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Current Applied Physics (15671739) 79pp. 66-76
This study uses molecular dynamics simulations to investigate the efficient separation of lithium (Li+) and sodium (Na+) ions in graphene-based nano-channels under the influence of an electric field. The effect of nano-channel dimensions, including length and width, on the ion separation performance was investigated. Our results show that nano-channels with a length of 12 nm and a width of 1.5 nm exhibit optimal ion separation at the present electric field intensity of 4 mV/Å, with lithium ions preferentially accumulating in the designated storage compartments. This separation efficiency is primarily due to the mass-dependent electrophoretic mobility of the ions, with lithium ions migrating faster than sodium ions in the same electric field due to their lower mass and higher acceleration. In addition, the narrow channel width provides a more controlled laminar flow, minimizing turbulence and improving ion transport selectivity. This study also highlights the role of thermal effects, ion diffusion, and electrostatic interactions with the graphene surface in improving the separation process. © 2025 Korean Physical Society
European Physical Journal B (14346028) 97(2)
Studying the phase transition process from free flow to congested state in communication networks is one of the hot topics of dynamically complex systems, and many related theoretical and computational efforts have been made to improve traffic systems’ organization and load management. A criterion to measure the organization efficiency of the system is the formation process of a global traffic flow cluster from local small clusters in a communication network which can be evaluated by measuring the percolation threshold. While little attention has been paid to percolation in such studies, in this research, the traffic percolation threshold is defined based on the system nodes’ loads to examine the influences of the network structures, different routing strategies, and distributions of transmission capacities on the efficiency of the communication networks. Considering the obtained results, it was found any variation in the network structure and traffic control strategies that leads to a rather diverse load distribution among the system’s nodes can organize traffic loads more efficiently. Graphical abstract: (Figure presented.) © The Author(s), under exclusive licence to EDP Sciences, SIF and Springer-Verlag GmbH Germany, part of Springer Nature 2024.
European Journal of Mechanics, B/Fluids (09977546) 103pp. 236-245
The droplet jumping on superhydrophobic surfaces is one of the attractive phenomena in academic and industrial research due to its various applications in engineering. The effect of the substrate hydrophobicity variation on the jumping of sub milliliter water droplets on smooth surfaces is computationally studied using a mass-spring-damper scheme. It is observed that above a critical substrate hydrophobicity variation, the interface area of the droplet-substrate decreases strongly, and the droplet jumps off the surface. In addition, the behavior of the droplets during the changing of substrate hydrophobicity is explained via an analytical energy-based model to predict and estimate the physical parameters at which droplet jumping is achieved. © 2023 Elsevier Masson SAS
European Physical Journal E (12928941) 46(1)
The aquaglyceroporin-7 (AQP7) protein channels facilitate the permeation of glycerol and water molecules through cell membranes by passive diffusion and play a crucial role in cell physiology. Considering the wide-spirit usage of radiofrequency electromagnetic fields in our daily life, in this study, the effects of constant and GHz electric fields were investigated on the dynamics of glycerol and water molecules inside the AQP7. To this end, four different molecular simulation groups were carried out in the absence and presence of electric fields. The results reveal that the free energy profile of the glycerol permeation inside the channel is reduced in the presence of the field of 0.2 mV/nm and the oscillating field of 10 GHz. In addition, exposing the channel to the electric field of 0.2 mV/nm assisted the water transport through the channel with no considerable effect on channel stability. These observations provide a framework for understanding how such fields could alter normal operation of protein channels, which may lead to disease beginning or being used in disease treatment. Graphical abstract: [Figure not available: see fulltext.]. © 2023, The Author(s), under exclusive licence to EDP Sciences, SIF and Springer-Verlag GmbH Germany, part of Springer Nature.
European Physical Journal E (12928941) 46(10)
Equilibrium molecular dynamics simulations were performed to explore the effects of external electric fields and confinement on water properties inside various carbon nanotubes (CNTs). Using different GHz electric field frequencies as well as various constant electric field strengths, the radial distribution function and density profile were investigated, by which the impact of the electric fields and confinement on the water structure are revealed. The results indicated water molecules inside the CNT form layered structures due to topological confinement applying external electric fields can disturb this ordered water molecules structure and increase the viscosity of confined water, particularly in the case of CNTs with a radius less than 13.5 Å. Conversely, for CNTs with a radius greater than13.5 Å, the viscosity decreases under the influence of external oscillating or constant electric fields. Graphical abstract: How dose the synergism of confinement and external electric fields affect the water properties inside the CNTs?[Figure not available: see fulltext.]. © 2023, The Author(s), under exclusive licence to EDP Sciences, SIF and Springer-Verlag GmbH Germany, part of Springer Nature.
Journal of Molecular Graphics and Modelling (10933263) 123
Alzheimer's disease is associated with accumulating different amyloid peptides on the nerve cell membranes. The non-thermal effects of the GHz electric fields in this topic have yet to be well recognized. Hence, in this study, the impacts of 1 and 5 GHz electric fields on the amyloid peptide proteins accumulation on the cell membrane have been investigated, utilizing molecular dynamics (MD) simulation. The obtained results indicated that this range of electric fields did not significantly affect the peptide structure. Moreover, it was found that the peptide penetration into the membrane was increased as the field frequency was increased when the system was exposed to a 20 mv/nm oscillating electric field. In addition, it was observed that the protein-membrane interaction is reduced significantly in the presence of the 70 mv/nm electric field. The molecular level results reported in this study could be helpful in better understanding Alzheimer's disease. © 2023 Elsevier Inc.
Journal of Molecular Graphics and Modelling (10933263) 125
In this study, inspired by the overall structure and operation of the aquaporin channel, graphene-based nanochannels are proposed to be used as potential membranes for the water purification process. To this end, an hourglass-shaped channel has been designed using the three-layer porous graphene sheets and the effects of some main channel's elements, such as the channel bending angle and attached functional groups to it, on the filtration performance have been examined by using molecular dynamics simulations. We find that a suitable bending channel shape can improve the channel efficiency, i.e. both the water permeability and the ion rejection rate of the suitable bent channels were more than for the straight channels. In addition, regarding the different functionalized channels, the half-functionalized channels were more efficient than the completed functionalized ones. Furthermore, by monitoring the dynamics of water molecules as they pass through the narrowest part of the channels, it was found that water molecule rotation assists water transport. © 2023 Elsevier Inc.
Physical Chemistry Chemical Physics (14639084) 25(3)pp. 2161-2166
The effect of substrate hydrophobicity on the dynamics of water nano-droplets is computationally studied using the molecular dynamics method. It is observed that the droplet moves upward by increasing the substrate hydrophobicity and then falls down onto the substrate, and during this process, the droplet-substrate interfacial area effectively declines. Moreover, the results indicate that above a critical substrate hydrophobicity, which depends on the droplet radius, the droplet completely detaches from the substrate. The droplet behavior is described at the molecular level using van der Waals attractions for the liquid-solid interface. © 2023 The Royal Society of Chemistry.
European Physical Journal Plus (21905444) 137(4)
Alzheimer’s disease is one of the widespread types of neurological dementia. The circumstances, which could influence Alzheimer’s risk and expression, have been frequently investigated in up-to-date research. A growing number of studies point to a relationship between cholesterol existence and the formation of amyloid plaques in the brain. The molecular dynamics simulations method examines the impact of embedded cholesterol molecules in a patch of cell membrane on the amyloid-beta (Aβ) oligomer aggregation. In addition, the influence of [AC0107] molecules as Aβ oligomer aggregation inhibitors is contemplated. It is found that the cholesterol interaction with the Aβ oligomer enhances the Aβ aggregation probability. Furthermore, the results acknowledge the protective feature of the [AC0107] molecules against the Aβ oligomer accumulation on the membrane. The outcomes show an increase in the interatomic interactions between the membrane molecules and the oligomers in the presence of cholesterol, while their reduction in the presence of [AC0107] molecules. Graphical abstract: [Figure not available: see fulltext.]. © 2022, The Author(s), under exclusive licence to Società Italiana di Fisica and Springer-Verlag GmbH Germany, part of Springer Nature.
Journal of Nano Research (16619897) 67pp. 89-96
The effects of the application of constant electric fields on the dynamics of a confined water droplet between two different surfaces are investigated, by using a molecular dynamics method. It is found that the water molecules responded to the electric field, which partially depends on the wettability of the different surfaces. The results reveal that the application of external electric fields causes to create extra pressure on the surfaces, which are theoretically justified. The induced pressure could be experienced by multilayer nano-filters, which are used in desalination processes, with the aid of an external electric field, and may reduce the water filters shelf life. © 2021 Trans Tech Publications Ltd, Switzerland.
International Journal of Modeling, Simulation, and Scientific Computing (17939623) 12(6)
In this study, we developed a SEIR model, including social interactions and individual human mobility in everyday activities. For this purpose, daily mobility of people was considered by using the molecular dynamic method and the virus spreading was modeled employing the ordinary SEIR scheme. Utilizing this model, the variation of population size, density, and health strategy as well as the effect of busy places such as malls, were considered. The results show that our flexible model is able to consider the effects of different parameters such as distance between peoples, local population density and health strategy in the outbreak. © 2021 World Scientific Publishing Company.
European Physical Journal Plus (21905444) 136(11)
Collective behavior, a significant issue in examinations of complex systems, has been considered in many recent investigations. However, different aspects of environmental parameters and individuals' interactions on the dynamics of systems are not completely clear. In this study, distance-based Lennard–Jones interaction types are used to simulate individuals’ collective motion, in the presence of thermal noise. Moreover, the individuals’ dynamics are examined in homogeneous and inhomogeneous environments, considering geometric and motional order parameters. The results show that as the noise amplitude enhances, the collective motion of the particles is disturbed, and the system shifts to an incoherent phase, while increasing the interaction strength raises the system coherency. Furthermore, it is observed that in the presence of an external attractive force, such as the feeding region, the system coherency and order are increased considerably. Finally, it is found that the range of particles' interactions can affect the collective behavior and the phase transition of the system. © 2021, The Author(s), under exclusive licence to Società Italiana di Fisica and Springer-Verlag GmbH Germany, part of Springer Nature.
Physical Chemistry Chemical Physics (14639084) 22(44)pp. 25859-25868
The dynamics of water molecules inside an Aquaporin channel, embedded within a stochastically fluctuating membrane, was modeled by means of the application of the molecular dynamics (MD) simulation method. We considered the effect of the existence and nonexistence of an external electric field, either constant or oscillating, on the stability of the channel. It was observed that the permeation of water molecules through the channel was increased when the channel was exposed to a constant electric field of strength -0.2 mV nm-1. Moreover, oscillating electric fields of 5 and 10 GHz frequencies, which is the range of field frequency generally present in our daily life, were applied to the channel, showing not significant effects on the stability of the channel and its important parts. In addition, we investigated the influence of the application of electric fields on the water molecule ordinations in the channels, and the results showed that the water molecule orientations were changed in response to the applied field. This journal is © the Owner Societies.
Journal Of Molecular Modeling (16102940) 26(9)
Using molecular dynamics method, the ion rejection and water flow inside flexible disjoint carbon-based channels were examined in the presence of electric fields. The effects of the carbon nanotube diameters and field magnitude on the nano-channel efficiency were investigated. It was observed that water flow through the filter was modified by increasing the radius of nanotubes, while the salt rejection was reduced. The particles’ behaviors inside the channel were described in view of Van der Waals interactions between the water molecules, ions, and carbon atoms. Furthermore, the results indicated that the ion rejection and water flow were increased under the application of proper magnitude of electric fields. [Figure not available: see fulltext.]. © 2020, Springer-Verlag GmbH Germany, part of Springer Nature.
Iranian Journal of Physics Research (16826957) 18(4)pp. 551-558
Calcium channels are cell membrane proteins that play an important role in controlling the Ca ion flux through the membrane. In this study, the effect of the external constant electric field on the dynamics of calcium ions in a L-type channel located within a stochastically fluctuating medium was modeled via the application of the molecular dynamics (MD) simulation method. The obtained results showed that application of the constant field of 0.03 V/nm did not show any significant effect on the ions motion. On the other hand, when the channel was exposed to a constant electric field of strength 0.3 V/nm, the ions directional motion along the applied field was observed. Furthermore, no net motion was observed when the field direction was changed. © 2019, Isfahan University of Technology. All rights reserved.
Journal Of Molecular Modeling (16102940) 25(9)
Understanding the mechanism of water and particle transport through thin-film membranes is essential to improve the water permeability and the salt rejection rate of the purification progress. In this research, mimicking from the structure and operation of the aquaporin channel, graphene-based nano-channels were designed to be used as a water filter. The effects of variation of the channel’s main elements, such as the width of the bottleneck and charges attached to the channel on its efficiency, were investigated via molecular dynamics simulations. We observe that the water flow through the channel decreases by increasing the charge, while the ion rejection rate of the channel is enhanced. Moreover, we find that the geometry and shape of the bottleneck part of the channel can affect the channel water flow and its selectivity. Finally, the pressure and the flow velocity in the channel were considered by using finite element models, and the results indicate that they are high at the entrance of the channel. The outcomes of this study can be used to improve the molecular knowledge of water desalination, which might be helpful in designing more efficient membranes. [Figure not available: see fulltext.]. © 2019, Springer-Verlag GmbH Germany, part of Springer Nature.
Indian Journal of Physics (09731458) 93(6)pp. 733-738
Functionalized graphene sheets have attracted increasing attention due to their novel micro-/nano-electromechanical applications. In this paper, the aggregation of the gold nano-clusters on the defected graphene sheet is studied by using the molecular dynamics simulation method. It is shown that a model defected graphene with randomly distributed vacancies can affect the formation and aggregation of the Au nano-clusters on the graphene sheet. It is found that the Au nano-clusters agglomerate on the pristine parts of the surface rather than on the defected parts. In addition, the results show that increasing the temperature amplifies the above result and varies the Au nano-cluster sizes. Moreover, it is observed that the aggregation of Au clusters changes the surface roughness. The results presented here would help to design more efficient functionalized graphene-based electronic devices. © 2018, Indian Association for the Cultivation of Science.
Physical Chemistry Chemical Physics (14639084) 21(6)pp. 3304-3309
Understanding the behavior of water molecule transport through artificial nano-channels is essential in designing novel nanofluidic devices that could be used especially in nanofiltration processes. In this study, using nonequilibrium molecular dynamics (MD) simulations, we simulated the water flow through different graphene-based channels to investigate the influences of some key factors such as the channel thickness and applied pressure on the water flow. It was demonstrated that the water flow was enhanced by increasing the applied pressure and channel thickness. Our results indicated that a third order polynomial curve could describe the variation of the water flow as a function of the channel thickness and the applied pressure. In addition, we improved the hydrodynamics equation used to consider the water flow through nano-channels, by adding two terms to describe the slip effect and the entrance/exit effect, in which the first term increased the water flow rate, while the second term reduced it. This study may be helpful in designing high-performance graphene-based membranes with some practical applications such as desalination. © the Owner Societies.
Neek-amal m., ,
Lohrasebi, A. ,
Mousaei m., ,
Shayeganfar f., ,
Radha b., ,
Peeters f.m., Applied Physics Letters (10773118) 113(11)
This article was originally published online on 20 August 2018 with an error in the affiliations for the last author. All online versions of this article were corrected on 27 August 2018; the article is correct as it appears above. © 2018 Author(s).
Neek-amal m., ,
Lohrasebi, A. ,
Mousaei m., ,
Shayeganfar f., ,
Radha b., ,
Peeters f.m., Applied Physics Letters (10773118) 113(8)
Water inside a nanocapillary becomes ordered, resulting in unconventional behavior. A profound enhancement of water flow inside nanometer thin capillaries made of graphene has been observed [Radha et al., Nature (London) 538, 222 (2016)]. Here, we explain this enhancement as due to the large density and the extraordinary viscosity of water inside the graphene nanocapillaries. Using the Hagen-Poiseuille theory with slippage-boundary condition and incorporating disjoining pressure term in combination with results from molecular dynamics simulations, we present an analytical theory that elucidates the origin of the enhancement of water flow inside hydrophobic nanocapillaries. Our work reveals a distinctive dependence of water flow in a nanocapillary on the structural properties of nanoconfined water in agreement with experiment, which opens a new avenue in nanofluidics. © 2018 Author(s).
Paclitaxel, one of the cancer chemotherapy drugs, stabilizes microtubule (MT) and changes its physical properties. Alteration in physical properties of MT and affinity of its associated motor proteins, such as kinesin, may be used as an effective approach in cancer treatment. In this paper, simultaneous influences of paclitaxel and oscillating GHz electric fields on flexibility of MT and on kinesin affinity to alpha beta-tubulin have been investigated, via using molecular dynamics simulation method. To approach to these purposes, a designed system consists of two alpha beta-tubulin stabilized by paclitaxel (SP alpha beta-tubulin) was exposed to electric fields in 1-10 GHz frequency range to examine MT flexibility. Then, another designed system was considered to study kinesin affinity to SP alpha beta-tubulin in three different structures, containing ATP, ADP and none of them. It was found that application of such fields changes flexibility of MT and changes kinesin affinity to SP alpha beta-tubulin. This variation in MT flexibility and kinesin affinity, due to the application of such fields, may perturb cancer treatment process, using paclitaxel.
Journal Of Molecular Modeling (16102940) 24(9)
Multilayer graphene membranes could be considered as an efficient membrane in water desalination processes based on the reverse osmosis (RO) method. In this study, we designed multilayer graphene channels using the molecular dynamics (MD) simulation approach. The effects of different parameters, such as channel width and length, and the pressure on the operation of the designed channels were examined, in the absence and presence of electric fields with various amplitudes and directions. The results indicated that the ion separation and water flow through the channels were modified under the application of the electric fields. Additionally, it has been shown that salt rejection and water flow could be controlled by the channel’s structural parameters mentioned above. The obtained results of this study at the molecular level can improve the knowledge of designing membranes for water purification processes. [Figure not available: see fulltext.]. © 2018, Springer-Verlag GmbH Germany, part of Springer Nature.
Nano Research (19980124) 11(4)pp. 2229-2236
Using molecular dynamics (MD) simulations, a porous graphene membrane was exposed to external electric fields to separate positive and negative ions from salt-water and to produce fresh water. It was observed that, by increasing the strength of the applied electric field, ion separation improved noticeably. In addition, to obtain fresh water, the designed system included two graphene membranes, which are exposed to two external electric fields in opposite directions. Ion rejection was found to be greater than 93% for the electric field of 10 mV/Å and higher. This atomic-level simulation increases the understanding of electric field effects on desalination using multilayer graphene membranes and can be helpful in designing more efficient membranes. © 2018, Tsinghua University Press and Springer-Verlag GmbH Germany, part of Springer Nature.
JOURNAL OF NANOSCIENCE AND NANOTECHNOLOGY (15334880) (8)pp. 5799-5803
Porous graphene sheets can be considered as an ultrathin membrane in reverse osmosis water desalination processes. In this paper, employing the molecular dynamics simulation method, the performance of multilayer porous graphene membranes with different pore sizes, layer separation, and layer number were investigated. We found that salt rejection and water flux through the membrane significantly depend on the graphene pore size and number of graphene layers, and controlling these parameters could improve the filtration process. It was shown that our 2-layer designed graphene membranes with the pore radius of 3.3 angstrom and layer separation of 20 angstrom, can reject more than 86% of ions. Also, no filtration process had occurred for graphene layer separation less than 5 angstrom. The results of this study that are described by ion hydration radius and water velocity distributions can be used to improve the knowledge of water desalination at the molecular level, which leads to design more efficient multilayer graphene membranes for water purification.
Physical Chemistry Chemical Physics (14639084) 19(39)pp. 26833-26838
The dynamics of a water nano-droplet on a flexible graphene sheet, in the presence of constant and alternative electric fields with various amplitudes and frequencies, was considered using a molecular dynamics method. It was found that because the water molecules respond to electric field, the nano-droplet elongates in the field direction for a field amplitude larger than 0.08 V Å-1, which is stronger than the predicted value from the Young-Laplace equation. This difference can be described by considering the van der Waals attractions between the droplet molecules and the substrate, which can be calculated by modifying the Young-Laplace equation. Furthermore, under the influence of an alternating field over the GHz frequency range, it was shown that the droplet shape will not change above a threshold frequency, which depends on the relaxation time of the water dipole. © 2017 the Owner Societies.
Biophysical Chemistry (03014622) 223pp. 17-24
Although, α2C adrenergic receptor (AR) mediates a number of physiological functions in vivo and has great therapeutic potential, the absence of its crystal structure is a major difficulty in the activation mechanism studies and drug design endeavors. Here, a homology model of α2C AR has been presented by means of multiple sequence alignment. The used templates were the latest crystal structures of the other ARs (Protein Data Bank IDs: 2R4R, 2RH1, 4GPO, 3P0G, 4BVN and 4LDO) that have 38.4% identity with the query. We then conducted docking simulations to understand and analyze the binding of noradrenaline (NOR), and its derivatives, namely arachidonoyl adrenalin (AA-AD) and arachidonoyl noradrenalin (AA-NOR) to the receptor. The existence of H-bonds between the ligands and SER218 residue implies the same binding site of derivatives with respect to the NOR. AA-AD and AA-NOR bind to the receptor with the larger binding affinities. The presence of salt bridge between ARG149 and GLU377 in the free receptor, obtained from molecular dynamics studies proved that the receptor still is in its basal state before binding process take places. The activation process is characterized by increasing in the RMSD values of the backbone receptor in the bound state, increasing the RMSF of the transmembrane involved in the activation process and the disappearance of the ARG149-GLU377 salt bridge. © 2017 Elsevier B.V.
Journal of Molecular Graphics and Modelling (10933263) 70pp. 122-128
Microtubule (MT) rigidity and response to 2450 MHz electric fields were investigated, via multi scale modeling approach. For this purpose, six systems were designed and simulated to consider all types of feasible interactions between α and β monomers in MT, by using all atom molecular dynamics method. Subsequently, coarse grain modeling was used to design different lengths of MT. Investigation of effects of external 2450 MHz electric field on MT showed MT less rigidity in the presence of such field, which may perturb its functions. Moreover, an additional computational setup was designed to study effects of 2450 MHz field on MT response to AFM tip. It was found, more tip velocity led to MT faster transformation and less time was required to change MT elastic response to plastic one, applying constant radius. Moreover it was observed smaller tip caused to increase required time to change MT elastic response to plastic one, considering constant velocity. Furthermore, exposing MT to 2450 MHz field led to no significant changes in MT response to AFM tip, but quick change in MT elastic response to plastic one. © 2016 Elsevier Inc.
Journal of Theoretical and Computational Chemistry (17936888) 15(2)
Using molecular dynamics simulation method, the effects of external electric fields of 900MHz and 2450 frequencies on αβ-tubulin dimer stabilized by paclitaxel, have been modeled. Due to this purpose, two systems, (A) αβ-tubulin dimer and (B) αβ-tubulin dimer stabilized by paclitaxel, were exposed to an external electric field of 0.01V/nm with frequency values of 900MHz and 2450MHz. It was found that application of these fields, which are in the range of cell phone and microwave frequencies, increased the flexibility of each system. Since paclitaxel, as chemotherapy drug, is used to increase the rigidity of dimer, application of such fields may disturb the effect of paclitaxel on the dimer. Consequently, negative side effects on the chemotherapy process may be observed. © 2016 World Scientific Publishing Company.
Journal of Superconductivity and Novel Magnetism (15571947) 28(3)pp. 777-780
The effect of an external magnetic field on a ferrofluid droplet is considered. The magnetic field causes the droplet to elongate depending on the values of its surface tension, susceptibility, and radius. Under the influence of an alternating magnetic field with certain frequency, it is shown that there is a critical frequency above which the droplet shape will not change. It is also shown that if an additional small magnetic field having a certain gradient is also present, the droplet will experience a force, which can be used to push it through channels with smaller diameters. Such a mechanism can have application in medical fields. © 2014, Springer Science+Business Media New York.
Journal Of Molecular Modeling (16102940) 21(4)pp. 1-7
The effects of external GHz electric fields on the mechanical properties of a microtubule (MT) have been modeled through the application of a molecular dynamics simulation method. To explore the properties of the MT, two different systems each consisting of a pair of dimers were exposed to an 0.03 V/nm electric field with a frequency ranging between 1 to 10 GHz. It was found that the Young’s modulus of each system, which is related to the flexibility of the MT, was lower at some frequencies and higher at others in comparison with normal biological conditions. Hence, the application of such an electric field with a frequency in this range may affect MT function, which could have positive or negative effects on cell health. Positive effects include its potential use in cancer treatment, where the application of such a field could lead to a decrease in MT rigidity, similar to the effect of Taxol on MTs. Negative effects include unwanted changes to the mechanical properties of MTs (e.g., disturbing the cell division process and in turn increasing the risk of cancer) upon the application of such a field. © 2015, Springer-Verlag Berlin Heidelberg.
Journal of Computational and Theoretical Nanoscience (15461955) 12(9)pp. 2437-2441
Molecular dynamics simulations, based on many-body inter-atomic potentials, have been performed to investigate the propagation of a Mode-I (edge) crack in a two-dimensional (2D) (111) plane of a random alloy of Pd and different percentage of Ir atoms. The Sutton-Chen many-body potential was used to simulate all inter-atomic interactions. We show that, fluctuations in the crack velocity, which lead to the phenomenon of crack branching, are also present in this alloy. Furthermore, it is found that as the percentage of Ir atoms increases, the critical stress for the initiation of crack propagation is increased, and the fluctuations in the crack velocity make their appearance sooner. © 2015 American Scientific Publishers All rights reserved.
Chinese Physics B (16741056) 24
Kinesin is a microtubule-associated motor protein which can respond to the external electric field due to its polarity. Using a molecular dynamics simulation method, the effect of such a field on the affinity of kinesin to the αβ-tubulin is investigated in this study. To consider kinesin affinity, the system is exposed to an electric field of 0.03 V/nm with frequency values of 1, 2, ..., 9, and 10 GHz. It is found that the applied electric field can change kinesin affinity to the microtubule. These changes could perturb the normal operation of kinesin, such as the processive motility of kinesin on the microtubule. © 2015 Chinese Physical Society and IOP Publishing Ltd.
Desalination (00119164) 365pp. 176-181
Using molecular dynamics simulations, we show that a designed graphene-charged carbon nanotube (CNT) membrane can act as a nanofilter with the efficiency more than 90%, to separate Na+/Mg+2/Fe+3 and Cl- ions from NaCl, MgCl2 and FeCl3 solutions. It is observed that there are two significant factors in ion separation process: the magnitude of charge density which covers the surface of the CNT and the velocity of the movable wall. The ion separation is improved by increasing the magnitude of surface charge density and decreasing the velocity of the movable wall. Also, it is found that, reducing the positive surface charge of the CNT will increase the percentage of passed water molecules through the CNT. © 2015 Elsevier B.V.
Journal of Theoretical and Computational Chemistry (17936888) 14(2)
KcsA potassium channel is a membrane protein that allows the passage of potassium ions and water molecules across the cellular membrane. Using molecular dynamics (MD) simulation method, the effect of an applied GHz oscillating electric field of strength 0.004 V/nm on the dynamics of K+ and water molecules in a KcsA channel was modeled. It was found that the application of GHz range electric field caused a change in the potential energy profile of the water molecules in the filter sites, causing an increase in the delay time of the water molecules in these sites. Therefore, exposing the channel to the GHz fields can perturb the dynamics of the water molecules in the filter, and consequently, the channel operation may be disturbed. Furthermore, the results show that the applied field has no major effects on the dipole orientation of water molecules in the channel. © 2015 World Scientific Publishing Company.
Molecular Simulation (08927022) 40(13)pp. 1067-1073
In this study, the potential energy profile of potassium ions in the selective filter part of a KcsA channel was investigated via the application of the molecular simulation method. For this purpose, using the molecular dynamics simulation, the effect of an applied electric field, either constant or oscillating, was studied on the dynamics of K ions in the filter. It was found that when the channel is exposed to a constant electric field of strength 0.03 V/nm, the ions experience a hopping motion. Furthermore, it was shown that the application of oscillating electric fields of 1 and 2.5 GHz, can increase the rigidity of the filter atomic bonds. By computing the potential energy of K ion in the filter, it was shown that the depth of the potential wells, corresponding to the filter sites, increased when an alternative field was applied. Therefore, exposing the channel to the GHz oscillating electric field could disturb the passing rate of ions through the filter, which in turn may affect the operation of these kinds of channels. © 2013 © 2013 Taylor & Francis.
Journal Of Molecular Modeling (16102940) 20
The mechanical properties of the αβ-tubulin dimer of microtubules was modeled by using the molecular dynamics (MD) simulation method. The effect on the mechanical properties of the dimer of the existence and nonexistence of an applied electric field, either constant or periodic, was studied. Since there are charged or polar groups in the dimer structure, the electric field can interact with the dimer. The elastic constant and Young's modulus of the dimer were decreased when the dimer was exposed to a constant electric field of 0.03 V/nm. Furthermore, applying an oscillating electric field in the 1 GHz range to the dimer increased the elastic constant and Young's modulus of the dimer. These parameters were related to dimer rigidity and, consequently, in this frequency range, the application of electric fields may affect the function of microtubules. © Springer-Verlag 2014.
Molecular Simulation (08927022) 40(5)pp. 399-407
The dynamics of potassium ions in a KcsA channel, located within a stochastically fluctuating medium, is modelled via the application of the molecular dynamics simulation method. We investigate the effect of presence and absence of an applied electric field, either constant or periodic, on the dynamics of the channel. It is found that the ions undergo a hopping motion when the channel is exposed to a constant electric field of strength 0.03 V/nm. Furthermore, an alternating electric field in the GHz range, normally present in the daily environment and encountered by most biological systems, is applied to the channel, showing that in this frequency range, the rigidity of the atomic bonds of the filter is increased, which in turn disturbs the ionic passage rate through the filter. Consequently, in this frequency range, the application of electric fields may affect the function of such channels. © 2013 Taylor & Francis.
AIP Advances (21583226) 4(5)
Crack propagation in a defected graphene sheet is investigated at finite temperature using molecular dynamics simulation. The effects of several initial cracks, temperature and different percentage of vacancies are considered. It is found that i) the critical load, which is a criteria for crack propagation, is larger when the load is applied on the zigzag direction, ii) the critical load decreases with increasing temperature, iii) a hole in the center of the sheet and the presence of randomly distributed vacancies reduce the critical load giving different crack propagation trajectory. Our new results would help to understand the crack propagation phenomena in defected graphene at finite temperature. © 2014 Author(s).
Journal Of Molecular Modeling (16102940) 18(9)pp. 4191-4197
The dynamics of a rotary nano ion pump, inspired by the F0 part of the F0F1-ATP synthase biomolecular motor, were investigated. This nanopump is composed of a rotor, which is constructed of two carbon nanotubes with benzene rings, and a stator, which is made of six graphene sheets. The molecular dynamics (MD) method was used to simulate the dynamics of the ion nanopump. When the rotor of the nanopump rotates mechanically, an ion gradient will be generated between the two sides of the nanopump. It is shown that the ion gradient generated by the nanopump is dependant on parameters such as the rotary frequency of the rotor, temperature and the amounts and locations of the positive and negative charges of the stator part of the nanopump. Also, an electrical potential difference is generated between the two sides of the pump as a result of its operation. © Springer-Verlag 2012.
Physica Medica (11201797) 28(3)pp. 221-229
We model the dynamics of the F0 component of the F0F1-ATPase mitochondrion-based nano-motor operating in a stochastically-fluctuating medium that represents the intracellular environment. The stochastic dynamics are modeled via Langevin equation of motion wherein fluctuations are treated as white noise. We have investigated the influence of an applied alternating electric field on the rotary motion of the F0 rotor in such an environment. The exposure to the field induces a temperature rise in the mitochondrion's membrane, within which the F0 is embedded. The external field also induces an electric potential that promotes a change in the mitochondrion's transmembrane potential (TMP). Both the induced temperature and the change in TMP contribute to a change in the dynamics of the F0. We have found that for external fields in the radio frequency (RF) range, normally present in the environment and encountered by biological systems, the contribution of the induced thermal effects, relative to that of the induced TMP, to the dynamics of the F0 is more significant. The changes in the dynamics of the F0 part affect the frequency of the rotary motion of the F0F1-ATPase protein motor which, in turn, affects the production rate of the ATP molecules. © 2011 Associazione Italiana di Fisica Medica.
Molecular Simulation (08927022) 38(10)pp. 850-855
The dynamics of an electrical-driven linear nanopump, consisting of a carbon nanotube, a C60 + molecule and a graphene sheet, has been simulated via the application of the molecular dynamics method. In this nanopump, the nanotube and the graphene sheet are used as the sleeve of the pump and the boundary between the two sides of the nanopump, respectively. By exposing the nanopump to an external alternative electric field, the C60 + molecule will be oscillating linearly in the nanotube. We found that the linear oscillating motion of the C60 + molecule causes the gas atoms to flow through the nanotube, and a density gradient is generated between the two sides of the nanopump. Also, it was observed that the frequency of the external alternative electric field affected the pump performance in the generation of the density gradient amount. The maximum performance occurred at a specific frequency of the electric field. This specific frequency can be computed by an analytical formula for given materials and temperatures. Moreover, the results indicate that the length of the nanotube can affect the gas pumping. © 2012 Copyright Taylor and Francis Group, LLC.
Journal of Molecular Graphics and Modelling (10933263) 29(8)pp. 1025-1029
The dynamics of a rotary nanopump, consisting of three coaxial carbon nanotubes and a number of graphene blades, has been simulated via application of the molecular dynamics (MD) method. In this nanopump the inner nanotube, the middle carbon nanotube with together the graphene blades and the outer nanotube are used as the shaft, rotor, and sleeve of the pump, respectively. The rotary motion of the rotor is due to the mechanical rotation of the two first carbon rings of the rotor's carbon nanotube. We found that this pump flow the gas atoms between two sides of the nanopump and it can produce an atomic gradient. Also it is observed that a rotary frequency of the rotor affected on the pump performance for generating the density gradient and the maximum performance is occurred at a special frequency of the rotor. This special rotary frequency can be computed by an analytical formula, for given material and temperatures. Moreover, the results indicate that the number of the rotor's graphene blades do not have a significant effect on the pumping capacity. Our finding provides a potentially useful mechanism for gas purification process. © 2011 Elsevier Inc. All rights reserved.
Physical Review E - Statistical, Nonlinear, and Soft Matter Physics (15502376) 83(4)
Nonequilibrium molecular dynamics simulations are used to study the motion of a C60 molecule on a graphene sheet subjected to a temperature gradient. The C60 molecule is actuated and moves along the system while it just randomly dances along the perpendicular direction. Increasing the temperature gradient increases the directed velocity of C60. It is found that the free energy decreases as the C60 molecule moves toward the cold end. The driving mechanism based on the temperature gradient suggests the construction of nanoscale graphene-based motors. © 2011 American Physical Society.
Journal of Molecular Graphics and Modelling (10933263) 27(2)pp. 116-123
The dynamics of an ion-driven rotary nanomotor, mimicking the F0 part of the ATPase biomolecular motor, in the presence, and absence, of an external electric field have been simulated via the application of the stochastic molecular dynamics (MD) method. The rotary motion of the proposed motor arises as a result of an ion gradient established between the outer and inner parts of the environment within which the motor is embedded. We show that the operation of this motor can be controlled by such parameters as the amount of the positive ions placed in the stator part of the motor, the density of the positive ions, and the strength and frequency of the applied electric field. © 2008 Elsevier Inc. All rights reserved.
Physica A: Statistical Mechanics and its Applications (03784371) 387(22)pp. 5466-5476
The rotary motion of the F0 part of the F0F1-ATPase motor that synthesizes the ATP molecules used by the intracellular stepping motors, such as kinesins, is modeled within a stochastically fluctuating medium via the application of the Langevin dynamics wherein the random intramembrane fluctuations are represented by a white noise. We have investigated the influence of an applied electric field and an applied electric current on this rotary motion, and the subsequent production rate of the ATP molecules. It is seen that the application of a field, or a current, changes both the elastic behavior of the cell membrane and the transmembrane potential. These changes in turn transform the dynamics of the F0 part of the motor. We have found that at low fields, the role of transmembrane potential becomes significant in the production rate of the ATP molecules, whereas at high fields the changes induced in the surface tension of the membrane also contribute to the production rate of the ATP. © 2008 Elsevier B.V. All rights reserved.
Physica A: Statistical Mechanics and its Applications (03784371) 381(1-2)pp. 239-254
The intracellular motion of the kinesin motor proteins, based on an asymmetric hand-over-hand mechanism, within a stochastically fluctuating medium is simulated via the Langevin dynamics in which the random intracellular fluctuations are represented by a white noise. The kinesin heads are subject to both a flashing ratchet potential, that represents their interaction with the microtubule track and models the random hydrolysis of the adenosine triphosphate (ATP) molecule that drives the motion forward, and a bistable potential that correlates their motion. Our computed results are in good agreement with the experimental data related to the hydrolysis of one ATP molecule per one step of motion, the space-time trajectories of the heads, the variation of the kinesin velocity with the applied external force, and the processivity nature of the kinesin motion. © 2007 Elsevier B.V. All rights reserved.
