New tricks for modelers from the crystallography toolkit: the particle mesh Ewald algorithm and its use in nucleic acid simulations

T Darden, L Perera, L Li, L Pedersen - Structure, 1999 - cell.com
The accurate simulation of DNA and RNA has been a goal of theoretical biophysicists for a
number of years. That is, given a high-resolution experimental structure, or perhaps a …

Dielectric relaxation and solvation dynamics of water in complex chemical and biological systems

N Nandi, K Bhattacharyya, B Bagchi - Chemical Reviews, 2000 - ACS Publications
Because of its unique properties, water drives many natural and biological processes. While
a detailed understanding of its precise role is still being unravelled, it is clear that the …

Theoretical methods for the description of the solvent effect in biomolecular systems

M Orozco, FJ Luque - Chemical Reviews, 2000 - ACS Publications
The environment plays a key role in the determination of the properties and reactivity of
substances in condensed phases. The complexity of chemical phenomena in solution has …

Direct measurement of the dielectric polarization properties of DNA

A Cuervo, PD Dans, JL Carrascosa… - Proceedings of the …, 2014 - National Acad Sciences
The electric polarizability of DNA, represented by the dielectric constant, is a key intrinsic
property that modulates DNA interaction with effector proteins. Surprisingly, it has so far …

Structure and interactions of biological helices

AA Kornyshev, DJ Lee, S Leikin, A Wynveen - Reviews of Modern Physics, 2007 - APS
Helices are essential building blocks of living organisms, be they molecular fragments of
proteins (α-helices), macromolecules (DNA and collagen), or multimolecular assemblies …

Dielectric constant of water confined in a nanocavity

S Senapati, A Chandra - The Journal of Physical Chemistry B, 2001 - ACS Publications
The dielectric constant of water confined in a nanodimensional spherical cavity is calculated
by means of molecular dynamics simulations. The simulations are carried out by using two …

Slow dynamics of constrained water in complex geometries

K Bhattacharyya, B Bagchi - The Journal of Physical Chemistry A, 2000 - ACS Publications
Although water is often hailed as the lubricant of life, a detailed understanding of its role in
many chemical and biological processes still eludes us. In many natural systems, water is …

Ion motions in molecular dynamics simulations on DNA

SY Ponomarev, KM Thayer… - Proceedings of the …, 2004 - National Acad Sciences
Counterions play a significant role in DNA structure and function, and molecular dynamics
(MD) simulations offer the prospect of detailed description of the dynamical structure of ions …

Label-free identification of single dielectric nanoparticles and viruses with ultraweak polarization forces

L Fumagalli, D Esteban-Ferrer, A Cuervo… - Nature materials, 2012 - nature.com
Label-free detection of the material composition of nanoparticles could be enabled by the
quantification of the nanoparticles' inherent dielectric response to an applied electric field …

Electrostatic correlations and fluctuations for ion binding to a finite length polyelectrolyte

ZJ Tan, SJ Chen - The Journal of chemical physics, 2005 - pubs.aip.org
Polyelectrolyte folding requires the proper ionic solution condition. It is essential to
understand how the ionic condition, such as ion concentration, ion size, and ion charges …