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Farimani RA, Ahmadian Dehaghani Z, Likos CN, Ejtehadi MR. Effects of Linking Topology on the Shear Response of Connected Ring Polymers: Catenanes and Bonded Rings Flow Differently. Phys Rev Lett 2024; 132:148101. [PMID: 38640389 DOI: 10.1103/physrevlett.132.148101] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/14/2023] [Revised: 10/09/2023] [Accepted: 02/15/2024] [Indexed: 04/21/2024]
Abstract
We perform computer simulations of mechanically linked (poly[2]catenanes, PC) and chemically bonded (bonded rings, BR) pairs of self-avoiding ring polymers in steady shear. We find that BRs develop a novel motif, termed gradient tumbling, rotating around the gradient axis. For the PCs the rings are stretched and display another new pattern, termed slip tumbling. The dynamics of BRs is continuous and oscillatory, whereas that of PCs is intermittent between slip-tumbling attempts. Our findings demonstrate the interplay between topology and hydrodynamics in dilute solutions of connected polymers.
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Affiliation(s)
- Reyhaneh A Farimani
- Department of Physics, Sharif University of Technology, Tehran, Iran
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, 1090 Vienna, Austria
| | | | - Christos N Likos
- Faculty of Physics, University of Vienna, Boltzmanngasse 5, 1090 Vienna, Austria
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2
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Rezaei M, Ghasemitarei M, Razzokov J, Yusupov M, Ghorbanalilu M, Ejtehadi MR. In silico study of the impact of oxidation on pyruvate transmission across the hVDAC1 protein channel. Arch Biochem Biophys 2024; 751:109835. [PMID: 38000492 DOI: 10.1016/j.abb.2023.109835] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2023] [Revised: 10/25/2023] [Accepted: 11/20/2023] [Indexed: 11/26/2023]
Abstract
The overexpression of voltage dependent anion channels (VDACs), particularly VDAC1, in cancer cells compared to normal cells, plays a crucial role in cancer cell metabolism, apoptosis regulation, and energy homeostasis. In this study, we used molecular dynamics (MD) simulations to investigate the effect of a low level of VDAC1 oxidation (induced e.g., by cold atmospheric plasma (CAP)) on the pyruvate (Pyr) uptake by VDAC1. Inhibiting Pyr uptake through VDAC1 can suppress cancer cell proliferation. Our primary target was to study the translocation of Pyr across the native and oxidized forms of hVDAC1, the human VDAC1. Specifically, we employed MD simulations to analyze the hVDAC1 structure by modifying certain cysteine residues to cysteic acids and methionine residues to methionine sulfoxides, which allowed us to investigate the effect of oxidation. Our results showed that the free energy barrier for Pyr translocation through the native and oxidized channel was approximately 4.3 ± 0.7 kJ mol-1 and 10.8 ± 1.8 kJ mol-1, respectively. An increase in barrier results in a decrease in rate of Pyr permeation through the oxidized channel. Thus, our results indicate that low levels of CAP oxidation reduce Pyr translocation, resulting in decreased cancer cell proliferation. Therefore, low levels of oxidation are likely sufficient to treat cancer cells given the inhibition of Pyr uptake.
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Affiliation(s)
- Mahsa Rezaei
- Department of Physics, Shahid Beheshti University, Tehran, 19839-69411, Iran
| | - Maryam Ghasemitarei
- Department of Physics, Sharif University of Technology, 14588-89694, Tehran, Iran; Research Group PLASMANT, Department of Chemistry, University of Antwerp, 2610, Antwerp, Belgium.
| | - Jamoliddin Razzokov
- Institute of Fundamental and Applied Research, National Research University TIIAME, 100000, Tashkent, Uzbekistan; School of Engineering, Central Asian University, Tashkent, 111221, Uzbekistan; Laboratory of Experimental Biophysics, Centre for Advanced Technologies, 100174, Tashkent, Uzbekistan; Department of Chemistry, Termez State University, 190111, Termez, Uzbekistan
| | - Maksudbek Yusupov
- School of Engineering, New Uzbekistan University, 100000, Tashkent, Uzbekistan; Department of Information Technologies, Tashkent International University of Education, 100207, Tashkent, Uzbekistan; Laboratory of Thermal Physics of Multiphase Systems, Arifov Institute of Ion-Plasma and Laser Technologies, Academy of Sciences of Uzbekistan, 100125, Tashkent, Uzbekistan; Department of Power Supply and Renewable Energy Sources, National Research University TIIAME, 100000, Tashkent, Uzbekistan
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3
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Ranjbar S, Salavati AH, Ashari Astani N, Naseri N, Davar N, Ejtehadi MR. Electrochromic Sensor Augmented with Machine Learning for Enzyme-Free Analysis of Antioxidants. ACS Sens 2023; 8:4281-4292. [PMID: 37963856 DOI: 10.1021/acssensors.3c01637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2023]
Abstract
Our study presents an electrochromic sensor that operates without the need for enzymes or multiple oxidant reagents. This sensor is augmented with machine learning algorithms, enabling the identification, classification, and prediction of six different antioxidants with high accuracy. We utilized polyaniline (PANI), Prussian blue (PB), and copper-Prussian blue analogues (Cu-PBA) at their respective oxidation states as electrochromic materials (ECMs). By designing three readout channels with these materials, we were able to achieve visual detection of antioxidants without relying on traditional "lock and key" specific interactions. Our sensing approach is based on the direct electrochemical reactions between oxidized electrochromic materials (ECMsox) as electron acceptors and various antioxidants, which act as electron donors. This interaction generates unique fingerprint patterns by switching the ECMsox to reduced electrochromic materials (ECMsred), causing their colors to change. Through the application of density functional theory (DFT), we demonstrated the molecular-level basis for the distinct multicolor patterns. Additionally, machine learning algorithms were employed to correlate the optical patterns with RGB data, enabling complex data analysis and the prediction of unknown samples. To demonstrate the practical applications of our design, we successfully used the EC sensor to diagnose antioxidants in serum samples, indicating its potential for the on-site monitoring of antioxidant-related diseases. This advancement holds promise for various applications, including the real-time monitoring of antioxidant levels in biological samples, the early diagnosis of antioxidant-related diseases, and personalized medicine. Furthermore, the success of our electrochromic sensor design highlights the potential for exploring similar strategies in the development of sensors for diverse analytes, showcasing the versatility and adaptability of this approach.
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Affiliation(s)
- Saba Ranjbar
- Department of Physics, Sharif University of Technology, Tehran 11365-9161, Iran
- Department of Industrial and Environmental Biotechnology, National Institute of Genetic Engineering and Biotechnology (NIGEB), Tehran 14965/161, Iran
| | - Amir Hesam Salavati
- Tehran Institute of Advanced Studies (TeIAS), Khatam University, Tehran 1991633357, Iran
| | - Negar Ashari Astani
- Departments of Physics and Energy Engineering, Amirkabir University of Technology, Tehran 15875-4413, Iran
| | - Naimeh Naseri
- Department of Physics, Sharif University of Technology, Tehran 11365-9161, Iran
- Department of Mechanical and Aerospace Engineering, Monash University, Clayton, VIC 3800, Australia
- ARC Research Hub for Advanced Manufacturing with Two-dimensional Materials (AM2D), Monash University, Clayton, VIC 3800, Australia
| | - Navid Davar
- Departments of Physics and Energy Engineering, Amirkabir University of Technology, Tehran 15875-4413, Iran
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Farnudi A, Ejtehadi MR, Everaers R. Dynamics of fluid bilayer vesicles: Soft meshes and robust curvature energy discretization. Phys Rev E 2023; 108:015301. [PMID: 37583159 DOI: 10.1103/physreve.108.015301] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2022] [Accepted: 05/26/2023] [Indexed: 08/17/2023]
Abstract
Continuum models like the Helfrich Hamiltonian are widely used to describe fluid bilayer vesicles. Here we study the molecular dynamics compatible dynamics of the vertices of two-dimensional meshes representing the bilayer, whose in-plane motion is only weakly constrained. We show (i) that Jülicher's discretization of the curvature energy offers vastly superior robustness for soft meshes compared to the commonly employed expression by Gommper and Kroll and (ii) that for sufficiently soft meshes, the typical behavior of fluid bilayer vesicles can emerge even if the mesh connectivity remains fixed throughout the simulations. In particular, soft meshes can accommodate large shape transformations, and the model can generate the typical ℓ^{-4} signal for the amplitude of surface undulation modes of nearly spherical vesicles all the way up to the longest wavelength modes. Furthermore, we compare results for Newtonian, Langevin, and Brownian dynamics simulations of the mesh vertices to demonstrate that the internal friction of the membrane model is negligible, making it suitable for studying the internal dynamics of vesicles via coupling to hydrodynamic solvers or particle-based solvent models.
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Affiliation(s)
- Ali Farnudi
- Department of Physics, Sharif University of Technology, P.O. Box 11155-9161, Tehran, Iran
| | - Mohammad Reza Ejtehadi
- Department of Physics, Sharif University of Technology, P.O. Box 11155-9161, Tehran, Iran
| | - Ralf Everaers
- Ecole Normale Supérieure (ENS) de Lyon, CNRS, Laboratoire de Physique and Centre Blaise Pascal de l'ENS de Lyon, F-69342 Lyon, France
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5
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Nemati H, Kaveh K, Ejtehadi MR. Counterintuitive properties of evolutionary measures: A stochastic process study in cyclic population structures with periodic environments. J Theor Biol 2023; 564:111436. [PMID: 36828246 DOI: 10.1016/j.jtbi.2023.111436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2022] [Revised: 01/26/2023] [Accepted: 02/05/2023] [Indexed: 02/24/2023]
Abstract
Local environmental interactions are a major factor in determining the success of a new mutant in structured populations. Spatial variations in the concentration of genotype-specific resources change the fitness of competing strategies locally and thus can drastically change the outcome of evolutionary processes in unintuitive ways. The question is how such local environmental variations in network population structures change the condition for selection and fixation probability of an advantageous (or deleterious) mutant. We consider linear graph structures and focus on the case where resources have a spatial periodic pattern. This is the simplest model with two parameters, length scale and fitness scales, representing heterogeneity. We calculate fixation probability and fixation times for a constant population birth-death process as fitness heterogeneity and period vary. Fixation probability is affected by not only the level of fitness heterogeneity but also spatial scale of resources variations set by period of distribution T. We identify conditions for which a previously a deleterious mutant (in a uniform environment) becomes beneficial as fitness heterogeneity is increased. We observe cases where the fixation probability of both mutant and resident types are more than their neutral value, 1/N, simultaneously. This coincides with exponential increase in time to fixation which points to potential coexistence of resident and mutant types. Finally, we discuss the effect of the 'fitness shift' where the fitness function of two types has a phase difference. We observe significant increases (or decreases) in the fixation probability of the mutant as a result of such phase shift.
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Affiliation(s)
- Hossein Nemati
- Sharif University of Technology, Physics Department, Iran
| | - Kamran Kaveh
- University of Washington, Department of Applied Mathematics, United States of America.
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6
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Vaezi M, Nejat Pishkenari H, Ejtehadi MR. Programmable Transport of C60 by Straining Graphene Substrate. Langmuir 2023; 39:4483-4494. [PMID: 36926912 DOI: 10.1021/acs.langmuir.3c00180] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/18/2023]
Abstract
Controlling the maneuverability of nanocars and molecular machines on the surface is essential for the targeted transportation of materials and energy at the nanoscale. Here, we evaluate the motion of fullerene, as the most popular candidate for use as a nanocar wheel, on the graphene nanoribbons with strain gradients based on molecular dynamics (MD), and theoretical approaches. The strain of the examined substrates linearly decreases by 20%, 16%, 12%, 8%, 4%, and 2%. MD calculations were performed with the open source LAMMPS solver. The essential physics of the interactions is captured by Lennard-Jones and Tersoff potentials. The motion of C60 on the graphene nanoribbon is simulated in canonical ensemble, which is implanted by using a Nose-Hoover thermostat. Since the potential energy of C60 is lower on the unstrained end of nanoribbons, this region is energetically more favorable for the molecule. As the strain gradient of the surface increases, the trajectories of the motion and the C60 velocity indicate more directed movements along the gradient of strain on the substrate. Based on the theoretical relations, it was shown that the driving force and diffusion coefficient of the C60 motion respectively find linear and quadratic growth with the increase of strain gradient, which is confirmed by MD simulations. To understand the effect of temperature, at each strain gradient of substrate, the simulations are repeated at the temperatures of 100, 200, 300, and 400 K. The large ratio of longitudinal speed to the transverse speed of fullerene at 100 and 200 K refers to the rectilinear motion of molecule at low temperatures. Using successive strain gradients on the graphene in perpendicular directions, we steered the motion of C60 to the desired target locations. The programmable transportation of nanomaterials on the surface has a significant role in different processes at the nanoscale, such as bottom-up assembly.
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Affiliation(s)
- Mehran Vaezi
- Institute for Nanoscience and Nanotechnology (INST), Sharif University of Technology, Tehran 11365-11155, Iran
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7
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Ranjbar S, Ashari Astani N, Atabay M, Naseri N, Esfandiar A, Reza Ejtehadi M. Electrochemical and computational studies of bio-mimicked Ti3C2Tx MXene-based sensor with multivalent interface. J Colloid Interface Sci 2022. [DOI: 10.1016/j.jcis.2022.05.033] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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8
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Vaezi M, Nejat Pishkenari H, Ejtehadi MR. Collective movement and thermal stability of fullerene clusters on the graphene layer. Phys Chem Chem Phys 2022; 24:11770-11781. [PMID: 35506871 DOI: 10.1039/d2cp00667g] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/16/2022]
Abstract
Understanding the motion characteristics of fullerene clusters on the graphene surface is critical for designing surface manipulation systems. Toward this purpose, using the molecular dynamics method, we evaluated six clusters of fullerenes including 1, 2, 3, 5, 10, and 25 molecules on the graphene surface, in the temperature range of 25 to 500 K. First, the surface motion of clusters is studied at 200 K and lower temperatures, in which fullerenes remain as a single group. The trajectories of the motion as well as the diffusion coefficients indicate the reduction of surface mobility as a response to the increase of the fullerene number. The clusters show normal diffusion at the temperature of 25 K, while they follow the super-diffusion regime at higher temperatures. The separation of fullerenes occurs at 300 K and higher temperatures. Due to the increase of vdW attraction with the increase of the fullerene number, the separation of fullerenes in larger clusters occurs at higher temperatures. The thermal energy at 500 K is sufficient to divide the large C60 clusters into smaller clusters. This energy level is related to the saturation of the interaction energy experienced by individual fullerenes, which can be estimated from the potential energy analysis. The results of simulations reveal that the separation occurs at the edge of clusters. Moreover, we studied the thermal stability of multilayer fullerene clusters on graphene. The simulation results indicate the tendency of multilayer clusters to locate on the surface, which implies the wetting property of C60s on the graphene layer.
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Affiliation(s)
- Mehran Vaezi
- Institute for Nanoscience and Nanotechnology (INST), Sharif University of Technology, Tehran, Iran
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9
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Hosseini AN, Lund M, Ejtehadi MR. A modified Jarzynski free-energy estimator to eliminate non-conservative forces and its application in nanoparticle-membrane interactions. Phys Chem Chem Phys 2022; 24:3647-3654. [PMID: 35103740 DOI: 10.1039/d1cp05218g] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Computational methods to understand interactions in bio-complex systems are however limited to time-scales typically much shorter than in Nature. For example, on the nanoscale level, interactions between nanoparticles (NPs)/molecules/peptides and membranes are central in complex biomolecular processes such as membrane-coated NPs or cellular uptake. This can be remedied by the application of e.g. Jarzynski's equality where thermodynamic properties are extracted from non-equilibrium simulations. Although, the out of equilibrium work leads to non-conservative forces. We here propose a correction Pair Forces method, that removes these forces. Our proposed method is based on the calculation of pulling forces in backward and forward directions for the Jarzynski free-energy estimator using steered molecular dynamics simulation. Our results show that this leads to much improvement for NP-membrane translocation free energies. Although here we have demonstrated the application of the method in molecular dynamics simulation, it could be applied for experimental approaches.
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Affiliation(s)
- Atiyeh Najla Hosseini
- Institute for Nanoscience and Nanotechnology, Sharif University of Technology, Tehran, Iran.
| | - Mikael Lund
- Division of Theoretical Chemistry, Lund University, Lund, Sweden.,LINXS - Lund Institute for Advanced Neutral and X-ray Scattering, Lund University, Sweden.
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10
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Ashkarran AA, Hosseini A, Loloee R, Perry G, Lee KB, Lund M, Ejtehadi MR, Mahmoudi M. Conformation- and phosphorylation-dependent electron tunnelling across self-assembled monolayers of tau peptides. J Colloid Interface Sci 2022; 606:2038-2050. [PMID: 34749450 DOI: 10.1016/j.jcis.2021.09.185] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Revised: 09/17/2021] [Accepted: 09/28/2021] [Indexed: 10/20/2022]
Abstract
We report on charge transport across self-assembled monolayers (SAMs) of short tau peptides by probing the electron tunneling rates and quantum mechanical simulation. We measured the electron tunneling rates across SAMs of carboxyl-terminated linker molecules (C6H12O2S) and short cis-tau (CT) and trans-tau (TT) peptides, supported on template-stripped gold (AuTS) bottom electrode, with Eutectic Gallium-Indium (EGaIn)(EGaIn) top electrode. Measurements of the current density across thousands of AuTS/linker/tau//Ga2O3/EGaIn single-molecule junctions show that the tunneling current across CT peptide is one order of magnitude lower than that of TT peptide. Quantum mechanical simulation demonstrated a wider energy bandgap of the CT peptide, as compared to the TT peptide, which causes a reduction in its electron tunneling current. Our findings also revealed the critical role of phosphorylation in altering the charge transport characteristics of short peptides; more specifically, we found that the presence of phosphate groups can reduce the energy band gap in tau peptides and alter their electrical properties. Our results suggest that conformational and phosphorylation of short peptides (e.g., tau) can significantly change their charge transport characteristics and energy levels.
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Affiliation(s)
- Ali Akbar Ashkarran
- Precision Health Program and Department of Radiology, Michigan State University, East Lansing, MI 48824, USA.
| | - Atiyeh Hosseini
- Division of Theoretical Chemistry, Lund University, Lund, Sweden; Institute for Nanoscience and Nanotechnology, Sharif University of Technology, Tehran, Iran
| | - Reza Loloee
- Department of Physics and Astronomy, Michigan State University, East Lansing, MI 48824, USA
| | - George Perry
- Department of Biology, The University of Texas at San Antonio, San Antonio, TX, USA
| | - Ki-Bum Lee
- Department of Chemistry and Chemical Biology, Rutgers, The State University of New Jersey, Piscataway, NJ 08854, USA
| | - Mikael Lund
- Division of Theoretical Chemistry, Lund University, Lund, Sweden.
| | | | - Morteza Mahmoudi
- Precision Health Program and Department of Radiology, Michigan State University, East Lansing, MI 48824, USA
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11
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Ghasemitarei M, Privat-Maldonado A, Yusupov M, Rahnama S, Bogaerts A, Ejtehadi MR. Effect of Cysteine Oxidation in SARS-CoV-2 Receptor-Binding Domain on Its Interaction with Two Cell Receptors: Insights from Atomistic Simulations. J Chem Inf Model 2022; 62:129-141. [PMID: 34965734 PMCID: PMC8751020 DOI: 10.1021/acs.jcim.1c00853] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Indexed: 12/15/2022]
Abstract
Binding of the SARS-CoV-2 S-glycoprotein to cell receptors is vital for the entry of the virus into cells and subsequent infection. ACE2 is the main cell receptor for SARS-CoV-2, which can attach to the C-terminal receptor-binding domain (RBD) of the SARS-CoV-2 S-glycoprotein. The GRP78 receptor plays an anchoring role, which attaches to the RBD and increases the chance of other RBDs binding to ACE2. Although high levels of reactive oxygen and nitrogen species (RONS) are produced during viral infections, it is not clear how they affect the RBD structure and its binding to ACE2 and GRP78. In this research, we apply molecular dynamics simulations to study the effect of oxidation of the highly reactive cysteine (Cys) amino acids of the RBD on its binding to ACE2 and GRP78. The interaction energy of both ACE2 and GRP78 with the whole RBD, as well as with the RBD main regions, is compared in both the native and oxidized RBDs. Our results show that the interaction energy between the oxidized RBD and ACE2 is strengthened by 155 kJ/mol, increasing the binding of the RBD to ACE2 after oxidation. In addition, the interaction energy between the RBD and GRP78 is slightly increased by 8 kJ/mol after oxidation, but this difference is not significant. Overall, these findings highlight the role of RONS in the binding of the SARS-CoV-2 S-glycoprotein to host cell receptors and suggest an alternative mechanism by which RONS could modulate the entrance of viral particles into the cells.
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Affiliation(s)
- Maryam Ghasemitarei
- Department
of Physics, Sharif University of Technology, Tehran 14588-89694, Iran
- Research
Group PLASMANT, Department of Chemistry, University of Antwerp, Universiteitsplein 1, B-2610 Antwerp, Belgium
| | - Angela Privat-Maldonado
- Research
Group PLASMANT, Department of Chemistry, University of Antwerp, Universiteitsplein 1, B-2610 Antwerp, Belgium
| | - Maksudbek Yusupov
- Research
Group PLASMANT, Department of Chemistry, University of Antwerp, Universiteitsplein 1, B-2610 Antwerp, Belgium
- Laboratory
of Thermal Physics of Multiphase Systems, Arifov Institute of Ion-Plasma
and Laser Technologies, Academy of Sciences
of Uzbekistan, Durmon
yuli str. 33, 100125 Tashkent, Uzbekistan
| | - Shadi Rahnama
- Institute
for Nanoscience & Nanotechnology (INST), Sharif University of Technology, Azadi Avenue, Tehran 14588-89694, Iran
| | - Annemie Bogaerts
- Research
Group PLASMANT, Department of Chemistry, University of Antwerp, Universiteitsplein 1, B-2610 Antwerp, Belgium
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12
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Vaezi M, Nejat Pishkenari H, Ejtehadi MR. Nanocar Swarm Movement on Graphene Surface. Phys Chem Chem Phys 2022; 24:27759-27771. [DOI: 10.1039/d2cp03856k] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Investigation of the nanomachines swarm motion is useful in the design of molecular transportation systems as well as in understanding the assembly process on the surface. Here, we evaluate the...
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13
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Hosseini N, Lund M, Ejtehadi MR. Polarization Switching Method for Effective Free Energy Calculation of Membrane Translocation on the Nano-scale. Phys Chem Chem Phys 2022; 24:12281-12292. [DOI: 10.1039/d2cp00056c] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
Abstract
Free-energy calculations are crucial for investigating biomolecular interactions on the Nano-scale level. However, in theoretical studies, the neglect of electronic polarization can jeopardize their accuracy and correct predictive capabilities, specifically...
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14
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Ghobadpour E, Kolb M, Ejtehadi MR, Everaers R. Monte Carlo simulation of a lattice model for the dynamics of randomly branching double-folded ring polymers. Phys Rev E 2021; 104:014501. [PMID: 34412203 DOI: 10.1103/physreve.104.014501] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/19/2020] [Accepted: 06/07/2021] [Indexed: 11/07/2022]
Abstract
Supercoiled DNA, crumpled interphase chromosomes, and topologically constrained ring polymers often adopt treelike, double-folded, randomly branching configurations. Here we study an elastic lattice model for tightly double-folded ring polymers, which allows for the spontaneous creation and deletion of side branches coupled to a diffusive mass transport, which is local both in space and on the connectivity graph of the tree. We use Monte Carlo simulations to study systems falling into three different universality classes: ideal double-folded rings without excluded volume interactions, self-avoiding double-folded rings, and double-folded rings in the melt state. The observed static properties are in good agreement with exact results, simulations, and predictions of Flory theory for randomly branching polymers. For example, in the melt state rings adopt compact configurations and exhibit territorial behavior. In particular, we show that the emergent dynamics is in excellent agreement with a recent scaling theory and illustrate the qualitative differences with the familiar reptation dynamics of linear chains.
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Affiliation(s)
- Elham Ghobadpour
- Université Grenoble Alpes, Centre National de la Recherche Scientifique (CNRS), TIMC, F-38000 Grenoble, France.,School of Nano Science, Institute for Research in Fundamental Sciences (IPM), 19395-5531, Tehran, Iran
| | - Max Kolb
- Université de Lyon, École Normale Supérieure (ENS) de Lyon, CNRS, Laboratoire de Physique and Centre Blaise Pascal de l'ENS de Lyon, F-69342 Lyon, France
| | | | - Ralf Everaers
- Université de Lyon, École Normale Supérieure (ENS) de Lyon, CNRS, Laboratoire de Physique and Centre Blaise Pascal de l'ENS de Lyon, F-69342 Lyon, France
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15
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Rahnama S, Azimzadeh Irani M, Amininasab M, Ejtehadi MR. S494 O-glycosylation site on the SARS-CoV-2 RBD affects the virus affinity to ACE2 and its infectivity; a molecular dynamics study. Sci Rep 2021; 11:15162. [PMID: 34312429 PMCID: PMC8313699 DOI: 10.1038/s41598-021-94602-w] [Citation(s) in RCA: 17] [Impact Index Per Article: 5.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2020] [Accepted: 07/13/2021] [Indexed: 12/23/2022] Open
Abstract
SARS-CoV-2 is a strain of Coronavirus family that caused the ongoing pandemic of COVID-19. Several studies showed that the glycosylation of virus spike (S) protein and the Angiotensin-Converting Enzyme 2 (ACE2) receptor on the host cell is critical for the virus infectivity. Molecular Dynamics (MD) simulations were used to explore the role of a novel mutated O-glycosylation site (D494S) on the Receptor Binding Domain (RBD) of S protein. This site was suggested as a key mediator of virus-host interaction. By exploring the dynamics of three O-glycosylated models and the control systems of unglcosylated S4944 and S494D complexes, it was shown that the decoration of S494 with elongated O-glycans results in stabilized interactions on the direct RBD-ACE2. Calculation of the distances between RBD and two major H1, H2 helices of ACE2 and the interacting pairs of amino acids in the interface showed that the elongated O-glycan maintains these interactions by forming several polar contacts with the neighbouring residues while it would not interfere in the direct binding interface. Relative binding free energy of RBD-ACE2 is also more favorable in the O-glycosylated models with longer glycans. The increase of RBD binding affinity to ACE2 depends on the size of attached O-glycan. By increasing the size of O-glycan, the RBD-ACE2 binding affinity will increase. Hence, this crucial factor must be taken into account for any further inhibitory approaches towards RBD-ACE2 interaction.
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Affiliation(s)
- Shadi Rahnama
- Institute for Nanoscience and Nanotechnology, Sharif University of Technology, Tehran, 14588, Iran
| | | | - Mehriar Amininasab
- Department of Cell and Molecular Biology, School of Biology, College of Science, University of Tehran, Tehran, Iran
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16
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Sajjadi S, Ejtehadi MR, Ghanbarnejad F. Impact of temporal correlations on high risk outbreaks of independent and cooperative SIR dynamics. PLoS One 2021; 16:e0253563. [PMID: 34283838 PMCID: PMC8291698 DOI: 10.1371/journal.pone.0253563] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2021] [Accepted: 06/08/2021] [Indexed: 11/18/2022] Open
Abstract
We first propose a quantitative approach to detect high risk outbreaks of independent and coinfective SIR dynamics on three empirical networks: a school, a conference and a hospital contact network. This measurement is based on the k-means clustering method and identifies proper samples for calculating the mean outbreak size and the outbreak probability. Then we systematically study the impact of different temporal correlations on high risk outbreaks over the original and differently shuffled counterparts of each network. We observe that, on the one hand, in the coinfection process, randomization of the sequence of the events increases the mean outbreak size of high-risk cases. On the other hand, these correlations do not have a consistent effect on the independent infection dynamics, and can either decrease or increase this mean. Randomization of the daily pattern correlations has no strong impact on the size of the outbreak in either the coinfection or the independent spreading cases. We also observe that an increase in the mean outbreak size does not always coincide with an increase in the outbreak probability; therefore, we argue that merely considering the mean outbreak size of all realizations may lead us into falsely estimating the outbreak risks. Our results suggest that some sort of contact randomization in the organizational level in schools, events or hospitals might help to suppress the spreading dynamics while the risk of an outbreak is high.
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Affiliation(s)
- Sina Sajjadi
- Department of Physics, Sharif University of Technology, Tehran, Iran
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17
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Mofidi SM, Nejat Pishkenari H, Ejtehadi MR, Akimov AV. Locomotion of the C 60-based nanomachines on graphene surfaces. Sci Rep 2021; 11:2576. [PMID: 33510367 PMCID: PMC7844297 DOI: 10.1038/s41598-021-82280-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2020] [Accepted: 01/19/2021] [Indexed: 01/30/2023] Open
Abstract
We provide a comprehensive computational characterization of surface motion of two types of nanomachines with four C60 "wheels": a flexible chassis Nanocar and a rigid chassis Nanotruck. We study the nanocars' lateral and rotational diffusion as well as the wheels' rolling motion on two kinds of graphene substrates-flexible single-layer graphene which may form surface ripples and an ideally flat graphene monolayer. We find that the graphene surface ripples facilitate the translational diffusion of Nanocar and Nanotruck, but have little effect on their surface rotation or the rolling of their wheels. The latter two types of motion are strongly affected by the structure of the nanomachines instead. Surface diffusion of both nanomachines occurs preferentially via a sliding mechanism whereas the rolling of the "wheels" contributes little. The axial rotation of all "wheels" is uncorrelated.
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Affiliation(s)
- Seyedeh Mahsa Mofidi
- grid.412553.40000 0001 0740 9747Institute for Nanoscience and Nanotechnology (INST), Sharif University of Technology, 14588-89694 Tehran, Iran
| | - Hossein Nejat Pishkenari
- grid.412553.40000 0001 0740 9747Mechanical Engineering Department, Sharif University of Technology, 11155-9567 Tehran, Iran
| | - Mohammad Reza Ejtehadi
- grid.412553.40000 0001 0740 9747Department of Physics, Sharif University of Technology, 11155-9161 Tehran, Iran
| | - Alexey V. Akimov
- grid.273335.30000 0004 1936 9887Department of Chemistry, University at Buffalo, State University of New York, Buffalo, 14260-3000 USA
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18
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Ashari Astani N, Najafi F, Maghsoumi A, Huma K, Azimi L, Karimi A, Ejtehadi MR, Gumbart JC, Naseri N. Molecular Machinery Responsible for Graphene Oxide’s Distinct Inhibitory Effects toward Pseudomonas aeruginosa and Staphylococcus aureus Pathogens. ACS Appl Bio Mater 2020. [DOI: 10.1021/acsabm.0c01203] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Affiliation(s)
- Negar Ashari Astani
- Department of Physics and Energy Engineering, Amirkabir University of Technology, Tehran 15875-4413, Iran
| | - Fahimeh Najafi
- Physics Department, Sharif University of Technology, Tehran 11365-9161, Iran
| | - Ali Maghsoumi
- Physics Department, Sharif University of Technology, Tehran 11365-9161, Iran
| | - Kinza Huma
- Physics Department, Sharif University of Technology, Tehran 11365-9161, Iran
| | - Leila Azimi
- Pediatric Infections Research Center, Research Institute for Children’s Health, Shahid Beheshti University of Medical Sciences, Tehran 19839-63113, Iran
| | - Abdollah Karimi
- Pediatric Infections Research Center, Research Institute for Children’s Health, Shahid Beheshti University of Medical Sciences, Tehran 19839-63113, Iran
| | | | - James. C. Gumbart
- School of Physics, Georgia Institute of Technology, Atlanta, Georgia 30332, United States
| | - Naimeh Naseri
- Physics Department, Sharif University of Technology, Tehran 11365-9161, Iran
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19
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Rafieiolhosseini N, Ejtehadi MR. Thermal conductivity of the cell membrane in the presence of cholesterol and amyloid precursor protein. Phys Rev E 2020; 102:042401. [PMID: 33212660 DOI: 10.1103/physreve.102.042401] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/04/2020] [Accepted: 09/16/2020] [Indexed: 12/11/2022]
Abstract
The cell membrane is responsible for the transportation of heat between inside and outside the cell. Whether the thermal properties of the cell membrane are affected by the cholesterol concentration or the membrane proteins has not been investigated so far. Although the experimental measurement of the membrane thermal conductivity was not available until very recently, computational methods have been widely used for this purpose. In this study, we carry out molecular dynamics simulations to investigate the relation between the concentration of cholesterol and the thermal conductivity of a model membrane. Our results suggest an increase in the membrane thermal conductivity upon increasing the concentration of cholesterol in the membrane. Moreover, we find that the asymmetric distribution of cholesterol in the two membrane leaflets decreases thermal conductivity. We also find a rectification effect when heat flows in opposite directions through a model membrane decorated with the amyloid precursor protein. The results of this study apply to the advancement of selective treatment methods, as well as the development of new materials such as biological rectifiers.
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Affiliation(s)
- Neda Rafieiolhosseini
- School of Nano Science, Institute for Research in Fundamental Sciences (IPM), P. O. Box 19395-5531, Tehran, Iran
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20
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Azimzadeh Irani M, Ejtehadi MR. Glycan-mediated functional assembly of IL-1RI: structural insights into completion of the current description for immune response. J Biomol Struct Dyn 2020; 40:2575-2585. [PMID: 33124956 DOI: 10.1080/07391102.2020.1841027] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
Interleukin 1 Receptor type I (IL-1RI) is a multi-domain transmembrane receptor that triggers the inflammatory response. Understanding its detailed mechanism of action is crucial for treating immune disorders. IL-1RI is activated upon formation of its functional assembly that occurs by binding of the IL-1 cytokine and the accessory protein (Il-1RAcP) to it. X-ray crystallography, small-Angle X-ray Scattering and molecular dynamics simulation studies showed that IL-1RI adopts two types of 'compact' and 'extended' conformational states in its dynamical pattern. Furthermore, glycosylation has shown to play a critical role in its activation process. Here, classical and accelerated atomistic molecular dynamics were carried out to examine the role of full glycosylation of IL-1RI and IL-1RAcP in arrangement of the functional assembly. Simulations showed that the 'compact' and 'extended' IL-1RI form two types of 'cytokine-inaccessible-non-signaling' and 'cytokine-accessible-signaling' assemblies with the IL-1RacP, respectively that are both abiding in the presence of glycans. Suggesting that the cytokine binding to IL-1RI is not required for the formation of IL-1RI-IL-1RAcP complex and the 'compact' complex could act as a down-regulatory mechanism. The 'extended' complex is maintained by formation of several persistent hydrogen bonds between the IL-1RI-IL-1RAcP inter-connected glycans. Taken together, it was shown that full glycosylation regulates formation of the IL-1RI functional assembly and play critical role in cytokine biding and triggering the IL-1RI involved downstream pathways in the cell.Communicated by Ramaswamy H. Sarma.
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Affiliation(s)
- Maryam Azimzadeh Irani
- Department of Animal Sciences and Marine Biology, Faculty of Life Sciences and Biotechnology, Shahid Beheshti University, Tehran, Iran
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21
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Azimzadeh Irani M, Ejtehadi MR. GAG positioning on IL-1RI; A mechanism regulated by dual effect of glycosylation. Glycobiology 2020; 29:803-812. [PMID: 31317192 DOI: 10.1093/glycob/cwz055] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2019] [Revised: 07/14/2019] [Accepted: 07/14/2019] [Indexed: 12/17/2022] Open
Abstract
IL-1RI is the signaling receptor for the IL-1 family of cytokines that are involved in establishment of the innate and acquired immune systems. Glycosylated extracellular (EC) domain of the IL-1RI binds to agonist such as IL-1β or antagonist ligands and the accessory protein to form the functional signaling complex. Dynamics and ligand binding of the IL-1RI is influenced by presence of the glycosaminoglycans (GAGs) of the EC matrix. Here a combination of molecular dockings and molecular dynamics simulations of the unglycosylated, partially N-glycosylated and fully N-glycosylated IL-1RI EC domain in the apo, GAG-bound and IL-1β-bound states were carried out to explain the co-occurring dynamical effect of receptor's glycosylation and GAGs. It was shown that the IL-1RI adopts two types of "extended" and "locked" conformations in its dynamical pattern, and glycosylation maintains the receptor in the latter form. Maintaining the receptor in the locked conformation disfavors IL-1β binding by burying its two binding site on the IL-1RI EC domain. Glycosylation disfavors GAG binding to the extended IL-1RI EC domain by sterically limiting the GAGs degrees of freedom in targeting its binding site, while it favors GAG binding to the locked IL-1RI by favorable packing interactions.
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22
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Ahmadian Dehaghani Z, Chubak I, Likos CN, Ejtehadi MR. Effects of topological constraints on linked ring polymers in solvents of varying quality. Soft Matter 2020; 16:3029-3038. [PMID: 32129365 DOI: 10.1039/c9sm02374g] [Citation(s) in RCA: 14] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
We investigate the effects of topological constraints in catenanes composed of interlinked ring polymers on their size in a good solvent as well as on the location of their θ-point when the solvent quality is worsened. We mainly focus on poly[n]catenanes consisting of n ring polymers each of length m interlocked in a linear fashion. Using molecular dynamics simulations, we study the scaling of the poly[n]catenane's radius of gyration in a good solvent, assuming in general that Rg∼mμnν and we find that μ = 0.65 ± 0.02 and ν = 0.60 ± 0.01 for the range of n and m considered. These findings are further rationalized with the help of a mean-field Flory-like theory yielding the values of μ = 16/25 and ν = 3/5, consistent with the numerical results. We show that individual rings within catenanes feature a surplus swelling due to the presence of NL topological links. Furthermore, we consider poly[n]catenanes in solvents of varying quality and we demonstrate that the presence of topological links leads to an increase of its θ-temperature in comparison to isolated linear and ring chains with the following ordering: T > T > T. Finally, we show that the presence of links similarly raises the θ-temperature of a single linked ring in comparison to an unlinked one, bringing its θ-temperature close to the one of a poly[n]catenane.
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23
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Ashari-Astani N, Jahanbakhshi F, Mladenović M, Alanazi AQM, Ahmadabadi I, Ejtehadi MR, Dar MI, Grätzel M, Rothlisberger U. Ruddlesden-Popper Phases of Methylammonium-Based Two-Dimensional Perovskites with 5-Ammonium Valeric Acid AVA 2MA n-1Pb nI 3 n+1 with n = 1, 2, and 3. J Phys Chem Lett 2019; 10:3543-3549. [PMID: 31194558 DOI: 10.1021/acs.jpclett.9b01111] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/09/2023]
Abstract
5-Ammonium valeric acid (AVA) is a frequently used additive in the preparation of lead halide perovskites. However, its microscopic role as passivating, cross-linking, or templating agent is far from clear. In this work, we provide density functional theory-based structural models for the Ruddlesden-Popper (RP) phases of AVA2(CH3NH3) n-1Pb nI3 n+1 for n = 1, 2, and 3 and validate with experimental data on polycrystalline samples for n = 1. The structural and electronic properties of the AVA-based RP phases are compared to the ones of other linker families. In contrast to aromatic and aliphatic spacers without additional functional groups, the RP phases of AVA are characterized by the formation of a regular and stable H-bonding network between the carbonyl head groups of adjacent AVA molecules in opposite layers. Because of these additional interactions, the penetration depth of the organic layer into the perovskite sheet is reduced with direct consequences for its crystalline phase. The possibility of forming strong interlinker hydrogen bonds may lead to an enhanced thermal stability.
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Affiliation(s)
- Negar Ashari-Astani
- Soft Condensed Matter (SCM) , Sharif University of Technology , Tehran , Iran
- Laboratory of Computational Chemistry and Biochemistry (LCBC) , École Polytechnique Fédérale de Lausanne (EPFL) , CH-1015 Lausanne , Switzerland
| | - Farzaneh Jahanbakhshi
- Laboratory of Computational Chemistry and Biochemistry (LCBC) , École Polytechnique Fédérale de Lausanne (EPFL) , CH-1015 Lausanne , Switzerland
| | - Marko Mladenović
- Laboratory of Computational Chemistry and Biochemistry (LCBC) , École Polytechnique Fédérale de Lausanne (EPFL) , CH-1015 Lausanne , Switzerland
- Scientific Computing Laboratory, Center for the Study of Complex Systems, Institute of Physics Belgrade , University of Belgrade , Pregrevica 118 , 11080 Belgrade , Serbia
| | - Anwar Q M Alanazi
- Laboratory of Photonics and Interfaces (LPI) , École Polytechnique Fédérale de Lausanne (EPFL) , CH-1015 Lausanne , Switzerland
| | - Iman Ahmadabadi
- Soft Condensed Matter (SCM) , Sharif University of Technology , Tehran , Iran
| | | | - M Ibrahim Dar
- Laboratory of Photonics and Interfaces (LPI) , École Polytechnique Fédérale de Lausanne (EPFL) , CH-1015 Lausanne , Switzerland
| | - Michael Grätzel
- Laboratory of Photonics and Interfaces (LPI) , École Polytechnique Fédérale de Lausanne (EPFL) , CH-1015 Lausanne , Switzerland
| | - Ursula Rothlisberger
- Laboratory of Computational Chemistry and Biochemistry (LCBC) , École Polytechnique Fédérale de Lausanne (EPFL) , CH-1015 Lausanne , Switzerland
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24
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Mohammad-Beigi H, Hosseini A, Adeli M, Ejtehadi MR, Christiansen G, Sahin C, Tu Z, Tavakol M, Dilmaghani-Marand A, Nabipour I, Farzadfar F, Otzen DE, Mahmoudi M, Hajipour MJ. Mechanistic Understanding of the Interactions between Nano-Objects with Different Surface Properties and α-Synuclein. ACS Nano 2019; 13:3243-3256. [PMID: 30810027 DOI: 10.1021/acsnano.8b08983] [Citation(s) in RCA: 28] [Impact Index Per Article: 5.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/24/2023]
Abstract
Aggregation of the natively unfolded protein α-synuclein (α-syn) is key to the development of Parkinson's disease (PD). Some nanoparticles (NPs) can inhibit this process and in turn be used for treatment of PD. Using simulation strategies, we show here that α-syn self-assembly is electrostatically driven. Dimerization by head-to-head monomer contact is triggered by dipole-dipole interactions and subsequently stabilized by van der Waals interactions and hydrogen bonds. Therefore, we hypothesized that charged nano-objects could interfere with this process and thus prevent α-syn fibrillation. In our simulations, positively and negatively charged graphene sheets or superparamagnetic iron oxide NPs first interacted with α-syn's N/C terminally charged residues and then with hydrophobic residues in the non-amyloid-β component (61-95) region. In the experimental setup, we demonstrated that the charged nano-objects have the capacity not only to strongly inhibit α-syn fibrillation (both nucleation and elongation) but also to disaggregate the mature fibrils. Through the α-syn fibrillation process, the charged nano-objects induced the formation of off-pathway oligomers.
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Affiliation(s)
- Hossein Mohammad-Beigi
- Interdisciplinary Nanoscience Centre (iNANO) , Aarhus University , Gustav Wieds Vej 14 , DK-8000 Aarhus C , Denmark
| | - Atiyeh Hosseini
- Institute for Nanoscience and Nanotechnology (INST) , Sharif University of Technology , Tehran 1458889694 , Iran
- Center of Excellence in Complex Systems and Condensed Matter (CSCM) , Sharif University of Technology , Tehran 1458889694 , Iran
| | - Mohsen Adeli
- Faculty of Science , Lorestan University , Khorramabad , Iran
- Department of Biology, Chemistry, Pharmacy, Institute of Chemistry and Biochemistry , Freie University Berlin , 14195 Berlin , Germany
| | - Mohammad Reza Ejtehadi
- School of Nano Science , Institute for Research in Fundamental Sciences (IPM) , P.O. Box 19395-5531, Tehran , Iran
- Department of Physics , Sharif University of Technology , P.O. Box 11155-9161, Tehran 1245 , Iran
| | - Gunna Christiansen
- Department of Biomedicine-Medical Microbiology and Immunology , Aarhus University , 8000 Aarhus C , Denmark
| | - Cagla Sahin
- Interdisciplinary Nanoscience Centre (iNANO) , Aarhus University , Gustav Wieds Vej 14 , DK-8000 Aarhus C , Denmark
- Science for Life Laboratory, Department of Microbiology, Tumor and Cell Biology , Karolinska Institutet , Solnavägen 9 , 171 65 Stockholm , Sweden
| | - Zhaoxu Tu
- Department of Biology, Chemistry, Pharmacy, Institute of Chemistry and Biochemistry , Freie University Berlin , 14195 Berlin , Germany
| | - Mahdi Tavakol
- Department of Mechanical Engineering , Sharif University of Technology , Tehran 1245 , Iran
| | - Arezou Dilmaghani-Marand
- Non-Communicable Diseases Research Center, Endocrinology and Metabolism Population Sciences Institute , Tehran University of Medical Sciences , Tehran 1411713137 , Iran
| | - Iraj Nabipour
- Persian Gulf Marine Biotechnology Research Center, The Persian Gulf Biomedical Sciences Research Institute , Bushehr University of Medical Sciences , Bushehr 75147 , Iran
| | - Farshad Farzadfar
- Non-Communicable Diseases Research Center, Endocrinology and Metabolism Population Sciences Institute , Tehran University of Medical Sciences , Tehran 1411713137 , Iran
| | - Daniel Erik Otzen
- Interdisciplinary Nanoscience Centre (iNANO) , Aarhus University , Gustav Wieds Vej 14 , DK-8000 Aarhus C , Denmark
- Department of Molecular Biology and Genetics , Aarhus University , Gustav Wieds Vej 14 , DK-8000 Aarhus C , Denmark
| | - Morteza Mahmoudi
- Department of Anesthesiology, Brigham and Women's Hospital , Harvard Medical School , Boston , Massachusetts 02115 , United States
| | - Mohammad Javad Hajipour
- Non-Communicable Diseases Research Center, Endocrinology and Metabolism Population Sciences Institute , Tehran University of Medical Sciences , Tehran 1411713137 , Iran
- Persian Gulf Marine Biotechnology Research Center, The Persian Gulf Biomedical Sciences Research Institute , Bushehr University of Medical Sciences , Bushehr 75147 , Iran
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25
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Derakhshankhah H, Hosseini A, Taghavi F, Jafari S, Lotfabadi A, Ejtehadi MR, Shahbazi S, Fattahi A, Ghasemi A, Barzegari E, Evini M, Saboury AA, Shahri SMK, Ghaemi B, Ng EP, Awala H, Omrani F, Nabipour I, Raoufi M, Dinarvand R, Shahpasand K, Mintova S, Hajipour MJ, Mahmoudi M. Molecular interaction of fibrinogen with zeolite nanoparticles. Sci Rep 2019; 9:1558. [PMID: 30733474 PMCID: PMC6367512 DOI: 10.1038/s41598-018-37621-4] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2018] [Accepted: 12/10/2018] [Indexed: 01/16/2023] Open
Abstract
Fibrinogen is one of the key proteins that participate in the protein corona composition of many types of nanoparticles (NPs), and its conformational changes are crucial for activation of immune systems. Recently, we demonstrated that the fibrinogen highly contributed in the protein corona composition at the surface of zeolite nanoparticles. Therefore, understanding the interaction of fibrinogen with zeolite nanoparticles in more details could shed light of their safe applications in medicine. Thus, we probed the molecular interactions between fibrinogen and zeolite nanoparticles using both experimental and simulation approaches. The results indicated that fibrinogen has a strong and thermodynamically favorable interaction with zeolite nanoparticles in a non-cooperative manner. Additionally, fibrinogen experienced a substantial conformational change in the presence of zeolite nanoparticles through a concentration-dependent manner. Simulation results showed that both E- and D-domain of fibrinogen are bound to the EMT zeolite NPs via strong electrostatic interactions, and undergo structural changes leading to exposing normally buried sequences. D-domain has more contribution in this interaction and the C-terminus of γ chain (γ377-394), located in D-domain, showed the highest level of exposure compared to other sequences/residues.
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Affiliation(s)
- Hossein Derakhshankhah
- Nano Drug Delivery Research Center, Kermanshah University of Medical Sciences, Kermanshah, Iran
- Pharmacutical Sciences Research Center, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Atiyeh Hosseini
- Institute for Nanoscience and Nanotechnology and Center of Excellence in Complex Systems and Condensed Matter (CSCM), Sharif University of Technology, Tehran, 1458889694, Iran
| | - Fereshteh Taghavi
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Samira Jafari
- Pharmacutical Sciences Research Center, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Alireza Lotfabadi
- Nano Drug Delivery Research Center, Kermanshah University of Medical Sciences, Kermanshah, Iran
- Pharmacutical Sciences Research Center, Kermanshah University of Medical Sciences, Kermanshah, Iran
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Mohammad Reza Ejtehadi
- Department of Physics, Sharif University of Technology, P. O. Box 11155-9161, Tehran, Iran
- Center of Excellence in Complex Systems and Condensed Matter (CSCM), Sharif University of Technology, Tehran, 1458889694, Iran
| | - Sahba Shahbazi
- School of Biology College of Science, University of Tehran, Tehran, Iran
| | - Ali Fattahi
- Pharmacutical Sciences Research Center, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Atiyeh Ghasemi
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Ebrahim Barzegari
- Pharmacutical Sciences Research Center, Kermanshah University of Medical Sciences, Kermanshah, Iran
| | - Mina Evini
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Ali Akbar Saboury
- Institute of Biochemistry and Biophysics, University of Tehran, Tehran, Iran
| | - Seyed Mehdi Kamali Shahri
- Department of Chemical Engineering, Pennsylvania State University, University Park, PA, 16802, United States
| | - Behnaz Ghaemi
- Department of Medical Nanotechnology, School of Advanced Technologies in Medicine (SATiM), Tehran University of Medical Sciences, Tehran, 1417755469, Iran
| | - Eng-Poh Ng
- School of Chemical Sciences, Universiti Sains Malaysia, Gelugor, 11800 USM, Malaysia
| | - Hussein Awala
- Laboratory of Catalysis and Spectroscopy, ENSICAEN, University of Caen, CNRS, 6 Boulevard du Marechal Juin, 14050, Caen, France
| | - Fatemeh Omrani
- Persian Gulf Marine Biotechnology Research Center, the Persian Gulf Biomedical Sciences Research Institute, Bushehr University of Medical Sciences, Bushehr, 75147, Iran
| | - Iraj Nabipour
- Persian Gulf Marine Biotechnology Research Center, the Persian Gulf Biomedical Sciences Research Institute, Bushehr University of Medical Sciences, Bushehr, 75147, Iran
| | - Mohammad Raoufi
- Nanotechnology Research Center, Faculty of Pharmacy, Department of Pharmaceutical Nanotechnology, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, 13169-43551, Iran
| | - Rassoul Dinarvand
- Nanotechnology Research Center, Faculty of Pharmacy, Department of Pharmaceutical Nanotechnology, Faculty of Pharmacy, Tehran University of Medical Sciences, Tehran, 13169-43551, Iran
| | - Koorosh Shahpasand
- Department of Brain and Cognitive Sciences, Cell Science Research Center, Royan Institute for Stem Cell Biology and Technology, ACECR, Tehran, Iran
| | - Svetlana Mintova
- Laboratory of Catalysis and Spectroscopy, ENSICAEN, University of Caen, CNRS, 6 Boulevard du Marechal Juin, 14050, Caen, France.
| | - Mohammad Javad Hajipour
- Persian Gulf Marine Biotechnology Research Center, the Persian Gulf Biomedical Sciences Research Institute, Bushehr University of Medical Sciences, Bushehr, 75147, Iran.
- Non-Communicable Diseases Research Center, Endocrinology and Metabolism Population Sciences Institute, Tehran University of Medical Sciences, Tehran, 13169-43551, Iran.
| | - Morteza Mahmoudi
- Department of Anesthesiology, Brigham and Women's Hospital, Harvard Medical School, Boston, Massachusetts, 02115, United States.
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26
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Alavizargar A, Berti C, Ejtehadi MR, Furini S. Molecular Dynamics Simulations of Orai Reveal How the Third Transmembrane Segment Contributes to Hydration and Ca 2+ Selectivity in Calcium Release-Activated Calcium Channels. J Phys Chem B 2018; 122:4407-4417. [PMID: 29600712 DOI: 10.1021/acs.jpcb.7b12453] [Citation(s) in RCA: 13] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022]
Abstract
Calcium release-activated calcium (CRAC) channels open upon depletion of Ca2+ from the endoplasmic reticulum, and when open, they are permeable to a selective flux of calcium ions. The atomic structure of Orai, the pore domain of CRAC channels, from Drosophila melanogaster has revealed many details about conduction and selectivity in this family of ion channels. However, it is still unclear how residues on the third transmembrane helix can affect the conduction properties of the channel. Here, molecular dynamics and Brownian dynamics simulations were employed to analyze how a conserved glutamate residue on the third transmembrane helix (E262) contributes to selectivity. The comparison between the wild-type and mutated channels revealed a severe impact of the mutation on the hydration pattern of the pore domain and on the dynamics of residues K270, and Brownian dynamics simulations proved that the altered configuration of residues K270 in the mutated channel impairs selectivity to Ca2+ over Na+. The crevices of water molecules, revealed by molecular dynamics simulations, are perfectly located to contribute to the dynamics of the hydrophobic gate and the basic gate, suggesting a possible role in channel opening and in selectivity function.
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Affiliation(s)
- Azadeh Alavizargar
- School of Nano Science , Institute for Research in Fundamental Sciences (IPM) , Tehran 1958914875 , Iran.,Department of Medical Biotechnologies , University of Siena , Siena 53100 , Italy
| | - Claudio Berti
- Department of Molecular Biophysics and Physiology , Rush University Medical Center , Chicago , Illinois 60612 , United States
| | - Mohammad Reza Ejtehadi
- School of Nano Science , Institute for Research in Fundamental Sciences (IPM) , Tehran 1958914875 , Iran.,Department of Physics , Sharif University of Technology , Tehran 11155-8639 , Iran
| | - Simone Furini
- Department of Medical Biotechnologies , University of Siena , Siena 53100 , Italy
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27
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Heydari T, Heidari M, Mashinchian O, Wojcik M, Xu K, Dalby MJ, Mahmoudi M, Ejtehadi MR. Development of a Virtual Cell Model to Predict Cell Response to Substrate Topography. ACS Nano 2017; 11:9084-9092. [PMID: 28742318 DOI: 10.1021/acsnano.7b03732] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Cells can sense and respond to changes in the topographical, chemical, and mechanical information in their environment. Engineered substrates are increasingly being developed that exploit these physical attributes to direct cell responses (most notably mesenchymal stem cells) and therefore control cell behavior toward desired applications. However, there are very few methods available for robust and accurate modeling that can predict cell behavior prior to experimental evaluations, and this typically means that many cell test iterations are needed to identify best material features. Here, we developed a unifying computational framework to create a multicomponent cell model, called the "virtual cell model" that has the capability to predict changes in whole cell and cell nucleus characteristics (in terms of shape, direction, and even chromatin conformation) on a range of cell substrates. Modeling data were correlated with cell culture experimental outcomes in order to confirm the applicability of the virtual cell model and demonstrating the ability to reflect the qualitative behavior of mesenchymal stem cells. This may provide a reliable, efficient, and fast high-throughput approach for the development of optimized substrates for a broad range of cellular applications including stem cell differentiation.
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Affiliation(s)
- Tiam Heydari
- Department of Physics, Sharif University of Technology , Tehran, 11155-9161, Iran
| | - Maziar Heidari
- Max Planck Institute for Polymer Research , Ackermannweg 10, 55128 Mainz, Germany
| | - Omid Mashinchian
- Nestlé Institute of Health Sciences (NIHS), EPFL , Innovation Park, 1015 Lausanne, Switzerland
- Doctoral Program in Biotechnology and Bioengineering, Institute of Bioengineering, École Polytechnique Fédérale de Lausanne (EPFL) , 1015 Lausanne, Switzerland
| | - Michal Wojcik
- Department of Chemistry, University of California , Berkeley, California 94720, United States
| | - Ke Xu
- Department of Chemistry, University of California , Berkeley, California 94720, United States
- Division of Molecular Biophysics and Integrated Bioimaging, Lawrence Berkeley National Laboratory , Berkeley, California 94720, United States
| | - Matthew John Dalby
- Centre for Cell Engineering, Institute of Molecular, Cell and Systems Biology, College of Medical Veterinary and Life Sciences, University of Glasgow , Joseph Black Building, Glasgow, G12 8QQ, U.K
| | - Morteza Mahmoudi
- Nanotechnology Research Center and Department of Nanotechnology, Faculty of Pharmacy, Tehran University of Medical Sciences , Tehran, 14155-6451, Iran
- Department of Anesthesiology, Brigham and Women's Hospital, Harvard Medical School , Boston, Massachusetts 02115, United States
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28
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Satarifard V, Heidari M, Mashaghi S, Tans SJ, Ejtehadi MR, Mashaghi A. Topology of polymer chains under nanoscale confinement. Nanoscale 2017; 9:12170-12177. [PMID: 28805849 DOI: 10.1039/c7nr04220e] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/07/2023]
Abstract
Spatial confinement limits the conformational space accessible to biomolecules but the implications for bimolecular topology are not yet known. Folded linear biopolymers can be seen as molecular circuits formed by intramolecular contacts. The pairwise arrangement of intra-chain contacts can be categorized as parallel, series or cross, and has been identified as a topological property. Using molecular dynamics simulations, we determine the contact order distributions and topological circuits of short semi-flexible linear and ring polymer chains with a persistence length of lp under a spherical confinement of radius Rc. At low values of lp/Rc, the entropy of the linear chain leads to the formation of independent contacts along the chain and accordingly, increases the fraction of series topology with respect to other topologies. However, at high lp/Rc, the fraction of cross and parallel topologies are enhanced in the chain topological circuits with cross becoming predominant. At an intermediate confining regime, we identify a critical value of lp/Rc, at which all topological states have equal probability. Confinement thus equalizes the probability of more complex cross and parallel topologies to the level of the more simple, non-cooperative series topology. Moreover, our topology analysis reveals distinct behaviours for ring- and linear polymers under weak confinement; however, we find no difference between ring- and linear polymers under strong confinement. Under weak confinement, ring polymers adopt parallel and series topologies with equal likelihood, while linear polymers show a higher tendency for series arrangement. The radial distribution analysis of the topology reveals a non-uniform effect of confinement on the topology of polymer chains, thereby imposing more pronounced effects on the core region than on the confinement surface. Additionally, our results reveal that over a wide range of confining radii, loops arranged in parallel and cross topologies have nearly the same contact orders. Such degeneracy implies that the kinetics and transition rates between the topological states cannot be solely explained by contact order. We expect these findings to be of general importance in understanding chaperone assisted protein folding, chromosome architecture, and the evolution of molecular folds.
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Affiliation(s)
- Vahid Satarifard
- Leiden Academic Centre for Drug Research, Faculty of Mathematics and Natural Sciences, Leiden University, Leiden, The Netherlands.
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29
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Abstract
Obtaining a reduced description with particle and momentum flux densities outgoing from the microscopic equations of motion of the particles requires approximations. The usual method, we refer to as truncation method, is to zero Fourier modes of the orientation distribution starting from a given number. Here we propose another method to derive continuum equations for interacting self-propelled particles. The derivation is based on a Gaussian approximation (GA) of the distribution of the direction of particles. First, by means of simulation of the microscopic model, we justify that the distribution of individual directions fits well to a wrapped Gaussian distribution. Second, we numerically integrate the continuum equations derived in the GA in order to compare with results of simulations. We obtain that the global polarization in the GA exhibits a hysteresis in dependence on the noise intensity. It shows qualitatively the same behavior as we find in particles simulations. Moreover, both global polarizations agree perfectly for low noise intensities. The spatiotemporal structures of the GA are also in agreement with simulations. We conclude that the GA shows qualitative agreement for a wide range of noise intensities. In particular, for low noise intensities the agreement with simulations is better as other approximations, making the GA to an acceptable candidates of describing spatially distributed self-propelled particles.
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Affiliation(s)
- Hamid Seyed-Allaei
- Department of Physics, Sharif University of Technology, P. O. Box 11155-9161, Tehran, Iran
| | - Lutz Schimansky-Geier
- Department of Physics, Humboldt-Universität zu Berlin, Newtonstrasse 15, 12489 Berlin, Germany
| | - Mohammad Reza Ejtehadi
- Department of Physics, Sharif University of Technology, P. O. Box 11155-9161, Tehran, Iran.,School of Nano Science, Institute for Research in Fundamental Sciences (IPM), P. O. Box 19395-5531, Tehran, Iran
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30
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Salari H, Eslami-Mossallam B, Ranjbar HF, Ejtehadi MR. Stiffer double-stranded DNA in two-dimensional confinement due to bending anisotropy. Phys Rev E 2017; 94:062407. [PMID: 28085439 DOI: 10.1103/physreve.94.062407] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2016] [Indexed: 11/07/2022]
Abstract
Using analytical approach and Monte Carlo (MC) simulations, we study the elastic behavior of the intrinsically twisted elastic ribbons with bending anisotropy, such as double-stranded DNA (dsDNA), in two-dimensional (2D) confinement. We show that, due to the bending anisotropy, the persistence length of dsDNA in 2D conformations is always greater than three-dimensional (3D) conformations. This result is in consistence with the measured values for DNA persistence length in 2D and 3D in equal biological conditions. We also show that in two dimensions, an anisotropic, intrinsically twisted polymer exhibits an implicit twist-bend coupling, which leads to the transient curvature increasing with a half helical turn periodicity along the bent polymer.
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Affiliation(s)
- H Salari
- Department of Physics, Sharif University of Technology, P.O. Box 11155-9161, Tehran, Iran
| | - B Eslami-Mossallam
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Lorentzweg 1, 2628 CJ Delft, the Netherlands
| | - H F Ranjbar
- Institute of Complex Systems (ICS-2), Forschungszentrum Jülich, Wilhelm-Johnen-Straße, 52425 Jülich, Germany
| | - M R Ejtehadi
- Department of Physics, Sharif University of Technology, P.O. Box 11155-9161, Tehran, Iran and School of Nano Science, Institute for Research in Fundamental Sciences (IPM), Tehran 19395-5531, Iran
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31
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Heidari M, Satarifard V, Tans SJ, Ejtehadi MR, Mashaghi S, Mashaghi A. Topology of internally constrained polymer chains. Phys Chem Chem Phys 2017; 19:18389-18393. [DOI: 10.1039/c7cp02145c] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
Abstract
An interacting partner can provide external control over folding rates and realized topologies.
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Affiliation(s)
- Maziar Heidari
- Leiden Academic Centre for Drug Research
- Faculty of Mathematics and Natural Sciences
- Leiden University
- Leiden
- The Netherlands
| | - Vahid Satarifard
- Leiden Academic Centre for Drug Research
- Faculty of Mathematics and Natural Sciences
- Leiden University
- Leiden
- The Netherlands
| | | | | | - Samaneh Mashaghi
- School of Engineering and Applied Sciences and Department of Physics
- Harvard University
- Cambridge
- USA
| | - Alireza Mashaghi
- Leiden Academic Centre for Drug Research
- Faculty of Mathematics and Natural Sciences
- Leiden University
- Leiden
- The Netherlands
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32
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Khatami M, Wolff K, Pohl O, Ejtehadi MR, Stark H. Active Brownian particles and run-and-tumble particles separate inside a maze. Sci Rep 2016; 6:37670. [PMID: 27876867 PMCID: PMC5120314 DOI: 10.1038/srep37670] [Citation(s) in RCA: 22] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2016] [Accepted: 11/01/2016] [Indexed: 11/09/2022] Open
Abstract
A diverse range of natural and artificial self-propelled particles are known and are used nowadays. Among them, active Brownian particles (ABPs) and run-and-tumble particles (RTPs) are two important classes. We numerically study non-interacting ABPs and RTPs strongly confined to different maze geometries in two dimensions. We demonstrate that by means of geometrical confinement alone, ABPs are separable from RTPs. By investigating Matryoshka-like mazes with nested shells, we show that a circular maze has the best filtration efficiency. Results on the mean first-passage time reveal that ABPs escape faster from the center of the maze, while RTPs reach the center from the rim more easily. According to our simulations and a rate theory, which we developed, ABPs in steady state accumulate in the outermost region of the Matryoshka-like mazes, while RTPs occupy all locations within the maze with nearly equal probability. These results suggest a novel technique for separating different types of self-propelled particles by designing appropriate confining geometries without using chemical or biological agents.
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Affiliation(s)
- Maryam Khatami
- Department of Physics, Sharif University of Technology, P.O. Box 11155-9161, Tehran, Iran
- Institut für Theoretische Physik, Technische Universität Berlin, Hardenbergstrasse 36, 10623 Berlin, Germany
| | - Katrin Wolff
- Institut für Theoretische Physik, Technische Universität Berlin, Hardenbergstrasse 36, 10623 Berlin, Germany
| | - Oliver Pohl
- Institut für Theoretische Physik, Technische Universität Berlin, Hardenbergstrasse 36, 10623 Berlin, Germany
| | - Mohammad Reza Ejtehadi
- Department of Physics, Sharif University of Technology, P.O. Box 11155-9161, Tehran, Iran
- School of Nano-Science, Institute for Research in Fundamental Sciences (IPM), P.O. Box 19395-5531, Tehran, Iran
| | - Holger Stark
- Institut für Theoretische Physik, Technische Universität Berlin, Hardenbergstrasse 36, 10623 Berlin, Germany
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33
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Abstract
Experimental data of the DNA cyclization (J-factor) at short length scales exceed the theoretical expectation based on the wormlike chain (WLC) model by several orders of magnitude. Here, we propose that asymmetric bending rigidity of the double helix in the groove direction can be responsible for extreme bendability of DNA at short length scales and it also facilitates DNA loop formation at these lengths. To account for the bending asymmetry, we consider the asymmetric elastic rod (AER) model which has been introduced and parametrized in an earlier study [B. Eslami-Mossallam and M. R. Ejtehadi, Phys. Rev. E 80, 011919 (2009)]. Exploiting a coarse grained representation of the DNA molecule at base pair (bp) level and using the Monte Carlo simulation method in combination with the umbrella sampling technique, we calculate the loop formation probability of DNA in the AER model. We show that the DNA molecule has a larger J-factor compared to the WLC model which is in excellent agreement with recent experimental data.
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Affiliation(s)
- H Salari
- Department of Physics, Sharif University of Technology, P.O. Box 11155-9161, Tehran, Iran
| | - B Eslami-Mossallam
- Department of Bionanoscience, Kavli Institute of Nanoscience, Delft University of Technology, Lorentzweg 1, 2628 CJ Delft, The Netherlands
| | - S Naderi
- Department of Physics, Sharif University of Technology, P.O. Box 11155-9161, Tehran, Iran
| | - M R Ejtehadi
- Department of Physics, Sharif University of Technology, P.O. Box 11155-9161, Tehran, Iran
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34
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Abstract
We study the formation of a vortex with fourfold symmetry in a minimal model of self-propelled particles, confined inside a squared box, using computer simulations and also theoretical analysis. In addition to the vortex pattern, we observe five other regimes in the system: a homogeneous gaseous phase, band structures, moving clumps, moving clusters, and vibrating rings. All six regimes emerge from controlling the strength of noise and from the contribution of repulsion and alignment interactions. We study the shape of the vortex and its symmetry in detail. The pattern shows exponential defect lines where incoming and outgoing flows of particles collide. We show that alignment and repulsion interactions between particles are necessary to form such patterns. We derive hydrodynamical equations with an introduction of the "small deviation" technique to describe the vortex phase. The method is applicable to other systems as well. Finally, we compare the theory with the results of both computer simulations and an experiment using Quincke rotors. A good agreement between the three is observed.
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Affiliation(s)
- Hamid Seyed-Allaei
- Department of Physics, Sharif University of Technology, P.O. Box 11155-9161, Tehran, Iran
| | - Mohammad Reza Ejtehadi
- Department of Physics, Sharif University of Technology, P.O. Box 11155-9161, Tehran, Iran
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35
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Abstract
von Willebrand factor (VWF) is a naturally collapsed protein that participates in primary haemostasis and coagulation events. The clotting process is triggered by the adsorption and conformational changes of the plasma VWFs localized to the collagen fibres found near the site of injury. We develop coarse-grained models to simulate the adsorption dynamics of VWF flowing near the adhesive collagen fibres at different shear rates and investigate the effect of factors such as interaction and cooperativity of VWFs on the success of adsorption events. The adsorption probability of a flowing VWF confined to the receptor field is enhanced when it encounters an adhered VWF in proximity to the collagen receptors. This enhancement is observed within a wide range of shear rates and is mostly controlled by the attractive van der Waals interactions rather than the hydrodynamic interactions among VWF monomers. The cooperativity between the VWFs acts as an effective mechanism for enhancing VWF adsorption to the collagen fibres. Additionally, this implies that the adsorption of such molecules is nonlinearly dependent on the density of flowing VWFs. These findings are important for studies of primary haemostasis as well as general adsorption dynamics processes in polymer physics.
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Affiliation(s)
- Maziar Heidari
- Molecular Cell Biomechanics Laboratory, Departments of Bioengineering and Mechanical Engineering, University of California, Berkeley, CA 94720, USA
| | - Mehrdad Mehrbod
- Molecular Cell Biomechanics Laboratory, Departments of Bioengineering and Mechanical Engineering, University of California, Berkeley, CA 94720, USA
| | - Mohammad Reza Ejtehadi
- Department of Physics and Center of Excellence in Complex Systems and Condensed Matter, Sharif University of Technology, Tehran, Iran
| | - Mohammad R K Mofrad
- Molecular Cell Biomechanics Laboratory, Departments of Bioengineering and Mechanical Engineering, University of California, Berkeley, CA 94720, USA
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36
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Ozmaian M, Fathizadeh A, Jalalvand M, Ejtehadi MR, Allaei SMV. Diffusion and self-assembly of C60 molecules on monolayer graphyne sheets. Sci Rep 2016; 6:21910. [PMID: 26912386 PMCID: PMC4766508 DOI: 10.1038/srep21910] [Citation(s) in RCA: 29] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/29/2015] [Accepted: 01/27/2016] [Indexed: 12/15/2022] Open
Abstract
The motion of a fullerene (C60) on 5 different types of graphyne is studied by all-atom molecular dynamics simulations and compared with former studies on the motion of C60 on graphene. The motion shows a diffusive behavior which consists of either a continuous motion or discrete movements between trapping sites depending on the type of the graphyne sheet. For graphyne-4 and graphyne-5, fullerenes could detach from the surface of the graphyne sheet at room temperature which was not reported for similar cases on graphene sheets. Collective motion of a group of fullerenes interacting with a graphyne studied and it is shown that fullerenes exhibit stable assemblies. Depending on the type of graphyne, these assemblies can have either single or double layers. The mobility of the assembled structures is also dependent on the type of the graphyne sheet. The observed properties of the motion suggests novel applications for the complexes of fullerene and monolayer graphynes.
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Affiliation(s)
- Masoumeh Ozmaian
- Institute for Nanoscience and Nanotechnology, Sharif University of Technology, Tehran, Iran
| | - Arman Fathizadeh
- School of physics, Institute for research in fundamental sciences (IPM), Tehran, Iran
| | | | - Mohammad Reza Ejtehadi
- Department of Physics, Sharif University of Technology, P.O. Box 11155-9161, Tehran, Iran.,Center of Excellence in Complex Systems and Condensed Matter (CSCM), Sharif University of Technology, Tehran 1458889694, Iran
| | - S Mehdi Vaez Allaei
- Department of physics, University of Tehran, Tehran 14395-547, Iran.,School of physics, Institute for research in fundamental sciences (IPM), Tehran, Iran
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37
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Kharazian B, Hadipour NL, Ejtehadi MR. Understanding the nanoparticle-protein corona complexes using computational and experimental methods. Int J Biochem Cell Biol 2016; 75:162-74. [PMID: 26873405 DOI: 10.1016/j.biocel.2016.02.008] [Citation(s) in RCA: 69] [Impact Index Per Article: 8.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2015] [Revised: 02/06/2016] [Accepted: 02/08/2016] [Indexed: 10/22/2022]
Abstract
Nanoparticles (NP) have capability to adsorb proteins from biological fluids and form protein layer, which is called protein corona. As the cell sees corona coated NPs, the protein corona can dictate biological response to NPs. The composition of protein corona is varied by physicochemical properties of NPs including size, shape, surface chemistry. Processing of protein adsorption is dynamic phenomena; to that end, a protein may desorb or leave a surface vacancy that is rapidly filled by another protein and cause changes in the corona composition mainly by the Vroman effect. In this review, we discuss the interaction between NP and proteins and the available techniques for identification of NP-bound proteins. Also we review current developed computational methods for understanding the NP-protein complex interactions.
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Affiliation(s)
- B Kharazian
- Department of Chemistry, Tarbiat Modares University, Tehran, Iran
| | - N L Hadipour
- Department of Chemistry, Tarbiat Modares University, P.O. Box 14115-175, Tehran, Iran.
| | - M R Ejtehadi
- Department of Physics, Sharif University of Technology, P.O. Box 11155-9161, Tehran, Iran; Center of Excellence in Complex Systems and Condensed Matter (CSCM), Sharif University of Technology, Tehran 1458889694, Iran
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38
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Abstract
To generalize simple bead-linker model of swimmers to higher dimensions and to demonstrate the chemotaxis ability of such swimmers, here we introduce a low-Reynolds predator, using a two-dimensional triangular bead-spring model. Two-state linkers as mechanochemical enzymes expand as a result of interaction with particular activator substances in the environment, causing the whole body to translate and rotate. The concentration of the chemical stimulator controls expansion versus the contraction rate of each arm and so affects the ability of the body for diffusive movements; also the variation of activator substance's concentration in the environment breaks the symmetry of linkers' preferred state, resulting in the drift of the random walker along the gradient of the density of activators. External food or danger sources may attract or repel the body by producing or consuming the chemical activators of the organism's enzymes, inducing chemotaxis behavior. Generalization of the model to three dimensions is straightforward.
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Affiliation(s)
- Mehran Ebrahimian
- Department of Management and Economics, Sharif University of Technology
| | | | - Mohammad Reza Ejtehadi
- Department of Physics and Center of Excellence in Complex systems and Condensed Matter, Sharif University of Technology, Tehran, 1458889694, Iran
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39
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Hashemi SM, Ejtehadi MR. Equilibrium state of a cylindrical particle with flat ends in nematic liquid crystals. Phys Rev E Stat Nonlin Soft Matter Phys 2015; 91:012503. [PMID: 25679634 DOI: 10.1103/physreve.91.012503] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/25/2014] [Indexed: 06/04/2023]
Abstract
A continuum theory is employed to numerically study the equilibrium orientation and defect structures of a circular cylindrical particle with flat ends under a homeotropic anchoring condition in a uniform nematic medium. Different aspect ratios of this colloidal geometry from thin discotic to long rodlike shapes and several colloidal length scales ranging from mesoscale to nanoscale are investigated. We show that the equilibrium state of this colloidal geometry is sensitive to the two geometrical parameters: aspect ratio and length scale of the particle. For a large enough mesoscopic particle, there is a specific asymptotic equilibrium angle associated to each aspect ratio. Upon reducing the particle size to nanoscale, the equilibrium angle follows a descending or ascending trend in such a way that the equilibrium angle of a particle with the aspect ratio bigger than 1:1 (a discotic particle) goes to a parallel alignment with respect to the far-field nematic, whereas the equilibrium angle for a particle with the aspect ratio 1:1 and smaller (a rodlike particle) tends toward a perpendicular alignment to the uniform nematic direction. The discrepancy between the equilibrium angles of the mesoscopic and nanoscopic particles originates from the significant differences between their defect structures. The possible defect structures related to mesoscopic and nanoscopic colloidal particles of this geometry are also introduced.
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Affiliation(s)
- S Masoomeh Hashemi
- Department of Physics, Sharif University of Technology, P. O. Box 11155-9161, Tehran, Iran
| | - Mohammad Reza Ejtehadi
- Department of Physics, Sharif University of Technology, P. O. Box 11155-9161, Tehran, Iran
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40
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Eskandari Z, Silvestre NM, Telo da Gama MM, Ejtehadi MR. Particle selection through topographic templates in nematic colloids. Soft Matter 2014; 10:9681-9687. [PMID: 25365252 DOI: 10.1039/c4sm02231a] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/04/2023]
Abstract
Liquid crystal colloids have been proposed as suitable candidates for responsive photonic crystals. Large scale growth of such colloidal systems is, however, a challenge and recently template-assisted assembly has been proposed to guide the growth of colloidal crystals, with controlled symmetries, in nematic liquid crystals. Known for their long-range anisotropic interactions, these colloidal systems are stabilized typically at the center of the cells due to strong particle-wall repulsion from the confining substrates. This behaviour is dramatically changed in the presence of topographic patterning. Here we propose the use of topographic modulation of surfaces to select and localize particles in nematic colloids. By considering convex and concave deformations of one of the confining surfaces we show that the colloid-flat surface repulsion may be enhanced or switched into an attraction. In particular, we find that when the colloidal particles have the same anchoring conditions as the patterned surfaces, they are strongly attracted to concave dimples, while if they exhibit different anchoring conditions they are pinned at the top of convex protrusions. Although dominated by elastic interactions the first mechanism is reminiscent of the depletion induced attraction or of the key-lock mechanism, while the second is specific to liquid crystal colloids. These long-ranged, highly tunable, surface-colloid interactions contribute to the development of template-assisted assembly of large colloidal crystals, with well defined symmetries, as required for applications.
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Affiliation(s)
- Z Eskandari
- Centro de Física Teórica e Computacional, Universidade de Lisboa, Avenida Professor Gama Pinto 2, PT-1649-003 Lisboa, Portugal.
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41
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Affiliation(s)
- Arman Fathizadeh
- School
of Physics, Institute for Research in Fundamental Sciences (IPM), Tehran, Iran
- Institute
for Nanoscience and Nanotechnology, Sharif University of Technology, Tehran, Iran
| | - Helmut Schiessel
- Instituut-Lorentz
for Theoretical Physics, P.O. Box 9506, 2300 RA Leiden, The Netherlands
| | - Mohammad Reza Ejtehadi
- Department
of Physics, Sharif University of Technology, P.O. Box 11155-8639, Tehran, Iran
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42
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Abstract
We study the conformations of a semiflexible chain, confined in nano-scaled spherical cavities, under two distinct processes of confinement. Radial contraction and packaging are employed as two confining procedures. The former method is performed by gradually decreasing the diameter of a spherical shell which envelopes a confined chain. The latter procedure is carried out by injecting the chain inside a spherical shell through a hole on the shell surface. The chain is modeled with a rigid body molecular dynamics simulation and its parameters are adjusted to DNA base-pair elasticity. Directional order parameter is employed to analyze and compare the confined chain and the conformations of the chain for two different sizes of the spheres are studied in both procedures. It is shown that for the confined chains in the sphere sizes of our study, they appear in spiral or tennis-ball structures, and the tennis-ball structure is more likely to be observed in more compact confinements. Our results also show that the dynamical procedure of confinement and the rate of the confinement are influential parameters of the structure of the chain inside spherical cavities.
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Affiliation(s)
- A Fathizadeh
- Sharif University of Technology, Institute for Nanoscience and Nanotechnology, P.O. Box 14588-89694, Tehran, Iran
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Seyednejad SR, Mozaffari MR, Ejtehadi MR. Confined nematic liquid crystal between two spherical boundaries with planar anchoring. Phys Rev E Stat Nonlin Soft Matter Phys 2013; 88:012508. [PMID: 23944475 DOI: 10.1103/physreve.88.012508] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/22/2013] [Indexed: 06/02/2023]
Abstract
Nematic shells of liquid crystals have been provided in microscales. Defect structures in the shells are very essential in the electro-optical applications of such colloidal objects. We have numerically minimized the free energy of symmetric and asymmetric spherical shells of the nematic liquid crystal. Considering degenerate planar anchoring on the surfaces and isotropic nematic elasticity, a variety of defect structures are observed by controlling or varying the thicknesses of the shell and its degree of asymmetry. In symmetric shells, our calculations show that boojums (bipolar) defects appear in thick shells and tetrahedral (baseball) defects in thin shells. In asymmetric shells, while we are in the bipolar regime, the boojums defects transform to trigonal configurations. Free energy landscape shows that in this regime the inner droplet is not stable in the center and it is trapped in an off-center minimum energy position. For the case of thin shells, there are two degenerate director textures with similar tetrahedral configuration of the disclination lines. The levels are split in asymmetric shells. The stability of the inner droplet in the center position depends on director texture. It is stable for one texture and unstable for the other one. For an unstable pattern there is no minimum energy position for the inner droplet and it moves until it touches the outer boundary.
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Affiliation(s)
- Seyed Reza Seyednejad
- Department of Physics, Sharif University of Technology, P.O. Box 11155-9161, Tehran, Iran
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Maftouni N, Amininasab M, Ejtehadi MR, Kowsari F, Dastvan R. Publisher's Note: “Nanomechanical properties of lipid bilayer: Asymmetric modulation of lateral pressure and surface tension due to protein insertion in one leaflet of a bilayer” [J. Chem. Phys. 138, 065101 (2013)]. J Chem Phys 2013. [DOI: 10.1063/1.4795259] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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Fathizadeh A, Berdy Besya A, Reza Ejtehadi M, Schiessel H. Rigid-body molecular dynamics of DNA inside a nucleosome. Eur Phys J E Soft Matter 2013; 36:21. [PMID: 23475204 DOI: 10.1140/epje/i2013-13021-4] [Citation(s) in RCA: 19] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/17/2012] [Revised: 02/13/2013] [Accepted: 02/15/2013] [Indexed: 06/01/2023]
Abstract
The majority of eukaryotic DNA, about three quarter, is wrapped around histone proteins forming so-called nucleosomes. To study nucleosomal DNA we introduce a coarse-grained molecular dynamics model based on sequence-dependent harmonic rigid base pair step parameters of DNA and nucleosomal binding sites. Mixed parametrization based on all-atom molecular dynamics and crystallographic data of protein-DNA structures is used for the base pair step parameters. The binding site parameters are adjusted by experimental B-factor values of the nucleosome crystal structure. The model is then used to determine the energy cost for placing a twist defect into the nucleosomal DNA which allows us to use Kramers theory to calculate nucleosome sliding caused by such defects. It is shown that the twist defect scenario together with the sequence-dependent elasticity of DNA can explain the slow time scales observed for nucleosome mobility along DNA. With this method we also show how the twist defect mechanism leads to a higher mobility of DNA in the presence of sin mutations near the dyad axis. Finally, by performing simulations on 5s rDNA, 601, and telomeric base pair sequences, it is demonstrated that the current model is a powerful tool to predict nucleosome positioning.
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Affiliation(s)
- Arman Fathizadeh
- Institute for Nanoscience and Nanotechnology, Sharif University of Technology, P.O. Box 14588-89694, Tehran, Iran
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Maftouni N, Amininasab M, Ejtehadi MR, Kowsari F, Dastvan R. Nanomechanical properties of lipid bilayer: Asymmetric modulation of lateral pressure and surface tension due to protein insertion in one leaflet of a bilayer. J Chem Phys 2013; 138:065101. [DOI: 10.1063/1.4776764] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
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47
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Fathizadeh A, Eslami-Mossallam B, Ejtehadi MR. Definition of the persistence length in the coarse-grained models of DNA elasticity. Phys Rev E Stat Nonlin Soft Matter Phys 2012; 86:051907. [PMID: 23214814 DOI: 10.1103/physreve.86.051907] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/23/2012] [Revised: 09/16/2012] [Indexed: 06/01/2023]
Abstract
By considering the detailed structure of DNA in the base pair level, two possible definitions of the persistence length are compared. One definition is related to the orientation of the terminal base pairs, and the other is based on the vectors which connect two adjacent base pairs at each end of the molecule. It is shown that although these definitions approach each other for long DNA molecules, they are dramatically different on short length scales. We show analytically that the difference mostly comes from the shear flexibility of the molecule and can be used to measure the shear modulus of DNA.
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Affiliation(s)
- A Fathizadeh
- Sharif University of Technology, Institue for Nanoscience and Nanotechnology, Post Office Box 14588-89694, Tehran, Iran
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Abstract
Monitoring conformational changes in ion channels is essential to understand their gating mechanism. Here, we explore the structural dynamics of four outer membrane proteins with different structures and functions in the slowest nonzero modes of vibration. Normal mode analysis was performed on the modified elastic network model of channel in the membrane. According to our results, when membrane proteins were analyzed in the dominant mode, the composed pores, TolC and α-hemolysin showed large motions at the intramembrane β-barrel region while, in other porins, OmpA and OmpF, largest motions observed in the region of external flexible loops. A criterion based on equipartition theorem was used to measure the possible amplitude of vibration in channel forming proteins. The current approach complements theoretical and experimental techniques including HOLE, Molecular Dynamics (MD), and voltage clamp used to address the channel's structure and dynamics and provides the means to conduct a theoretical simultaneous study of the structure and function of the channel. An animated interactive 3D complement (I3DC) is available in Proteopedia at http://proteopedia.org/w/Journal:JBSD:3.
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Affiliation(s)
- A B Besya
- Institute for Nano Science and Technology, Sharif University of Technology, P.O. Box 14588-89694, Tehran, Iran
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Laurent S, Ejtehadi MR, Rezaei M, Kehoe PG, Mahmoudi M. Interdisciplinary challenges and promising theranostic effects of nanoscience in Alzheimer's disease. RSC Adv 2012. [DOI: 10.1039/c2ra01374f] [Citation(s) in RCA: 44] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/29/2022] Open
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Abdolvahab RH, Metzler R, Ejtehadi MR. First passage time distribution of chaperone driven polymer translocation through a nanopore: Homopolymer and heteropolymer cases. J Chem Phys 2011; 135:245102. [DOI: 10.1063/1.3669427] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [What about the content of this article? (0)] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022] Open
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