Advances in the understanding of protein misfolding and aggregation through molecular dynamics simulation

A Rahman, B Saikia, CR Gogoi, A Baruah - Progress in Biophysics and …, 2022 - Elsevier
Aberrant protein folding known as protein misfolding is counted as one of the striking factors
of neurodegenerative diseases. The extensive range of pathologies caused by protein …

From system modeling to system analysis: The impact of resolution level and resolution distribution in the computer-aided investigation of biomolecules

M Giulini, M Rigoli, G Mattiotti, R Menichetti… - Frontiers in Molecular …, 2021 - frontiersin.org
The ever increasing computer power, together with the improved accuracy of atomistic force
fields, enables researchers to investigate biological systems at the molecular level with …

Molecular simulation of ultrathin polymeric films near the glass transition

JA Torres, PF Nealey, JJ de Pablo - Physical Review Letters, 2000 - APS
Abstract Properties such as the glass transition temperature (T g) and the diffusion
coefficient of ultrathin polymeric films are shown to depend on the dimensions of the system …

Molecular dynamics simulations of spontaneous fibril formation by random-coil peptides

HD Nguyen, CK Hall - … of the National Academy of Sciences, 2004 - National Acad Sciences
Assembly of normally soluble proteins into amyloid fibrils is a cause or associated symptom
of numerous human disorders, including Alzheimer's and the prion diseases. We report …

Modeling viral capsid assembly

MF Hagan - Advances in Chemical Physics: Volume 155, 2014 - Wiley Online Library
Viruses play a role in a significant portion of human diseases, as well as those of other
animals, plants, and bacteria. This chapter focuses on the use of theoretical and …

The event scheduling problem in molecular dynamic simulation

DC Rapaport - Journal of Computational Physics, 1980 - Elsevier
Molecular dynamics simulation studies of hard sphere and related many-body systems tend
to be heavy consumers of computer time. In order to perform event-driven simulations of this …

Deciphering the kinetic mechanism of spontaneous self-assembly of icosahedral capsids

HD Nguyen, VS Reddy, CL Brooks - Nano letters, 2007 - ACS Publications
Self-assembly of viral proteins into icosahedral capsids is an interesting yet poorly
understood phenomenon of which elucidation may aid the exploration of beneficial …

α‐Helix formation: Discontinuous molecular dynamics on an intermediate‐resolution protein model

A Voegler Smith, CK Hall - Proteins: Structure, Function, and …, 2001 - Wiley Online Library
An intermediate‐resolution model of small, homogeneous peptides is introduced, and
discontinuous molecular dynamics simulation is applied to study secondary structure …

Computer simulation of self‐avoiding walks: testing the scanning method

H Meirovitch - The Journal of chemical physics, 1983 - pubs.aip.org
The scanning method is a computer simulation technique for macromolecules suggested
recently. The method is described here in detail and its applicability (in contrast to other …

Historical perspective and current outlook for molecular dynamics as a chemical engineering tool

EJ Maginn, JR Elliott - Industrial & engineering chemistry …, 2010 - ACS Publications
On the occasion of the AIChE's 100th anniversary, we review the status of molecular
dynamics simulation. The development of molecular dynamics has been highly …