ferdinando Pezzoli, Michele Migliore, Olivier Richard Hagens, Stefano Maximiliano Antonel, Szabolcs Kali, Carmen Alina Lupascu, Rosanna Migliore, Luca Leonardo Bologna, Audrey Mercer

Every neuron is part of a network, exerting its function by transforming multiple spatiotemporal synaptic input patterns into a single spiking output. This function is specified by the particular shape and passive electrical properties of the neuronal memb ...

2018

Polyglutamine expansion affects huntingtin conformation in multiple Huntington’s disease models

Hilal Lashuel, Lara Petricca, Sean Michael Deguire

Conformational changes in disease-associated or mutant proteins represent a key pathological aspect of Huntington's disease (HD) and other protein misfolding diseases. Using immunoassays and biophysical approaches, we and others have recently reported that ...

Springer Nature2017

Phage Selection of Cyclic Peptides for Application in Research and Drug Development

Christian Heinis, Xudong Kong, Kaycie Marie Butler

Cyclic peptides can bind to protein targets with high affinities and selectivities, which makes them an attractive modality for the development of research reagents and therapeutics. Additional properties, including low inherent toxicity, efficient chemica ...

2017

From Neuron Biophysics to Orientation Selectivity in Electrically Coupled Networks of Neocortical L2/3 Large Basket Cells

Henry Markram, Eilif Benjamin Muller, Idan Segev, Werner Alfons Hilda Van Geit, Oren Amsalem

In the neocortex, inhibitory interneurons of the same subtype are electrically coupled with each other via dendritic gap junctions (GJs). The impact of multiple GJs on the biophysical properties of interneurons and thus on their input processing is unclear ...

Oxford University Press (OUP)2016

Integrating gene synthesis and microfluidic protein analysis for rapid protein engineering

Sebastian Maerkl, Ekaterina Emilova Petrova, Bruno Emanuel Ferreira De Sousa Correia, Matthew Christopher Blackburn

The capability to rapidly design proteins with novel functions will have a significant impact on medicine, biotechnology and synthetic biology. Synthetic genes are becoming a commodity, but integrated approaches have yet to be developed that take full adva ...

Oxford Univ Press2016

Accelerated Microstructure Imaging via Convex Optimization (AMICO) from diffusion MRI data

Jean-Philippe Thiran, Alessandro Daducci, Erick Jorge Canales Rodriguez, Tim Bjørn Dyrby, Hui Zhang

Microstructure imaging from diffusion magnetic resonance (MR) data represents an invaluable tool to study non-invasively the morphology of tissues and to provide a biological insight into their microstructural organization. In recent years, a variety of bi ...

Elsevier2015