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#### Surface balance laws of linear and angular momenta and Cauchy's stress theorem

, Article Scientia Iranica ; Volume 11, Issue 1-2 , 2004 , Pages 21-25 ; 10263098 (ISSN) ; Yavari, A ; Sharif University of Technology
Sharif University of Technology
2004

Abstract

Using Helmholtz's decomposition theorem, the laws of balance of linear and angular momenta are restated as surface integrals over the closed surface of an arbitrary subregion in a continuum. Newton's law of action and reaction and Cauchy's theorem for stress and couple-stress are proved as corollaries of these surface balance laws. © Sharif University of Technology

#### Basis free relations for the conjugate stresses of the strains based on the right stretch tensor

, Article International Journal of Solids and Structures ; Volume 40, Issue 22 , 2003 , Pages 5887-5900 ; 00207683 (ISSN) ; Naghdabadi, R ; Sharif University of Technology
Elsevier Ltd
2003

Abstract

In this paper, general relations between two different stress tensors Tf and Tg, respectively conjugate to strain measure tensors f(U) and g(U) are found. The strain class f(U) is based on the right stretch tensor U which includes the Seth-Hill strain tensors. The method is based on the definition of energy conjugacy and Hill's principal axis method. The relations are derived for the cases of distinct as well as coalescent principal stretches. As a special case, conjugate stresses of the Seth-Hill strain measures are then more investigated in their general form. The relations are first obtained in the principal axes of the tensor U. Then they are used to obtain basis free tensorial equations...

#### Solubility of CO2 in 1-(2-hydroxyethyl)-3-methylimidazolium ionic liquids with different anions

, Article Journal of Chemical Thermodynamics ; Volume 42, Issue 6 , June , 2010 , Pages 787-791 ; 00219614 (ISSN) ; Mehdizadeh, A ; Shokouhi, M ; Sakhaeinia, H ; Taghikhani, V ; Sharif University of Technology
2010

Abstract

The solubility of carbon dioxide in a series of 1-(2-hydroxyethyl)-3-methylimidazolium ([hemim]+) based ionic liquids (ILs) with different anions, viz. hexafluorophosphate ([PF6]-), trifluoromethanesulfonate ([OTf]-), and bis-(trifluoromethyl)sulfonylimide ([Tf2N]-) at temperatures ranging from 303.15 K to 353.15 K and pressures up to 1.3 MPa were determined. The solubility data were correlated using the Krichevsky-Kasarnovsky equation and Henry's law constants were obtained at different temperatures. Using the solubility data, the partial molar thermodynamic functions of solution such as Gibbs free energy, enthalpy, and entropy were calculated. Comparison showed that the solubility of CO2...

#### Calculation of Free Energy Barrier for Base Flipping of Thymine Dimer Outward the DNA Double Strand Using Molecular Dynamics

, M.Sc. Thesis Sharif University of Technology ; Parsafar, Golam Abbas (Supervisor)
Abstract

Formation of Cyclobutane Pyrimidine Dimer (CPD), one of the most abundant types of damages in DNA double helices, is caused by UV radiation and plays a major role in causing skin cancer. DNA photolyase is an efficient enzyme that repairs this UV-induced damaged DNA-base. Previous studies have shown that the enzyme flips the dimer out of the DNA double helix into its binding pocket.

In this project, several nanoseconds of molecular dynamics simulations was performed to investigate the process of base flipping energetically. These simulations are consist of equilibration of repaired and damaged double strands for 3 and 8 nanoseconds respectively. All these simulations ran over NVT...

In this project, several nanoseconds of molecular dynamics simulations was performed to investigate the process of base flipping energetically. These simulations are consist of equilibration of repaired and damaged double strands for 3 and 8 nanoseconds respectively. All these simulations ran over NVT...

#### Comparison of the mechanical properties of NiTi/Cu bilayer by nanoindentation and tensile test: Molecular dynamics simulation

, Article Materials Research Express ; Volume 3, Issue 12 , 2016 ; 20531591 (ISSN) ; Vahedpour, M ; Sadrnezhaad, S. K ; Sharif University of Technology
Institute of Physics Publishing
2016

Abstract

Molecular dynamics simulation was used to study of mechanical properties of NiTi/Cu bilayer by nanoindentation and tensile testing. A comparison has been made among mechanical properties measured and plastic deformation process at different copper thickness during nanoindnetation and tensile test of the samples. Embedded atom method potentials for describing of inter-Atomic interaction and Nose-Hoover thermostat and barostat are employed in the simulation at 400 K. The results showed that as the copper film thickness decreased, the maximum load and hardness values increased during nanoindetation. Saha and Nix model is used to describe reduced young's modulus behaviour of the bilayer system...

#### Solubility of H2S in ionic liquids [hmim][PF6], [hmim][BF4], and [hmim][Tf2N]

, Article Journal of Chemical Thermodynamics ; Volume 41, Issue 9 , 2009 , Pages 1052-1055 ; 00219614 (ISSN) ; Ghotbi, C ; Hosseini Jenab, M ; Ahmadi, A. N ; Jalili, A. H ; Sharif University of Technology
2009

Abstract

The solubility of hydrogen sulphide in three ionic liquids, viz. 1-hexyl-3-methylilmidazolium hexafluorophosphate ([hmim][PF6]), 1-hexyl-3-methylimidazolium tetrafluoroborate ([hmim][BF4]), and 1-hexyl-3-methylimidazolium bis(trifluoromethanesulfonyl)imide ([hmim][Tf2N]), at temperatures ranging from 303.15 K to 343.15 K and pressures up to 1.1 MPa were determined. The solubility values were correlated using the Krichevsky-Kasarnovsky equation and Henry's constants were obtained at different temperatures. Partial molar thermodynamic functions of solvation such as standard Gibbs free energy, enthalpy, and entropy were calculated from the solubility results. Comparison of the values obtained...

#### Prediction of interfacial tensions of binary and ternary liquid-liquid systems by using UNIQUAC Excess Gibbs Free energy model

, Article Iranian Journal of Science and Technology, Transaction B: Technology ; Volume 27, Issue 2 , 2003 , Pages 261-268 ; 03601307 (ISSN) ; Ghotbi, C ; Hatefi Rad, P ; Sharif University of Technology
2003

Abstract

Interfacial tension of both 36 binary and 6 ternary liquid-liquid systems at 298 K, has been predicted through a reliable thermodynamic model. To properly predict interfacial tension, it is necessary to calculate interfacial area of each constituent of the mixtures. For such estimation, two empirical correlations have been proposed for binary mixtures whose one component is water and experimental data have been used to calculate interfacial area of ternary mixtures. The UNIQUAUC Excess Gibbs Free energy model and its parameters have been used to calculate the concentration and activity coefficients in the bulk and interface phases. The overall average deviation of the predicted binary...

#### Confined nematic liquid crystal between two spherical boundaries with planar anchoring

, Article Physical Review E - Statistical, Nonlinear, and Soft Matter Physics ; Volume 88, Issue 1 , 2013 ; 15393755 (ISSN) ; Mozaffari, M. R ; Ejtehadi, M. R ; Sharif University of Technology
2013

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...

#### Modeling of austenite to ferrite transformation

, Article Bulletin of Materials Science ; Volume 35, Issue 3 , 2012 , Pages 395-398 ; 02504707 (ISSN) ; Sharif University of Technology
2012

Abstract

In this research, an algorithm based on the Q-state Potts model is presented for modeling the austenite to ferrite transformation. In the algorithm, it is possible to exactly track boundary migration of the phase formed during transformation. In the algorithm, effects of changes in chemical free energy, strain free energy and interfacial energies of austenite-austenite, ferrite-ferrite and austenite-ferrite during transformation are considered. From the algorithm, the kinetics of transformation and mean ferrite grain size for different cooling rates are calculated. It is found that there is a good agreement between the calculated and experimental results

#### DFT study of nitrogen monoxide adsorption and dissociation on Rh[sbnd]Cu nano clusters

, Article Journal of Alloys and Compounds ; Volume 695 , 2017 , Pages 1924-1929 ; 09258388 (ISSN) ; Nahali, M ; Gobal, F ; Sharif University of Technology
Abstract

Adsorption and dissociation of NO on RhxCu4-x(x = 0–4) nano clusters were investigated using density functional theory. Adsorption energy, total charge on NO, NO bond length, and NO vibrational frequency for various modes of NO adsorption were analyzed. Adsorption from the nitrogen end of NO on the Rh atom(s) of the clusters are more favored and adsorption energies are in the −1.02 eV to −2.59 eV range. NO binds stronger to Rh-Cu mixed clusters compared to pure Cu4 cluster, so N[sbnd]O bond is significantly weakened upon adsorption on the former. NO binding to more atoms of the clusters results in a corresponding decrease of the N[sbnd]O vibrational frequency. Dissociation of NO was also...

#### Microscopic structure and solubility predictions of multifunctional solids in supercritical carbon dioxide: a molecular simulation study

, Article Journal of Physical Chemistry B ; Volume 121, Issue 7 , 2017 , Pages 1660-1674 ; 15206106 (ISSN) ; Paluch, A. S ; Sharif University of Technology
Abstract

Molecular dynamics simulations were employed to both estimate the solubility of nonelectrolyte solids, such as acetanilide, acetaminophen, phenacetin, methylparaben, and lidocaine, in supercritical carbon dioxide and understand the underlying molecular-level driving forces. The solubility calculations involve the estimation of the solute's limiting activity coefficient, which may be computed using conventional staged free-energy calculations. For the case of lidocaine, wherein the infinite dilution approximation is not appropriate, we demonstrate how the activity coefficient at finite concentrations may be estimated without additional effort using the dilute solution approximation and how...

#### Investigation of the interactions between Melittin and the PLGA and PLA polymers: Molecular dynamic simulation and binding free energy calculation

, Article Materials Research Express ; Volume 6, Issue 5 , 2019 ; 20531591 (ISSN) ; Moosavi, A ; Sharif University of Technology
Institute of Physics Publishing
2019

Abstract

Nanobiotechnology is the application of nanotechnology in nanomedicine. Recently, the use of antimicrobial peptides as a substitute for antibiotics and anticancer drugs has attracted increasing attention. Therefore, the study of the structural behavior of these peptides such as Melittin and their interactions with biocompatible and biodegradable polymers is important. This study was performed to evaluate the critical interactions in the formation of the Melittin-polymers complexes. The aim of the current study was to investigate molecular mechanisms of Melittin encapsulation in biopolymers by molecular dynamics (MD) simulation. The results indicated that the basic residues of Melittin could...

#### Investigation of the interactions between Melittin and the PLGA and PLA polymers: Molecular dynamic simulation and binding free energy calculation

, Article Materials Research Express ; Volume 6, Issue 5 , 2019 ; 20531591 (ISSN) ; Moosavi, A ; Sharif University of Technology
Institute of Physics Publishing
2019

Abstract

Nanobiotechnology is the application of nanotechnology in nanomedicine. Recently, the use of antimicrobial peptides as a substitute for antibiotics and anticancer drugs has attracted increasing attention. Therefore, the study of the structural behavior of these peptides such as Melittin and their interactions with biocompatible and biodegradable polymers is important. This study was performed to evaluate the critical interactions in the formation of the Melittin-polymers complexes. The aim of the current study was to investigate molecular mechanisms of Melittin encapsulation in biopolymers by molecular dynamics (MD) simulation. The results indicated that the basic residues of Melittin could...

#### A thermodynamically consistent electro-chemo-mechanical theory for modeling axonal swelling

, Article Journal of the Mechanics and Physics of Solids ; Volume 145 , 2020 ; Naghdabadi, R ; Sohrabpour, S ; Li, Y ; Hu, Y ; Sharif University of Technology
Elsevier Ltd
2020

Abstract

In the present study, for the first time, a thermodynamically consistent large deformation theory is developed to model the multi physics problem of axonal swelling which is the hallmark of most of the brain diseases. To this end, the relevant axonal compartments are first explained and the corresponding model parts are introduced. Next, the problem is formulated as an open thermodynamic system and the corresponding constitutive and evolution equations are extracted utilizing the balance laws. Here, a multiplicative decomposition of the deformation gradient is used to capture the active behavior of the axonal actin cortex. Specific free energy functions are given for the model parts to...

#### Extended gibbs free energy and laplace pressure of ordered hexagonal close-packed spherical particles: A wettability study

, Article Langmuir ; Volume 37, Issue 28 , 2021 , Pages 8382-8392 ; 07437463 (ISSN) ; Ebrahimi, M ; Rahemi Ardekani, S ; Saievar Iranizad, E ; Zaker Moshfegh, A ; Sharif University of Technology
American Chemical Society
2021

Abstract

The wetting property of spherical particles in a hexagonal close-packed (HCP) ordering from extended Gibbs free energy (GFE) and Laplace pressure view points is studied. A formalism is proposed to predict the contact angle (θ) of a droplet on the HCP films and penetration angle (α) of the liquid on the spherical particles. Then, the extended Laplace pressure for the layered HCP ordering is calculated and a correlation between the wetting angle, sign of pressure, and pressure gradient is achieved. Our results show that the sign and the slope of pressure are important criteria for determining the wettability state and it is found that the contact angle is independent of the particle radius, as...

#### A model for inhomogeneous large deformation of photo-thermal sensitive hydrogels

, Article Acta Mechanica ; Volume 232, Issue 8 , 2021 , Pages 2955-2972 ; 00015970 (ISSN) ; Namdar, A. H ; Ghasemkhani, A ; Sharif University of Technology
Springer
2021

Abstract

The current study develops a 3D constitutive model for photo-thermal sensitive hydrogels based on free energy decomposition. The hydrogel under study is PNIPAM network with copper chlorophyllin nanoparticle agents attached to the network. The effect of light intensity is considered as a rise in temperature since chlorophyllin nanoparticle agents absorb light irradiation and convert it to heat. Moreover, it is necessary to consider the effect of dissociation of these agents on the hydrogel’s free energy function; therefore, a term is added to the free energy function. After introducing the model, some problems, including the free swelling and uniaxial loading problems, are studied, and the...

#### Investigation uncovered the impact of anions on CO2 absorption by low viscous ether functionalized pyridinium ionic liquids

, Article Journal of Molecular Liquids ; Volume 336 , August , 2021 ; 01677322 (ISSN) ; Dong, H ; Zeng, S ; Umair Ahmad, M ; Khurum Shehzad, F ; Wu, H ; Zhang, Y ; Sharif University of Technology
Elsevier B. V
2021

Abstract

Ionic liquids, which are designable and nonvolatile, have become a hot topic in the field of CO2 separation from industrial gases. In order to utilize the nonvolatile and low heat capacity of ionic liquids, it is necessary to solve the problem of high viscosity of pure ionic liquids. In the present study, ether functionalized pyridinium ion [E1Py]+ with good biodegradability and low viscosity was selected as cation. Ions containing cyano groups were used as anions, such as thiocyanate ion [SCN]-, dicyanamide ion [N(CN)2]-, tricyanomethanide ion [C(CN)3]-. Three ionic liquids with low viscosity were synthesized and characterized by 1HNMR, 13CNMR and FTIR. The physiochemical properties of...

#### Solvation thermodynamics of hydroxyl and carbonyl group in supercritical CO2 by Monte Carlo simulations

, Article Chemical Physics Letters ; Volume 458, Issue 4-6 , 2008 , Pages 308-312 ; 00092614 (ISSN) ; Khanlarkhani, A ; Sharif University of Technology
2008

Abstract

The Helmholtz free energy of solvation (ΔslvA) of 2-propanol and acetone in supercritical CO2 were calculated by expanded-ensemble method. For both solute molecules, ΔslvA is well represented by the polynomial equation of the third power of density and the density value correspond to the maximum stability decreases with increasing temperature. In all states under study acetone is more stable than 2-propanol. At low densities the solvation of acetone is more exothermic than 2-propanol while at high densities it come with less entropic penalty. The solvent reorganization energy is more favorable in 2-propanol case, although the role of solute-solvent interactions is dominant in both cases. ©...

#### A computational thermodynamics approach to the Gibbs-Thomson effect

, Article Materials Science and Engineering A ; Volume 443, Issue 1-2 , 2007 , Pages 178-184 ; 09215093 (ISSN) ; Nategh, S ; Sharif University of Technology
2007

Abstract

In two-phase system, curvature of interface leads to increase of solute concentration in matrix. This effect plays a significant role in solidification, precipitation, nucleation and growth and coarsening. There are number of models and formulas for Gibbs-Thomson effect in binary alloys. In this paper with the help of CALPHAD calculations, new approach for describing this effect in binary and multicomponent systems is proposed. In this generalized method no traditional simplifying assumption are considered and this yield to more accurate result for Gibbs-Thomson phenomenon. This model is compared with previous formulas in some case alloying systems. © 2006 Elsevier B.V. All rights reserved

#### Protein folding rates correlate with heterogeneity of folding mechanism

, Article Physical Review Letters ; Volume 93, Issue 20 , 2004 , Pages 208105-1-208105-4 ; 00319007 (ISSN) ; Ejtehadi, M. R ; Plotkin, S. S ; Sharif University of Technology
American Physical Society
2004

Abstract

The folding rates of protein were shown to correlate with the degree of heterogeneity in the formation of native contacts. It was shown that both experimental rates and simulated free energy barriers for 2-state proteins depend on the degree of heterogeneity present in the folding process. Heterogeneity due to variance in the distribution of native loop lengths, and variance in the distribution of φ values, were observed to increase folding rates and reduce folding barriers. The observed effect due to φ variance was found to be the most statistically significant, because φ variance captures both heterogeneity arising from native topology and that arising from energetics