Article
Neurosciences
Maria Italia, Elena Ferrari, Monica Di Luca, Fabrizio Gardoni
Summary: AMPARs play a crucial role in excitatory synaptic transmission in the mammalian brain, with the GluA3 subunit being widely expressed and functionally relevant. Modulation of GluA3 through pharmacological means may offer a new approach for addressing altered glutamatergic synapses associated with neurodegenerative and neurodevelopmental disorders.
NEUROBIOLOGY OF DISEASE
(2021)
Article
Chemistry, Physical
Aditi Khot, Brett M. Savoie
Summary: Coarse-grained molecular dynamics (CGMD) simulations address critical lengthscales and timescales in chemical and material applications. The development of black-box CGMD methodologies similar to density functional theory for electronic structure is still lacking. Machine learning (ML)-based CGMD potentials show promise in simplifying model development, but they have yet to outperform physics-based CGMD methods. In this study, λ-learning models are explored to combine the advantages of both approaches. The λ-models outperform ML-only CGMD models and provide essentially free gains in reproducing atomistic properties. However, neither the λ-learning models nor the ML-only models significantly outperform elementary pairwise models in reproducing atomistic properties due to the large irreducible force errors associated with coarse-graining.
JOURNAL OF CHEMICAL PHYSICS
(2023)
Review
Neurosciences
Agnes L. Nishimura, Natalia Arias
Summary: Amyotrophic Lateral Sclerosis (ALS) is a complex neurodegenerative disease caused by motor neuron degeneration. Loss of C9orf72 function and toxic effects of repeat expansions may contribute to the pathogenesis of ALS, leading to neurotransmission deficiencies.
FRONTIERS IN CELLULAR NEUROSCIENCE
(2021)
Article
Neurosciences
Min Yang, Peijia Lin, Wei Jing, Haokun Guo, Hongnian Chen, Yuanyuan Chen, Yi Guo, Yixue Gu, Miaoqing He, Junhong Wu, Xuejun Jiang, Zhen Zou, Xin Xu, Chengzhi Chen, Fei Xiao, Xuefeng Wang, Xin Tian
Summary: In this study, increased expression of Beclin1 in brain tissues from patients with temporal lobe epilepsy (TLE) was detected. Heterozygous disruption of beclin1 decreased susceptibility to epilepsy and suppressed seizure activity in two mouse epilepsy models. Additionally, Beclin1 participates in synaptic transmission, and dendritic spine development may be a biological function of Beclin1 independent of its role in autophagy.
FRONTIERS IN MOLECULAR NEUROSCIENCE
(2022)
Article
Mechanics
Fernando F. Grinstein, Juan A. Saenz, Massimo Germano
Summary: The study revisits coarse-grained simulation strategies for turbulent material mixing involving shock-driven turbulence, using newly available LMC-xRAGE hydrodynamics. Improved simulated mixing and turbulence levels on coarser grids were achieved, with the more accurate models requiring less resolution and resulting in grid-coarsening savings for mixing prediction.
Article
Clinical Neurology
Jorge Arriagada-Diaz, Carolina Flores-Munoz, Barbara Gomez-Soto, Marjorie Labrana-Allende, Michelle Mattar-Araos, Lorena Prado-Vega, Fernando Hinostroza, Ivana Gajardo, Maria Jose Guerra-Fernandez, Jorge A. Bevilacqua, Ana M. Cardenas, Marc Bitoun, Alvaro O. Ardiles, Arlek M. Gonzalez-Jamett
Summary: This study investigates the effect of the dynamin-2 p.R465W mutation on CNS function and suggests that it disrupts synaptic and cognitive function. The mutation leads to changes in neuronal morphology and impaired excitatory synaptic transmission.
NEUROPATHOLOGY AND APPLIED NEUROBIOLOGY
(2023)
Article
Clinical Neurology
Jorge Arriagada-Diaz, Carolina Flores-Munoz, Barbara Gomez-Soto, Marjorie Labrana-Allende, Michelle Mattar-Araos, Lorena Prado-Vega, Fernando Hinostroza, Ivana Gajardo, Maria Jose Guerra-Fernandez, Jorge A. Bevilacqua, Ana M. Cardenas, Marc Bitoun, Alvaro O. Ardiles, Arlek M. Gonzalez-Jamett
Summary: This study investigated the effect of a mutation in the dynamin-2 gene on central nervous system function. The mutation was found to reduce dendritic arborisation and spine density, as well as impair excitatory synaptic transmission and recognition memory in a mouse model. These findings highlight the role of dynamin-2 in regulating neuronal morphology and synaptic transmission in the hippocampus.
NEUROPATHOLOGY AND APPLIED NEUROBIOLOGY
(2023)
Article
Chemistry, Physical
Yangyang Zhang, Donghui Liu, Yiyang Zhang, Yachong Guo, Wenfei Li, Fabrice Thalmann
Summary: This article describes a coarse-grained model of POPC and DOPC lipid peroxides and discusses their predicted structure and the influence of hydration. In addition, electron and neutron scattering length density profiles of the simulated bilayers are provided.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Neurosciences
Naila Kuhlmann, Miriam Wagner Valladolid, Lucia Quesada-Ramirez, Matthew J. Farrer, Austen J. Milnerwood
Summary: The plasticity of excitatory striatal synapses is influenced by both facilitative and inhibitory factors. Excessive or persistent silencing leads to decreased dendritic spine density, while activation of NMDA receptors enhances synaptic structural plasticity.
FRONTIERS IN CELLULAR NEUROSCIENCE
(2021)
Article
Chemistry, Physical
Valery Lutsyk, Pawel Wolski, Wojciech Plazinski
Summary: This article presents a coarse-grained force field dedicated to glucopyranose-based carbohydrates, compatible with the Martini force field. The new model successfully displays spontaneous formation of aggregates with experimentally identified features and accurately identifies binding pockets in carbohydrate-binding proteins.
JOURNAL OF CHEMICAL THEORY AND COMPUTATION
(2022)
Article
Chemistry, Physical
Michael R. DeLyser, W. G. Noid
Summary: Investigated a new class of one-body potentials called square gradient (SG) potentials that can improve the accuracy and transferability of coarse-grained (CG) models. These SG potentials can tune interfacial properties and enhance the performance of various models.
JOURNAL OF CHEMICAL PHYSICS
(2022)
Article
Multidisciplinary Sciences
Amanda Toupin, Serine Benachenhou, Armita Abolghasemi, Asma Laroui, Luc Galarneau, Thamas Fulop, Francois Corbin, Artuela Caku
Summary: Fragile X syndrome (FXS) is a common genetic disorder that causes intellectual disability and autism spectrum disorder (ASD). This study found that individuals with FXS have decreased cholesterol content in lipid rafts (LRs), and this alteration is associated with autistic traits and adaptive behavior.
SCIENTIFIC REPORTS
(2022)
Article
Physics, Fluids & Plasmas
Enrico Skoruppa, Aderik Voorspoels, Jocelyne Vreede, Enrico Carlon
Summary: Investigations on the influence of nonlocal couplings on DNA torsional and bending elasticities revealed strong off-site couplings for tilt-tilt and twist-twist, while they were weaker in the roll-roll case. Analysis indicated that off-site interactions generate a length-scale-dependent elasticity in DNA models. Simulation-generated data predicted significant length-scale-dependent effect on torsional fluctuations, but only a modest effect on bending fluctuations, consistent with experimental observations probing DNA mechanics.
Article
Engineering, Multidisciplinary
Son Pham-Ba, Jean-Francois Molinari
Summary: The use of molecular dynamics (MD) simulations and the discrete element method (DEM) can unravel the atomistic origins of adhesive wear. MD simulations have a high computational cost and are limited to a narrow time and length scale, while DEM can reduce the computational cost and have larger particle diameters and system sizes. Single asperity wear simulations performed with MD can be successfully reproduced with DEM, validating the coarse-graining procedure. DEM allows for more complex simulations and reaching scales inaccessible to MD in the context of adhesive wear.
COMPUTER METHODS IN APPLIED MECHANICS AND ENGINEERING
(2022)
Review
Construction & Building Technology
Katerina Ioannidou, Christophe Labbez, Enrico Masoero
Summary: This manuscript reviews the current state of the art in coarse-grained and mesoscale simulations of C-S-H, and highlights opportunities for future research.
CEMENT AND CONCRETE RESEARCH
(2022)
Article
Biochemistry & Molecular Biology
Alessandro Pagliuso, To Nam Tham, Julia K. Stevens, Thibault Lagache, Roger Persson, Audrey Salles, Jean-Christophe Olivo-Marin, Stephane Oddos, Anne Spang, Pascale Cossart, Fabrizia Stavru
Article
Physics, Mathematical
T. Lagache, D. Holcman
JOURNAL OF STATISTICAL PHYSICS
(2017)
Article
Nanoscience & Nanotechnology
Krishna Jayant, Jan J. Hirtz, Ilan Jen-La Plante, David M. Tsai, Wieteke D. A. M. De Boer, Alexa Semonche, Darcy S. Peterka, Jonathan S. Owen, Ozgur Sahin, Kenneth L. Shepard, Rafael Yuste
NATURE NANOTECHNOLOGY
(2017)
Article
Multidisciplinary Sciences
Thibault Lagache, Alexandre Grassart, Stephane Dallongeville, Orestis Faklaris, Nathalie Sauvonnet, Alexandre Dufour, Lydia Danglot, Jean-Christophe Olivo-Marin
NATURE COMMUNICATIONS
(2018)
Article
Cell Biology
Krishna Jayant, Michael Wenzel, Yuki Bando, Jordan P. Hamm, Nicola Mandriota, Jake H. Rabinowitz, Ilan Jen-La Plante, Jonathan S. Owen, Ozgur Sahin, Kenneth L. Shepard, Rafael Yuste
Article
Cell Biology
Claudia Demarta-Gatsi, Anna Rivkin, Vincenzo Di Bartolo, Roger Peronet, Shuai Ding, Pierre-Henri Commere, Francois Guillonneau, Jacques Bellalou, Sebastien Brule, Paula Abou Karam, Sidney R. Cohen, Thibault Lagache, Chris J. Janse, Neta Regev-Rudzki, Salaheddine Mecheri
CELLULAR MICROBIOLOGY
(2019)
Article
Engineering, Biomedical
Fabrice de Chaumont, Elodie Ey, Nicolas Torquet, Thibault Lagache, Stephane Dallongeville, Albane Imbert, Thierry Legou, Anne-Marie Le Sourd, Philippe Faure, Thomas Bourgeron, Jean-Christophe Olivo-Marin
NATURE BIOMEDICAL ENGINEERING
(2019)
Article
Chemistry, Physical
Jake Rabinowitz, Martin A. Edwards, Elizabeth Whittier, Krishna Jayant, Kenneth L. Shepard
JOURNAL OF PHYSICAL CHEMISTRY A
(2019)
Article
Cell Biology
Jingliang Zhang, Xiaoling Chen, Muriel Eaton, Jiaxiang Wu, Zhixiong Ma, Shirong Lai, Anthony Park, Talha S. Ahmad, Zhefu Que, Ji Hea Lee, Tiange Xiao, Yuansong Li, Yujia Wang, Maria Olivero-Acosta, James A. Schaber, Krishna Jayant, Chongli Yuan, Zhuo Huang, Nadia A. Lanman, William C. Skarnes, Yang Yang
Summary: Severe Na(V)1.2 deficiency unexpectedly results in increased neuronal excitability, which can be reversed by genetic restoration. This neuronal hyperexcitability may serve as a cellular basis underlying Na(V)1.2 deficiency-related seizures.
Article
Multidisciplinary Sciences
Jake Rabinowitz, Elizabeth Whittier, Zheng Liu, Krishna Jayant, Joachim Frank, Kenneth Shepard
Article
Engineering, Electrical & Electronic
Siddharth Shekar, Krishna Jayant, M. Angeles Rabadan, Raju Tomer, Rafael Yuste, Kenneth L. Shepard
NATURE ELECTRONICS
(2019)
Proceedings Paper
Biochemical Research Methods
Thibault Lagache, Giacomo Nardi, Laetitia Bertot, Alexandre Grassart, Nathalie Sauvonnet, Jean-Christophe Olivo-Marin
2017 IEEE 14TH INTERNATIONAL SYMPOSIUM ON BIOMEDICAL IMAGING (ISBI 2017)
(2017)
Article
Microbiology
Pedro Escoll, Ok-Ryul Song, Flavia Viana, Bernhard Steiner, Thibault Lagache, Jean-Christophe Olivo-Marin, Francis Impens, Priscille Brodin, Hubert Hilbi, Carmen Buchrieser
CELL HOST & MICROBE
(2017)