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molecular-model
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Multiscale Modeling of Carbon Nano Structures Using Tersoff Potential Function
, M.Sc. Thesis Sharif University of Technology ; Khoei, Amir Reza (Supervisor)
Abstract
During the last decade, thanks to a combination of exploding computational power and improved physical insight into material behavior, continuum and atomistic simulations improved greatly. Both classes of methods are now used to solve problems, which are more complicated than ever with greater accuracy than ever before. Nevertheless, there still exist problems for which neither method alone is sufficient. In general, atomistic simulations cannot be used for such length scales due to the restrictions on the number of atoms that can be simulated, along with the time scales, which they can be simulated for. In contrast, continuum simulations tend to fail at the atomic scale, for example due to...
Water dispersed magnetic nanoparticles (H2O-DMNPs) of γ-Fe2O3 for multicomponent coupling reactions: A green, single-pot technique for the synthesis of tetrahydro-4H-chromenes and hexahydroquinoline carboxylates
, Article Tetrahedron Letters ; Volume 54, Issue 26 , 2013 , Pages 3344-3347 ; 00404039 (ISSN) ; Nuri, A ; Xin, H ; Pourjavadi, A ; Hosseini, S. H ; Sharif University of Technology
2013
Abstract
Water dispersed magnetic nanoparticles (DMNPs) of γ-Fe 2O3 represent a simple and green catalyst for the rapid three-component synthesis of tetrahydro-4H-chromene and hexahydroquinoline carboxylate skeletons via single-pot domino Knoevenagel-Michael-cyclization reactions
Vibrational analysis of single-layered graphene sheets
, Article Nanotechnology ; Volume 19, Issue 8 , 2008 ; 09574484 (ISSN) ; Ahmadian, M. T ; Naghdabadi, R ; Sharif University of Technology
2008
Abstract
A molecular structural mechanics method has been implemented to investigate the vibrational behavior of single-layered graphene sheets. By adopting this approach, mode shapes and natural frequencies are obtained. Vibrational analysis is performed with different chirality and boundary conditions. Numerical results from the atomistic modeling are employed to develop predictive equations via a statistical nonlinear regression model. With the proposed equations, fundamental frequencies of single-layered graphene sheets with considered boundary conditions can be predicted within 3% difference with respect to the atomistic simulation. © IOP Publishing Ltd
Three-body interactions improve the prediction of rate and mechanism in protein folding models
, Article Proceedings of the National Academy of Sciences of the United States of America ; Volume 101, Issue 42 , 2004 , Pages 15088-15093 ; 00278424 (ISSN) ; Avall, S. P ; Plotkin, S. S ; Sharif University of Technology
2004
Abstract
Here we study the effects of many-body interactions on rate and mechanism in protein folding by using the results of molecular dynamics simulations on numerous coarse-grained Cα-model single-domain proteins. After adding three-body interactions explicitly as a perturbation to a Gō-like Hamiltonian with native pairwise interactions only, we have found (i) a significantly increased correlation with experimental φ values and folding rates, (ii) a stronger correlation of folding rate with contact order, matching the experimental range in rates when the fraction of three-body energy in the native state is ≈20%, and (iii) a considerably larger amount of three-body energy present in chymotripsin...
Synthesis and characterization of 1-amidino-O-alkylureas metal complexes as α- glucosidase Inhibitors: Structure-activity relationship, molecular docking, and kinetic studies
, Article Journal of Molecular Structure ; Volume 1250 , 2022 ; 00222860 (ISSN) ; Daneshfar, M ; Daneshfar, Z ; Iraji, A ; Samandari Najafabad, A ; Faramarzi, M. A ; Mahdavi, M ; Sharif University of Technology
Elsevier B.V
2022
Abstract
In the present study, metal complexes of 1-amidino-O-alkylureas were designed, synthesized and characterized by elemental analyses, FT-IR spectra, XRD, Mass analyses and scanning electron microscopy (SEM). All synthesized complexes were screen as α-Glucosidase inhibitors. According to the in vitro results, the Cu (II) complexes showed superior potency compared to other tested metal complexes. Particularly, [Cu(L-Me)2](Cl)2 (1b) showed the strongest inhibition against α-Glucosidase with an IC50 value of 2.75 ± 0.3 µM which was comparable to that of acarbose (IC50 = 750 µM). These findings are supported by the ligands and enzyme interactions through molecular docking. © 2021 Elsevier B.V
Synthesis, crystal structure and DNA interaction of a new water-soluble derivative of pyrazino[2,3-f][1,10] phenanthroline; theoretical calculations, experimental and molecular docking studies
, Article Journal of Molecular Structure ; Volume 1165 , 2018 , Pages 267-275 ; 00222860 (ISSN) ; Eslami, A ; Kia, R ; Aleeshah, R ; Sharif University of Technology
Elsevier B.V
2018
Abstract
The new water-soluble derivative of pyrazino[2,3-f][1,10] phenanthroline has been synthesized and characterized by conductivity measurement, elemental analysis, FT-IR, 1H NMR, 13C NMR spectroscopic studies, as well as single crystal x-ray crystallography. Theoretical calculations have been performed using the density functional theory (DFT) in order to confirm the structure and understand the electronic structure of the synthesized compound. The DNA binding properties of the compound were investigated by absorption spectroscopy, melting temperature and viscosity measurements. The intrinsic binding constant, Kb, was determined as 7.84 × 103 M−1 at 298 K. Thermodynamic parameters showed that...
Simulation of rarefied gas flows in MEMS/NEMS using a molecular method
, Article Proceedings of the ASME Fluids Engineering Division Summer Conference 2009, FEDSM2009, 2 August 2009 through 6 August 2009 ; Volume 1, Issue PART B , 2009 , Pages 1039-1044 ; 9780791843727 (ISBN) ; Ebrahimi, R ; Shams, A ; Sharif University of Technology
Abstract
In this work, the development of a two-dimensional Direct Simulation Monte Carlo (DSMC) Program for pressure boundaries using unstructured cells and its applications to typical micro-scale gas flows are described. For the molecular collision kinetics, variable hard sphere molecular model and no time counter collision sampling scheme have been used. Applications to micro-scale gas flows include micro-nozzel, nano channel and slider air bearing.The aim is to further test the treatment of pressure boundaries. For slider air bearing gas flows of the computer hard drive, the simulated gas pressures, at different rotating speeds, have a very good agreement with previous studies. The applicability...
Simulation of manual materials handling: Biomechanial assessment under different lifting conditions
, Article Technology and Health Care ; Volume 13, Issue 1 , 2005 , Pages 57-66 ; 09287329 (ISSN) ; Anderson, K. S ; Parnianpour, M ; Sharif University of Technology
IOS Press
2005
Abstract
Manual material handling (MMH) tasks were evaluated and compared under different lifting conditions. For the theoretical evaluations, a two-dimensional sagittally symmetric human-body model was established to compute the moment and joint load time histories for MMH tasks for a variety of different lift specifications and constraints such as lifting durations, loads, and modes. Nonlinear control techniques and genetic algorithms were utilized in the optimizations to explore optimal lifting patterns. Since the kinetic measures such as joint moments are vital metrics in the assessment of the likelihood of injury, the simulation results obtained may be compared using these metrics for each lift...
Ramsey interferometry with a two-level generalized Tonks-Girardeau gas
, Article Physical Review A - Atomic, Molecular, and Optical Physics ; Volume 76, Issue 3 , 2007 ; 10502947 (ISSN) ; Del Campo, A ; Lizuain, I ; Muga, J. G ; Sharif University of Technology
2007
Abstract
We propose a solvable generalization of the Tonks-Girardeau model that describes a coherent one-dimensional (1D) gas of cold two-level bosons which interact with two external fields in a Ramsey interferometer. They also interact among themselves by idealized, infinitely strong contact potentials, with interchange of momentum and internal state. We study the corresponding Ramsey fringes and the quantum projection noise which, essentially unaffected by the interactions, remains that for ideal bosons. The dual system of this gas, an ideal gas of two-level fermions coupled by the interaction with the separated fields, produces the same fringes and noise fluctuations. The cases of time-separated...
Predictive models for permeability and diffusivity of CH4 through imidazolium-based supported ionic liquid membranes
, Article Journal of Membrane Science ; Volume 371, Issue 1-2 , 2011 , Pages 127-133 ; 03767388 (ISSN) ; Barghi, S.H ; Rashtchian, D ; Sharif University of Technology
Abstract
Experimental permeability and diffusivity values for CO2 and CH4 through imidazolium-based ionic liquid 1-hexyl-3-methylimidazolium bis(trifluoromethanesulfonyl)imide ([hmim][Tf2N]) were determined in the temperature range of 300-320K using temperature correction factor defined in our previous study. According to literature, experimental values of permeability and diffusivity obtained in this study for CO2 in [hmim][Tf2N], showed good agreement with predictive models reported by other researchers. In addition, experimental values of permeability and diffusivity for CH4 in [hmim][Tf2N] as a function of pressure have been reported in this study. Considering the results of present study and...
Prediction of absolute entropy of ideal gas at 298 K of pure chemicals through GAMLR and FFNN
, Article Energy Conversion and Management ; Volume 52, Issue 1 , 2011 , Pages 630-634 ; 01968904 (ISSN) ; Bagheri, M ; Ghaniyari-Benis, S ; Aslebagh, R ; Kamaloo, E ; Sharif University of Technology
2011
Abstract
Thermodynamical optimization for energy conversion system can be performed by decreasing entropy generation. For calculation of entropy, we need to know entropy of ideal gases at 298 K as a reference point. Entropy is a thermodynamic quantity which is not easily measured and prediction of entropy by molecular structures for new designed molecules may be a challenge. An easy and accurate equation for prediction of absolute entropy of pure ideal gas at 298 K was introduced for the first time based on the quantitative structure property relationship (QSPR) approach. Thousand seven hundred pure chemical compounds and 3224 molecular descriptors were used for finding this easy equation by genetic...
New Karplus equations for 2JHH, 3JHH, 2JCH, 3JCH, 3JCOCH, 3JCSCH, and 3JCCCH in some aldohexopyranoside derivatives as determined using NMR spectroscopy and density functional theory calculations
, Article Carbohydrate Research ; 2007 , Pages 2086-2096 ; 00086215 (ISSN) ; Volume 342, Issue 14 ; Ghiasi, M ; Sharif University of Technology
2007
Abstract
The 1H-13C coupling constants of methyl α- and β-pyranosides of d-glucose and d-galactose have been measured by one-dimensional and two-dimensional 1H-13C heteronuclear zero and double quantum, phase sensitive J-HMBC spectra to determine a complete set of coupling constants (1JCH, 2JCH, 3JCH, 2JHH, and 3JHH) within the exocyclic hydroxymethyl group (CH2OH) for each compound. In parallel with these experimental studies, structure, energy, and potential energy surfaces of the hydroxymethyl group for these compounds were determined employing quantum mechanical calculations at the B3LYP level using the 6-311++G** basis set. Values of the vicinal coupling constants involving 1H and 13C in the...
Molecular dynamics study of 'success evaluation' for metallic nanoparticles manipulation on gold substrate
, Article Micro and Nano Letters ; Volume 5, Issue 5 , 2010 , Pages 286-290 ; 17500443 (ISSN) ; Meghdari, A ; Jalili, N ; Amiri, F ; Sharif University of Technology
2010
Abstract
One of the key factors in the assembly of nanoparticles and controlled construction of such systems is their positioning by a manipulation system. The response of clusters that are subjected to this process is of great importance. In this study, the behaviour of metallic nanoparticles during the manipulation process on an Au substrate is investigated using molecular dynamics. Two criteria are proposed for the evaluation of success in a pushing process regarding the intactness of a nanoparticle/substrate pair. The effects of cluster material, temperature and manipulation speed on the success of the process are investigated based on the simulation results
Modeling of retention behaviors of most frequent components of essential oils in polar and non-polar stationary phases
, Article Journal of Separation Science ; Volume 34, Issue 13 , 2011 , Pages 1538-1546 ; 16159306 (ISSN) ; Ebrahimi Najafabadi, H ; Sharif University of Technology
2011
Abstract
The gas chromatography retention indices of 100 different components of essential oils, on three columns with stationary phases of different polarities, were used to develop robust quantitative structure-retention relationship (QSRR) models. Two linear models with only one variable, i.e. solvation entropy, were developed, which explain 95 and 94% of variances of the test set for dimethyl silicone and dimethyl silicone with 5% phenyl group columns, respectively. These models are extremely simple and easy to interpret, but they show higher errors compared with more robust models such as partial least square (PLS) and ridge regressions. For the third column (polyethylene glycol (PEG)), 24...
Mechanical differences between ATP and ADP actin states: A molecular dynamics study
, Article Journal of Theoretical Biology ; Volume 448 , 2018 , Pages 94-103 ; 00225193 (ISSN) ; Shamloo, A ; Sharif University of Technology
Academic Press
2018
Abstract
This paper aims to give a comprehensive atomistic modeling of the nanomechanical behavior of actin monomer. Actin is a ubiquitous and essential component of cytoskeleton which forms many different cellular structures. Despite for several years great effort has been devoted to the investigation of mechanical properties of the actin filament, studies on the nanomechanical behavior of actin monomer are still lacking. These scales are, however, important for a complete understanding of the role of actin as an important component in the cytoskeleton structure. Based on the accuracy of atomistic modeling methods such as molecular dynamics simulations, steered molecular dynamics method is performed...
Gating and conduction of nano-channel forming proteins: A computational approach
, Article Journal of Biomolecular Structure and Dynamics ; Volume 31, Issue 8 , 2013 , Pages 818-828 ; 07391102 (ISSN) ; Mobasheri, H ; Ejtehadi, M. R ; Sharif University of Technology
2013
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...
Electrokinetic properties of asphaltene colloidal particles: determining the electric charge using micro electrophoresis technique
, Article Colloids and Surfaces A: Physicochemical and Engineering Aspects ; Volume 541 , 2018 , Pages 68-77 ; 09277757 (ISSN) ; Abolghasemi, E ; Hosseini, A ; Ayatollahi, S ; Dehghani, F ; Sharif University of Technology
Elsevier B.V
2018
Abstract
In this work, the electrokinetic properties of asphaltene particles have been investigated. Micro-electrophoresis method by applying DC electric field, was utilized to different mixtures containing asphaltene to determine its electric charge. It was observed that in the case of using n-heptane and its mixture with toluene (heptol), the asphaltene particles were showed to be positively charged however for toluene itself, they expressed no tendency toward the electrodes. While it is expected that larger asphaltene aggregates carry higher electric charge, the results contradictorily showed that they are mainly governed by gravity rather than electro-static force and that “aggregation” reduces...
Drug loading onto ion-exchange microspheres: Modeling study and experimental verification
, Article Biomaterials ; Volume 27, Issue 19 , 2006 , Pages 3652-3662 ; 01429612 (ISSN) ; Wu, X. Y ; Sharif University of Technology
2006
Abstract
A new mathematical model was developed and an exact analytical solution without approximations of previous work was derived for the description of the kinetics and equilibrium characteristics of drug loading from a finite external solution onto ion-exchange microspheres. The influence of important parameters pertinent to material properties and loading conditions on the kinetics, efficiency, and equilibrium of drug loading was analyzed using the developed model and equations. The numerical results showed that the rate of drug loading increased with increasing initial drug concentration in the solution or with the relative volume of the external solution and the microsphere. The maximum...
Discovering dominant pathways and signal-response relationships in signaling networks through nonparametric approaches
, Article Genomics ; Volume 102, Issue 4 , October , 2013 , Pages 195-201 ; 08887543 (ISSN) ; Masoudi Nejad, A ; Jalili, M ; Moeini, A ; Sharif University of Technology
2013
Abstract
A signaling pathway is a sequence of proteins and passenger molecules that transmits information from the cell surface to target molecules. Understanding signal transduction process requires detailed description of the involved pathways. Several methods and tools resolved this problem by incorporating genomic and proteomic data. However, the difficulty of obtaining prior knowledge of complex signaling networks limited the applicability of these tools. In this study, based on the simulation of signal flow in signaling network, we introduce a method for determining dominant pathways and signal response to stimulations. The model uses topology-weighted transit compartment approach and comprises...
Development of a novel nano-sized anti-VEGFA nanobody with enhanced physicochemical and pharmacokinetic properties
, Article Artificial Cells, Nanomedicine and Biotechnology ; Volume 46, Issue 7 , 2018 , Pages 1402-1414 ; 21691401 (ISSN) ; Norouzian, D ; Vaziri, B ; Ahangari Cohan, R ; Sardari, S ; Mahboudi, F ; Behdani, M ; Mansouri, K ; Mehdizadeh, A ; Sharif University of Technology
Abstract
Since physiological and pathological processes occur at nano-environments, nanotechnology has considered as an efficient tool for designing of next generation specific biomolecules with enhanced pharmacodynamic and pharmacodynamic properties. In the current investigation, by control of the size and hydrodynamic volume at the nanoscale, for the first time, physicochemical and pharmacokinetic properties of an anti-VEGFA nanobody was remarkably improved by attachment of a Proline-Alanine-Serine (PAS) rich sequence. The results elucidated unexpected impressive effects of PAS sequence on physicochemical properties especially on size, hydrodynamics radius, and even solubility of nanobody. CD...