Taming the Ewald sum in the computer simulation of charged systems

Adams, David J.; Dubey, Girija S.

doi:10.1016/0021-9991(87)90076-3

Cited by 171 publications

(86 citation statements)

References 30 publications

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“…In order to explain spectacular features in frequency shifts, band shapes, and bandwidths of the components the OH stretching modes the linear and nonlinear response theory [43][44][45], quantum ab inito calculations for possible cluster structures [62][63][64][65][66][67][68], classical [69][70][71][72][73] and mixed quantum/classical molecular dynamics simulations [74][75][76] have been used.…”

Section: Discussionmentioning

confidence: 99%

Hydrogen bonds of interfacial water in human breast cancer tissue compared to lipid and DNA interfaces

Abramczyk¹,

Brożek-Płuska²,

Surmacki³

et al. 2011

JBPC

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The paper presents the results for water confined in a human breast cancerous tissue, a single stranded DNA, a double stranded DNA and in phospholipids (DPPC-D--Phosphatidylcholine, dipalmitoyl). The interfacial water in DNA and lipids is represented by a double band in the region of the OH stretching mode of water corresponding to the symmetric and asymmetric vibrational modes, in contrast to water confined in the cancerous breast tissue where only one band at 3311 cm -1 has been recorded. The marked red-shift of the maximum peak position of the OH stretching mode confirms that the vibrational properties of the interfacial water observed in restricted biological environment differ drastically from those in bulk water. The change of vibrational pattern of behavior may be due to the decoupling of the vibrations of the OH bonds in water molecule or change of the vibrational selection rules at biological interfaces. According to our knowledge Raman vibrational properties of water confined in the normal and cancerous breast tissue of the same patient have not been reported in literature yet. Here we have also presented the first Raman 'optical biopsy' images of the non-cancerous and cancerous (infiltrating ductal cancer) human breast tissues.

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Section: Discussionmentioning

confidence: 99%

Hydrogen bonds of interfacial water in human breast cancer tissue compared to lipid and DNA interfaces

Abramczyk¹,

Brożek-Płuska²,

Surmacki³

et al. 2011

JBPC

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“…We computed the electrostatics of the system using Ewald summation procedure of Adams and Dubey. 49 The equations of motion were integrated using (2) where ξ(t) is the Gaussian random noise satisfying . Figure 2B).…”

Section: Brownian Dynamics Simulationsmentioning

confidence: 99%

Charge Density of Divalent Metal Cations Determines RNA Stability

et al. 2007

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RNA molecules are exquisitely sensitive to the properties of counterions. The folding equilibrium of the Tetrahymena ribozyme is measured by non-denaturing gel electrophoresis in the presence of divalent group IIA metal cations. The stability of the folded ribozyme increases with the charge density (ζ) of the cation. Similar scaling is found when the free energy of the RNA folded in small and large metal cations is measured by urea denaturation. Brownian dynamics simulations of a polyelectrolyte show that the experimental observations can be explained by non-specific ion-RNA interactions in the absence of site-specific metal chelation. The experimental and simulation results establish that RNA stability is largely determined by a combination of counterion charge and the packing efficiency of condensed cations that depends on the excluded volume of the cations.

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“…3 Several methods have been proposed to tackle the first problem, e.g., tabulation of the complete Ewald potential 4 or the use of polynomial approximations, in particular expansion of the nonspherical contributions to the Ewald potential in cubic harmonics. 4,5 Apart from the difficulty of a computational overhead which might strongly increase with the desired accuracy, all these methods do not solve the second problem: the unfavorable scaling with particle number.…”

Section: Introductionmentioning

confidence: 99%

How to mesh up Ewald sums. I. A theoretical and numerical comparison of various particle mesh routines

Deserno¹,

Holm²

1998

The Journal of Chemical Physics

617

622

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Standard Ewald sums, which calculate, e.g., the electrostatic energy or the force in periodically closed systems of charged particles, can be efficiently speeded up by the use of the fast Fourier transformation ͑FFT͒. In this article we investigate three algorithms for the FFT-accelerated Ewald sum, which have attracted widespread attention, namely, the so-called particle-particle-particle mesh ͑P 3 M), particle mesh Ewald ͑PME͒, and smooth PME method. We present a unified view of the underlying techniques and the various ingredients which comprise those routines. Additionally, we offer detailed accuracy measurements, which shed some light on the influence of several tuning parameters and also show that the existing methods -although similar in spirit -exhibit remarkable differences in accuracy. We propose a set of combinations of the individual components, mostly relying on the P 3 M approach, that we regard to be the most flexible. The issue of estimating the errors connected with particle mesh routines is reserved to paper II.

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Taming the Ewald sum in the computer simulation of charged systems

Cited by 171 publications

References 30 publications

Hydrogen bonds of interfacial water in human breast cancer tissue compared to lipid and DNA interfaces

Hydrogen bonds of interfacial water in human breast cancer tissue compared to lipid and DNA interfaces

Charge Density of Divalent Metal Cations Determines RNA Stability

How to mesh up Ewald sums. I. A theoretical and numerical comparison of various particle mesh routines

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