[HTML][HTML] Simulating realistic membrane shapes

W Pezeshkian, SJ Marrink - Current opinion in cell biology, 2021 - Elsevier
Biological membranes exhibit diversity in their shapes and complexity in chemical
compositions that are linked to many cellular functions. These two central features of …

Mitochondrial DNA replication stress triggers a pro-inflammatory endosomal pathway of nucleoid disposal

LE Newman, S Weiser Novak, GR Rojas… - Nature Cell …, 2024 - nature.com
Mitochondrial DNA (mtDNA) encodes essential subunits of the oxidative phosphorylation
system, but is also a major damage-associated molecular pattern (DAMP) that engages …

The many faces of membrane tension: Challenges across systems and scales

P Rangamani - Biochimica et Biophysica Acta (BBA)-Biomembranes, 2022 - Elsevier
Our understanding of the role of membrane tension in the field of membrane biophysics is
rapidly evolving from a passive construct to an active player in a variety of cellular …

Backmapping triangulated surfaces to coarse-grained membrane models

W Pezeshkian, M König, TA Wassenaar… - Nature …, 2020 - nature.com
Many biological processes involve large-scale changes in membrane shape. Computer
simulations of these processes are challenging since they occur across a wide range of …

Generative multiscale analysis of de novo proteome-inspired molecular structures and nanomechanical optimization using a VoxelPerceiver transformer model

Z Yang, YC Hsu, MJ Buehler - Journal of the Mechanics and Physics of …, 2023 - Elsevier
We report a method to generate de novo protein designs through a generative adversarial
neural network, MolShapeGAN, that can rapidly produce a large variety of nanoarchitected …

Systems modeling predicts that mitochondria ER contact sites regulate the postsynaptic energy landscape

A Leung, D Ohadi, G Pekkurnaz… - NPJ systems biology and …, 2021 - nature.com
Spatiotemporal compartmentation of calcium dynamics is critical for neuronal function,
particularly in postsynaptic spines. This exquisite level of Ca2+ compartmentalization is …

Multiscale simulation approaches to modeling drug–protein binding

BR Jagger, SE Kochanek, S Haldar, RE Amaro… - Current opinion in …, 2020 - Elsevier
Highlights•Drug binding is inherently multiscale as it occurs over a broad range of length
and time scales.•Multiscale simulation methods combine molecular descriptions to access …

Biophysical Modeling of Synaptic Plasticity

CT Lee, M Bell, M Bonilla-Quintana… - Annual Review of …, 2024 - annualreviews.org
Dendritic spines are small, bulbous compartments that function as postsynaptic sites and
undergo intense biochemical and biophysical activity. The role of the myriad signaling …

Violation of the ultrastructural size principle in the dorsolateral prefrontal cortex underlies working memory impairment in the aged common marmoset (Callithrix …

C Glavis-Bloom, CR Vanderlip… - Frontiers in Aging …, 2023 - frontiersin.org
Morphology and function of the dorsolateral prefrontal cortex (dlPFC), and corresponding
working memory performance, are affected early in the aging process, but nearly half of …

Dendritic spine morphology regulates calcium-dependent synaptic weight change

MK Bell, MV Holst, CT Lee, P Rangamani - Journal of General …, 2022 - rupress.org
Dendritic spines act as biochemical computational units and must adapt their responses
according to their activation history. Calcium influx acts as the first signaling step during …