Search for: molecular-model
Total 23 records
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
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...
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
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...
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
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...
Multiscale Modeling of Carbon Nano Structures Using Tersoff Potential Function, M.Sc. Thesis Sharif University of Technology ; Khoei, Amir Reza
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...
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
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
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
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...
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
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...
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
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...
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
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
Binding assessment of two arachidonic-based synthetic derivatives of adrenalin with β-lactoglobulin: Molecular modeling and chemometrics approach, Article Biophysical Chemistry ; Volume 207 , 2015 , Pages 97-106 ; 03014622 (ISSN) ; Bordbar, A. K ; Akvan, N ; Parastar, H ; Fani, N ; Gretskaya, N. M ; Bezuglov, V. V ; Haertlé, T ; Sharif University of Technology
A computational approach to predict the main binding modes of two adrenalin derivatives, arachidonoyl adrenalin (AA-AD) and arachidonoyl noradrenalin (AA-NOR) with the β-lactoglubuline (BLG) as a nano-milk protein carrier is presented and assessed by comparison to the UV-Vis absorption spectroscopic data using chemometric analysis. Analysis of the spectral data matrices by using the multivariate curve resolution-alternating least squares (MCR-ALS) algorithm led to the pure concentration calculation and spectral profiles resolution of the chemical constituents and the apparent equilibrium constants computation. The negative values of entropy and enthalpy changes for both compound indicated...
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
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...
Cis-trans proline isomers in the catalytic domain of calcineurin, Article FEBS Journal ; Volume 286, Issue 6 , 2019 , Pages 1230-1239 ; 1742464X (ISSN) ; Guasch, A ; Biçer, A ; Aranguren Ibáñez, Á ; Chashmniam, S ; Paniagua, J. C ; Pérez Riba, M ; Fita, I ; Pons, M ; Sharif University of Technology
Blackwell Publishing Ltd 2019
Calcineurin is an essential calcium-activated serine/threonine phosphatase. The six NMR-observable methionine methyl groups in the catalytic domain of human calcineurin Aα (CNA) were assigned and used as reporters of the presence of potential cis-trans isomers in solution. Proline 84 is found in the cis conformation in most calcineurin X-ray structures, and proline 309, which is part of a highly conserved motif in phosphoprotein phosphatases, was modeled with a cis peptide bond in one of the two molecules present in the asymmetric unit of CNA. We mutated each of the two prolines to alanine to force the trans conformation. Solution NMR shows that the P84A CNA mutant exists in two forms,...
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
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
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
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...
Conservation of statistical results under the reduction of pair-contact interactions to solvation interactions, Article Physical Review E - Statistical, Nonlinear, and Soft Matter Physics ; Volume 72, Issue 6 , 2005 ; 15393755 (ISSN) ; Farzami, R. R ; Ejtehadi, M. R ; Sharif University of Technology
We show that the hydrophobicity of sequences is the leading term in Miyazawa-Jernigan interactions. Being the source of additive (solvation) terms in pair-contact interactions, they were used to reduce the energy parameters while resulting in a clear vector manipulation of energy. The reduced (additive) potential performs considerably successful in predicting the statistical properties of arbitrary structures. The evaluated designabilities of the structures by both models are highly correlated. Suggesting geometrically nondegenerate vectors (structures) as proteinlike structures, the additive model is a powerful tool for protein design. Moreover, a crossing point in the log-linear diagram of...
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
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...
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
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...
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
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...
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
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...
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
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...