Browsing by Subject "thermodynamics"

Now showing 1 - 4 of 4

Open Access
A radiotracer study of the adsorption behavior of aqueous Ba2+ ions on nanoparticles of zero-valent iron
(2007) Çelebi O.; Üzüm, C.; Shahwan, T.; Erten H.N.
Recently, iron nanoparticles are increasingly being tested as adsorbents for various types of organic and inorganic pollutants. In this study, nanoparticles of zero-valent iron (NZVI) synthesized under atmospheric conditions were employed for the removal of Ba2+ ions in a concentration range 10-3 to 10-6 M. Throughout the study, 133Ba was used as a tracer to study the effects of time, concentration, and temperature. The obtained data was analyzed using various kinetic models and adsorption isotherms. Pseudo-second-order kinetics and Dubinin-Radushkevich isotherm model provided the best correlation with the obtained data. Observed thermodynamic parameters showed that the process is exothermic and hence enthalpy-driven. © 2007 Elsevier B.V. All rights reserved.
Open Access
Some exact solutions of colliding waves, black holes and their thermodynamical properties in Dilaton gravity
(1998) Sermutlu, Emre
We consider all possible theories in spherically symmetric Riemannian geometry in D-dimensions. We find solutions to such theories, in particular black hole solutions of the low energy limit of the string theory in Ddimensions and study their uniqueness. We find for the first time in literature, exact solutions of colliding Dilaton-Einstein-Maxwell Plane Waves. We investigate thermodynamical properties of four and five dimensional black hole solutions of toroidally compactified string theory. We find the explicit expression of the first law of black hole thermodynamics. We calculate the temperature T, angula,r velocity ÎÎ and the electromagnetic potentials on the horizon using two different methods. Collision of plane waves in dilaton gravity theories and low energy limit of string theory is considered. The formulation of the problem and some exact solutions are presented
Open Access
Structures and free energy landscapes of the wild-type and A30P mutant-type α-synuclein proteins with dynamics
(2013) Wise-Scira O.; Aloglu, A.K.; Dunn, A.; Sakallioglu I.T.; Coskuner O.
The genetic missense A30P mutation of the wild-type α-synuclein protein results in the replacement of the 30th amino acid residue from alanine (Ala) to proline (Pro) and was initially found in the members of a German family who developed Parkinson's disease. Even though the structures of these proteins have been measured before, detailed understanding about the structures and their relationships with free energy landscapes is lacking, which is of interest to provide insights into the pathogenic mechanism of Parkinson's disease. We report the secondary and tertiary structures and conformational free energy landscapes of the wild-type and A30P mutant-type α-synuclein proteins in an aqueous solution environment via extensive parallel tempering molecular dynamics simulations along with thermodynamic calculations. In addition, we present the residual secondary structure component transition stabilities at the atomic level with dynamics in terms of free energy change calculations using a new strategy that we reported most recently. Our studies yield new interesting results; for instance, we find that the A30P mutation has local as well as long-range effects on the structural properties of the wild-type α-synuclein protein. The helical content at Ala18-Gly31 is less prominent in comparison to the wild-type α-synuclein protein. The β-sheet structure abundance decreases in the N-terminal region upon A30P mutation of the wild-type α-synuclein, whereas the NAC and C-terminal regions possess larger tendencies for β-sheet structure formation. Long-range intramolecular protein interactions are less abundant upon A30P mutation, especially between the NAC and C-terminal regions, which is linked to the less compact and less stable structures of the A30P mutant-type rather than the wild-type α-synuclein protein. Results including the usage of our new strategy for secondary structure transition stabilities show that the A30P mutant-type α-synuclein tendency toward aggregation is higher than the wild-type α-synuclein but we also find that the C-terminal and NAC regions of the A30P mutant-type α-synuclein are reactive toward fibrillzation and aggregation based on atomic level studies with dynamics in an aqueous solution environment. Therefore, we propose that small molecules or drugs blocking the specific residues, which we report herein, located in the NAC- and C-terminal regions of the A30P mutant-type α-synuclein protein might help to reduce the toxicity of the A30P mutant-type α-synuclein protein. © 2013 American Chemical Society.
Open Access
Structures of the E46K mutant-type α-synuclein protein and impact of E46K mutation on the structures of the wild-type α-synuclein protein
(2013) Wise-Scira O.; Dunn, A.; Aloglu, A.K.; Sakallioglu I.T.; Coskuner O.
The E46K genetic missense mutation of the wild-type α-synuclein protein was recently identified in a family of Spanish origin with hereditary Parkinson's disease. Detailed understanding of the structures of the monomeric E46K mutant-type α-synuclein protein as well as the impact of the E46K missense mutation on the conformations and free energy landscapes of the wild-type α-synuclein are required for gaining insights into the pathogenic mechanism of Parkinson's disease. In this study, we use extensive parallel tempering molecular dynamics simulations along with thermodynamic calculations to assess the secondary and tertiary structural properties as well as the conformational preferences of the monomeric wild-type and E46K mutant-type α-synuclein proteins in an aqueous solution environment. We also present the residual secondary structure component conversion stabilities with dynamics using a theoretical strategy, which we most recently developed. To the best of our knowledge, this study presents the first detailed comparison of the structural and thermodynamic properties of the wild-type and E46K mutant-type α-synuclein proteins in an aqueous solution environment at the atomic level with dynamics. We find that the E46K mutation results not only in local but also in long-range changes in the structural properties of the wild-type α-synuclein protein. The mutation site shows a significant decrease in helical content as well as a large increase in β-sheet structure formation upon E46K mutation. In addition, the β-sheet content of the C-terminal region increases significantly in the E46K mutant-type αS in comparison to the wild-type αS. Our theoretical strategy developed to assess the thermodynamic preference of secondary structure transitions indicates that this shift in secondary structure is the result of a decrease in the thermodynamic preference of turn to helix conversions while the coil to β-sheet preference increases for these residues. Long-range intramolecular protein interactions of the C-terminal with the N-terminal and NAC regions increase upon E46K mutation, resulting in more compact structures for the E46K mutant-type rather than wild-type αS. However, the E46K mutant-type αS structures are less stable than the wild-type αS. Overall, our results show that the E46K mutant-type αS has a higher propensity to aggregate than the wild-type αS and that the N-terminal and C-terminal regions are reactive toward fibrillization and aggregation upon E46K mutation and we explain the associated reasons based on the structural properties herein. Small molecules or drugs that can block the specific residues forming abundant β-sheet structure, which we report here, might help to reduce the reactivity of these intrinsically disordered fibrillogenic proteins toward aggregation and their toxicity. © 2013 American Chemical Society.