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 Ballistic Heat Transport in Nanocomposite: The Role of the Shape and Interconnection of Nanoinclusions

Nanomaterials ◽  
2021 ◽  
Vol 11 (8) ◽  
pp. 1982
Author(s):  
Paul Desmarchelier ◽  
Alice Carré ◽  
Konstantinos Termentzidis ◽  
Anne Tanguy
Keyword(s):  
Thermal Conductivity ◽  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Free Path ◽  
Mean Free Path ◽  
Strong Increase ◽  
Moderate Increase ◽  
Energy Propagation ◽  
The Mean ◽  
Dynamics Simulations

In this article, the effect on the vibrational and thermal properties of gradually interconnected nanoinclusions embedded in an amorphous silicon matrix is studied using molecular dynamics simulations. The nanoinclusion arrangement ranges from an aligned sphere array to an interconnected mesh of nanowires. Wave-packet simulations scanning different polarizations and frequencies reveal that the interconnection of the nanoinclusions at constant volume fraction induces a strong increase of the mean free path of high frequency phonons, but does not affect the energy diffusivity. The mean free path and energy diffusivity are then used to estimate the thermal conductivity, showing an enhancement of the effective thermal conductivity due to the existence of crystalline structural interconnections. This enhancement is dominated by the ballistic transport of phonons. Equilibrium molecular dynamics simulations confirm the tendency, although less markedly. This leads to the observation that coherent energy propagation with a moderate increase of the thermal conductivity is possible. These findings could be useful for energy harvesting applications, thermal management or for mechanical information processing.

scholarly journals Exploiting correlated molecular-dynamics networks to counteract enzyme activity–stability trade-off

2018 ◽  
Vol 115 (52) ◽  
pp. E12192-E12200 ◽  
Author(s):  
Haoran Yu ◽  
Paul A. Dalby
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Active Site ◽  
Dynamic Networks ◽  
Aromatic Aldehydes ◽  
Active Site Residues ◽  
Trade Off ◽  
Highly Correlated ◽  
Dynamics Simulations ◽  
The Impact

The directed evolution of enzymes for improved activity or substrate specificity commonly leads to a trade-off in stability. We have identified an activity–stability trade-off and a loss in unfolding cooperativity for a variant (3M) of Escherichia coli transketolase (TK) engineered to accept aromatic substrates. Molecular dynamics simulations of 3M revealed increased flexibility in several interconnected active-site regions that also form part of the dimer interface. Mutating the newly flexible active-site residues to regain stability risked losing the new activity. We hypothesized that stabilizing mutations could be targeted to residues outside of the active site, whose dynamics were correlated with the newly flexible active-site residues. We previously stabilized WT TK by targeting mutations to highly flexible regions. These regions were much less flexible in 3M and would not have been selected a priori as targets using the same strategy based on flexibility alone. However, their dynamics were highly correlated with the newly flexible active-site regions of 3M. Introducing the previous mutations into 3M reestablished the WT level of stability and unfolding cooperativity, giving a 10.8-fold improved half-life at 55 °C, and increased midpoint and aggregation onset temperatures by 3 °C and 4.3 °C, respectively. Even the activity toward aromatic aldehydes increased up to threefold. Molecular dynamics simulations confirmed that the mutations rigidified the active-site via the correlated network. This work provides insights into the impact of rigidifying mutations within highly correlated dynamic networks that could also be useful for developing improved computational protein engineering strategies.

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 Molecular Dynamics Simulations Studies of the Proton Channel Otopetrin and Other Mechanically-Activated Ion Channels

2020 ◽  
Vol 118 (3) ◽  
pp. 274a-275a
Author(s):  
Che Chun (Alex) Tsui ◽  
Kei Saotome ◽  
Bochuan Teng ◽  
Wen-Hsin Lee ◽  
Yu-Hsiang Tu ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Ion Channels ◽  
Molecular Dynamics Simulations ◽  
Proton Channel ◽  
Dynamics Simulations

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 In-Silico Electrophysiology: On the Activation of Voltage-Gated Ion Channels using Molecular Dynamics Simulations

2016 ◽  
Vol 110 (3) ◽  
pp. 107a ◽  
Author(s):  
Mounir Tarek ◽  
Lucie Delemotte ◽  
Marina Kasimova ◽  
Michael L. Klein ◽  
Vincenzo Carnevale
Keyword(s):  
Molecular Dynamics ◽  
Ion Channels ◽  
Molecular Dynamics Simulations ◽  
In Silico ◽  
Voltage Gated ◽  
Voltage Gated Ion Channels ◽  
Dynamics Simulations ◽  
Gated Ion Channels
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