scholarly journals “On-the-fly” coupled cluster path-integral molecular dynamics: impact of nuclear quantum effects on the protonated water dimer

2015 ◽  
Vol 17 (22) ◽  
pp. 14355-14359 ◽  
Author(s):  
Thomas Spura ◽  
Hossam Elgabarty ◽  
Thomas D. Kühne
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Path Integral ◽  
Effective Potential ◽  
Water Dimer ◽  
Coupled Cluster ◽  
Single Well ◽  
Cluster Path ◽  
Dynamics Simulations ◽  
Nuclear Quantum Effects

“On-the-fly” coupled cluster-based path-integral molecular dynamics simulations predict that the effective potential of the protonated water–dimer has a single-well only.

scholarly journals Correction: “On-the-fly” coupled cluster path-integral molecular dynamics: impact of nuclear quantum effects on the protonated water dimer

2015 ◽  
Vol 17 (29) ◽  
pp. 19673-19674 ◽  
Author(s):  
Thomas Spura ◽  
Hossam Elgabarty ◽  
Thomas D. Kühne
Keyword(s):  
Molecular Dynamics ◽  
Path Integral ◽  
Quantum Effects ◽  
Chem Phys ◽  
Water Dimer ◽  
Coupled Cluster ◽  
Cluster Path ◽  
Nuclear Quantum Effects ◽  
Phys Chem Chem Phys

Correction for “On-the-fly” coupled cluster path-integral molecular dynamics: impact of nuclear quantum effects on the protonated water dimer` by Thomas Spura et al., Phys. Chem. Chem. Phys., 2015, 17, 14355–14359.

scholarly journals Effects of Topological Constraints on Penetration Structures of Semi-Flexible Ring Polymers

Polymers ◽  
2020 ◽  
Vol 12 (11) ◽  
pp. 2659
Author(s):  
Fuchen Guo ◽  
Ke Li ◽  
Jiaxin Wu ◽  
Linli He ◽  
Linxi Zhang
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Effective Potential ◽  
Topological Constraints ◽  
Chain Stiffness ◽  
Ring Polymers ◽  
Dynamics Simulations ◽  
Flexible Ring ◽  
Peak Value ◽  
Improved Algorithm

The effects of topological constraints on penetration structures of semi-flexible ring polymers in a melt are investigated using molecular dynamics simulations, considering simultaneously the effects of the chain stiffness. Three topology types of rings are considered: 01-knot (the unknotted), 31-knot and 61-knot ring polymers, respectively. With the improved algorithm to detect and quantify the inter-ring penetration (or inter-ring threading), the degree of ring threading does not increase monotonously with the chain stiffness, existing a peak value at the intermediate stiffness. It indicates that rings interpenetrate most at intermediate stiffness where there is a balance between coil expansion (favoring penetrations) and stiffness (inhibiting penetrations). Meanwhile, the inter-ring penetration would be suppressed with the knot complexity of the rings. The analysis of effective potential between the rings provides a better understanding for this non-monotonous behavior in inter-ring penetration.

scholarly journals From the Potential of the Mean Force to a Quasiparticle’s Effective Potential in Narrow Ion Channels

2019 ◽  
Vol 18 (02) ◽  
pp. 1940006 ◽  
Author(s):  
M. L. Barabash ◽  
W. A. T. Gibby ◽  
C. Guardiani ◽  
D. G. Luchinsky ◽  
P. V. E. McClintock
Keyword(s):  
Molecular Dynamics ◽  
Ion Channels ◽  
Molecular Dynamics Simulations ◽  
Strong Interaction ◽  
Effective Potential ◽  
Current Voltage ◽  
Ionic Motion ◽  
The Mean ◽  
Highly Correlated ◽  
Dynamics Simulations

We consider the selective permeation of ions through narrow water-filled channels in the presence of strong interaction between the ions. These interactions lead to highly correlated ionic motion, which can conveniently be described via the concept of a quasiparticle. Here, we connect the quasiparticle’s effective potential and the multi-ion potential of the mean force, found through molecular dynamics simulations, and we validate the method on an analytical toy model of the KcsA channel. Possible future applications of the method to the connection between molecular dynamical calculations and the experimentally measured current-voltage and current-concentration characteristics of the channel are discussed.

scholarly journals QM/MM description of periodic systems

2015 ◽  
Vol 14 (07) ◽  
pp. 1550054 ◽  
Author(s):  
K. Doll ◽  
T. Jacob
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Molecular Mechanics ◽  
Liquid Water ◽  
Three Dimensional ◽  
Water Dimer ◽  
Periodic Systems ◽  
Quantum Mechanical ◽  
Dynamics Simulations

A quantum mechanical molecular mechanics (QM/MM) implementation for periodic systems is reported. This is done for the case of molecules and for systems with two and three-dimensional periodicity, which is suitable to model electrolytes in contact with electrodes. Tests on different water-containing systems, ranging from the water dimer up to liquid water indicate the correctness of the scheme. Furthermore, molecular dynamics simulations are performed, as a possible direction to study realistic systems.

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