scholarly journals Translocation of Charged Polymers through a Nanopore in Monovalent and Divalent Salt Solutions: A Scaling Study Exploring over the Entire Driving Force Regimes

Polymers ◽  
2018 ◽  
Vol 10 (11) ◽  
pp. 1229 ◽  
Author(s):  
Pai-Yi Hsiao
Keyword(s):  
Driving Force ◽  
Scaling Theory ◽  
Salt Solutions ◽  
Diffusion Behavior ◽  
Charged Polymers ◽  
The Mean ◽  
Translocation Time ◽  
Dynamics Simulations ◽  
Usual Experimental Condition ◽  
Comparison With Experiments

Langevin dynamics simulations are performed to study polyelectrolytes driven through a nanopore in monovalent and divalent salt solutions. The driving electric field E is applied inside the pore, and the strength is varied to cover the four characteristic force regimes depicted by a rederived scaling theory, namely the unbiased (UB) regime, the weakly-driven (WD) regime, the strongly-driven trumpet (SD(T)) regime and the strongly-driven isoflux (SD(I)) regime. By changing the chain length N, the mean translocation time is studied under the scaling form ⟨ τ ⟩ ∼ N α E − δ . The exponents α and δ are calculated in each force regime for the two studied salt cases. Both of them are found to vary with E and N and, hence, are not universal in the parameter’s space. We further investigate the diffusion behavior of translocation. The subdiffusion exponent γ p is extracted. The three essential exponents ν s , q, z p are then obtained from the simulations. Together with γ p , the validness of the scaling theory is verified. Through a comparison with experiments, the location of a usual experimental condition on the scaling plot is pinpointed.

Isomorphous replacement in electron diffraction of wet crystals of rat hemoglobin

1983 ◽  
Vol 41 ◽  
pp. 446-447
Author(s):  
William F. Tivol ◽  
Murray Vernon King ◽  
D. F. Parsons
Keyword(s):  
Electron Diffraction ◽  
Heavy Atom ◽  
Isomorphous Substitution ◽  
X Ray Diffraction ◽  
Salt Solutions ◽  
X Ray ◽  
Isomorphous Replacement ◽  
Structure Factors ◽  
Diffraction Structure ◽  
The Mean

Feasibility of isomorphous substitution in electron diffraction is supported by a calculation of the mean alteration of the electron-diffraction structure factors for hemoglobin crystals caused by substituting two mercury atoms per molecule, following Green, Ingram & Perutz, but with allowance for the proportionality of f to Z3/4 for electron diffraction. This yields a mean net change in F of 12.5%, as contrasted with 22.8% for x-ray diffraction.Use of the hydration chamber in electron diffraction opens prospects for examining many proteins that yield only very thin crystals not suitable for x-ray diffraction. Examination in the wet state avoids treatments that could cause translocation of the heavy-atom labels or distortion of the crystal. Combined with low-fluence techniques, it enables study of the protein in a state as close to native as possible.We have undertaken a study of crystals of rat hemoglobin by electron diffraction in the wet state. Rat hemoglobin offers a certain advantage for hydration-chamber work over other hemoglobins in that it can be crystallized from distilled water instead of salt solutions.

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.

Diffusion Behavior of Methanol Molecules Confined in Cross-Linked Phenolic Resins Studied Using Neutron Scattering and Molecular Dynamics Simulations

2018 ◽  
Vol 51 (16) ◽  
pp. 6334-6343 ◽  
Author(s):  
Yasuyuki Shudo ◽  
Atsushi Izumi ◽  
Katsumi Hagita ◽  
Takeshi Yamada ◽  
Kaoru Shibata ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Neutron Scattering ◽  
Molecular Dynamics Simulations ◽  
Phenolic Resins ◽  
Diffusion Behavior ◽  
Dynamics Simulations

INVESTIGATING DYNAMIC VORTEX TRANSITIONS IN 2D SUPERCONDUCTORS

2009 ◽  
Vol 23 (19) ◽  
pp. 2399-2408
Author(s):  
I. M. OBAIDAT ◽  
U. AL KHAWAJA ◽  
M. BENKRAOUDA
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Driving Force ◽  
Critical Currents ◽  
Flow State ◽  
Pinning Centers ◽  
Average Speed ◽  
Vortex States ◽  
Dynamics Simulations ◽  
2D Superconductors

Extensive molecular dynamics simulations were performed on superconducting samples with periodic square arrays of pinning centers where several strengths, sizes, and densities of the pinning centers were considered. By calculating the average speed of the vortices as the driving force increases, we defined two critical currents that divide the states of the vortices into three different states with respect to the magnitude of the driving current. These vortex states are a pinned state, a disordered flow state where only some of the vortices flow in some vortex channels, and an ordered flow state where all the vortices flow in an ordered and collective manner. We have clarified the roles of the number of vortices, the size, the strength, and the number of pinning centers in these three states at several temperatures.

An Investigation on Thermal Conductivity of Fluid in a Nanochannel by Nonequilibrium Molecular Dynamics Simulations

2020 ◽  
Vol 142 (3) ◽  
Author(s):  
Mohammad Bagheri Motlagh ◽  
Mohammad Kalteh
Keyword(s):  
Thermal Conductivity ◽  
Molecular Dynamics ◽  
Molecular Dynamics Simulation ◽  
Poiseuille Flow ◽  
Driving Force ◽  
Dynamics Simulation ◽  
Nonequilibrium Molecular Dynamics ◽  
Wall Roughness ◽  
Dynamics Simulations ◽  
Effect Of Copper

Abstract In this paper, molecular dynamics simulation is used to investigate the effect of copper and argon nanochannels size on the thermal conductivity of argon. Thermal conductivity is calculated by nonequilibrium molecular dynamics (NEMD) simulation. Simulations are performed for different distances between the walls. Results for both copper and argon walls are investigated individually. Results show that the existence of argon walls has little effect on the thermal conductivity. However, the amount of it for the argon confined between the copper walls is affected by the distance between the two walls. In the same way, the effect of wall roughness on the thermal conductivity is investigated, which shows that roughness is effective only for low distances between the walls. Also, the thermal conductivity of argon under Poiseuille flow in a nanochannel is studied. The results indicate that by increasing the driving force, the thermal conductivity increases and the increase ratio is higher for larger forces.

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.

Diffusion behavior in a liquid-liquid interfacial crystallization by molecular dynamics simulations

2009 ◽  
Vol 131 (17) ◽  
pp. 174707 ◽  
Author(s):  
Akira Kitayama ◽  
Shinya Yamanaka ◽  
Kazunori Kadota ◽  
Atsuko Shimosaka ◽  
Yoshiyuki Shirakawa ◽  
...  
Keyword(s):  
Molecular Dynamics ◽  
Molecular Dynamics Simulations ◽  
Diffusion Behavior ◽  
Dynamics Simulations
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