Multiscale simulation of DNA
Highlights•We describe the most recent methods to study DNA from electrons to
chromosomes.•Methods were classified as: electronic, atomistic, coarse grained, and …
chromosomes.•Methods were classified as: electronic, atomistic, coarse grained, and …
Conformational Thermodynamics of DNA Strands in Hydrophilic Nanopores
Enhanced sampling techniques spanning a submicrosecond time scale reveal that a double-
stranded DNA dodecamer can be spontaneously encapsulated into (51, 0) and (40, 0) …
stranded DNA dodecamer can be spontaneously encapsulated into (51, 0) and (40, 0) …
Electric-Field-Induced protein translocation via a conformational transition in SecDF: An MD study
E Ficici, D Jeong, I Andricioaei - Biophysical Journal, 2017 - cell.com
SecDF is an important component of the Sec protein translocation machinery embedded in
the bacterial membrane, which is associated with many functions, such as stabilizing other …
the bacterial membrane, which is associated with many functions, such as stabilizing other …
Partial Denaturation of Double-Stranded DNA on Pristine Graphene under Physiological-like Conditions
Interactions between DNA and graphene are paramount for a wide range of applications,
such as biosensing and nanoelectronics; nonetheless, the molecular details of such …
such as biosensing and nanoelectronics; nonetheless, the molecular details of such …
Computational Studies of Biomolecular Conformational Changes Through Potential of Mean Force Calculations and Accelerated Molecular Dynamics Simulations
E Ficici - 2015 - escholarship.org
Molecular dynamics (MD) simulations have made significant contributions to our
understanding of biomolecular structures, functions and processes during the last few …
understanding of biomolecular structures, functions and processes during the last few …