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] Scalable molecular dynamics on CPU and GPU architectures with NAMD

JC Phillips, DJ Hardy, JDC Maia, JE Stone… - The Journal of …, 2020 - pubs.aip.org
NAMD is a molecular dynamics program designed for high-performance simulations of very
large biological objects on CPU-and GPU-based architectures. NAMD offers scalable …

Lipid–protein interactions are unique fingerprints for membrane proteins

V Corradi, E Mendez-Villuendas, HI Ingólfsson… - ACS central …, 2018 - ACS Publications
Cell membranes contain hundreds of different proteins and lipids in an asymmetric
arrangement. Our current understanding of the detailed organization of cell membranes …

[HTML][HTML] Albumin/vaccine nanocomplexes that assemble in vivo for combination cancer immunotherapy

G Zhu, GM Lynn, O Jacobson, K Chen, Y Liu… - Nature …, 2017 - nature.com
Subunit vaccines have been investigated in over 1000 clinical trials of cancer
immunotherapy, but have shown limited efficacy. Nanovaccines may improve efficacy but …

The role of protein loops and linkers in conformational dynamics and allostery

E Papaleo, G Saladino, M Lambrughi… - Chemical …, 2016 - ACS Publications
Proteins are dynamic entities that undergo a plethora of conformational changes that may
take place on a wide range of time scales. These changes can be as small as the rotation of …

Coupling of mechanical deformation and electromagnetic fields in biological cells

M Torbati, K Mozaffari, L Liu, P Sharma - Reviews of Modern Physics, 2022 - APS
The cell, as the most fundamental unit of life, is a microcosm of biology in which the
confluence of nearly all aspects of classical physics (mechanics, statistical physics …

[HTML][HTML] Tinker-HP: a massively parallel molecular dynamics package for multiscale simulations of large complex systems with advanced point dipole polarizable force …

L Lagardère, LH Jolly, F Lipparini, F Aviat, B Stamm… - Chemical …, 2018 - pubs.rsc.org
We present Tinker-HP, a massively MPI parallel package dedicated to classical molecular
dynamics (MD) and to multiscale simulations, using advanced polarizable force fields (PFF) …

New tricks for old dogs: improving the accuracy of biomolecular force fields by pair-specific corrections to non-bonded interactions

J Yoo, A Aksimentiev - Physical Chemistry Chemical Physics, 2018 - pubs.rsc.org
In contrast to ordinary polymers, the vast majority of biological macromolecules adopt highly
ordered three-dimensional structures that define their functions. The key to folding of a …

[HTML][HTML] Bringing molecular dynamics simulation data into view

PW Hildebrand, AS Rose, JKS Tiemann - Trends in Biochemical Sciences, 2019 - cell.com
Molecular dynamics (MD) simulations monitor time-resolved motions of macromolecules.
While visualization of MD trajectories allows an instant and intuitive understanding of …