Simulation of DNA-nanotube interactions
H Gao, Y Kong - Annu. Rev. Mater. Res., 2004 - annualreviews.org
▪ Abstract Carbon nanotubes functionalized with biological molecules (such as protein
peptides and nucleic acids) show great potential for application in bioengineering and …
peptides and nucleic acids) show great potential for application in bioengineering and …
Empirical amide I vibrational frequency map: application to 2D-IR line shapes for isotope-edited membrane peptide bundles
The amide I vibrational mode, primarily associated with peptide-bond carbonyl stretches,
has long been used to probe the structures and dynamics of peptides and proteins by …
has long been used to probe the structures and dynamics of peptides and proteins by …
GROMACS 3.0: a package for molecular simulation and trajectory analysis
GROMACS 3.0 is the latest release of a versatile and very well optimized package for
molecular simulation. Much effort has been devoted to achieving extremely high …
molecular simulation. Much effort has been devoted to achieving extremely high …
A biomolecular force field based on the free enthalpy of hydration and solvation: the GROMOS force‐field parameter sets 53A5 and 53A6
Successive parameterizations of the GROMOS force field have been used successfully to
simulate biomolecular systems over a long period of time. The continuing expansion of …
simulate biomolecular systems over a long period of time. The continuing expansion of …
Improving efficiency of large time‐scale molecular dynamics simulations of hydrogen‐rich systems
KA Feenstra, B Hess… - Journal of computational …, 1999 - Wiley Online Library
A systematic analysis is performed on the effectiveness of removing degrees of freedom
from hydrogen atoms and/or increasing hydrogen masses to increase the efficiency of …
from hydrogen atoms and/or increasing hydrogen masses to increase the efficiency of …
A systematic study of water models for molecular simulation: derivation of water models optimized for use with a reaction field
D Van der Spoel, PJ Van Maaren… - The Journal of chemical …, 1998 - pubs.aip.org
We have performed long molecular dynamics simulations of water using four popular water
models, namely simple point charge (SPC), extended simple point charge (SPC/E), and the …
models, namely simple point charge (SPC), extended simple point charge (SPC/E), and the …
Efficient algorithms for Langevin and DPD dynamics
N Goga, AJ Rzepiela, AH De Vries… - Journal of chemical …, 2012 - ACS Publications
In this article, we present several algorithms for stochastic dynamics, including Langevin
dynamics and different variants of Dissipative Particle Dynamics (DPD), applicable to …
dynamics and different variants of Dissipative Particle Dynamics (DPD), applicable to …
The antibacterial peptide pyrrhocoricin inhibits the ATPase actions of DnaK and prevents chaperone-assisted protein folding
Recently, we documented that the short, proline-rich antibacterial peptides pyrrhocoricin,
drosocin, and apidaecin interact with the bacterial heat shock protein DnaK, and peptide …
drosocin, and apidaecin interact with the bacterial heat shock protein DnaK, and peptide …
Molecular dynamics simulations of phospholipid bilayers with cholesterol
To investigate the microscopic interactions between cholesterol and lipids in biological
membranes, we have performed a series of molecular dynamics simulations of large …
membranes, we have performed a series of molecular dynamics simulations of large …
Tunable water desalination across graphene oxide framework membranes
The performance of graphene oxide framework (GOF) membranes for water desalination is
assessed using classical molecular dynamics (MD) simulations. The coupling between …
assessed using classical molecular dynamics (MD) simulations. The coupling between …