Computational modeling of realistic cell membranes

SJ Marrink, V Corradi, PCT Souza, HI Ingolfsson… - Chemical …, 2019 - ACS Publications
Cell membranes contain a large variety of lipid types and are crowded with proteins,
endowing them with the plasticity needed to fulfill their key roles in cell functioning. The …

Multiscale simulations of biological membranes: the challenge to understand biological phenomena in a living substance

G Enkavi, M Javanainen, W Kulig, T Róg… - Chemical …, 2019 - ACS Publications
Biological membranes are tricky to investigate. They are complex in terms of molecular
composition and structure, functional over a wide range of time scales, and characterized by …

[HTML][HTML] The interplay between membrane topology and mechanical forces in regulating T cell receptor activity

MA Al-Aghbar, AK Jainarayanan, ML Dustin… - Communications …, 2022 - nature.com
T cells are critically important for host defense against infections. T cell activation is specific
because signal initiation requires T cell receptor (TCR) recognition of foreign antigen …

Universal relation between instantaneous diffusivity and radius of gyration of proteins in aqueous solution

E Yamamoto, T Akimoto, A Mitsutake, R Metzler - Physical review letters, 2021 - APS
Protein conformational fluctuations are highly complex and exhibit long-term correlations.
Here, molecular dynamics simulations of small proteins demonstrate that these …

Machine-learning solutions for the analysis of single-particle diffusion trajectories

H Seckler, J Szwabinski, R Metzler - The Journal of Physical …, 2023 - ACS Publications
Single-particle traces of the diffusive motion of molecules, cells, or animals are by now
routinely measured, similar to stochastic records of stock prices or weather data …

[HTML][HTML] Binding revisited—avidity in cellular function and signaling

S Erlendsson, K Teilum - Frontiers in molecular biosciences, 2021 - frontiersin.org
When characterizing biomolecular interactions, avidity, is an umbrella term used to describe
the accumulated strength of multiple specific and unspecific interactions between two or …

Crossover from anomalous to normal diffusion: truncated power-law noise correlations and applications to dynamics in lipid bilayers

D Molina-Garcia, T Sandev, H Safdari… - New Journal of …, 2018 - iopscience.iop.org
The emerging diffusive dynamics in many complex systems show a characteristic crossover
behaviour from anomalous to normal diffusion which is otherwise fitted by two independent …

The more the merrier: effects of macromolecular crowding on the structure and dynamics of biological membranes

M Löwe, M Kalacheva, AJ Boersma… - The FEBS …, 2020 - Wiley Online Library
Proteins are essential and abundant components of cellular membranes. Being densely
packed within the limited surface area, proteins fulfil essential tasks for life, which include …

[HTML][HTML] Extracting, quantifying, and comparing dynamical and biomechanical properties of living matter through single particle tracking

S Scott, M Weiss, C Selhuber-Unkel… - Physical Chemistry …, 2023 - pubs.rsc.org
A panoply of new tools for tracking single particles and molecules has led to an explosion of
experimental data, leading to novel insights into physical properties of living matter …

Assembly and analysis of cell-scale membrane envelopes

JV Vermaas, CG Mayne, E Shinn… - Journal of chemical …, 2021 - ACS Publications
The march toward exascale computing will enable routine molecular simulation of larger
and more complex systems, for example, simulation of entire viral particles, on the scale of …