Computational modeling of realistic cell membranes
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 …
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
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 …
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
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 …
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 …
arrangement. Our current understanding of the detailed organization of cell membranes …
[HTML][HTML] Albumin/vaccine nanocomplexes that assemble in vivo for combination cancer immunotherapy
Subunit vaccines have been investigated in over 1000 clinical trials of cancer
immunotherapy, but have shown limited efficacy. Nanovaccines may improve efficacy but …
immunotherapy, but have shown limited efficacy. Nanovaccines may improve efficacy but …
The role of protein loops and linkers in conformational dynamics and allostery
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 …
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
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 …
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 …
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) …
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 …
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 …
While visualization of MD trajectories allows an instant and intuitive understanding of …