International journal of automotive engineering, 2017
Proton exchange membrane (PEM) fuel cells being employed in fuel cell vehicles (FCVs) are promisi... more Proton exchange membrane (PEM) fuel cells being employed in fuel cell vehicles (FCVs) are promising power generators producing electric power from fuel stream via porous electrodes. Structure of carbon paper gas diffusion layers (GDLs) applying in the porous electrodes can have a great influence on the PEM fuel cell performance and distribution of temperature, especially at the cathode side where the electrochemical reaction is more sluggish. To discover the role of carbon paper GDL structure, different cathode electrodes with dissimilar anisotropy parameter are simulated via lattice Boltzmann method (LBM). The distributions of temperature through the GDL as well as the distribution of temperature on the catalyst layer are presented and analyzed. The results indicate that when the carbon fibres are more likely oriented normal to the catalyst layer the distribution of temperature becomes more uniform. Besides, the maximum temperature occurs in this case.
Abstract The effect of interaction between immobile nanoparticle and polymer on the translocation... more Abstract The effect of interaction between immobile nanoparticle and polymer on the translocation process was investigated using a three dimensional Langevin molecular dynamics. Several parameters for describing the translocation time, the polymer shape, and the dispersion of polymer were calculated. Placing a purely repulsive nanoparticle in front of the nanopore not only increases the translocation time but also cause the translocation process to be longer than the translocation process without the presence of nanoparticle. On the other hand, the attractive–repulsive nanoparticle decreases the translocation time for both having a bigger nanoparticle and stronger interaction between polymer and nanoparticle. Simulation results show that the nanoparticle effect on the translocation velocity depends on the binding energy (BE) and by increasing the BE it changes from a decelerator to an accelerator. Moreover, the waiting time plots show a significant difference between the translocation with or without the nanoparticle and change from step-like to the bell-shaped. Analyzing the center of the mass and shape factor, show that increasing the nanoparticle–nanopore distance will elongate the polymer and manifest itself on the shape of the polymer.
In the study of viral epidemics, having information about the structural evolution of the virus c... more In the study of viral epidemics, having information about the structural evolution of the virus can be very helpful in controlling the disease and making vaccines. Various deep learning and natural language processing techniques (NLP) can be used to analyze genetic structure of viruses, namely to predict their mutations. In this paper, by using Sequence-to-Sequence (Seq2Seq) model with Long Short-Term Memory (LSTM) cell and Transformer model with the attention mechanism, we investigate the spike protein mutations of SARS-CoV-2 virus. We make time-series datasets of the spike protein sequences of this virus and generate upcoming spike protein sequences. We also determine the mutations of the generated spike protein sequences, by comparing these sequences with the Wuhan spike protein sequence. We train the models to make predictions in December 2021, February 2022, and October 2022. Furthermore, we find that some of our generated spike protein sequences have been reported in December ...
Chaperones are binding proteins which work as a driving force to bias the biopolymer translocatio... more Chaperones are binding proteins which work as a driving force to bias the biopolymer translocation by binding to it near the pore and preventing its backsliding. Chaperones may have different spatial distribution. Recently we show the importance of their spatial distribution in translocation and how it effects on sequence dependency of the translocation time. Here we focus on homopolymers and exponential distribution. As a result of the exponential distribution of chaperones, energy dependency of the translocation time will changed and one see a minimum in translocation time versus effective energy curve. The same trend can be seen in scaling exponent of time versus polymer length, β (T∼β). Interestingly in some special cases e.g. chaperones of size λ=6 and with exponential distribution rate of α=5, the minimum reaches even to amount of less than 1 (β<1). We explain the possibility of this rare result and base on a theoretical discussion we show that by taking into account the ve...
We employ a three-dimensional molecular dynamics to simulate translocation of a polymer through a... more We employ a three-dimensional molecular dynamics to simulate translocation of a polymer through a nanopore driven by an external force. The translocation is investigated for different three pore diameter and two different external forces. In order to see the polymer and pore interaction effects on translocation time, we studied 9 different interaction energies. Moreover, to better understand the simulation results we investigate polymer center of mass, shape factor and the monomer distribution through the translocation. Our results unveil that while increasing the polymer-pore interaction energy slows down the translocation, expanding the pore diameter, makes the translocation faster. The shape analysis of the results reveals that the polymer shape is very sensitive to the interaction energy. In high interactions, the monomers come close to the pore from both sides. As a result, the translocation becomes fast at first and slows down at last.
Chaperone-assisted biopolymer translocation is the main model proposed for translocation in vivo.... more Chaperone-assisted biopolymer translocation is the main model proposed for translocation in vivo. A dynamical Monte Carlo method is used to simulate the translocation of a stiff homopolymer through a nanopore driven by chaperones. Chaperones are proteins that bind to the polymer near the wall and prevent its backsliding through Cis side. The important parameters include binding energy, size and the local concentration of the chaperones. The profile of these local concentrations, build up the chaperones distribution. Here we investigate the effects of binding energy, size and the exponential distribution of chaperones in their equilibration in each step of the polymer translocation needed for stable translocation time. The simulation results show that in case of chaperones with the size of a monomer (λ=1) and/or positive effective binding energy and/or uniform distribution, the chaperones binding equilibration rate/frequency is less than 5 times per monomer. However, in some special ...
Abstract In this paper, the device characteristics of Cu2BaSnSSe3 (CBT(S,Se3)) solar cells have b... more Abstract In this paper, the device characteristics of Cu2BaSnSSe3 (CBT(S,Se3)) solar cells have been simulated using SCAPS-1D. The simulated results have been validated by comparison with the experimental data reported in the literature. For improving the cell performance and boosting the efficiency, adding different Back Surface Field (BSF) layers is suggested on the absorber layer. Inserting a BSF layer with optimum parameters causes enhancement of open-circuit voltage (VOC), in particular, causes better efficiency on the cell's performance. For this purpose, we optimize the MoSe2 layer, which is formed at the interface between CBT(S,Se3) absorber layer and Mo back contact. Investigation of MoSe2 helps us to represent optimum ranges for bandgap (Eg), electron affinity (χ), charge carrier density, thickness, the mobility of electron and hole (μe and μh) and the effective density of states of conduction band and valence band (NC and NV) of a material to choose as a BSF layer which can be inserted in CBT(S,Se3) solar cells and other types of cells like CZTSSe, perovskite and CIGS. Based on the optimum parameters for an appropriate BSF layer, Cu2BaSnSSe3 solar cell has been simulated by inserting SnS as a BSF layer, and the results indicated improvement in the cell's parameters. We recorded PCE = 7.31%, VOC = 0.867 V, JSC = 16.986 mA/cm2, and FF = 49.63.
In this research study, we prepared different thin films of ZnO:Cu, ZnO:Mo, and Zno:Mo:Cu using a... more In this research study, we prepared different thin films of ZnO:Cu, ZnO:Mo, and Zno:Mo:Cu using a magnetron co-sputtering method. At the best of our knowledge, it is the first time that one prepared co-sputtered Zno:Mo:Cu thin films. We also annealed the samples at 100, 200, 400, and 800 °C. The samples were both theoretically and experimentally. We investigate the AFM results of the samples in the above-mentioned temperatures and compare different parameters of saturation roughness, height density function, and permutation entropy. The results demonstrated that the height density function became wider and the roughness decreased at higher temperatures. Moreover, the plot of permutation entropy versus roughness enabled us to distinguish between our samples.
Here using LAMMPS molecular dynamics (MD) software, we simulate polymer translocation in 2 dimens... more Here using LAMMPS molecular dynamics (MD) software, we simulate polymer translocation in 2 dimensions. We do the simulations for weak and moderate forces and for different pore diameters. Our results show that in both non-equilibrium and equilibrium initial conditions, translocation time will always increase by increasing binding energy and or increasing pore diameter. Moreover, scaling exponent of time versus force is -0.9531 in accordance to our predecessors. The comparison between equilibrium and non-equilibrium initial condition shows that the translocation time is very sensitive to the initial condition. Translocation time of the relaxed polymers for interaction energy of 8k_B T is smaller from the non-equilibrium case even in the small energy of 1k_B T.
International journal of automotive engineering, 2017
Proton exchange membrane (PEM) fuel cells being employed in fuel cell vehicles (FCVs) are promisi... more Proton exchange membrane (PEM) fuel cells being employed in fuel cell vehicles (FCVs) are promising power generators producing electric power from fuel stream via porous electrodes. Structure of carbon paper gas diffusion layers (GDLs) applying in the porous electrodes can have a great influence on the PEM fuel cell performance and distribution of temperature, especially at the cathode side where the electrochemical reaction is more sluggish. To discover the role of carbon paper GDL structure, different cathode electrodes with dissimilar anisotropy parameter are simulated via lattice Boltzmann method (LBM). The distributions of temperature through the GDL as well as the distribution of temperature on the catalyst layer are presented and analyzed. The results indicate that when the carbon fibres are more likely oriented normal to the catalyst layer the distribution of temperature becomes more uniform. Besides, the maximum temperature occurs in this case.
Abstract The effect of interaction between immobile nanoparticle and polymer on the translocation... more Abstract The effect of interaction between immobile nanoparticle and polymer on the translocation process was investigated using a three dimensional Langevin molecular dynamics. Several parameters for describing the translocation time, the polymer shape, and the dispersion of polymer were calculated. Placing a purely repulsive nanoparticle in front of the nanopore not only increases the translocation time but also cause the translocation process to be longer than the translocation process without the presence of nanoparticle. On the other hand, the attractive–repulsive nanoparticle decreases the translocation time for both having a bigger nanoparticle and stronger interaction between polymer and nanoparticle. Simulation results show that the nanoparticle effect on the translocation velocity depends on the binding energy (BE) and by increasing the BE it changes from a decelerator to an accelerator. Moreover, the waiting time plots show a significant difference between the translocation with or without the nanoparticle and change from step-like to the bell-shaped. Analyzing the center of the mass and shape factor, show that increasing the nanoparticle–nanopore distance will elongate the polymer and manifest itself on the shape of the polymer.
In the study of viral epidemics, having information about the structural evolution of the virus c... more In the study of viral epidemics, having information about the structural evolution of the virus can be very helpful in controlling the disease and making vaccines. Various deep learning and natural language processing techniques (NLP) can be used to analyze genetic structure of viruses, namely to predict their mutations. In this paper, by using Sequence-to-Sequence (Seq2Seq) model with Long Short-Term Memory (LSTM) cell and Transformer model with the attention mechanism, we investigate the spike protein mutations of SARS-CoV-2 virus. We make time-series datasets of the spike protein sequences of this virus and generate upcoming spike protein sequences. We also determine the mutations of the generated spike protein sequences, by comparing these sequences with the Wuhan spike protein sequence. We train the models to make predictions in December 2021, February 2022, and October 2022. Furthermore, we find that some of our generated spike protein sequences have been reported in December ...
Chaperones are binding proteins which work as a driving force to bias the biopolymer translocatio... more Chaperones are binding proteins which work as a driving force to bias the biopolymer translocation by binding to it near the pore and preventing its backsliding. Chaperones may have different spatial distribution. Recently we show the importance of their spatial distribution in translocation and how it effects on sequence dependency of the translocation time. Here we focus on homopolymers and exponential distribution. As a result of the exponential distribution of chaperones, energy dependency of the translocation time will changed and one see a minimum in translocation time versus effective energy curve. The same trend can be seen in scaling exponent of time versus polymer length, β (T∼β). Interestingly in some special cases e.g. chaperones of size λ=6 and with exponential distribution rate of α=5, the minimum reaches even to amount of less than 1 (β<1). We explain the possibility of this rare result and base on a theoretical discussion we show that by taking into account the ve...
We employ a three-dimensional molecular dynamics to simulate translocation of a polymer through a... more We employ a three-dimensional molecular dynamics to simulate translocation of a polymer through a nanopore driven by an external force. The translocation is investigated for different three pore diameter and two different external forces. In order to see the polymer and pore interaction effects on translocation time, we studied 9 different interaction energies. Moreover, to better understand the simulation results we investigate polymer center of mass, shape factor and the monomer distribution through the translocation. Our results unveil that while increasing the polymer-pore interaction energy slows down the translocation, expanding the pore diameter, makes the translocation faster. The shape analysis of the results reveals that the polymer shape is very sensitive to the interaction energy. In high interactions, the monomers come close to the pore from both sides. As a result, the translocation becomes fast at first and slows down at last.
Chaperone-assisted biopolymer translocation is the main model proposed for translocation in vivo.... more Chaperone-assisted biopolymer translocation is the main model proposed for translocation in vivo. A dynamical Monte Carlo method is used to simulate the translocation of a stiff homopolymer through a nanopore driven by chaperones. Chaperones are proteins that bind to the polymer near the wall and prevent its backsliding through Cis side. The important parameters include binding energy, size and the local concentration of the chaperones. The profile of these local concentrations, build up the chaperones distribution. Here we investigate the effects of binding energy, size and the exponential distribution of chaperones in their equilibration in each step of the polymer translocation needed for stable translocation time. The simulation results show that in case of chaperones with the size of a monomer (λ=1) and/or positive effective binding energy and/or uniform distribution, the chaperones binding equilibration rate/frequency is less than 5 times per monomer. However, in some special ...
Abstract In this paper, the device characteristics of Cu2BaSnSSe3 (CBT(S,Se3)) solar cells have b... more Abstract In this paper, the device characteristics of Cu2BaSnSSe3 (CBT(S,Se3)) solar cells have been simulated using SCAPS-1D. The simulated results have been validated by comparison with the experimental data reported in the literature. For improving the cell performance and boosting the efficiency, adding different Back Surface Field (BSF) layers is suggested on the absorber layer. Inserting a BSF layer with optimum parameters causes enhancement of open-circuit voltage (VOC), in particular, causes better efficiency on the cell's performance. For this purpose, we optimize the MoSe2 layer, which is formed at the interface between CBT(S,Se3) absorber layer and Mo back contact. Investigation of MoSe2 helps us to represent optimum ranges for bandgap (Eg), electron affinity (χ), charge carrier density, thickness, the mobility of electron and hole (μe and μh) and the effective density of states of conduction band and valence band (NC and NV) of a material to choose as a BSF layer which can be inserted in CBT(S,Se3) solar cells and other types of cells like CZTSSe, perovskite and CIGS. Based on the optimum parameters for an appropriate BSF layer, Cu2BaSnSSe3 solar cell has been simulated by inserting SnS as a BSF layer, and the results indicated improvement in the cell's parameters. We recorded PCE = 7.31%, VOC = 0.867 V, JSC = 16.986 mA/cm2, and FF = 49.63.
In this research study, we prepared different thin films of ZnO:Cu, ZnO:Mo, and Zno:Mo:Cu using a... more In this research study, we prepared different thin films of ZnO:Cu, ZnO:Mo, and Zno:Mo:Cu using a magnetron co-sputtering method. At the best of our knowledge, it is the first time that one prepared co-sputtered Zno:Mo:Cu thin films. We also annealed the samples at 100, 200, 400, and 800 °C. The samples were both theoretically and experimentally. We investigate the AFM results of the samples in the above-mentioned temperatures and compare different parameters of saturation roughness, height density function, and permutation entropy. The results demonstrated that the height density function became wider and the roughness decreased at higher temperatures. Moreover, the plot of permutation entropy versus roughness enabled us to distinguish between our samples.
Here using LAMMPS molecular dynamics (MD) software, we simulate polymer translocation in 2 dimens... more Here using LAMMPS molecular dynamics (MD) software, we simulate polymer translocation in 2 dimensions. We do the simulations for weak and moderate forces and for different pore diameters. Our results show that in both non-equilibrium and equilibrium initial conditions, translocation time will always increase by increasing binding energy and or increasing pore diameter. Moreover, scaling exponent of time versus force is -0.9531 in accordance to our predecessors. The comparison between equilibrium and non-equilibrium initial condition shows that the translocation time is very sensitive to the initial condition. Translocation time of the relaxed polymers for interaction energy of 8k_B T is smaller from the non-equilibrium case even in the small energy of 1k_B T.
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