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Far-from-equilibrium measurements of thermodynamic length

Description: Thermodynamic length is a path function that generalizes the notion of length to the surface of thermodynamic states. Here, we show how to measure thermodynamic length in far-from-equilibrium experiments using the work fluctuation relations. For these microscopic systems, it proves necessary to define the thermodynamic length in terms of the Fisher information. Consequently, the thermodynamic length can be directly related to the magnitude of fluctuations about equilibrium. The work fluctuation relations link the work and the free energy change during an external perturbation on a system. We use this result to determine equilibrium averages at intermediate points of the protocol in which the system is out-of-equilibrium. This allows us to extend Bennett's method to determine the potential of mean force, as well as the thermodynamic length, in single molecule experiments.
Date: November 5, 2008
Creator: Feng, Edward H. & Crooks, Gavin E.
Partner: UNT Libraries Government Documents Department

Comments on "Solvation Parameters. 2. A Simplified Molecular Topology to Generate Easily Optimized Values"

Description: This article provides comments on "Solvation Parameters. 2. A Simplified Molecular Topology to Generate Easily Optimized Values," published in the Journal of Chemical Information and Modeling.
Date: September 8, 2006
Creator: Mintz, Christina; Acree, William E. (William Eugene) & Abraham, M. H. (Michael H.)
Partner: UNT College of Arts and Sciences

Spacetime thermodynamics and subsystem observables in akinetically constrained model of glassy systems

Description: In a recent article it was argued that dynamic heterogeneity in d-dimensional glass formers is a manifestation of an order-disorder phenomenon in the d+1 dimensions of spacetime. By considering a dynamical analogue of the free energy, evidence was found for phase coexistence between active and inactive regions of spacetime, and it was suggested that this phenomenon underlies the glass transition. Here we develop these ideas further by investigating in detail the one-dimensional Fredrickson-Andersen (FA) model in which the active and inactive phases originate in the reducibility of the dynamics. We illustrate the phase coexistence by considering the distributions of mesoscopic spacetime observables. We show how the analogy with phase coexistence can be strengthened by breaking microscopic reversibility in the FA model, leading to a non-equilibrium theory in the directed percolation universality class.
Date: October 4, 2006
Creator: Jack, Robert L.; Garrahan, Juan P. & Chandler, David
Partner: UNT Libraries Government Documents Department

Water at an electrochemical interface - a simulation study

Description: The results of molecular dynamics simulations of the properties of water in an aqueous ionic solution close to an interface with a model metallic electrode are described. In the simulations the electrode behaves as an ideally polarizable hydrophilic metal, supporting image charge interactions with charged species, and it is maintained at a constant electrical potential with respect to the solution so that the model is a textbook representation of an electrochemical interface through which no current is passing. We show how water is strongly attracted to and ordered at the electrode surface. This ordering is different to the structure that might be imagined from continuum models of electrode interfaces. Further, this ordering significantly affects the probability of ions reaching the surface. We describe the concomitant motion and configurations of the water and ions as functions of the electrode potential, and we analyze the length scales over which ionic atmospheres fluctuate. The statistics of these fluctuations depend upon surface structure and ionic strength. The fluctuations are large, sufficiently so that the mean ionic atmosphere is a poor descriptor of the aqueous environment near a metal surface. The importance of this finding for a description of electrochemical reactions is examined by calculating, directly from the simulation, Marcus free energy profiles for transfer of charge between the electrode and a redox species in the solution and comparing the results with the predictions of continuum theories. Significant departures from the electrochemical textbook descriptions of the phenomenon are found and their physical origins are characterized from the atomistic perspective of the simulations.
Date: August 22, 2008
Creator: Willard, Adam; Reed, Stewart; Madden, Paul & Chandler, David
Partner: UNT Libraries Government Documents Department

Supplemental Material: Enthalpy of Solvation Correlations for Gaseous Solutes Dissolved in Alcohol Solvents Based on the Abraham Model

Description: This document includes supplemental material to an article titled "Enthalpy of solvation correlations for gaseous solutes dissolved in alcohol solvents based on the Abraham model," published in QSAR & Combinatorial Science.
Date: December 7, 2007
Creator: Mintz, Christina; Ladlie, Tara; Burton, Katherine; Clark, Michael; Acree, William E. (William Eugene) & Abraham, M. H. (Michael H.)
Partner: UNT College of Arts and Sciences

Characterization of the sorption of gaseous and organic solutes onto polydimethyl siloxane solid-phase microextraction surfaces using the Abraham model

Description: Article on the characterization of the sorption of gaseous and organic solutes onto polydimethyl siloxane solid-phase microextraction surfaces using the Abraham model.
Date: December 21, 2007
Creator: Sprunger, Laura M.; Proctor, Amy; Acree, William E. (William Eugene) & Abraham, M. H. (Michael H.)
Partner: UNT College of Arts and Sciences

Free energy calculations of Cu-Sn interfaces

Description: Excess free energies of solid Cu-Solid Sn and Solid Cu-liquid Sn have been calculated employing an adiabatic switching formalism in a Molecular Dynamics framework. The atomic interactions are described by modified embedded atom method potentials which includes the angular dependence of the electron density to describe bond bending forces necessary to model covalent materials.
Date: December 31, 1995
Creator: Ravelo, R. & Baskes, M.
Partner: UNT Libraries Government Documents Department

Partition of solutes from the gas phase and from water to wet and dry di-n-butyl ether: a linear free energy relationship analysis

Description: Article on the partition of solutes from the gas phase and from water to wet and dry di-n-butyl ether and a linear free energy relationship analysis.
Date: August 13, 2001
Creator: Abraham, M. H. (Michael H.); Zissimos, Andreas M. & Acree, William E. (William Eugene)
Partner: UNT College of Arts and Sciences

1st-Principles Step- and Kink-Formation Energies on Cu(111)

Description: In rough agreement with experimental values derived from Cu island shapes vs. temperature, ab-initio calculations yield formation energies of 0.27 and 0.26 eV/ step-edge-atom for (100)- and (111)-micro facet steps on Cu(lll), and 0.09 and 0.12 eV per kink in those steps. Comparison to ab-initio results for Al and Pt shows that as a rule, the average formation energy of straight steps on a close-packed metal surface equals -7% of the metal's cohesive energy.
Date: May 26, 1999
Creator: Feibelman, Peter J.
Partner: UNT Libraries Government Documents Department

Activity Coefficients at Infinite Dilution of Organic Compounds in Trihexyl(tetradecyl)phosphonium Bis(trifluoromethylsulfonyl)imide Using Inverse Gas Chromatography

Description: Article on activity coefficients at infinite dilution of organic compounds in trihexyl(tetradecyl)phosphonium Bis(trifluoromethylsulfonyl)imide using inverse gas chromatography.
Date: February 2, 2009
Creator: Revelli, Anne-Laure; Sprunger, Laura M.; Gibbs, Jennifer; Acree, William E. (William Eugene); Baker, Gary A. & Mutelet, Fabrice
Partner: UNT College of Arts and Sciences

Linear Free Energy Relationship Correlations for Enthalpies of Solvation of Organic Solutes into Room-Temperature Ionic Liquids Based on the Abraham Model with Ion-Specific Equation Coefficients

Description: Article discussing the linear free energy relationship correlations for enthalpies of solvation of organic solutes into room-temperature ionic liquids based on the Abraham model with ion-specific equation coefficients.
Date: August 3, 2009
Creator: Sprunger, Laura M.; Achi, Sai S.; Acree, William E. (William Eugene) & Abraham, M. H. (Michael H.)
Partner: UNT College of Arts and Sciences

An NMR Method for Quantitative Assessment of Intramolecular Hydrogen Bonding; Application to Physiochemical, Environmental, and Biochemical Properties

Description: Article on an NMR method for the quantitative assessment of intramolecular hydrogen bonding and an application to physiochemical, environmental, and biochemical properties.
Date: October 30, 2014
Creator: Abraham, M. H. (Michael H.); Abraham, Raymond J.; Acree, William E. (William Eugene); Aliev, Abil E.; Leo, Albert J. & Whaley, William L.
Partner: UNT College of Arts and Sciences

Examination and Development of the Correlation Consistent Composite Approach

Description: The primary focus of this dissertation is the advancement of the correlation consistent composite approach (ccCA) methodology from its original formulation to the current implementation. Although for large main group test sets which contained both first- (Li-Ne) and second-row (Na-Ar) species ccCA produced chemical accuracy (generally estimated as a deviation of ~1 kcal mol-1 from reliable experiment), the second-row species were smaller in molecular size in comparison to their corresponding first-row species. Previous theoretical work has shown that the accuracy for theoretical calculations involving second-row species (specifically sulfur-containing species) are more basis set dependent than first-row species. Therefore, an analysis of the accuracy of ccCA for sulfur-containing species is warranted. The ccCA methodology is used to evaluate both enthalpies of formation and bond dissociation energies of sulfur-containing species as well as examine isomerization energies for three sets of sulfur-containing isomers. During the testing of ccCA for sulfur-containing species two observations were made which led to further investigations. First, there is no agreement between different theoretical methodologies on the lowest energetic isomer between SNO and NSO. In fact, G3 and G3B3 which differ only by the geometry of the single-point calculations do not agree on the lowest isomer. For this reason, larger, more complete theoretical treatments of SNO and NSO are investigated. Second, for open-shell sulfur-containing systems the accuracy of the ccCA methodology begins to degrade when spin-contamination becomes non-negligible. Therefore, we investigate the accuracy of the ccCA methodology when spin-contamination is removed from the wavefunction. Finally, the ccCA methodology is utilized in a multilayer ONIOM approach as the high level of theory in conjunction with density functional theory as the low level for the C-H bond dissociation energies of anthracene and fluorene analogues.
Date: December 2010
Creator: Williams, T. Gavin
Partner: UNT Libraries

Insights into the structural function of the complex of HIV-1 protease with TMC-126: molecular dynamics simulations and free-energy calculations

Description: The binding properties of the protein-inhibitor complex of human immunodeficiency virus type 1 (HIV-1) protease with the inhibitor TMC-126 are investigated by combining computational alanine scanning (CAS) mutagenesis with binding free-energy decomposition (BFED). The calculated results demonstrate that the flap region (residues 38-58) and the active site region (residues 23-32) in HIV-1 protease contribute 63.72% of the protease to the binding of the inhibitor. In particular, the mechanisms for the interactions of key residues of these species are fully explored and analyzed. Interestingly, the regression analyses show that both CAS and BFED based on the generalized Born model yield similar results, with a correlation coefficient of 0.94. However, compared to CAS, BFED is faster and can decompose the per-residue binding free-energy contributions into backbone and sidechain contributions. The results obtained in this study are useful for studying the binding mechanism between receptor and ligand and for designing potent inhibitors that can combat diseases.
Date: May 1, 2012
Creator: Li, Dan; Han, Ju-Guang; Chen, Hang; Li, Liang; Zhao, Run-Ning Zhao; Liu, Guang et al.
Partner: UNT Libraries Government Documents Department

Adhesion and Surface Energy Profiles of Large-area Atomic Layers of Two-dimensional MoS2 on Rigid Substrates by Facile Methods

Description: Two-dimensional (2D) transition metal dichalcogenides (TMDs) show great potential for the future electronics, optoelectronics and energy applications. But, the studies unveiling their interactions with the host substrates are sparse and limits their practical use for real device applications. We report the facile nano-scratch method to determine the adhesion energy of the wafer scale MoS2 atomic layers attached to the SiO2/Si and sapphire substrates. The practical adhesion energy of monolayer MoS2 on the SiO2/Si substrate is 7.78 J/m2. The practical adhesion energy was found to be an increasing function of the MoS2 thickness. Unlike SiO2/Si substrates, MoS2 films grown on the sapphire possess higher bonding energy, which is attributed to the defect-free growth and less number of grain boundaries, as well as less stress and strain stored at the interface owing to the similarity of Thermal Expansion Coefficient (TEC) between MoS2 films and sapphire substrate. Furthermore, we calculated the surface free energy of 2D MoS2 by the facile contact angle measurements and Neumann model fitting. A surface free energy ~85.3 mJ/m2 in few layers thick MoS2 manifests the hydrophilic nature of 2D MoS2. The high surface energy of MoS2 helps explain the good bonding strength at MoS2/substrate interface. This simple adhesion energy and surface energy measurement methodology could further apply to other TMDs for their widespread use.
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Date: May 2016
Creator: Wu, Min
Partner: UNT Libraries

Comment on"Elucidating the Mechanism of Nucleation near the Gas-Liquid Spinodal"

Description: In a recent Letter [1], Bhimalapuram, Chakrabarty and Bagchi (BCB) study the phase transformation mechanism of the Lennard-Jones fluid and the non-conserved Ising model. They compute the free energy as a function of the size of the largest droplet of the stable phase. In apparent contradiction to classical nucleation theory (CNT), they find that in both systems the free energy develops a minimum at subcritical cluster sizes. In this Comment we argue that this minimum is specific to the chosen order parameter, and that the observed behavior is in fact consistent with CNT. CNT states that the free energy F(N) of a single cluster of size N is a concave function with a maximum at the critical nucleus size N{sub c}. BCB, on the other hand, calculate the probability distribution of N*, the size of the largest cluster in the system, and compute the free energy {beta}F*(N*) = -ln P(N*), where {beta} = 1/k{sub B}T. This order parameter does not measure the size of a single cluster. Instead, when sampling small values of N*, one measures the statistical weight of configurations in which all clusters are at most N* in size. Hence a free energy penalty is incurred when one constrains N* to values smaller than the largest average cluster in the simulation volume V. It is this penalty that causes the sudden increase of F* as N* {yields} 0 and the minimum at intermediate values of N*. We now illustrate how F(N) can be calculated from simulations. Our argument is intuitive but not exact, a formal derivation that yields an equivalent result can be found in Ref. 2. We choose the Ising model for concreteness. We aim to compute the probability that a given cluster has size N, where we imagine the center of the cluster to be fixed ...
Date: June 18, 2008
Creator: Maibaum, Lutz & Maibaum, Lutz
Partner: UNT Libraries Government Documents Department