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Sample records for linear free-energy relations

  1. Free energy of activation. Definition, properties, and dependent variables with special reference to linear free energy relations

    International Nuclear Information System (INIS)

    Levine, R.D.

    1979-01-01

    The reaction rate constant is expressed as Z exp(-G/sub a//RT). Z is the binary collision frequency. G/sub a/, the free energy of activation, is shown to be the difference between the free energy of the reactive reactants and the free energy of all reactants. The results are derived from both a statistical mechanical and a collision theoretic point of view. While the later is more suitable for an ab-initio computation of the reaction rate, it is the former that lends itself to the search of systematics and of correlations and to compaction of data. Different thermodynamic-like routes to the characterization of G/sub a/ are thus explored. The two most promising ones appear to be the use of thermodynamic type cycles and the changes of dependent variables using the Legendre transform technique. The dependence of G/sub a/ on ΔG 0 , the standard free energy change in the reaction, is examined from the later point of view. It is shown that one can rigorously express this dependence as G/sub a/ = αΔG 0 + G/sub a/ 0 M(α). Here α is the Bronsted slope, α = -par. delta ln k(T)/par. delta(ΔG 0 /RT), G/sub a/ 0 is independent of ΔG 0 and M(α), the Legendre transform of G/sub a/, is a function only of α. For small changes in ΔG 0 , the general result reduces to the familiar ''linear'' free energy relation delta G/sub a/ = α delta ΔG 0 . It is concluded from general considerations that M(α) is a symmetric, convex function of α and hence that α is a monotonically increasing function of ΔG 0 . Experimental data appear to conform well to the form α = 1/[1 + exp(-ΔG 0 /G/sub s/ 0 )]. A simple interpretation of the ΔG 0 dependence of G/sub a/, based on an interpolation of the free energy from that of the reagents to that of the products, is offered. 4 figures, 69 references

  2. Guaiacol hydrodeoxygenation mechanism on Pt(111): insights from density functional theory and linear free energy relations.

    Science.gov (United States)

    Lee, Kyungtae; Gu, Geun Ho; Mullen, Charles A; Boateng, Akwasi A; Vlachos, Dionisios G

    2015-01-01

    Density functional theory is used to study the adsorption of guaiacol and its initial hydrodeoxygenation (HDO) reactions on Pt(111). Previous Brønsted-Evans-Polanyi (BEP) correlations for small open-chain molecules are inadequate in estimating the reaction barriers of phenolic compounds except for the side group (methoxy) carbon-dehydrogenation. New BEP relations are established using a select group of phenolic compounds. These relations are applied to construct a potential-energy surface of guaiacol-HDO to catechol. Analysis shows that catechol is mainly produced via dehydrogenation of the methoxy functional group followed by the CHx (x<3) removal of the functional group and hydrogenation of the ring carbon, in contrast to a hypothesis of a direct demethylation path. Dehydroxylation and demethoxylation are slow, implying that phenol is likely produced from catechol but not through its direct dehydroxylation followed by aromatic carbon-ring hydrogenation. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  3. Linear free energy relationships in glass corrosion

    International Nuclear Information System (INIS)

    Abrajano, T.A. Jr.; Bates, J.K.; Bohlke, J.K.

    1988-01-01

    Various theoretical models that have been proposed to correlate glass durability to their composition for a wide variety of silicate, borosilicate, and aluminosilicate glasses are examined. Comparisons are made between the predictions of these models and those of an empirical formulation extracted from existing data in the present work. The empirical approach provides independent confirmation of the relative accuracy of the silica release rate predictions of the different theoretical models in static leaching systems. Extension of the empirical approach used in this work are discussed. 23 refs., 2 figs., 1 tab

  4. Implicit ligand theory for relative binding free energies

    Science.gov (United States)

    Nguyen, Trung Hai; Minh, David D. L.

    2018-03-01

    Implicit ligand theory enables noncovalent binding free energies to be calculated based on an exponential average of the binding potential of mean force (BPMF)—the binding free energy between a flexible ligand and rigid receptor—over a precomputed ensemble of receptor configurations. In the original formalism, receptor configurations were drawn from or reweighted to the apo ensemble. Here we show that BPMFs averaged over a holo ensemble yield binding free energies relative to the reference ligand that specifies the ensemble. When using receptor snapshots from an alchemical simulation with a single ligand, the new statistical estimator outperforms the original.

  5. Linear free energy relationships between aqueous phase hydroxyl radical reaction rate constants and free energy of activation.

    Science.gov (United States)

    Minakata, Daisuke; Crittenden, John

    2011-04-15

    The hydroxyl radical (HO(•)) is a strong oxidant that reacts with electron-rich sites on organic compounds and initiates complex radical chain reactions in aqueous phase advanced oxidation processes (AOPs). Computer based kinetic modeling requires a reaction pathway generator and predictions of associated reaction rate constants. Previously, we reported a reaction pathway generator that can enumerate the most important elementary reactions for aliphatic compounds. For the reaction rate constant predictor, we develop linear free energy relationships (LFERs) between aqueous phase literature-reported HO(•) reaction rate constants and theoretically calculated free energies of activation for H-atom abstraction from a C-H bond and HO(•) addition to alkenes. The theoretical method uses ab initio quantum mechanical calculations, Gaussian 1-3, for gas phase reactions and a solvation method, COSMO-RS theory, to estimate the impact of water. Theoretically calculated free energies of activation are found to be within approximately ±3 kcal/mol of experimental values. Considering errors that arise from quantum mechanical calculations and experiments, this should be within the acceptable errors. The established LFERs are used to predict the HO(•) reaction rate constants within a factor of 5 from the experimental values. This approach may be applied to other reaction mechanisms to establish a library of rate constant predictions for kinetic modeling of AOPs.

  6. A study of the linear free energy model for DNA structures using the generalized Hamiltonian formalism

    Energy Technology Data Exchange (ETDEWEB)

    Yavari, M., E-mail: yavari@iaukashan.ac.ir [Islamic Azad University, Kashan Branch (Iran, Islamic Republic of)

    2016-06-15

    We generalize the results of Nesterenko [13, 14] and Gogilidze and Surovtsev [15] for DNA structures. Using the generalized Hamiltonian formalism, we investigate solutions of the equilibrium shape equations for the linear free energy model.

  7. Development of linear free energy relationships for aqueous phase radical-involved chemical reactions.

    Science.gov (United States)

    Minakata, Daisuke; Mezyk, Stephen P; Jones, Jace W; Daws, Brittany R; Crittenden, John C

    2014-12-02

    Aqueous phase advanced oxidation processes (AOPs) produce hydroxyl radicals (HO•) which can completely oxidize electron rich organic compounds. The proper design and operation of AOPs require that we predict the formation and fate of the byproducts and their associated toxicity. Accordingly, there is a need to develop a first-principles kinetic model that can predict the dominant reaction pathways that potentially produce toxic byproducts. We have published some of our efforts on predicting the elementary reaction pathways and the HO• rate constants. Here we develop linear free energy relationships (LFERs) that predict the rate constants for aqueous phase radical reactions. The LFERs relate experimentally obtained kinetic rate constants to quantum mechanically calculated aqueous phase free energies of activation. The LFERs have been applied to 101 reactions, including (1) HO• addition to 15 aromatic compounds; (2) addition of molecular oxygen to 65 carbon-centered aliphatic and cyclohexadienyl radicals; (3) disproportionation of 10 peroxyl radicals, and (4) unimolecular decay of nine peroxyl radicals. The LFERs correlations predict the rate constants within a factor of 2 from the experimental values for HO• reactions and molecular oxygen addition, and a factor of 5 for peroxyl radical reactions. The LFERs and the elementary reaction pathways will enable us to predict the formation and initial fate of the byproducts in AOPs. Furthermore, our methodology can be applied to other environmental processes in which aqueous phase radical-involved reactions occur.

  8. Competition Experiments as a Means of Evaluating Linear Free Energy Relationships

    Science.gov (United States)

    Mullins, Richard J.; Vedernikov, Andrei; Viswanathan, Rajesh

    2004-01-01

    The use of competition experiments as a means of evaluating linear free energy relationship in the undergraduate teaching laboratory is reported. The use of competition experiments proved to be a reliable method for the construction of Hammett plots with good correlation providing great flexibility with regard to the compounds and reactions that…

  9. Linear free energy relationship applied to trivalent cations with lanthanum and actinium oxide and hydroxide structure

    International Nuclear Information System (INIS)

    Ragavan, Anpalaki J.

    2006-01-01

    Linear free energy relationships for trivalent cations with crystalline M 2 O 3 and, M(OH) 3 phases of lanthanides and actinides were developed from known thermodynamic properties of the aqueous trivalent cations, modifying the Sverjensky and Molling equation. The linear free energy relationship for trivalent cations is as ΔG f,MvX 0 =a MvX ΔG n,M 3+ 0 +b MvX +β MvX r M 3+ , where the coefficients a MvX , b MvX , and β MvX characterize a particular structural family of MvX, r M 3+ is the ionic radius of M 3+ cation, ΔG f,MvX 0 is the standard Gibbs free energy of formation of MvX and ΔG n,M 3+ 0 is the standard non-solvation free energy of the cation. The coefficients for the oxide family are: a MvX =0.2705, b MvX =-1984.75 (kJ/mol), and β MvX =197.24 (kJ/molnm). The coefficients for the hydroxide family are: a MvX =0.1587, b MvX =-1474.09 (kJ/mol), and β MvX =791.70 (kJ/molnm).

  10. Use of linear free energy relationship to predict Gibbs free energies of formation of pyrochlore phases (CaMTi2O7)

    International Nuclear Information System (INIS)

    Xu, H.; Wang, Y.

    1999-01-01

    In this letter, a linear free energy relationship is used to predict the Gibbs free energies of formation of crystalline phases of pyrochlore and zirconolite families with stoichiometry of MCaTi 2 O 7 (or, CaMTi 2 O 7 ,) from the known thermodynamic properties of aqueous tetravalent cations (M 4+ ). The linear free energy relationship for tetravalent cations is expressed as ΔG f,M v X 0 =a M v X ΔG n,M 4+ 0 +b M v X +β M v X r M 4+ , where the coefficients a M v X , b M v X , and β M v X characterize a particular structural family of M v X, r M 4+ is the ionic radius of M 4+ cation, ΔG f,M v X 0 is the standard Gibbs free energy of formation of M v X, and ΔG n,M 4+ 0 is the standard non-solvation energy of cation M 4+ . The coefficients for the structural family of zirconolite with the stoichiometry of M 4+ CaTi 2 O 7 are estimated to be: a M v X =0.5717, b M v X =-4284.67 (kJ/mol), and β M v X =27.2 (kJ/mol nm). The coefficients for the structural family of pyrochlore with the stoichiometry of M 4+ CaTi 2 O 7 are estimated to be: a M v X =0.5717, b M v X =-4174.25 (kJ/mol), and β M v X =13.4 (kJ/mol nm). Using the linear free energy relationship, the Gibbs free energies of formation of various zirconolite and pyrochlore phases are calculated. (orig.)

  11. Linear free energy correlations for fission product release from the Fukushima-Daiichi nuclear accident.

    Science.gov (United States)

    Abrecht, David G; Schwantes, Jon M

    2015-03-03

    This paper extends the preliminary linear free energy correlations for radionuclide release performed by Schwantes et al., following the Fukushima-Daiichi Nuclear Power Plant accident. Through evaluations of the molar fractionations of radionuclides deposited in the soil relative to modeled radionuclide inventories, we confirm the initial source of the radionuclides to the environment to be from active reactors rather than the spent fuel pool. Linear correlations of the form In χ = −α ((ΔGrxn°(TC))/(RTC)) + β were obtained between the deposited concentrations, and the reduction potentials of the fission product oxide species using multiple reduction schemes to calculate ΔG°rxn (TC). These models allowed an estimate of the upper bound for the reactor temperatures of TC between 2015 and 2060 K, providing insight into the limiting factors to vaporization and release of fission products during the reactor accident. Estimates of the release of medium-lived fission products 90Sr, 121mSn, 147Pm, 144Ce, 152Eu, 154Eu, 155Eu, and 151Sm through atmospheric venting during the first month following the accident were obtained, indicating that large quantities of 90Sr and radioactive lanthanides were likely to remain in the damaged reactor cores.

  12. Bounding the electrostatic free energies associated with linear continuum models of molecular solvation.

    Science.gov (United States)

    Bardhan, Jaydeep P; Knepley, Matthew G; Anitescu, Mihai

    2009-03-14

    The importance of electrostatic interactions in molecular biology has driven extensive research toward the development of accurate and efficient theoretical and computational models. Linear continuum electrostatic theory has been surprisingly successful, but the computational costs associated with solving the associated partial differential equations (PDEs) preclude the theory's use in most dynamical simulations. Modern generalized-Born models for electrostatics can reproduce PDE-based calculations to within a few percent and are extremely computationally efficient but do not always faithfully reproduce interactions between chemical groups. Recent work has shown that a boundary-integral-equation formulation of the PDE problem leads naturally to a new approach called boundary-integral-based electrostatics estimation (BIBEE) to approximate electrostatic interactions. In the present paper, we prove that the BIBEE method can be used to rigorously bound the actual continuum-theory electrostatic free energy. The bounds are validated using a set of more than 600 proteins. Detailed numerical results are presented for structures of the peptide met-enkephalin taken from a molecular-dynamics simulation. These bounds, in combination with our demonstration that the BIBEE methods accurately reproduce pairwise interactions, suggest a new approach toward building a highly accurate yet computationally tractable electrostatic model.

  13. Bounding the electrostatic free energies associated with linear continuum models of molecular solvation.

    Energy Technology Data Exchange (ETDEWEB)

    Bardhan, J. P.; Knepley, M. G.; Anitescu, M. (Biosciences Division); ( MCS); (Rush Univ.)

    2009-03-01

    The importance of electrostatic interactions in molecular biology has driven extensive research toward the development of accurate and efficient theoretical and computational models. Linear continuum electrostatic theory has been surprisingly successful, but the computational costs associated with solving the associated partial differential equations (PDEs) preclude the theory's use in most dynamical simulations. Modern generalized-Born models for electrostatics can reproduce PDE-based calculations to within a few percent and are extremely computationally efficient but do not always faithfully reproduce interactions between chemical groups. Recent work has shown that a boundary-integral-equation formulation of the PDE problem leads naturally to a new approach called boundary-integral-based electrostatics estimation (BIBEE) to approximate electrostatic interactions. In the present paper, we prove that the BIBEE method can be used to rigorously bound the actual continuum-theory electrostatic free energy. The bounds are validated using a set of more than 600 proteins. Detailed numerical results are presented for structures of the peptide met-enkephalin taken from a molecular-dynamics simulation. These bounds, in combination with our demonstration that the BIBEE methods accurately reproduce pairwise interactions, suggest a new approach toward building a highly accurate yet computationally tractable electrostatic model.

  14. A Python tool to set up relative free energy calculations in GROMACS.

    Science.gov (United States)

    Klimovich, Pavel V; Mobley, David L

    2015-11-01

    Free energy calculations based on molecular dynamics (MD) simulations have seen a tremendous growth in the last decade. However, it is still difficult and tedious to set them up in an automated manner, as the majority of the present-day MD simulation packages lack that functionality. Relative free energy calculations are a particular challenge for several reasons, including the problem of finding a common substructure and mapping the transformation to be applied. Here we present a tool, alchemical-setup.py, that automatically generates all the input files needed to perform relative solvation and binding free energy calculations with the MD package GROMACS. When combined with Lead Optimization Mapper (LOMAP; Liu et al. in J Comput Aided Mol Des 27(9):755-770, 2013), recently developed in our group, alchemical-setup.py allows fully automated setup of relative free energy calculations in GROMACS. Taking a graph of the planned calculations and a mapping, both computed by LOMAP, our tool generates the topology and coordinate files needed to perform relative free energy calculations for a given set of molecules, and provides a set of simulation input parameters. The tool was validated by performing relative hydration free energy calculations for a handful of molecules from the SAMPL4 challenge (Mobley et al. in J Comput Aided Mol Des 28(4):135-150, 2014). Good agreement with previously published results and the straightforward way in which free energy calculations can be conducted make alchemical-setup.py a promising tool for automated setup of relative solvation and binding free energy calculations.

  15. Modeling bioaccumulation in humans using poly-parameter linear free energy relationships (PPLFERS)

    Energy Technology Data Exchange (ETDEWEB)

    Undeman, Emma, E-mail: emma.undeman@itm.su.se; Czub, Gertje; McLachlan, Michael S.

    2011-04-01

    Chemical partition coefficients between environmental media and biological tissues are a key component of bioaccumulation models. The single-parameter linear free energy relationships (spLFERs) commonly used for predicting partitioning are often derived using apolar chemicals and may not accurately capture polar chemicals. In this study, a poly-parameter LFER (ppLFER) based model of organic chemical bioaccumulation in humans is presented. Chemical partitioning was described by an air-body partition coefficient that was a volume weighted average of ppLFER based partition coefficients for the major organs and tissues constituting the human body. This model was compared to a spLFER model treating the body as a mixture of lipid ({approx} octanol) and water. Although model agreement was good for hydrophobic chemicals (average difference 15% for log K{sub OW} > 4 and log K{sub OA} > 8), the ppLFER model predicted {approx} 90% lower body burdens for hydrophilic chemicals (log K{sub OW} < 0). This was mainly due to lower predictions of muscle and adipose tissue sorption capacity for these chemicals. A comparison of the predicted muscle and adipose tissue sorption capacities of hydrophilic chemicals with measurements indicated that the ppLFER and spLFER models' uncertainties were similar. Consequently, little benefit from the implementation of ppLFERs in this model was identified. - Research Highlights: {yields}Implementation of ppLFERs resulted in on average 90% lower predicted body burdens. {yields}Uncertainties in spLFER and ppLFER predictions were similar. {yields}The benefit from implementation of ppLFERs in bioaccumulation models was limited.

  16. Tinker-OpenMM: Absolute and relative alchemical free energies using AMOEBA on GPUs.

    Science.gov (United States)

    Harger, Matthew; Li, Daniel; Wang, Zhi; Dalby, Kevin; Lagardère, Louis; Piquemal, Jean-Philip; Ponder, Jay; Ren, Pengyu

    2017-09-05

    The capabilities of the polarizable force fields for alchemical free energy calculations have been limited by the high computational cost and complexity of the underlying potential energy functions. In this work, we present a GPU-based general alchemical free energy simulation platform for polarizable potential AMOEBA. Tinker-OpenMM, the OpenMM implementation of the AMOEBA simulation engine has been modified to enable both absolute and relative alchemical simulations on GPUs, which leads to a ∼200-fold improvement in simulation speed over a single CPU core. We show that free energy values calculated using this platform agree with the results of Tinker simulations for the hydration of organic compounds and binding of host-guest systems within the statistical errors. In addition to absolute binding, we designed a relative alchemical approach for computing relative binding affinities of ligands to the same host, where a special path was applied to avoid numerical instability due to polarization between the different ligands that bind to the same site. This scheme is general and does not require ligands to have similar scaffolds. We show that relative hydration and binding free energy calculated using this approach match those computed from the absolute free energy approach. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

  17. Application of a linear free energy relationship to crystalline solids of MO2 and M(OH)4

    International Nuclear Information System (INIS)

    Xu Huifang; Barton, L.L.

    1999-01-01

    In this letter, a linear free energy relationship developed by Sverjensky and Molling is used to predict the Gibbs free energies of formation of crystalline phases of M 4+ O 2 and M 4+ (OH) 4 from the known thermodynamic properties of aqueous tetravalent cations (M 4+ ). The modified Sverjensky and Molling equation for tetravalent cations is expressed as ΔG 0 f,M v X = a M v X ΔG 0 n,M 4+ + b M v X + β M v X r M 4+ , where the coefficients a M v X , b M v X and β M v X characterize a particular structural family of M v X, r M 4+ is the ionic radius of M 4+ cation, ΔG 0 f,M v X is the standard Gibbs free energy of formation of M v X, and ΔG 0 n,M 4+ is the standard non-solvation energy of cation M 4+ . By fitting the equation to the existing thermodynamic data, the coefficients in the equation for the MO 2 family minerals are estimated to be: a M v X = 0.670, β M v X = 32 (kcal/mol A), and b = -430.02 (kcal/mol). The constrained relationship can be used to predict the standard Gibbs free energies of formation of crystalline phases and fictive phases (i.e., phases which are thermodynamically unstable and do not occur at standard conditions) within the isostructural families of M 4+ O 2 and M 4+ (OH) 4 if the standard Gibbs free energies of formation of the tetravalent cations are known. (orig.)

  18. Efficient Determination of Free Energy Landscapes in Multiple Dimensions from Biased Umbrella Sampling Simulations Using Linear Regression.

    Science.gov (United States)

    Meng, Yilin; Roux, Benoît

    2015-08-11

    The weighted histogram analysis method (WHAM) is a standard protocol for postprocessing the information from biased umbrella sampling simulations to construct the potential of mean force with respect to a set of order parameters. By virtue of the WHAM equations, the unbiased density of state is determined by satisfying a self-consistent condition through an iterative procedure. While the method works very effectively when the number of order parameters is small, its computational cost grows rapidly in higher dimension. Here, we present a simple and efficient alternative strategy, which avoids solving the self-consistent WHAM equations iteratively. An efficient multivariate linear regression framework is utilized to link the biased probability densities of individual umbrella windows and yield an unbiased global free energy landscape in the space of order parameters. It is demonstrated with practical examples that free energy landscapes that are comparable in accuracy to WHAM can be generated at a small fraction of the cost.

  19. Computing Relative Free Energies of Solvation using Single Reference Thermodynamic Integration Augmented with Hamiltonian Replica Exchange.

    Science.gov (United States)

    Khavrutskii, Ilja V; Wallqvist, Anders

    2010-11-09

    This paper introduces an efficient single-topology variant of Thermodynamic Integration (TI) for computing relative transformation free energies in a series of molecules with respect to a single reference state. The presented TI variant that we refer to as Single-Reference TI (SR-TI) combines well-established molecular simulation methodologies into a practical computational tool. Augmented with Hamiltonian Replica Exchange (HREX), the SR-TI variant can deliver enhanced sampling in select degrees of freedom. The utility of the SR-TI variant is demonstrated in calculations of relative solvation free energies for a series of benzene derivatives with increasing complexity. Noteworthy, the SR-TI variant with the HREX option provides converged results in a challenging case of an amide molecule with a high (13-15 kcal/mol) barrier for internal cis/trans interconversion using simulation times of only 1 to 4 ns.

  20. Relative Free Energies for Hydration of Monovalent Ions from QM and QM/MM Simulations.

    Science.gov (United States)

    Lev, Bogdan; Roux, Benoît; Noskov, Sergei Yu

    2013-09-10

    Methods directly evaluating the hydration structure and thermodynamics of physiologically relevant cations (Na(+), K(+), Cl(-), etc.) have wide ranging applications in the fields of inorganic, physical, and biological chemistry. All-atom simulations based on accurate potential energy surfaces appear to offer a viable option for assessing the chemistry of ion solvation. Although MD and free energy simulations of ion solvation with classical force fields have proven their usefulness, a number of challenges still remain. One of them is the difficulty of force field benchmarking and validation against structural and thermodynamic data obtained for a condensed phase. Hybrid quantum mechanical/molecular mechanical (QM/MM) models combined with sampling algorithms have the potential to provide an accurate solvation model and to incorporate the effects from the surrounding, which is often missing in gas-phase ab initio computations. Herein, we report the results from QM/MM free energy simulations of Na(+)/K(+) and Cl(-)/Br(-) hydration where we simultaneously characterized the relative thermodynamics of ion solvation and changes in the solvation structure. The Flexible Inner Region Ensemble Separator (FIRES) method was used to impose a spatial separation between QM region and the outer sphere of solvent molecules treated with the CHARMM27 force field. FEP calculations based on QM/MM simulations utilizing the CHARMM/deMon2k interface were performed with different basis set combinations for K(+)/Na(+) and Cl(-)/Br(-) perturbations to establish the dependence of the computed free energies on the basis set level. The dependence of the computed relative free energies on the size of the QM and MM regions is discussed. The current methodology offers an accurate description of structural and thermodynamic aspects of the hydration of alkali and halide ions in neat solvents and can be used to obtain thermodynamic data on ion solvation in condensed phase along with underlying

  1. Relative Binding Free Energy Calculations in Drug Discovery: Recent Advances and Practical Considerations.

    Science.gov (United States)

    Cournia, Zoe; Allen, Bryce; Sherman, Woody

    2017-12-26

    Accurate in silico prediction of protein-ligand binding affinities has been a primary objective of structure-based drug design for decades due to the putative value it would bring to the drug discovery process. However, computational methods have historically failed to deliver value in real-world drug discovery applications due to a variety of scientific, technical, and practical challenges. Recently, a family of approaches commonly referred to as relative binding free energy (RBFE) calculations, which rely on physics-based molecular simulations and statistical mechanics, have shown promise in reliably generating accurate predictions in the context of drug discovery projects. This advance arises from accumulating developments in the underlying scientific methods (decades of research on force fields and sampling algorithms) coupled with vast increases in computational resources (graphics processing units and cloud infrastructures). Mounting evidence from retrospective validation studies, blind challenge predictions, and prospective applications suggests that RBFE simulations can now predict the affinity differences for congeneric ligands with sufficient accuracy and throughput to deliver considerable value in hit-to-lead and lead optimization efforts. Here, we present an overview of current RBFE implementations, highlighting recent advances and remaining challenges, along with examples that emphasize practical considerations for obtaining reliable RBFE results. We focus specifically on relative binding free energies because the calculations are less computationally intensive than absolute binding free energy (ABFE) calculations and map directly onto the hit-to-lead and lead optimization processes, where the prediction of relative binding energies between a reference molecule and new ideas (virtual molecules) can be used to prioritize molecules for synthesis. We describe the critical aspects of running RBFE calculations, from both theoretical and applied perspectives

  2. Use of linear free energy relationship to predict Gibbs free energies of formation of zirconolite phases (MZrTi2O7 and MHfTi2O7)

    International Nuclear Information System (INIS)

    Xu, H.

    1999-01-01

    In this letter, the Sverjensky-Molling equation derived from a linear free energy relationship is used to calculate the Gibbs free energies of formation of zirconolite crystalline phases (MZrTi 2 O 7 and MHfTi 2 O 7 ) from the known thermodynamic properties of the corresponding aqueous divalent cations (M 2+ ). Sverjensky-Molling equation is expressed as ΔG 0 f,M v X =a M v X ΔG 0 n,M 2+ +b M v X +β M v X r M 2+ , where the coefficients a M v X , b M v X , and β M v X characterize a particular structural family of M v X, r M 2+ is the ionic radius of M 2+ cation, ΔG f,M v X 0 is the standard Gibbs free energy of formation of M v X, and ΔG 0 n,M 2+ is the standard non-solvation energy of cation M 2+ . This relationship can be used to predict the Gibbs free energies of formation of various fictive phases (such as BaZrTi 2 O 7 , SrZrTi 2 O 7 , PbZrTi 2 O 7 , etc.) that may form solid solution with CaZrTi 2 O 7 in actual Synroc-based nuclear waste forms. Based on obtained linear free energy relationships, it is predicted that large cations (e.g., Ba and Ra) prefer to be in perovskite structure, and small cations (e.g., Ca, Zn, and Cd) prefer to be in zirconolite structure. (orig.)

  3. Low dielectric and low surface free energy flexible linear aliphatic alkoxy core bridged bisphenol cyanate ester based POSS nanocomposites

    Directory of Open Access Journals (Sweden)

    Muthukaruppan eAlagar

    2013-10-01

    Full Text Available The aim of the present work is to develop a new type of flexible linear aliphatic alkoxy core bridged bisphenol cyanate ester (AECE based POSS nanocomposites for low k applications. The POSS-AECE nanocomposites were developed by incorporating varying weight percentages (0, 5 and 10 wt % of octakis (dimethylsiloxypropylglycidylether silsesquioxane (OG-POSS into cyanate esters. Data from thermal and dielectric studies imply that the POSS reinforced nanocomposite exhibits higher thermal stability and low dielectric value of k=2.4 (10 wt% POSS-AECE4 compared than those of neat AECE. From the contact angle measurement, it is inferred that, the increase in the percentage incorporation of POSS in to AECE, the values of water contact angle was enhanced. Further, the value of surface free energy was lower when compared to that of neat AECE. The molecular level dispersion of POSS into AECE was ascertained from SEM and TEM analyses.

  4. Computation of free energy

    NARCIS (Netherlands)

    van Gunsteren, WF; Daura, [No Value; Mark, AE

    2002-01-01

    Many quantities that are standardly used to characterize a chemical system are related to free-energy differences between particular states of the system. By statistical mechanics, free-energy differences may be expressed in terms of averages over ensembles of atomic configurations for the molecular

  5. Evaluating the environmental fate of pharmaceuticals using a level III model based on poly-parameter linear free energy relationships

    International Nuclear Information System (INIS)

    Zukowska, Barbara; Breivik, Knut; Wania, Frank

    2006-01-01

    We recently proposed how to expand the applicability of multimedia models towards polar organic chemicals by expressing environmental phase partitioning with the help of poly-parameter linear free energy relationships (PP-LFERs). Here we elaborate on this approach by applying it to three pharmaceutical substances. A PP-LFER-based version of a Level III fugacity model calculates overall persistence, concentrations and intermedia fluxes of polar and non-polar organic chemicals between air, water, soil and sediments at steady-state. Illustrative modeling results for the pharmaceuticals within a defined coastal region are presented and discussed. The model results are highly sensitive to the degradation rate in water and the equilibrium partitioning between organic carbon and water, suggesting that an accurate description of this particular partitioning equilibrium is essential in order to obtain reliable predictions of environmental fate. The PP-LFER based modeling approach furthermore illustrates that the greatest mobility in aqueous phases may be experienced by pharmaceuticals that combines a small molecular size with strong H-acceptor properties

  6. Evaluating the environmental fate of pharmaceuticals using a level III model based on poly-parameter linear free energy relationships

    Energy Technology Data Exchange (ETDEWEB)

    Zukowska, Barbara [Department of Analytical Chemistry, Chemical Faculty, Gdansk University of Technology, 11/12 G. Narutowicza St., 80-952 Gdansk (Poland); Breivik, Knut [NILU- Norwegian Institute for Air Research, P.O. Box 100, NO-2027 Kjeller (Norway)]. E-mail: knut.breivik@nilu.no; Wania, Frank [Department of Physical and Environmental Sciences, University of Toronto at Scarborough, 1265 Military Trail, Scarborough, Ontario, M1C 1A4 (Canada)

    2006-04-15

    We recently proposed how to expand the applicability of multimedia models towards polar organic chemicals by expressing environmental phase partitioning with the help of poly-parameter linear free energy relationships (PP-LFERs). Here we elaborate on this approach by applying it to three pharmaceutical substances. A PP-LFER-based version of a Level III fugacity model calculates overall persistence, concentrations and intermedia fluxes of polar and non-polar organic chemicals between air, water, soil and sediments at steady-state. Illustrative modeling results for the pharmaceuticals within a defined coastal region are presented and discussed. The model results are highly sensitive to the degradation rate in water and the equilibrium partitioning between organic carbon and water, suggesting that an accurate description of this particular partitioning equilibrium is essential in order to obtain reliable predictions of environmental fate. The PP-LFER based modeling approach furthermore illustrates that the greatest mobility in aqueous phases may be experienced by pharmaceuticals that combines a small molecular size with strong H-acceptor properties.

  7. Determination of polyparameter linear free energy relationship (pp-LFER) substance descriptors for established and alternative flame retardants.

    Science.gov (United States)

    Stenzel, Angelika; Goss, Kai-Uwe; Endo, Satoshi

    2013-02-05

    Polyparameter linear free energy relationships (pp-LFERs) can predict partition coefficients for a multitude of environmental and biological phases with high accuracy. In this work, the pp-LFER substance descriptors of 40 established and alternative flame retardants (e.g., polybrominated diphenyl ethers, hexabromocyclododecane, bromobenzenes, trialkyl phosphates) were determined experimentally. In total, 251 data for gas-chromatographic (GC) retention times and liquid/liquid partition coefficients (K) were measured and used to calibrate the pp-LFER substance descriptors. Substance descriptors were validated through a comparison between predicted and experimental log K for the systems octanol/water (K(ow)), water/air (K(wa)), organic carbon/water (K(oc)) and liposome/water (K(lipw)), revealing a high reliability of pp-LFER predictions based on our descriptors. For instance, the difference between predicted and experimental log K(ow) was <0.3 log units for 17 out of 21 compounds for which experimental values were available. Moreover, we found an indication that the H-bond acceptor value (B) depends on the solvent for some compounds. Thus, for predicting environmentally relevant partition coefficients it is important to determine B values using measurements in aqueous systems. The pp-LFER descriptors calibrated in this study can be used to predict partition coefficients for which experimental data are unavailable, and the predicted values can serve as references for further experimental measurements.

  8. Development of polyparameter linear free energy relationship models for octanol-air partition coefficients of diverse chemicals.

    Science.gov (United States)

    Jin, Xiaochen; Fu, Zhiqiang; Li, Xuehua; Chen, Jingwen

    2017-03-22

    The octanol-air partition coefficient (K OA ) is a key parameter describing the partition behavior of organic chemicals between air and environmental organic phases. As the experimental determination of K OA is costly, time-consuming and sometimes limited by the availability of authentic chemical standards for the compounds to be determined, it becomes necessary to develop credible predictive models for K OA . In this study, a polyparameter linear free energy relationship (pp-LFER) model for predicting K OA at 298.15 K and a novel model incorporating pp-LFERs with temperature (pp-LFER-T model) were developed from 795 log K OA values for 367 chemicals at different temperatures (263.15-323.15 K), and were evaluated with the OECD guidelines on QSAR model validation and applicability domain description. Statistical results show that both models are well-fitted, robust and have good predictive capabilities. Particularly, the pp-LFER model shows a strong predictive ability for polyfluoroalkyl substances and organosilicon compounds, and the pp-LFER-T model maintains a high predictive accuracy within a wide temperature range (263.15-323.15 K).

  9. Relative solvation free energies calculated using an ab initio QM/MM-based free energy perturbation method: dependence of results on simulation length.

    Science.gov (United States)

    Reddy, M Rami; Erion, Mark D

    2009-12-01

    Molecular dynamics (MD) simulations in conjunction with thermodynamic perturbation approach was used to calculate relative solvation free energies of five pairs of small molecules, namely; (1) methanol to ethane, (2) acetone to acetamide, (3) phenol to benzene, (4) 1,1,1 trichloroethane to ethane, and (5) phenylalanine to isoleucine. Two studies were performed to evaluate the dependence of the convergence of these calculations on MD simulation length and starting configuration. In the first study, each transformation started from the same well-equilibrated configuration and the simulation length was varied from 230 to 2,540 ps. The results indicated that for transformations involving small structural changes, a simulation length of 860 ps is sufficient to obtain satisfactory convergence. In contrast, transformations involving relatively large structural changes, such as phenylalanine to isoleucine, require a significantly longer simulation length (>2,540 ps) to obtain satisfactory convergence. In the second study, the transformation was completed starting from three different configurations and using in each case 860 ps of MD simulation. The results from this study suggest that performing one long simulation may be better than averaging results from three different simulations using a shorter simulation length and three different starting configurations.

  10. How to deal with multiple binding poses in alchemical relative protein-ligand binding free energy calculations.

    Science.gov (United States)

    Kaus, Joseph W; Harder, Edward; Lin, Teng; Abel, Robert; McCammon, J Andrew; Wang, Lingle

    2015-06-09

    Recent advances in improved force fields and sampling methods have made it possible for the accurate calculation of protein–ligand binding free energies. Alchemical free energy perturbation (FEP) using an explicit solvent model is one of the most rigorous methods to calculate relative binding free energies. However, for cases where there are high energy barriers separating the relevant conformations that are important for ligand binding, the calculated free energy may depend on the initial conformation used in the simulation due to the lack of complete sampling of all the important regions in phase space. This is particularly true for ligands with multiple possible binding modes separated by high energy barriers, making it difficult to sample all relevant binding modes even with modern enhanced sampling methods. In this paper, we apply a previously developed method that provides a corrected binding free energy for ligands with multiple binding modes by combining the free energy results from multiple alchemical FEP calculations starting from all enumerated poses, and the results are compared with Glide docking and MM-GBSA calculations. From these calculations, the dominant ligand binding mode can also be predicted. We apply this method to a series of ligands that bind to c-Jun N-terminal kinase-1 (JNK1) and obtain improved free energy results. The dominant ligand binding modes predicted by this method agree with the available crystallography, while both Glide docking and MM-GBSA calculations incorrectly predict the binding modes for some ligands. The method also helps separate the force field error from the ligand sampling error, such that deviations in the predicted binding free energy from the experimental values likely indicate possible inaccuracies in the force field. An error in the force field for a subset of the ligands studied was identified using this method, and improved free energy results were obtained by correcting the partial charges assigned to the

  11. How To Deal with Multiple Binding Poses in Alchemical Relative Protein–Ligand Binding Free Energy Calculations

    Science.gov (United States)

    2016-01-01

    Recent advances in improved force fields and sampling methods have made it possible for the accurate calculation of protein–ligand binding free energies. Alchemical free energy perturbation (FEP) using an explicit solvent model is one of the most rigorous methods to calculate relative binding free energies. However, for cases where there are high energy barriers separating the relevant conformations that are important for ligand binding, the calculated free energy may depend on the initial conformation used in the simulation due to the lack of complete sampling of all the important regions in phase space. This is particularly true for ligands with multiple possible binding modes separated by high energy barriers, making it difficult to sample all relevant binding modes even with modern enhanced sampling methods. In this paper, we apply a previously developed method that provides a corrected binding free energy for ligands with multiple binding modes by combining the free energy results from multiple alchemical FEP calculations starting from all enumerated poses, and the results are compared with Glide docking and MM-GBSA calculations. From these calculations, the dominant ligand binding mode can also be predicted. We apply this method to a series of ligands that bind to c-Jun N-terminal kinase-1 (JNK1) and obtain improved free energy results. The dominant ligand binding modes predicted by this method agree with the available crystallography, while both Glide docking and MM-GBSA calculations incorrectly predict the binding modes for some ligands. The method also helps separate the force field error from the ligand sampling error, such that deviations in the predicted binding free energy from the experimental values likely indicate possible inaccuracies in the force field. An error in the force field for a subset of the ligands studied was identified using this method, and improved free energy results were obtained by correcting the partial charges assigned to the

  12. Classifying Linear Canonical Relations

    OpenAIRE

    Lorand, Jonathan

    2015-01-01

    In this Master's thesis, we consider the problem of classifying, up to conjugation by linear symplectomorphisms, linear canonical relations (lagrangian correspondences) from a finite-dimensional symplectic vector space to itself. We give an elementary introduction to the theory of linear canonical relations and present partial results toward the classification problem. This exposition should be accessible to undergraduate students with a basic familiarity with linear algebra.

  13. Calculation of Relative Binding Free Energy in the Water-Filled Active Site of Oligopeptide-Binding Protein A.

    Science.gov (United States)

    Maurer, Manuela; de Beer, Stephanie B A; Oostenbrink, Chris

    2016-04-15

    The periplasmic oligopeptide binding protein A (OppA) represents a well-known example of water-mediated protein-ligand interactions. Here, we perform free-energy calculations for three different ligands binding to OppA, using a thermodynamic integration approach. The tripeptide ligands share a high structural similarity (all have the sequence KXK), but their experimentally-determined binding free energies differ remarkably. Thermodynamic cycles were constructed for the ligands, and simulations conducted in the bound and (freely solvated) unbound states. In the unbound state, it was observed that the difference in conformational freedom between alanine and glycine leads to a surprisingly slow convergence, despite their chemical similarity. This could be overcome by increasing the softness parameter during alchemical transformations. Discrepancies remained in the bound state however, when comparing independent simulations of the three ligands. These difficulties could be traced to a slow relaxation of the water network within the active site. Fluctuations in the number of water molecules residing in the binding cavity occur mostly on a timescale larger than the simulation time along the alchemical path. After extensive simulations, relative binding free energies that were converged to within thermal noise could be obtained, which agree well with available experimental data.

  14. Free Energies by Thermodynamic Integration Relative to an Exact Solution, Used to Find the Handedness-Switching Salt Concentration for DNA.

    Science.gov (United States)

    Berryman, Joshua T; Schilling, Tanja

    2013-01-08

    Sets of free energy differences are useful for finding the equilibria of chemical reactions, while absolute free energies have little physical meaning. However finding the relative free energy between two macrostates by subtraction of their absolute free energies is a valuable strategy in certain important cases. We present calculations of absolute free energies of biomolecules, using a combination of the well-known Einstein molecule method (for treating the solute) with a conceptually related method of recent genesis for computing free energies of liquids (to treat the solvent and counterions). The approach is based on thermodynamic integration from a detailed atomistic model to one which is simplified but analytically solvable, thereby giving the absolute free energy as that of the tractable model plus a correction term found numerically. An example calculation giving the free energy with respect to salt concentration for the B- and Z-isomers of all-atom duplex DNA in explicit solvent and counterions is presented. The coexistence salt concentration is found with unprecedented accuracy.

  15. Calculation of relative free energies for ligand-protein binding, solvation, and conformational transitions using the GROMOS software.

    Science.gov (United States)

    Riniker, Sereina; Christ, Clara D; Hansen, Halvor S; Hünenberger, Philippe H; Oostenbrink, Chris; Steiner, Denise; van Gunsteren, Wilfred F

    2011-11-24

    The calculation of the relative free energies of ligand-protein binding, of solvation for different compounds, and of different conformational states of a polypeptide is of considerable interest in the design or selection of potential enzyme inhibitors. Since such processes in aqueous solution generally comprise energetic and entropic contributions from many molecular configurations, adequate sampling of the relevant parts of configurational space is required and can be achieved through molecular dynamics simulations. Various techniques to obtain converged ensemble averages and their implementation in the GROMOS software for biomolecular simulation are discussed, and examples of their application to biomolecules in aqueous solution are given. © 2011 American Chemical Society

  16. Linear rate-equilibrium relations arising from ion channel-bilayer energetic coupling

    DEFF Research Database (Denmark)

    Greisen, Per Junior; Lum, Kevin; Ashrafuzzaman, Md

    2011-01-01

    Linear rate-equilibrium (RE) relations, also known as linear free energy relations, are widely observed in chemical reactions, including protein folding, enzymatic catalysis, and channel gating. Despite the widespread occurrence of linear RE relations, the principles underlying the linear relatio...

  17. Organic Carbon/Water and Dissolved Organic Carbon/Water Partitioning of Cyclic Volatile Methylsiloxanes: Measurements and Polyparameter Linear Free Energy Relationships.

    Science.gov (United States)

    Panagopoulos, Dimitri; Jahnke, Annika; Kierkegaard, Amelie; MacLeod, Matthew

    2015-10-20

    The sorption of cyclic volatile methyl siloxanes (cVMS) to organic matter has a strong influence on their fate in the aquatic environment. We report new measurements of the partition ratios between freshwater sediment organic carbon and water (KOC) and between Aldrich humic acid dissolved organic carbon and water (KDOC) for three cVMS, and for three polychlorinated biphenyls (PCBs) that were used as reference chemicals. Our measurements were made using a purge-and-trap method that employs benchmark chemicals to calibrate mass transfer at the air/water interface in a fugacity-based multimedia model. The measured log KOC of octamethylcyclotetrasiloxane (D4), decamethylcyclopentasiloxane (D5), and dodecamethylcyclohexasiloxane (D6) were 5.06, 6.12, and 7.07, and log KDOC were 5.05, 6.13, and 6.79. To our knowledge, our measurements for KOC of D6 and KDOC of D4 and D6 are the first reported. Polyparameter linear free energy relationships (PP-LFERs) derived from training sets of empirical data that did not include cVMS generally did not predict our measured partition ratios of cVMS accurately (root-mean-squared-error (RMSE) for logKOC 0.76 and for logKDOC 0.73). We constructed new PP-LFERs that accurately describe partition ratios for the cVMS as well as for other chemicals by including our new measurements in the existing training sets (logKOC RMSEcVMS: 0.09, logKDOC RMSEcVMS: 0.12). The PP-LFERs we have developed here should be further evaluated and perhaps recalibrated when experimental data for other siloxanes become available.

  18. D3R Grand Challenge 2: blind prediction of protein-ligand poses, affinity rankings, and relative binding free energies

    Science.gov (United States)

    Gaieb, Zied; Liu, Shuai; Gathiaka, Symon; Chiu, Michael; Yang, Huanwang; Shao, Chenghua; Feher, Victoria A.; Walters, W. Patrick; Kuhn, Bernd; Rudolph, Markus G.; Burley, Stephen K.; Gilson, Michael K.; Amaro, Rommie E.

    2018-01-01

    The Drug Design Data Resource (D3R) ran Grand Challenge 2 (GC2) from September 2016 through February 2017. This challenge was based on a dataset of structures and affinities for the nuclear receptor farnesoid X receptor (FXR), contributed by F. Hoffmann-La Roche. The dataset contained 102 IC50 values, spanning six orders of magnitude, and 36 high-resolution co-crystal structures with representatives of four major ligand classes. Strong global participation was evident, with 49 participants submitting 262 prediction submission packages in total. Procedurally, GC2 mimicked Grand Challenge 2015 (GC2015), with a Stage 1 subchallenge testing ligand pose prediction methods and ranking and scoring methods, and a Stage 2 subchallenge testing only ligand ranking and scoring methods after the release of all blinded co-crystal structures. Two smaller curated sets of 18 and 15 ligands were developed to test alchemical free energy methods. This overview summarizes all aspects of GC2, including the dataset details, challenge procedures, and participant results. We also consider implications for progress in the field, while highlighting methodological areas that merit continued development. Similar to GC2015, the outcome of GC2 underscores the pressing need for methods development in pose prediction, particularly for ligand scaffolds not currently represented in the Protein Data Bank (http://www.pdb.org), and in affinity ranking and scoring of bound ligands.

  19. Uncertainty Quantification in Alchemical Free Energy Methods.

    Science.gov (United States)

    Bhati, Agastya P; Wan, Shunzhou; Hu, Yuan; Sherborne, Brad; Coveney, Peter V

    2018-05-02

    Alchemical free energy methods have gained much importance recently from several reports of improved ligand-protein binding affinity predictions based on their implementation using molecular dynamics simulations. A large number of variants of such methods implementing different accelerated sampling techniques and free energy estimators are available, each claimed to be better than the others in its own way. However, the key features of reproducibility and quantification of associated uncertainties in such methods have barely been discussed. Here, we apply a systematic protocol for uncertainty quantification to a number of popular alchemical free energy methods, covering both absolute and relative free energy predictions. We show that a reliable measure of error estimation is provided by ensemble simulation-an ensemble of independent MD simulations-which applies irrespective of the free energy method. The need to use ensemble methods is fundamental and holds regardless of the duration of time of the molecular dynamics simulations performed.

  20. Are automated molecular dynamics simulations and binding free energy calculations realistic tools in lead optimization? An evaluation of the linear interaction energy (LIE) method

    NARCIS (Netherlands)

    Stjernschantz, E.M.; Marelius, J.; Medina, C.; Jacobsson, M.; Vermeulen, N.P.E.; Oostenbrink, C.

    2006-01-01

    An extensive evaluation of the linear interaction energy (LIE) method for the prediction of binding affinity of docked compounds has been performed, with an emphasis on its applicability in lead optimization. An automated setup is presented, which allows for the use of the method in an industrial

  1. The new view of hydrophobic free energy.

    Science.gov (United States)

    Baldwin, Robert L

    2013-04-17

    In the new view, hydrophobic free energy is measured by the work of solute transfer of hydrocarbon gases from vapor to aqueous solution. Reasons are given for believing that older values, measured by solute transfer from a reference solvent to water, are not quantitatively correct. The hydrophobic free energy from gas-liquid transfer is the sum of two opposing quantities, the cavity work (unfavorable) and the solute-solvent interaction energy (favorable). Values of the interaction energy have been found by simulation for linear alkanes and are used here to find the cavity work, which scales linearly with molar volume, not accessible surface area. The hydrophobic free energy is the dominant factor driving folding as judged by the heat capacity change for transfer, which agrees with values for solvating hydrocarbon gases. There is an apparent conflict with earlier values of hydrophobic free energy from studies of large-to-small mutations and an explanation is given. Copyright © 2013 Federation of European Biochemical Societies. Published by Elsevier B.V. All rights reserved.

  2. SOCIAL EQUIVALENT OF FREE ENERGY

    Directory of Open Access Journals (Sweden)

    Josip Stepanic

    2004-06-01

    Full Text Available Characterisation of unbounded resources of a social system within the sociological interpretation has resulted in a large number of different notions, which are relevant in different situations. From the view point of statistical mechanics, these notions resemble free energy. In this paper the concept of social free energy is introduced and first steps toward its development presented. The social free energy is a function equal to physical free energy appropriately determined for the social system, with intrinsically sociological interpretation as a measure of social action obtainable in a given social system without changes in its structure. Its construction is a consequence of response of a social system to recognised parts of environment dynamics. It is argued that development of a social system response resembles exciting the normal modes of a general, physical system.

  3. Interfacial free energy governs single polystyrene chain collapse in water and aqueous solutions.

    Science.gov (United States)

    Li, Isaac T S; Walker, Gilbert C

    2010-05-12

    The hydrophobic interaction is significantly responsible for driving protein folding and self-assembly. To understand it, the thermodynamics, the role of water structure, the dewetting process surrounding hydrophobes, and related aspects have undergone extensive investigations. Here, we examine the hypothesis that polymer-solvent interfacial free energy is adequate to describe the energetics of the collapse of a hydrophobic homopolymer chain at fixed temperature, which serves as a much simplified model for studying the hydrophobic collapse of a protein. This implies that changes in polymer-solvent interfacial free energy should be directly proportional to the force to extend a collapsed polymer into a bad solvent. To test this hypothesis, we undertook single-molecule force spectroscopy on a collapsed, single, polystyrene chain in water-ethanol and water-salt mixtures where we measured the monomer solvation free energy from an ensemble average conformations. Different proportions within the binary mixture were used to create solvents with different interfacial free energies with polystyrene. In these mixed solvents, we observed a linear correlation between the interfacial free energy and the force required to extend the chain into solution, which is a direct measure of the solvation free energy per monomer on a single chain at room temperature. A simple analytical model compares favorably with the experimental results. This knowledge supports a common assumption that explicit water solvent may not be necessary for cases whose primary concerns are hydrophobic interactions and hydrophobic hydration.

  4. Binding free energy predictions of farnesoid X receptor (FXR) agonists using a linear interaction energy (LIE) approach with reliability estimation: application to the D3R Grand Challenge 2

    Science.gov (United States)

    Rifai, Eko Aditya; van Dijk, Marc; Vermeulen, Nico P. E.; Geerke, Daan P.

    2018-01-01

    Computational protein binding affinity prediction can play an important role in drug research but performing efficient and accurate binding free energy calculations is still challenging. In the context of phase 2 of the Drug Design Data Resource (D3R) Grand Challenge 2 we used our automated eTOX ALLIES approach to apply the (iterative) linear interaction energy (LIE) method and we evaluated its performance in predicting binding affinities for farnesoid X receptor (FXR) agonists. Efficiency was obtained by our pre-calibrated LIE models and molecular dynamics (MD) simulations at the nanosecond scale, while predictive accuracy was obtained for a small subset of compounds. Using our recently introduced reliability estimation metrics, we could classify predictions with higher confidence by featuring an applicability domain (AD) analysis in combination with protein-ligand interaction profiling. The outcomes of and agreement between our AD and interaction-profile analyses to distinguish and rationalize the performance of our predictions highlighted the relevance of sufficiently exploring protein-ligand interactions during training and it demonstrated the possibility to quantitatively and efficiently evaluate if this is achieved by using simulation data only.

  5. Evaluation of several two-step scoring functions based on linear interaction energy, effective ligand size, and empirical pair potentials for prediction of protein-ligand binding geometry and free energy.

    Science.gov (United States)

    Rahaman, Obaidur; Estrada, Trilce P; Doren, Douglas J; Taufer, Michela; Brooks, Charles L; Armen, Roger S

    2011-09-26

    The performances of several two-step scoring approaches for molecular docking were assessed for their ability to predict binding geometries and free energies. Two new scoring functions designed for "step 2 discrimination" were proposed and compared to our CHARMM implementation of the linear interaction energy (LIE) approach using the Generalized-Born with Molecular Volume (GBMV) implicit solvation model. A scoring function S1 was proposed by considering only "interacting" ligand atoms as the "effective size" of the ligand and extended to an empirical regression-based pair potential S2. The S1 and S2 scoring schemes were trained and 5-fold cross-validated on a diverse set of 259 protein-ligand complexes from the Ligand Protein Database (LPDB). The regression-based parameters for S1 and S2 also demonstrated reasonable transferability in the CSARdock 2010 benchmark using a new data set (NRC HiQ) of diverse protein-ligand complexes. The ability of the scoring functions to accurately predict ligand geometry was evaluated by calculating the discriminative power (DP) of the scoring functions to identify native poses. The parameters for the LIE scoring function with the optimal discriminative power (DP) for geometry (step 1 discrimination) were found to be very similar to the best-fit parameters for binding free energy over a large number of protein-ligand complexes (step 2 discrimination). Reasonable performance of the scoring functions in enrichment of active compounds in four different protein target classes established that the parameters for S1 and S2 provided reasonable accuracy and transferability. Additional analysis was performed to definitively separate scoring function performance from molecular weight effects. This analysis included the prediction of ligand binding efficiencies for a subset of the CSARdock NRC HiQ data set where the number of ligand heavy atoms ranged from 17 to 35. This range of ligand heavy atoms is where improved accuracy of predicted ligand

  6. Free energy of formation of lanthanum nickelate

    International Nuclear Information System (INIS)

    Sreedharan, O.M.; Chandrasekharaiah, M.S.; Karkhanavala, M.D.

    1976-01-01

    The ΔG 0 /sub f/ of La 2 NiO 4 (s) was determined from the measured emf in the range 1123 to 1373 0 K of the solid oxide electrolyte galvanic cell. The emf data were fitted to a linear equation by the method of least squares. From these data, the standard free-energy change, ΔG 0 , for the reaction NiO(s) + La 2 O 3 (s) = La 2 NiO 4 (s) was calculated. Combining these emf data with the best available free energy of formation data for NiO(s) and La 2 O 3 (s), the following expression for ΔG 0 /sub f/(La 2 NiO 4 (s)) was derived as ΔG 0 /sub f/(La 2 NiO 4 (s)/kJ mole -1 = -2057.0 + 322.8 x 10 -3 T +- 17.30

  7. Interfacial free energy and stiffness of aluminum during rapid solidification

    International Nuclear Information System (INIS)

    Brown, Nicholas T.; Martinez, Enrique; Qu, Jianmin

    2017-01-01

    Using molecular dynamics simulations and the capillary fluctuation method, we have calculated the anisotropic crystal-melt interfacial free energy and stiffness of aluminum in a rapid solidification system where a temperature gradient is applied to enforce thermal non-equilibrium. To calculate these material properties, the standard capillary fluctuation method typically used for systems in equilibrium has been modified to incorporate a second-order Taylor expansion of the interfacial free energy term. The result is a robust method for calculating interfacial energy, stiffness and anisotropy as a function of temperature gradient using the fluctuations in the defined interface height. This work includes the calculation of interface characteristics for temperature gradients ranging from 11 to 34 K/nm. The captured results are compared to a thermal equilibrium case using the same model and simulation technique with a zero gradient definition. We define the temperature gradient as the change in temperature over height perpendicular to the crystal-melt interface. The gradients are applied in MD simulations using defined thermostat regions on a stable solid-liquid interface initially in thermal equilibrium. The results of this work show that the interfacial stiffness and free energy for aluminum are dependent on the magnitude of the temperature gradient, however the anisotropic parameters remain independent of the non-equilibrium conditions applied in this analysis. As a result, the relationships of the interfacial free energy/stiffness are determined to be linearly related to the thermal gradient, and can be interpolated to find material characteristics at additional temperature gradients.

  8. Integrodifferential relations in linear elasticity

    CERN Document Server

    Kostin, Georgy V

    2012-01-01

    This work treats the elasticity of deformed bodies, including the resulting interior stresses and displacements.It also takes into account that some of constitutive relations can be considered in a weak form. To discuss this problem properly, the method of integrodifferential relations is used, and an advanced numerical technique for stress-strain analysis is presented and evaluated using various discretization techniques. The methods presented in this book are of importance for almost all elasticity problems in materials science and mechanical engineering.

  9. Calculating Free Energies Using Average Force

    Science.gov (United States)

    Darve, Eric; Pohorille, Andrew; DeVincenzi, Donald L. (Technical Monitor)

    2001-01-01

    A new, general formula that connects the derivatives of the free energy along the selected, generalized coordinates of the system with the instantaneous force acting on these coordinates is derived. The instantaneous force is defined as the force acting on the coordinate of interest so that when it is subtracted from the equations of motion the acceleration along this coordinate is zero. The formula applies to simulations in which the selected coordinates are either unconstrained or constrained to fixed values. It is shown that in the latter case the formula reduces to the expression previously derived by den Otter and Briels. If simulations are carried out without constraining the coordinates of interest, the formula leads to a new method for calculating the free energy changes along these coordinates. This method is tested in two examples - rotation around the C-C bond of 1,2-dichloroethane immersed in water and transfer of fluoromethane across the water-hexane interface. The calculated free energies are compared with those obtained by two commonly used methods. One of them relies on determining the probability density function of finding the system at different values of the selected coordinate and the other requires calculating the average force at discrete locations along this coordinate in a series of constrained simulations. The free energies calculated by these three methods are in excellent agreement. The relative advantages of each method are discussed.

  10. Free energy and heat capacity

    International Nuclear Information System (INIS)

    Kurata, M.; Devanathan, R.

    2015-01-01

    Free energy and heat capacity of actinide elements and compounds are important properties for the evaluation of the safety and reliable performance of nuclear fuel. They are essential inputs for models that describe complex phenomena that govern the behaviour of actinide compounds during nuclear fuels fabrication and irradiation. This chapter introduces various experimental methods to measure free energy and heat capacity to serve as inputs for models and to validate computer simulations. This is followed by a discussion of computer simulation of these properties, and recent simulations of thermophysical properties of nuclear fuel are briefly reviewed. (authors)

  11. Free Energy in Introductory Physics

    Science.gov (United States)

    Prentis, Jeffrey J.; Obsniuk, Michael J.

    2016-01-01

    Energy and entropy are two of the most important concepts in science. For all natural processes where a system exchanges energy with its environment, the energy of the system tends to decrease and the entropy of the system tends to increase. Free energy is the special concept that specifies how to balance the opposing tendencies to minimize energy…

  12. Free energy surfaces in the superconducting mixed state

    Science.gov (United States)

    Finnemore, D. K.; Fang, M. M.; Bansal, N. P.; Farrell, D. E.

    1989-01-01

    The free energy surface for Tl2Ba2Ca2Cu3O1O has been measured as a function of temperature and magnetic field to determine the fundamental thermodynamic properties of the mixed state. The change in free energy, G(H)-G(O), is found to be linear in temperature over a wide range indicating that the specific heat is independent of field.

  13. Free energy profiles from single-molecule pulling experiments.

    Science.gov (United States)

    Hummer, Gerhard; Szabo, Attila

    2010-12-14

    Nonequilibrium pulling experiments provide detailed information about the thermodynamic and kinetic properties of molecules. We show that unperturbed free energy profiles as a function of molecular extension can be obtained rigorously from such experiments without using work-weighted position histograms. An inverse Weierstrass transform is used to relate the system free energy obtained from the Jarzynski equality directly to the underlying molecular free energy surface. An accurate approximation for the free energy surface is obtained by using the method of steepest descent to evaluate the inverse transform. The formalism is applied to simulated data obtained from a kinetic model of RNA folding, in which the dynamics consists of jumping between linker-dominated folded and unfolded free energy surfaces.

  14. Computing the Free Energy Barriers for Less by Sampling with a Coarse Reference Potential while Retaining Accuracy of the Target Fine Model.

    Science.gov (United States)

    Plotnikov, Nikolay V

    2014-08-12

    Proposed in this contribution is a protocol for calculating fine-physics (e.g., ab initio QM/MM) free-energy surfaces at a high level of accuracy locally (e.g., only at reactants and at the transition state for computing the activation barrier) from targeted fine-physics sampling and extensive exploratory coarse-physics sampling. The full free-energy surface is still computed but at a lower level of accuracy from coarse-physics sampling. The method is analytically derived in terms of the umbrella sampling and the free-energy perturbation methods which are combined with the thermodynamic cycle and the targeted sampling strategy of the paradynamics approach. The algorithm starts by computing low-accuracy fine-physics free-energy surfaces from the coarse-physics sampling in order to identify the reaction path and to select regions for targeted sampling. Thus, the algorithm does not rely on the coarse-physics minimum free-energy reaction path. Next, segments of high-accuracy free-energy surface are computed locally at selected regions from the targeted fine-physics sampling and are positioned relative to the coarse-physics free-energy shifts. The positioning is done by averaging the free-energy perturbations computed with multistep linear response approximation method. This method is analytically shown to provide results of the thermodynamic integration and the free-energy interpolation methods, while being extremely simple in implementation. Incorporating the metadynamics sampling to the algorithm is also briefly outlined. The application is demonstrated by calculating the B3LYP//6-31G*/MM free-energy barrier for an enzymatic reaction using a semiempirical PM6/MM reference potential. These modifications allow computing the activation free energies at a significantly reduced computational cost but at the same level of accuracy compared to computing full potential of mean force.

  15. Ascent, descent, nullity, defect, and related notions for linear relations in linear spaces

    NARCIS (Netherlands)

    Sandovici, Adrian; de Snoo, Henk; Winkler, Henrik

    2007-01-01

    For a linear relation in a linear space the concepts of ascent, descent, nullity, and defect are introduced and studied. It is shown that the results of A.E. Taylor and M.A. Kaashoek concerning the relationship between ascent, descent, nullity, and defect for the case of linear operators remain

  16. Diffusion in multicomponent systems: a free energy approach

    International Nuclear Information System (INIS)

    Emmanuel, Simon; Cortis, Andrea; Berkowitz, Brian

    2004-01-01

    This work examines diffusion in ternary non-ideal systems and derives coupled non-linear equations based on a non-equilibrium thermodynamic approach in which an explicit expression for the free energy is substituted into standard diffusion equations. For ideal solutions, the equations employ four mobility parameters (M aa , M ab , M ba , and M bb ), and uphill diffusion is predicted for certain initial conditions and combinations of mobilities. For the more complex case of ternary Simple Mixtures, two non-ideality parameters (χ ac and χ bc ) that are directly related to the excess free energy of mixing are introduced. The solution of the equations is carried out by means of two different numerical schemes: (1) spectral collocation and (2) finite element. An error minimization technique is coupled with the spectral collocation method and applied to diffusional profiles to extract the M and χ parameters. The model satisfactorily reproduces diffusional profiles from published data for silicate melts. Further improvements in numerical and experimental techniques are then suggested

  17. Surface free energy for systems with integrable boundary conditions

    International Nuclear Information System (INIS)

    Goehmann, Frank; Bortz, Michael; Frahm, Holger

    2005-01-01

    The surface free energy is the difference between the free energies for a system with open boundary conditions and the same system with periodic boundary conditions. We use the quantum transfer matrix formalism to express the surface free energy in the thermodynamic limit of systems with integrable boundary conditions as a matrix element of certain projection operators. Specializing to the XXZ spin-1/2 chain we introduce a novel 'finite temperature boundary operator' which characterizes the thermodynamical properties of surfaces related to integrable boundary conditions

  18. Free energy of hydration of niobium oxide

    International Nuclear Information System (INIS)

    Plodinec, M.J.

    1996-01-01

    Some of the glasses being formulated by SRTC researchers contain niobium oxide. In this report, the free energy of hydration of the oxide is calculated from the free energies of formation of the oxide, the hydroxide, and water. This value can be used in calculations of the free energy of hydration of glasses containing niobium

  19. Probing Free-Energy Surfaces with Differential Scanning Calorimetry

    Science.gov (United States)

    Sanchez-Ruiz, Jose M.

    2011-05-01

    Many aspects of protein folding can be understood in terms of projections of the highly dimensional energy landscape onto a few (or even only one) particularly relevant coordinates. These free-energy surfaces can be probed conveniently from experimental differential scanning calorimetry (DSC) thermograms, as DSC provides a direct relation with the protein partition function. Free-energy surfaces thus obtained are consistent with two fundamental scenarios predicted by the energy-landscape perspective: (a) well-defined macrostates separated by significant free-energy barriers, in some cases, and, in many other cases, (b) marginal or even vanishingly small barriers, which furthermore show a good correlation with kinetics for fast- and ultrafast-folding proteins. Overall, the potential of DSC to assess free-energy surfaces for a wide variety of proteins makes it possible to address fundamental issues, such as the molecular basis of the barrier modulations produced by natural selection in response to functional requirements or to ensure kinetic stability.

  20. Linear time relational prototype based learning.

    Science.gov (United States)

    Gisbrecht, Andrej; Mokbel, Bassam; Schleif, Frank-Michael; Zhu, Xibin; Hammer, Barbara

    2012-10-01

    Prototype based learning offers an intuitive interface to inspect large quantities of electronic data in supervised or unsupervised settings. Recently, many techniques have been extended to data described by general dissimilarities rather than Euclidean vectors, so-called relational data settings. Unlike the Euclidean counterparts, the techniques have quadratic time complexity due to the underlying quadratic dissimilarity matrix. Thus, they are infeasible already for medium sized data sets. The contribution of this article is twofold: On the one hand we propose a novel supervised prototype based classification technique for dissimilarity data based on popular learning vector quantization (LVQ), on the other hand we transfer a linear time approximation technique, the Nyström approximation, to this algorithm and an unsupervised counterpart, the relational generative topographic mapping (GTM). This way, linear time and space methods result. We evaluate the techniques on three examples from the biomedical domain.

  1. From free energy to expected energy: Improving energy-based value function approximation in reinforcement learning.

    Science.gov (United States)

    Elfwing, Stefan; Uchibe, Eiji; Doya, Kenji

    2016-12-01

    Free-energy based reinforcement learning (FERL) was proposed for learning in high-dimensional state and action spaces. However, the FERL method does only really work well with binary, or close to binary, state input, where the number of active states is fewer than the number of non-active states. In the FERL method, the value function is approximated by the negative free energy of a restricted Boltzmann machine (RBM). In our earlier study, we demonstrated that the performance and the robustness of the FERL method can be improved by scaling the free energy by a constant that is related to the size of network. In this study, we propose that RBM function approximation can be further improved by approximating the value function by the negative expected energy (EERL), instead of the negative free energy, as well as being able to handle continuous state input. We validate our proposed method by demonstrating that EERL: (1) outperforms FERL, as well as standard neural network and linear function approximation, for three versions of a gridworld task with high-dimensional image state input; (2) achieves new state-of-the-art results in stochastic SZ-Tetris in both model-free and model-based learning settings; and (3) significantly outperforms FERL and standard neural network function approximation for a robot navigation task with raw and noisy RGB images as state input and a large number of actions. Copyright © 2016 The Author(s). Published by Elsevier Ltd.. All rights reserved.

  2. Mapping the conformational free energy of aspartic acid in the gas phase and in aqueous solution.

    Science.gov (United States)

    Comitani, Federico; Rossi, Kevin; Ceriotti, Michele; Sanz, M Eugenia; Molteni, Carla

    2017-04-14

    The conformational free energy landscape of aspartic acid, a proteogenic amino acid involved in a wide variety of biological functions, was investigated as an example of the complexity that multiple rotatable bonds produce even in relatively simple molecules. To efficiently explore such a landscape, this molecule was studied in the neutral and zwitterionic forms, in the gas phase and in water solution, by means of molecular dynamics and the enhanced sampling method metadynamics with classical force-fields. Multi-dimensional free energy landscapes were reduced to bi-dimensional maps through the non-linear dimensionality reduction algorithm sketch-map to identify the energetically stable conformers and their interconnection paths. Quantum chemical calculations were then performed on the minimum free energy structures. Our procedure returned the low energy conformations observed experimentally in the gas phase with rotational spectroscopy [M. E. Sanz et al., Phys. Chem. Chem. Phys. 12, 3573 (2010)]. Moreover, it provided information on higher energy conformers not accessible to experiments and on the conformers in water. The comparison between different force-fields and quantum chemical data highlighted the importance of the underlying potential energy surface to accurately capture energy rankings. The combination of force-field based metadynamics, sketch-map analysis, and quantum chemical calculations was able to produce an exhaustive conformational exploration in a range of significant free energies that complements the experimental data. Similar protocols can be applied to larger peptides with complex conformational landscapes and would greatly benefit from the next generation of accurate force-fields.

  3. Mapping the conformational free energy of aspartic acid in the gas phase and in aqueous solution

    Science.gov (United States)

    Comitani, Federico; Rossi, Kevin; Ceriotti, Michele; Sanz, M. Eugenia; Molteni, Carla

    2017-04-01

    The conformational free energy landscape of aspartic acid, a proteogenic amino acid involved in a wide variety of biological functions, was investigated as an example of the complexity that multiple rotatable bonds produce even in relatively simple molecules. To efficiently explore such a landscape, this molecule was studied in the neutral and zwitterionic forms, in the gas phase and in water solution, by means of molecular dynamics and the enhanced sampling method metadynamics with classical force-fields. Multi-dimensional free energy landscapes were reduced to bi-dimensional maps through the non-linear dimensionality reduction algorithm sketch-map to identify the energetically stable conformers and their interconnection paths. Quantum chemical calculations were then performed on the minimum free energy structures. Our procedure returned the low energy conformations observed experimentally in the gas phase with rotational spectroscopy [M. E. Sanz et al., Phys. Chem. Chem. Phys. 12, 3573 (2010)]. Moreover, it provided information on higher energy conformers not accessible to experiments and on the conformers in water. The comparison between different force-fields and quantum chemical data highlighted the importance of the underlying potential energy surface to accurately capture energy rankings. The combination of force-field based metadynamics, sketch-map analysis, and quantum chemical calculations was able to produce an exhaustive conformational exploration in a range of significant free energies that complements the experimental data. Similar protocols can be applied to larger peptides with complex conformational landscapes and would greatly benefit from the next generation of accurate force-fields.

  4. Exploration, Novelty, Surprise and Free Energy Minimisation

    Directory of Open Access Journals (Sweden)

    Philipp eSchwartenbeck

    2013-10-01

    Full Text Available This paper reviews recent developments under the free energy principle that introduce a normative perspective on classical economic (utilitarian decision-making based on (active Bayesian inference. It has been suggested that the free energy principle precludes novelty and complexity, because it assumes that biological systems – like ourselves - try to minimise the long-term average of surprise to maintain their homeostasis. However, recent formulations show that minimising surprise leads naturally to concepts such as exploration and novelty bonuses. In this approach, agents infer a policy that minimises surprise by minimising the difference (or relative entropy between likely and desired outcomes, which involves both pursuing the goal-state that has the highest expected utility (often termed ‘exploitation’ and visiting a number of different goal-states (‘exploration’. Crucially, the opportunity to visit new states increases the value of the current state. Casting decision-making problems within a variational framework, therefore, predicts that our behaviour is governed by both the entropy and expected utility of future states. This dissolves any dialectic between minimising surprise and exploration or novelty seeking.

  5. QM/MM free energy simulations: recent progress and challenges

    Science.gov (United States)

    Lu, Xiya; Fang, Dong; Ito, Shingo; Okamoto, Yuko; Ovchinnikov, Victor

    2016-01-01

    Due to the higher computational cost relative to pure molecular mechanical (MM) simulations, hybrid quantum mechanical/molecular mechanical (QM/MM) free energy simulations particularly require a careful consideration of balancing computational cost and accuracy. Here we review several recent developments in free energy methods most relevant to QM/MM simulations and discuss several topics motivated by these developments using simple but informative examples that involve processes in water. For chemical reactions, we highlight the value of invoking enhanced sampling technique (e.g., replica-exchange) in umbrella sampling calculations and the value of including collective environmental variables (e.g., hydration level) in metadynamics simulations; we also illustrate the sensitivity of string calculations, especially free energy along the path, to various parameters in the computation. Alchemical free energy simulations with a specific thermodynamic cycle are used to probe the effect of including the first solvation shell into the QM region when computing solvation free energies. For cases where high-level QM/MM potential functions are needed, we analyze two different approaches: the QM/MM-MFEP method of Yang and co-workers and perturbative correction to low-level QM/MM free energy results. For the examples analyzed here, both approaches seem productive although care needs to be exercised when analyzing the perturbative corrections. PMID:27563170

  6. Accelerated weight histogram method for exploring free energy landscapes

    Energy Technology Data Exchange (ETDEWEB)

    Lindahl, V.; Lidmar, J.; Hess, B. [Department of Theoretical Physics and Swedish e-Science Research Center, KTH Royal Institute of Technology, 10691 Stockholm (Sweden)

    2014-07-28

    Calculating free energies is an important and notoriously difficult task for molecular simulations. The rapid increase in computational power has made it possible to probe increasingly complex systems, yet extracting accurate free energies from these simulations remains a major challenge. Fully exploring the free energy landscape of, say, a biological macromolecule typically requires sampling large conformational changes and slow transitions. Often, the only feasible way to study such a system is to simulate it using an enhanced sampling method. The accelerated weight histogram (AWH) method is a new, efficient extended ensemble sampling technique which adaptively biases the simulation to promote exploration of the free energy landscape. The AWH method uses a probability weight histogram which allows for efficient free energy updates and results in an easy discretization procedure. A major advantage of the method is its general formulation, making it a powerful platform for developing further extensions and analyzing its relation to already existing methods. Here, we demonstrate its efficiency and general applicability by calculating the potential of mean force along a reaction coordinate for both a single dimension and multiple dimensions. We make use of a non-uniform, free energy dependent target distribution in reaction coordinate space so that computational efforts are not wasted on physically irrelevant regions. We present numerical results for molecular dynamics simulations of lithium acetate in solution and chignolin, a 10-residue long peptide that folds into a β-hairpin. We further present practical guidelines for setting up and running an AWH simulation.

  7. Microscopically derived free energy of dislocations

    NARCIS (Netherlands)

    Kooiman, M.; Hütter, M.; Geers, M.G.D.

    2015-01-01

    The dynamics of large amounts of dislocations is the governing mechanism in metal plasticity. The free energy of a continuous dislocation density profile plays a crucial role in the description of the dynamics of dislocations, as free energy derivatives act as the driving forces of dislocation

  8. Gravitational Wave in Linear General Relativity

    Science.gov (United States)

    Cubillos, D. J.

    2017-07-01

    General relativity is the best theory currently available to describe the interaction due to gravity. Within Albert Einstein's field equations this interaction is described by means of the spatiotemporal curvature generated by the matter-energy content in the universe. Weyl worked on the existence of perturbations of the curvature of space-time that propagate at the speed of light, which are known as Gravitational Waves, obtained to a first approximation through the linearization of the field equations of Einstein. Weyl's solution consists of taking the field equations in a vacuum and disturbing the metric, using the Minkowski metric slightly perturbed by a factor ɛ greater than zero but much smaller than one. If the feedback effect of the field is neglected, it can be considered as a weak field solution. After introducing the disturbed metric and ignoring ɛ terms of order greater than one, we can find the linearized field equations in terms of the perturbation, which can then be expressed in terms of the Dalambertian operator of the perturbation equalized to zero. This is analogous to the linear wave equation in classical mechanics, which can be interpreted by saying that gravitational effects propagate as waves at the speed of light. In addition to this, by studying the motion of a particle affected by this perturbation through the geodesic equation can show the transversal character of the gravitational wave and its two possible states of polarization. It can be shown that the energy carried by the wave is of the order of 1/c5 where c is the speed of light, which explains that its effects on matter are very small and very difficult to detect.

  9. The free energy principle, negative energy modes, and stability

    International Nuclear Information System (INIS)

    Morrison, P.J.; Kotschenreuther, M.

    1990-01-01

    This paper is concerned with instability of equilibria of Hamiltonian, fluid and plasma dynamical systems. Usually the dynamical equilibrium of interest is not the state of thermodynamic equilibrium, and does not correspond to a free energy minimum. The relaxation of this type of equilibrium is conventionally considered to be initiated by linear instability. However, there are many cases where linear instability is not present, but the equilibrium is nonlinearly unstable to arbitrarily small perturbations. This paper is about general free energy expressions for determining the presence of linear or nonlinear instabilities. These expressions are simple and practical, and can be obtained for all equilibria of all ideal fluid and plasma models. By free energy, we mean the energy change upon perturbations of the equilibrium that respect dynamical phase space constraints. This quantity is measured by a self-adjoint quadratic form, called δ 2 F. The free energy can result in instability when δ 2 F is indefinite; i.e. there exist accessible perturbations that lower the free energy of the system. A primary purpose of this paper is to tie together three manifestations of what we will refer to as negative energy modes. The first is the conventional plasma physics notion of negative energy mode that is based on the definition of the energy in a homogeneous dielectric medium. A negative energy mode is a normal mode of the medium (plasma) that possesses negative dielectric energy. The second manifestation occurs in finite degree-of-freedom Hamiltonian normal form theory. The quadratic part of a Hamiltonian in the vicinity of an equilibrium point, which possesses only distinct oscillatory eigenvalues, has an invariant signature. Thus in cases where the quadratic form is indefinite, it is natural to refer to the modes corresponding to the negative signature as negative energy modes

  10. Structure-based prediction of free energy changes of binding of PTP1B inhibitors

    Science.gov (United States)

    Wang, Jing; Ling Chan, Shek; Ramnarayan, Kal

    2003-08-01

    The goals were (1) to understand the driving forces in the binding of small molecule inhibitors to the active site of PTP1B and (2) to develop a molecular mechanics-based empirical free energy function for compound potency prediction. A set of compounds with known activities was docked onto the active site. The related energy components and molecular surface areas were calculated. The bridging water molecules were identified and their contributions were considered. Linear relationships were explored between the above terms and the binding free energies of compounds derived based on experimental inhibition constants. We found that minimally three terms are required to give rise to a good correlation (0.86) with predictive power in five-group cross-validation test (q2 = 0.70). The dominant terms are the electrostatic energy and non-electrostatic energy stemming from the intra- and intermolecular interactions of solutes and from those of bridging water molecules in complexes.

  11. Mechanism of active transport: free energy dissipation and free energy transduction.

    OpenAIRE

    Tanford, C

    1982-01-01

    The thermodynamic pathway for "chemiosmotic" free energy transduction in active transport is discussed with an ATP-driven Ca2+ pump as an illustrative example. Two innovations are made in the analysis. (i) Free energy dissipated as heat is rigorously excluded from overall free energy bookkeeping by focusing on the dynamic equilibrium state of the chemiosmotic process. (ii) Separate chemical potential terms for free energy donor and transported ions are used to keep track of the thermodynamic ...

  12. Finite-size corrections to the free energies of crystalline solids

    NARCIS (Netherlands)

    Polson, J.M.; Trizac, E.; Pronk, S.; Frenkel, D.

    2000-01-01

    We analyze the finite-size corrections to the free energy of crystals with a fixed center of mass. When we explicitly correct for the leading (ln N/N) corrections, the remaining free energy is found to depend linearly on 1/N. Extrapolating to the thermodynamic limit (N → ∞), we estimate the free

  13. Exploration, Sampling, And Reconstruction of Free Energy Surfaces with Gaussian Process Regression.

    Science.gov (United States)

    Mones, Letif; Bernstein, Noam; Csányi, Gábor

    2016-10-11

    Practical free energy reconstruction algorithms involve three separate tasks: biasing, measuring some observable, and finally reconstructing the free energy surface from those measurements. In more than one dimension, adaptive schemes make it possible to explore only relatively low lying regions of the landscape by progressively building up the bias toward the negative of the free energy surface so that free energy barriers are eliminated. Most schemes use the final bias as their best estimate of the free energy surface. We show that large gains in computational efficiency, as measured by the reduction of time to solution, can be obtained by separating the bias used for dynamics from the final free energy reconstruction itself. We find that biasing with metadynamics, measuring a free energy gradient estimator, and reconstructing using Gaussian process regression can give an order of magnitude reduction in computational cost.

  14. Converging ligand-binding free energies obtained with free-energy perturbations at the quantum mechanical level.

    Science.gov (United States)

    Olsson, Martin A; Söderhjelm, Pär; Ryde, Ulf

    2016-06-30

    In this article, the convergence of quantum mechanical (QM) free-energy simulations based on molecular dynamics simulations at the molecular mechanics (MM) level has been investigated. We have estimated relative free energies for the binding of nine cyclic carboxylate ligands to the octa-acid deep-cavity host, including the host, the ligand, and all water molecules within 4.5 Å of the ligand in the QM calculations (158-224 atoms). We use single-step exponential averaging (ssEA) and the non-Boltzmann Bennett acceptance ratio (NBB) methods to estimate QM/MM free energy with the semi-empirical PM6-DH2X method, both based on interaction energies. We show that ssEA with cumulant expansion gives a better convergence and uses half as many QM calculations as NBB, although the two methods give consistent results. With 720,000 QM calculations per transformation, QM/MM free-energy estimates with a precision of 1 kJ/mol can be obtained for all eight relative energies with ssEA, showing that this approach can be used to calculate converged QM/MM binding free energies for realistic systems and large QM partitions. © 2016 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc. © 2016 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.

  15. Variational Approach to Enhanced Sampling and Free Energy Calculations

    Science.gov (United States)

    Valsson, Omar; Parrinello, Michele

    2014-08-01

    The ability of widely used sampling methods, such as molecular dynamics or Monte Carlo simulations, to explore complex free energy landscapes is severely hampered by the presence of kinetic bottlenecks. A large number of solutions have been proposed to alleviate this problem. Many are based on the introduction of a bias potential which is a function of a small number of collective variables. However constructing such a bias is not simple. Here we introduce a functional of the bias potential and an associated variational principle. The bias that minimizes the functional relates in a simple way to the free energy surface. This variational principle can be turned into a practical, efficient, and flexible sampling method. A number of numerical examples are presented which include the determination of a three-dimensional free energy surface. We argue that, beside being numerically advantageous, our variational approach provides a convenient and novel standpoint for looking at the sampling problem.

  16. Free Energy and Internal Combustion Engine Cycles

    OpenAIRE

    Harris, William D.

    2012-01-01

    The performance of one type (Carnot) of Internal Combustion Engine (ICE) cycle is analyzed within the framework of thermodynamic free energies. ICE performance is different from that of an External Combustion Engine (ECE) which is dictated by Carnot's rule.

  17. Virtual substitution scan via single-step free energy perturbation.

    Science.gov (United States)

    Chiang, Ying-Chih; Wang, Yi

    2016-02-05

    With the rapid expansion of our computing power, molecular dynamics (MD) simulations ranging from hundreds of nanoseconds to microseconds or even milliseconds have become increasingly common. The majority of these long trajectories are obtained from plain (vanilla) MD simulations, where no enhanced sampling or free energy calculation method is employed. To promote the 'recycling' of these trajectories, we developed the Virtual Substitution Scan (VSS) toolkit as a plugin of the open-source visualization and analysis software VMD. Based on the single-step free energy perturbation (sFEP) method, VSS enables the user to post-process a vanilla MD trajectory for a fast free energy scan of substituting aryl hydrogens by small functional groups. Dihedrals of the functional groups are sampled explicitly in VSS, which improves the performance of the calculation and is found particularly important for certain groups. As a proof-of-concept demonstration, we employ VSS to compute the solvation free energy change upon substituting the hydrogen of a benzene molecule by 12 small functional groups frequently considered in lead optimization. Additionally, VSS is used to compute the relative binding free energy of four selected ligands of the T4 lysozyme. Overall, the computational cost of VSS is only a fraction of the corresponding multi-step FEP (mFEP) calculation, while its results agree reasonably well with those of mFEP, indicating that VSS offers a promising tool for rapid free energy scan of small functional group substitutions. This article is protected by copyright. All rights reserved. © 2016 Wiley Periodicals, Inc.

  18. Direct measurement of the free energy of aging hard sphere colloidal glasses.

    Science.gov (United States)

    Zargar, Rojman; Nienhuis, Bernard; Schall, Peter; Bonn, Daniel

    2013-06-21

    The nature of the glass transition is one of the most important unsolved problems in condensed matter physics. The difference between glasses and liquids is believed to be caused by very large free energy barriers for particle rearrangements; however, so far it has not been possible to confirm this experimentally. We provide the first quantitative determination of the free energy for an aging hard sphere colloidal glass. The determination of the free energy allows for a number of new insights in the glass transition, notably the quantification of the strong spatial and temporal heterogeneity in the free energy. A study of the local minima of the free energy reveals that the observed variations are directly related to the rearrangements of the particles. Our main finding is that the probability of particle rearrangements shows a power law dependence on the free energy changes associated with the rearrangements similar to the Gutenberg-Richter law in seismology.

  19. Good Practices in Free-energy Calculations

    Science.gov (United States)

    Pohorille, Andrew; Jarzynski, Christopher; Chipot, Christopher

    2013-01-01

    As access to computational resources continues to increase, free-energy calculations have emerged as a powerful tool that can play a predictive role in drug design. Yet, in a number of instances, the reliability of these calculations can be improved significantly if a number of precepts, or good practices are followed. For the most part, the theory upon which these good practices rely has been known for many years, but often overlooked, or simply ignored. In other cases, the theoretical developments are too recent for their potential to be fully grasped and merged into popular platforms for the computation of free-energy differences. The current best practices for carrying out free-energy calculations will be reviewed demonstrating that, at little to no additional cost, free-energy estimates could be markedly improved and bounded by meaningful error estimates. In energy perturbation and nonequilibrium work methods, monitoring the probability distributions that underlie the transformation between the states of interest, performing the calculation bidirectionally, stratifying the reaction pathway and choosing the most appropriate paradigms and algorithms for transforming between states offer significant gains in both accuracy and precision. In thermodynamic integration and probability distribution (histogramming) methods, properly designed adaptive techniques yield nearly uniform sampling of the relevant degrees of freedom and, by doing so, could markedly improve efficiency and accuracy of free energy calculations without incurring any additional computational expense.

  20. Spectral analysis of linear relations and degenerate operator semigroups

    International Nuclear Information System (INIS)

    Baskakov, A G; Chernyshov, K I

    2002-01-01

    Several problems of the spectral theory of linear relations in Banach spaces are considered. Linear differential inclusions in a Banach space are studied. The construction of the phase space and solutions is carried out with the help of the spectral theory of linear relations, ergodic theorems, and degenerate operator semigroups

  1. Free energy analysis of cell spreading.

    Science.gov (United States)

    McEvoy, Eóin; Deshpande, Vikram S; McGarry, Patrick

    2017-10-01

    In this study we present a steady-state adaptation of the thermodynamically motivated stress fiber (SF) model of Vigliotti et al. (2015). We implement this steady-state formulation in a non-local finite element setting where we also consider global conservation of the total number of cytoskeletal proteins within the cell, global conservation of the number of binding integrins on the cell membrane, and adhesion limiting ligand density on the substrate surface. We present a number of simulations of cell spreading in which we consider a limited subset of the possible deformed spread-states assumed by the cell in order to examine the hypothesis that free energy minimization drives the process of cell spreading. Simulations suggest that cell spreading can be viewed as a competition between (i) decreasing cytoskeletal free energy due to strain induced assembly of cytoskeletal proteins into contractile SFs, and (ii) increasing elastic free energy due to stretching of the mechanically passive components of the cell. The computed minimum free energy spread area is shown to be lower for a cell on a compliant substrate than on a rigid substrate. Furthermore, a low substrate ligand density is found to limit cell spreading. The predicted dependence of cell spread area on substrate stiffness and ligand density is in agreement with the experiments of Engler et al. (2003). We also simulate the experiments of Théry et al. (2006), whereby initially circular cells deform and adhere to "V-shaped" and "Y-shaped" ligand patches. Analysis of a number of different spread states reveals that deformed configurations with the lowest free energy exhibit a SF distribution that corresponds to experimental observations, i.e. a high concentration of highly aligned SFs occurs along free edges, with lower SF concentrations in the interior of the cell. In summary, the results of this study suggest that cell spreading is driven by free energy minimization based on a competition between decreasing

  2. Free energy of superfluid 3He

    International Nuclear Information System (INIS)

    Rainer, D.; Serene, J.W.

    1976-01-01

    A systematic scheme is presented for calculating the free energy of superfluid Fermi liquids by an asymptotic expansion in the small parameter T/subc//T/subF/. This scheme is used to evaluate the strong-coupling corrections to the free energy of superfluid 3 He. It is shown that the leading corrections can be expressed in terms of the normal-state quasiparticle scattering amplitude, and the strong-coupling results are discussed using the s-p approximation for the scattering amplitude

  3. Linear free energy relationships in heterogeneous catalysis--13. The dehydration of aliphatic alcohols over silica-alumina. [N-butyl alcohol, sec. -butyl or isopropyl alcohol, tert. -butyl alcolol

    Energy Technology Data Exchange (ETDEWEB)

    Take, J; Matsumoto, T; Yoneda, Y

    1978-01-01

    The dehydration of n-butyl alcohol at 120/sup 0/-166/sup 0/C, sec.-butyl or isopropyl alcohol at 100/sup 0/-145/sup 0/C, and tert.-butyl alcohol at 54/sup 0/-80/sup 0/C, over silica/alumina catalyst was zero order in alcohol at 0.01-0.1 atm, and the activation energies were 35.3, 31.7, 32.0, and 29.9 kcal/mol, respectively. The zero-order rate constants were mainly affected by the activation energies since the preexponential factors varied little except for tert.-butyl alcohol. A linear relationship was found between the activation energy or the logarithm of the zero-order rate constant and the heterolytic bond dissociation energy for the carbon-oxygen bond in alcohols D(R/sup +/OH/sup -/). The activation energy increased and the rate constant decreased with increasing D(R/sup +/OH/sup -/). The results indicate that dehydration is E1 over this catalyst, but a similar correlation was observed based on published data for dehydration over alumina, which follows an E2 mechanism, indicating that heterolytic cleavage of the C-O bond is rate-determining in both mechanisms.

  4. Free energy functionals for polarization fluctuations: Pekar factor revisited.

    Science.gov (United States)

    Dinpajooh, Mohammadhasan; Newton, Marshall D; Matyushov, Dmitry V

    2017-02-14

    The separation of slow nuclear and fast electronic polarization in problems related to electron mobility in polarizable media was considered by Pekar 70 years ago. Within dielectric continuum models, this separation leads to the Pekar factor in the free energy of solvation by the nuclear degrees of freedom. The main qualitative prediction of Pekar's perspective is a significant, by about a factor of two, drop of the nuclear solvation free energy compared to the total (electronic plus nuclear) free energy of solvation. The Pekar factor enters the solvent reorganization energy of electron transfer reactions and is a significant mechanistic parameter accounting for the solvent effect on electron transfer. Here, we study the separation of the fast and slow polarization modes in polar molecular liquids (polarizable dipolar liquids and polarizable water force fields) without relying on the continuum approximation. We derive the nonlocal free energy functional and use atomistic numerical simulations to obtain nonlocal, reciprocal space electronic and nuclear susceptibilities. A consistent transition to the continuum limit is introduced by extrapolating the results of finite-size numerical simulation to zero wavevector. The continuum nuclear susceptibility extracted from the simulations is numerically close to the Pekar factor. However, we derive a new functionality involving the static and high-frequency dielectric constants. The main distinction of our approach from the traditional theories is found in the solvation free energy due to the nuclear polarization: the anticipated significant drop of its magnitude with increasing liquid polarizability does not occur. The reorganization energy of electron transfer is either nearly constant with increasing the solvent polarizability and the corresponding high-frequency dielectric constant (polarizable dipolar liquids) or actually noticeably increases (polarizable force fields of water).

  5. Free energy functionals for polarization fluctuations: Pekar factor revisited

    International Nuclear Information System (INIS)

    Dinpajooh, Mohammadhasan; Newton, Marshall D.; Matyushov, Dmitry V.

    2017-01-01

    The separation of slow nuclear and fast electronic polarization in problems related to electron mobility in polarizable media was considered by Pekar 70 years ago. This separation leads to the Pekar factor in the free energy of solvation by the nuclear degrees of freedom, within dielectric continuum models. The main qualitative prediction of Pekar’s perspective is a significant, by about a factor of two, drop of the nuclear solvation free energy compared to the total (electronic plus nuclear) free energy of solvation. The Pekar factor enters the solvent reorganization energy of electron transfer reactions and is a significant mechanistic parameter accounting for the solvent effect on electron transfer. We study the separation of the fast and slow polarization modes in polar molecular liquids (polarizable dipolar liquids and polarizable water force fields) without relying on the continuum approximation. We derive the nonlocal free energy functional and use atomistic numerical simulations to obtain nonlocal, reciprocal space electronic and nuclear susceptibilities. A consistent transition to the continuum limit is introduced by extrapolating the results of finite-size numerical simulation to zero wavevector. The continuum nuclear susceptibility extracted from the simulations is numerically close to the Pekar factor. But, we derive a new functionality involving the static and high-frequency dielectric constants. The main distinction of our approach from the traditional theories is found in the solvation free energy due to the nuclear polarization: the anticipated significant drop of its magnitude with increasing liquid polarizability does not occur. The reorganization energy of electron transfer is either nearly constant with increasing the solvent polarizability and the corresponding high-frequency dielectric constant (polarizable dipolar liquids) or actually noticeably increases (polarizable force fields of water).

  6. Using physics-based pose predictions and free energy perturbation calculations to predict binding poses and relative binding affinities for FXR ligands in the D3R Grand Challenge 2

    Science.gov (United States)

    Athanasiou, Christina; Vasilakaki, Sofia; Dellis, Dimitris; Cournia, Zoe

    2018-01-01

    Computer-aided drug design has become an integral part of drug discovery and development in the pharmaceutical and biotechnology industry, and is nowadays extensively used in the lead identification and lead optimization phases. The drug design data resource (D3R) organizes challenges against blinded experimental data to prospectively test computational methodologies as an opportunity for improved methods and algorithms to emerge. We participated in Grand Challenge 2 to predict the crystallographic poses of 36 Farnesoid X Receptor (FXR)-bound ligands and the relative binding affinities for two designated subsets of 18 and 15 FXR-bound ligands. Here, we present our methodology for pose and affinity predictions and its evaluation after the release of the experimental data. For predicting the crystallographic poses, we used docking and physics-based pose prediction methods guided by the binding poses of native ligands. For FXR ligands with known chemotypes in the PDB, we accurately predicted their binding modes, while for those with unknown chemotypes the predictions were more challenging. Our group ranked #1st (based on the median RMSD) out of 46 groups, which submitted complete entries for the binding pose prediction challenge. For the relative binding affinity prediction challenge, we performed free energy perturbation (FEP) calculations coupled with molecular dynamics (MD) simulations. FEP/MD calculations displayed a high success rate in identifying compounds with better or worse binding affinity than the reference (parent) compound. Our studies suggest that when ligands with chemical precedent are available in the literature, binding pose predictions using docking and physics-based methods are reliable; however, predictions are challenging for ligands with completely unknown chemotypes. We also show that FEP/MD calculations hold predictive value and can nowadays be used in a high throughput mode in a lead optimization project provided that crystal structures of

  7. Analysis of the Bogoliubov free energy functional

    DEFF Research Database (Denmark)

    Reuvers, Robin

    In this thesis, we analyse a variational reformulation of the Bogoliubov approximation that is used to describe weakly-interacting translationally-invariant Bose gases. For the resulting model, the `Bogoliubov free energy functional', we demonstrate existence of minimizers as well as the presence...

  8. Gibbs free energy of formation of liquid lanthanide-bismuth alloys

    International Nuclear Information System (INIS)

    Sheng Jiawei; Yamana, Hajimu; Moriyama, Hirotake

    2001-01-01

    The linear free energy relationship developed by Sverjensky and Molling provides a way to predict Gibbs free energies of liquid Ln-Bi alloys formation from the known thermodynamic properties of aqueous trivalent lanthanides (Ln 3(5(6+ ). The Ln-Bi alloys are divided into two isostructural families named as the LnBi 2 (Ln=La, Ce, Pr, Nd and Pm) and LnBi (Ln=Sm, Eu, Gd, Tb, Dy, Ho, Er, Tm and Yb). The calculated Gibbs free energy values are well agreed with experimental data

  9. Free energy change of a dislocation due to a Cottrell atmosphere

    Science.gov (United States)

    Sills, R. B.; Cai, W.

    2018-06-01

    The free energy reduction of a dislocation due to a Cottrell atmosphere of solutes is computed using a continuum model. We show that the free energy change is composed of near-core and far-field components. The far-field component can be computed analytically using the linearized theory of solid solutions. Near the core the linearized theory is inaccurate, and the near-core component must be computed numerically. The influence of interactions between solutes in neighbouring lattice sites is also examined using the continuum model. We show that this model is able to reproduce atomistic calculations of the nickel-hydrogen system, predicting hydride formation on dislocations. The formation of these hydrides leads to dramatic reductions in the free energy. Finally, the influence of the free energy change on a dislocation's line tension is examined by computing the equilibrium shape of a dislocation shear loop and the activation stress for a Frank-Read source using discrete dislocation dynamics.

  10. The mathematical structure of the approximate linear response relation

    International Nuclear Information System (INIS)

    Yasuda, Muneki; Tanaka, Kazuyuki

    2007-01-01

    In this paper, we study the mathematical structures of the linear response relation based on Plefka's expansion and the cluster variation method in terms of the perturbation expansion, and we show how this linear response relation approximates the correlation functions of the specified system. Moreover, by comparing the perturbation expansions of the correlation functions estimated by the linear response relation based on these approximation methods with exact perturbative forms of the correlation functions, we are able to explain why the approximate techniques using the linear response relation work well

  11. Correcting for the free energy costs of bond or angle constraints in molecular dynamics simulations.

    Science.gov (United States)

    König, Gerhard; Brooks, Bernard R

    2015-05-01

    Free energy simulations are an important tool in the arsenal of computational biophysics, allowing the calculation of thermodynamic properties of binding or enzymatic reactions. This paper introduces methods to increase the accuracy and precision of free energy calculations by calculating the free energy costs of constraints during post-processing. The primary purpose of employing constraints for these free energy methods is to increase the phase space overlap between ensembles, which is required for accuracy and convergence. The free energy costs of applying or removing constraints are calculated as additional explicit steps in the free energy cycle. The new techniques focus on hard degrees of freedom and use both gradients and Hessian estimation. Enthalpy, vibrational entropy, and Jacobian free energy terms are considered. We demonstrate the utility of this method with simple classical systems involving harmonic and anharmonic oscillators, four-atomic benchmark systems, an alchemical mutation of ethane to methanol, and free energy simulations between alanine and serine. The errors for the analytical test cases are all below 0.0007kcal/mol, and the accuracy of the free energy results of ethane to methanol is improved from 0.15 to 0.04kcal/mol. For the alanine to serine case, the phase space overlaps of the unconstrained simulations range between 0.15 and 0.9%. The introduction of constraints increases the overlap up to 2.05%. On average, the overlap increases by 94% relative to the unconstrained value and precision is doubled. The approach reduces errors arising from constraints by about an order of magnitude. Free energy simulations benefit from the use of constraints through enhanced convergence and higher precision. The primary utility of this approach is to calculate free energies for systems with disparate energy surfaces and bonded terms, especially in multi-scale molecular mechanics/quantum mechanics simulations. This article is part of a Special Issue

  12. Electrostatic solvation free energies of charged hard spheres using molecular dynamics with density functional theory interactions

    Science.gov (United States)

    Duignan, Timothy T.; Baer, Marcel D.; Schenter, Gregory K.; Mundy, Chistopher J.

    2017-10-01

    Determining the solvation free energies of single ions in water is one of the most fundamental problems in physical chemistry and yet many unresolved questions remain. In particular, the ability to decompose the solvation free energy into simple and intuitive contributions will have important implications for models of electrolyte solution. Here, we provide definitions of the various types of single ion solvation free energies based on different simulation protocols. We calculate solvation free energies of charged hard spheres using density functional theory interaction potentials with molecular dynamics simulation and isolate the effects of charge and cavitation, comparing to the Born (linear response) model. We show that using uncorrected Ewald summation leads to unphysical values for the single ion solvation free energy and that charging free energies for cations are approximately linear as a function of charge but that there is a small non-linearity for small anions. The charge hydration asymmetry for hard spheres, determined with quantum mechanics, is much larger than for the analogous real ions. This suggests that real ions, particularly anions, are significantly more complex than simple charged hard spheres, a commonly employed representation.

  13. The Bogoliubov free energy functional II

    DEFF Research Database (Denmark)

    Napiórkowski, Marcin; Reuvers, Robin; Solovej, Jan Philip

    2018-01-01

    We analyse the canonical Bogoliubov free energy functional at low temperatures in the dilute limit. We prove existence of a first order phase transition and, in the limit $a_0\\to a$, we determine the critical temperature to be $T_{\\rm{c}}=T_{\\rm{fc}}(1+1.49(\\rho^{1/3}a))$ to leading order. Here, $T......_{\\rm{fc}}$ is the critical temperature of the free Bose gas, $\\rho$ is the density of the gas, $a$ is the scattering length of the pair-interaction potential $V$, and $a_0=(8\\pi)^{-1}\\widehat{V}(0)$ its first order approximation. We also prove asymptotic expansions for the free energy. In particular, we recover the Lee...

  14. Linear free energy relationship in reactions between diphenyl amine ...

    Indian Academy of Sciences (India)

    Unknown

    Frost A A and Pearson R G 1970 Kinetics and mechanism 2nd edn (New Delhi: Wiley Eastern) p. 37. 9. Nakanishi K and Solomon P H 1977 Infrared absorp- tion spectroscopy (Holden Day) p. 50. 10. Hammett L P 1935 Chem. Rev. 17 125. 11. Shorter J 1973 Correlation analysis in organic che- mistry (Oxford: Clarendon).

  15. Holographic free energy and thermodynamic geometry

    Science.gov (United States)

    Ghorai, Debabrata; Gangopadhyay, Sunandan

    2016-12-01

    We obtain the free energy and thermodynamic geometry of holographic superconductors in 2+1 dimensions. The gravitational theory in the bulk dual to this 2+1-dimensional strongly coupled theory lives in the 3+1 dimensions and is that of a charged AdS black hole together with a massive charged scalar field. The matching method is applied to obtain the nature of the fields near the horizon using which the holographic free energy is computed through the gauge/gravity duality. The critical temperature is obtained for a set of values of the matching point of the near horizon and the boundary behaviour of the fields in the probe limit approximation which neglects the back reaction of the matter fields on the background spacetime geometry. The thermodynamic geometry is then computed from the free energy of the boundary theory. From the divergence of the thermodynamic scalar curvature, the critical temperature is obtained once again. We then compare this result for the critical temperature with that obtained from the matching method.

  16. Holographic free energy and thermodynamic geometry

    International Nuclear Information System (INIS)

    Ghorai, Debabrata; Gangopadhyay, Sunandan

    2016-01-01

    We obtain the free energy and thermodynamic geometry of holographic superconductors in 2 + 1 dimensions. The gravitational theory in the bulk dual to this 2 + 1-dimensional strongly coupled theory lives in the 3 + 1 dimensions and is that of a charged AdS black hole together with a massive charged scalar field. The matching method is applied to obtain the nature of the fields near the horizon using which the holographic free energy is computed through the gauge/gravity duality. The critical temperature is obtained for a set of values of the matching point of the near horizon and the boundary behaviour of the fields in the probe limit approximation which neglects the back reaction of the matter fields on the background spacetime geometry. The thermodynamic geometry is then computed from the free energy of the boundary theory. From the divergence of the thermodynamic scalar curvature, the critical temperature is obtained once again. We then compare this result for the critical temperature with that obtained from the matching method. (orig.)

  17. Holographic free energy and thermodynamic geometry

    Energy Technology Data Exchange (ETDEWEB)

    Ghorai, Debabrata [S.N. Bose National Centre for Basic Sciences, Kolkata (India); Gangopadhyay, Sunandan [Indian Institute of Science Education and Research, Kolkata, Nadia (India); West Bengal State University, Department of Physics, Barasat (India); Inter University Centre for Astronomy and Astrophysics, Pune (India)

    2016-12-15

    We obtain the free energy and thermodynamic geometry of holographic superconductors in 2 + 1 dimensions. The gravitational theory in the bulk dual to this 2 + 1-dimensional strongly coupled theory lives in the 3 + 1 dimensions and is that of a charged AdS black hole together with a massive charged scalar field. The matching method is applied to obtain the nature of the fields near the horizon using which the holographic free energy is computed through the gauge/gravity duality. The critical temperature is obtained for a set of values of the matching point of the near horizon and the boundary behaviour of the fields in the probe limit approximation which neglects the back reaction of the matter fields on the background spacetime geometry. The thermodynamic geometry is then computed from the free energy of the boundary theory. From the divergence of the thermodynamic scalar curvature, the critical temperature is obtained once again. We then compare this result for the critical temperature with that obtained from the matching method. (orig.)

  18. Determination of partial molar volumes from free energy perturbation theory.

    Science.gov (United States)

    Vilseck, Jonah Z; Tirado-Rives, Julian; Jorgensen, William L

    2015-04-07

    Partial molar volume is an important thermodynamic property that gives insights into molecular size and intermolecular interactions in solution. Theoretical frameworks for determining the partial molar volume (V°) of a solvated molecule generally apply Scaled Particle Theory or Kirkwood-Buff theory. With the current abilities to perform long molecular dynamics and Monte Carlo simulations, more direct methods are gaining popularity, such as computing V° directly as the difference in computed volume from two simulations, one with a solute present and another without. Thermodynamically, V° can also be determined as the pressure derivative of the free energy of solvation in the limit of infinite dilution. Both approaches are considered herein with the use of free energy perturbation (FEP) calculations to compute the necessary free energies of solvation at elevated pressures. Absolute and relative partial molar volumes are computed for benzene and benzene derivatives using the OPLS-AA force field. The mean unsigned error for all molecules is 2.8 cm(3) mol(-1). The present methodology should find use in many contexts such as the development and testing of force fields for use in computer simulations of organic and biomolecular systems, as a complement to related experimental studies, and to develop a deeper understanding of solute-solvent interactions.

  19. Determination of partial molar volumes from free energy perturbation theory†

    Science.gov (United States)

    Vilseck, Jonah Z.; Tirado-Rives, Julian

    2016-01-01

    Partial molar volume is an important thermodynamic property that gives insights into molecular size and intermolecular interactions in solution. Theoretical frameworks for determining the partial molar volume (V°) of a solvated molecule generally apply Scaled Particle Theory or Kirkwood–Buff theory. With the current abilities to perform long molecular dynamics and Monte Carlo simulations, more direct methods are gaining popularity, such as computing V° directly as the difference in computed volume from two simulations, one with a solute present and another without. Thermodynamically, V° can also be determined as the pressure derivative of the free energy of solvation in the limit of infinite dilution. Both approaches are considered herein with the use of free energy perturbation (FEP) calculations to compute the necessary free energies of solvation at elevated pressures. Absolute and relative partial molar volumes are computed for benzene and benzene derivatives using the OPLS-AA force field. The mean unsigned error for all molecules is 2.8 cm3 mol−1. The present methodology should find use in many contexts such as the development and testing of force fields for use in computer simulations of organic and biomolecular systems, as a complement to related experimental studies, and to develop a deeper understanding of solute–solvent interactions. PMID:25589343

  20. Characterizing structural transitions using localized free energy landscape analysis.

    Directory of Open Access Journals (Sweden)

    Nilesh K Banavali

    Full Text Available Structural changes in molecules are frequently observed during biological processes like replication, transcription and translation. These structural changes can usually be traced to specific distortions in the backbones of the macromolecules involved. Quantitative energetic characterization of such distortions can greatly advance the atomic-level understanding of the dynamic character of these biological processes.Molecular dynamics simulations combined with a variation of the Weighted Histogram Analysis Method for potential of mean force determination are applied to characterize localized structural changes for the test case of cytosine (underlined base flipping in a GTCAGCGCATGG DNA duplex. Free energy landscapes for backbone torsion and sugar pucker degrees of freedom in the DNA are used to understand their behavior in response to the base flipping perturbation. By simplifying the base flipping structural change into a two-state model, a free energy difference of upto 14 kcal/mol can be attributed to the flipped state relative to the stacked Watson-Crick base paired state. This two-state classification allows precise evaluation of the effect of base flipping on local backbone degrees of freedom.The calculated free energy landscapes of individual backbone and sugar degrees of freedom expectedly show the greatest change in the vicinity of the flipping base itself, but specific delocalized effects can be discerned upto four nucleotide positions away in both 5' and 3' directions. Free energy landscape analysis thus provides a quantitative method to pinpoint the determinants of structural change on the atomic scale and also delineate the extent of propagation of the perturbation along the molecule. In addition to nucleic acids, this methodology is anticipated to be useful for studying conformational changes in all macromolecules, including carbohydrates, lipids, and proteins.

  1. Mass and free energy of Lovelock black holes

    International Nuclear Information System (INIS)

    Kastor, David; Traschen, Jennie; Ray, Sourya

    2011-01-01

    An explicit formula for the ADM mass of an asymptotically AdS black hole in a generic Lovelock gravity theory is presented, identical in form to that in Einstein gravity, but multiplied by a function of the Lovelock coupling constants and the AdS curvature radius. A Gauss' law-type formula relates the mass, which is an integral at infinity, to an expression depending instead on the horizon radius. This and other thermodynamic quantities, such as the free energy, are then analyzed in the limits of small and large horizon radius, yielding results that are independent of the detailed choice of Lovelock couplings. In even dimensions, the temperature diverges in both limits, implying the existence of a minimum temperature for black holes. The negative free energy of sufficiently large black holes implies the existence of a Hawking-Page transition. In odd dimensions, the temperature still diverges for large black holes, which again have negative free energy. However, the temperature vanishes as the horizon radius tends to zero and sufficiently small black holes have positive specific heat.

  2. Time signal filtering by relative neighborhood graph localized linear approximation

    DEFF Research Database (Denmark)

    Sørensen, John Aasted

    1994-01-01

    A time signal filtering algorithm based on the relative neighborhood graph (RNG) used for localization of linear filters is proposed. The filter is constructed from a training signal during two stages. During the first stage an RNG is constructed. During the second stage, localized linear filters...

  3. Relation of deformed nonlinear algebras with linear ones

    International Nuclear Information System (INIS)

    Nowicki, A; Tkachuk, V M

    2014-01-01

    The relation between nonlinear algebras and linear ones is established. For a one-dimensional nonlinear deformed Heisenberg algebra with two operators we find the function of deformation for which this nonlinear algebra can be transformed to a linear one with three operators. We also establish the relation between the Lie algebra of total angular momentum and corresponding nonlinear one. This relation gives a possibility to simplify and to solve the eigenvalue problem for the Hamiltonian in a nonlinear case using the reduction of this problem to the case of linear algebra. It is demonstrated in an example of a harmonic oscillator. (paper)

  4. Free-energy analysis of spin models on hyperbolic lattice geometries.

    Science.gov (United States)

    Serina, Marcel; Genzor, Jozef; Lee, Yoju; Gendiar, Andrej

    2016-04-01

    We investigate relations between spatial properties of the free energy and the radius of Gaussian curvature of the underlying curved lattice geometries. For this purpose we derive recurrence relations for the analysis of the free energy normalized per lattice site of various multistate spin models in the thermal equilibrium on distinct non-Euclidean surface lattices of the infinite sizes. Whereas the free energy is calculated numerically by means of the corner transfer matrix renormalization group algorithm, the radius of curvature has an analytic expression. Two tasks are considered in this work. First, we search for such a lattice geometry, which minimizes the free energy per site. We conjecture that the only Euclidean flat geometry results in the minimal free energy per site regardless of the spin model. Second, the relations among the free energy, the radius of curvature, and the phase transition temperatures are analyzed. We found out that both the free energy and the phase transition temperature inherit the structure of the lattice geometry and asymptotically approach the profile of the Gaussian radius of curvature. This achievement opens new perspectives in the AdS-CFT correspondence theories.

  5. Prediction of trypsin/molecular fragment binding affinities by free energy decomposition and empirical scores

    Science.gov (United States)

    Benson, Mark L.; Faver, John C.; Ucisik, Melek N.; Dashti, Danial S.; Zheng, Zheng; Merz, Kenneth M.

    2012-05-01

    Two families of binding affinity estimation methodologies are described which were utilized in the SAMPL3 trypsin/fragment binding affinity challenge. The first is a free energy decomposition scheme based on a thermodynamic cycle, which included separate contributions from enthalpy and entropy of binding as well as a solvent contribution. Enthalpic contributions were estimated with PM6-DH2 semiempirical quantum mechanical interaction energies, which were modified with a statistical error correction procedure. Entropic contributions were estimated with the rigid-rotor harmonic approximation, and solvent contributions to the free energy were estimated with several different methods. The second general methodology is the empirical score LISA, which contains several physics-based terms trained with the large PDBBind database of protein/ligand complexes. Here we also introduce LISA+, an updated version of LISA which, prior to scoring, classifies systems into one of four classes based on a ligand's hydrophobicity and molecular weight. Each version of the two methodologies (a total of 11 methods) was trained against a compiled set of known trypsin binders available in the Protein Data Bank to yield scaling parameters for linear regression models. Both raw and scaled scores were submitted to SAMPL3. Variants of LISA showed relatively low absolute errors but also low correlation with experiment, while the free energy decomposition methods had modest success when scaling factors were included. Nonetheless, re-scaled LISA yielded the best predictions in the challenge in terms of RMS error, and six of these models placed in the top ten best predictions by RMS error. This work highlights some of the difficulties of predicting binding affinities of small molecular fragments to protein receptors as well as the benefit of using training data.

  6. Exploring the ab initio/classical free energy perturbation method: The hydration free energy of water

    International Nuclear Information System (INIS)

    Sakane, Shinichi; Yezdimer, Eric M.; Liu, Wenbin; Barriocanal, Jose A.; Doren, Douglas J.; Wood, Robert H.

    2000-01-01

    The ab initio/classical free energy perturbation (ABC-FEP) method proposed previously by Wood et al. [J. Chem. Phys. 110, 1329 (1999)] uses classical simulations to calculate solvation free energies within an empirical potential model, then applies free energy perturbation theory to determine the effect of changing the empirical solute-solvent interactions to corresponding interactions calculated from ab initio methods. This approach allows accurate calculation of solvation free energies using an atomistic description of the solvent and solute, with interactions calculated from first principles. Results can be obtained at a feasible computational cost without making use of approximations such as a continuum solvent or an empirical cavity formation energy. As such, the method can be used far from ambient conditions, where the empirical parameters needed for approximate theories of solvation may not be available. The sources of error in the ABC-FEP method are the approximations in the ab initio method, the finite sample of configurations, and the classical solvent model. This article explores the accuracy of various approximations used in the ABC-FEP method by comparing to the experimentally well-known free energy of hydration of water at two state points (ambient conditions, and 973.15 K and 600 kg/m3). The TIP4P-FQ model [J. Chem. Phys. 101, 6141 (1994)] is found to be a reliable solvent model for use with this method, even at supercritical conditions. Results depend strongly on the ab initio method used: a gradient-corrected density functional theory is not adequate, but a localized MP2 method yields excellent agreement with experiment. Computational costs are reduced by using a cluster approximation, in which ab initio pair interaction energies are calculated between the solute and up to 60 solvent molecules, while multi-body interactions are calculated with only a small cluster (5 to 12 solvent molecules). Sampling errors for the ab initio contribution to

  7. Inference with minimal Gibbs free energy in information field theory

    International Nuclear Information System (INIS)

    Ensslin, Torsten A.; Weig, Cornelius

    2010-01-01

    Non-linear and non-Gaussian signal inference problems are difficult to tackle. Renormalization techniques permit us to construct good estimators for the posterior signal mean within information field theory (IFT), but the approximations and assumptions made are not very obvious. Here we introduce the simple concept of minimal Gibbs free energy to IFT, and show that previous renormalization results emerge naturally. They can be understood as being the Gaussian approximation to the full posterior probability, which has maximal cross information with it. We derive optimized estimators for three applications, to illustrate the usage of the framework: (i) reconstruction of a log-normal signal from Poissonian data with background counts and point spread function, as it is needed for gamma ray astronomy and for cosmography using photometric galaxy redshifts, (ii) inference of a Gaussian signal with unknown spectrum, and (iii) inference of a Poissonian log-normal signal with unknown spectrum, the combination of (i) and (ii). Finally we explain how Gaussian knowledge states constructed by the minimal Gibbs free energy principle at different temperatures can be combined into a more accurate surrogate of the non-Gaussian posterior.

  8. Calculation of free-energy differences from computer simulations of initial and final states

    International Nuclear Information System (INIS)

    Hummer, G.; Szabo, A.

    1996-01-01

    A class of simple expressions of increasing accuracy for the free-energy difference between two states is derived based on numerical thermodynamic integration. The implementation of these formulas requires simulations of the initial and final (and possibly a few intermediate) states. They involve higher free-energy derivatives at these states which are related to the moments of the probability distribution of the perturbation. Given a specified number of such derivatives, these integration formulas are optimal in the sense that they are exact to the highest possible order of free-energy perturbation theory. The utility of this approach is illustrated for the hydration free energy of water. This problem provides a quite stringent test because the free energy is a highly nonlinear function of the charge so that even fourth order perturbation theory gives a very poor estimate of the free-energy change. Our results should prove most useful for complex, computationally demanding problems where free-energy differences arise primarily from changes in the electrostatic interactions (e.g., electron transfer, charging of ions, protonation of amino acids in proteins). copyright 1996 American Institute of Physics

  9. Free Energy, Enthalpy and Entropy from Implicit Solvent End-Point Simulations.

    Science.gov (United States)

    Fogolari, Federico; Corazza, Alessandra; Esposito, Gennaro

    2018-01-01

    Free energy is the key quantity to describe the thermodynamics of biological systems. In this perspective we consider the calculation of free energy, enthalpy and entropy from end-point molecular dynamics simulations. Since the enthalpy may be calculated as the ensemble average over equilibrated simulation snapshots the difficulties related to free energy calculation are ultimately related to the calculation of the entropy of the system and in particular of the solvent entropy. In the last two decades implicit solvent models have been used to circumvent the problem and to take into account solvent entropy implicitly in the solvation terms. More recently outstanding advancement in both implicit solvent models and in entropy calculations are making the goal of free energy estimation from end-point simulations more feasible than ever before. We review briefly the basic theory and discuss the advancements in light of practical applications.

  10. Free Energy, Enthalpy and Entropy from Implicit Solvent End-Point Simulations

    Directory of Open Access Journals (Sweden)

    Federico Fogolari

    2018-02-01

    Full Text Available Free energy is the key quantity to describe the thermodynamics of biological systems. In this perspective we consider the calculation of free energy, enthalpy and entropy from end-point molecular dynamics simulations. Since the enthalpy may be calculated as the ensemble average over equilibrated simulation snapshots the difficulties related to free energy calculation are ultimately related to the calculation of the entropy of the system and in particular of the solvent entropy. In the last two decades implicit solvent models have been used to circumvent the problem and to take into account solvent entropy implicitly in the solvation terms. More recently outstanding advancement in both implicit solvent models and in entropy calculations are making the goal of free energy estimation from end-point simulations more feasible than ever before. We review briefly the basic theory and discuss the advancements in light of practical applications.

  11. The Magnetic Free Energy in Active Regions

    Science.gov (United States)

    Metcalf, Thomas R.; Mickey, Donald L.; LaBonte, Barry J.

    2001-01-01

    The magnetic field permeating the solar atmosphere governs much of the structure, morphology, brightness, and dynamics observed on the Sun. The magnetic field, especially in active regions, is thought to provide the power for energetic events in the solar corona, such as solar flares and Coronal Mass Ejections (CME) and is believed to energize the hot coronal plasma seen in extreme ultraviolet or X-rays. The question remains what specific aspect of the magnetic flux governs the observed variability. To directly understand the role of the magnetic field in energizing the solar corona, it is necessary to measure the free magnetic energy available in active regions. The grant now expiring has demonstrated a new and valuable technique for observing the magnetic free energy in active regions as a function of time.

  12. Generalized formulation of free energy and application to photosynthesis

    Science.gov (United States)

    Zhang, Hwe Ik; Choi, M. Y.

    2018-03-01

    The origin of free energy on the earth is solar radiation. However, the amount of free energy it contains has seldom been investigated, because the free energy concept was believed to be inappropriate for a system of photons. Instead, the origin of free energy has been sought in the process of photosynthesis, imposing a limit of conversion given by the Carnot efficiency. Here we present a general formulation, capable of not only assessing accurately the available amount of free energy in the photon gas but also explaining the primary photosynthetic process more succinctly. In this formulation, the problem of "photosynthetic conversion of the internal energy of photons into the free energy of chlorophyll" is replaced by simple "free energy transduction" between the photons and chlorophyll. An analytic expression for the photosynthetic efficiency is derived and shown to deviate from the Carnot efficiency. Some predictions verifiable possibly by observation are also suggested.

  13. Knot soliton in DNA and geometric structure of its free-energy density.

    Science.gov (United States)

    Wang, Ying; Shi, Xuguang

    2018-03-01

    In general, the geometric structure of DNA is characterized using an elastic rod model. The Landau model provides us a new theory to study the geometric structure of DNA. By using the decomposition of the arc unit in the helical axis of DNA, we find that the free-energy density of DNA is similar to the free-energy density of a two-condensate superconductor. By using the φ-mapping topological current theory, the torus knot soliton hidden in DNA is demonstrated. We show the relation between the geometric structure and free-energy density of DNA and the Frenet equations in differential geometry theory are considered. Therefore, the free-energy density of DNA can be expressed by the curvature and torsion of the helical axis.

  14. A fast tomographic method for searching the minimum free energy path

    International Nuclear Information System (INIS)

    Chen, Changjun; Huang, Yanzhao; Xiao, Yi; Jiang, Xuewei

    2014-01-01

    Minimum Free Energy Path (MFEP) provides a lot of important information about the chemical reactions, like the free energy barrier, the location of the transition state, and the relative stability between reactant and product. With MFEP, one can study the mechanisms of the reaction in an efficient way. Due to a large number of degrees of freedom, searching the MFEP is a very time-consuming process. Here, we present a fast tomographic method to perform the search. Our approach first calculates the free energy surfaces in a sequence of hyperplanes perpendicular to a transition path. Based on an objective function and the free energy gradient, the transition path is optimized in the collective variable space iteratively. Applications of the present method to model systems show that our method is practical. It can be an alternative approach for finding the state-to-state MFEP

  15. A linearized dispersion relation for orthorhombic pseudo-acoustic modeling

    KAUST Repository

    Song, Xiaolei; Alkhalifah, Tariq Ali

    2012-01-01

    Wavefield extrapolation in acoustic orthorhombic anisotropic media suffers from wave-mode coupling and stability limitations in the parameter range. We introduce a linearized form of the dispersion relation for acoustic orthorhombic media to model acoustic wavefields. We apply the lowrank approximation approach to handle the corresponding space-wavenumber mixed-domain operator. Numerical experiments show that the proposed wavefield extrapolator is accurate and practically free of dispersions. Further, there is no coupling of qSv and qP waves, because we use the analytical dispersion relation. No constraints on Thomsen's parameters are required for stability. The linearized expression may provide useful application for parameter estimation in orthorhombic media.

  16. Rigorous bounds on the free energy of electron-phonon models

    NARCIS (Netherlands)

    Raedt, Hans De; Michielsen, Kristel

    1997-01-01

    We present a collection of rigorous upper and lower bounds to the free energy of electron-phonon models with linear electron-phonon interaction. These bounds are used to compare different variational approaches. It is shown rigorously that the ground states corresponding to the sharpest bounds do

  17. Variationally Optimized Free-Energy Flooding for Rate Calculation

    Science.gov (United States)

    McCarty, James; Valsson, Omar; Tiwary, Pratyush; Parrinello, Michele

    2015-08-01

    We propose a new method to obtain kinetic properties of infrequent events from molecular dynamics simulation. The procedure employs a recently introduced variational approach [Valsson and Parrinello, Phys. Rev. Lett. 113, 090601 (2014)] to construct a bias potential as a function of several collective variables that is designed to flood the associated free energy surface up to a predefined level. The resulting bias potential effectively accelerates transitions between metastable free energy minima while ensuring bias-free transition states, thus allowing accurate kinetic rates to be obtained. We test the method on a few illustrative systems for which we obtain an order of magnitude improvement in efficiency relative to previous approaches and several orders of magnitude relative to unbiased molecular dynamics. We expect an even larger improvement in more complex systems. This and the ability of the variational approach to deal efficiently with a large number of collective variables will greatly enhance the scope of these calculations. This work is a vindication of the potential that the variational principle has if applied in innovative ways.

  18. Modeling patterns in data using linear and related models

    International Nuclear Information System (INIS)

    Engelhardt, M.E.

    1996-06-01

    This report considers the use of linear models for analyzing data related to reliability and safety issues of the type usually associated with nuclear power plants. The report discusses some of the general results of linear regression analysis, such as the model assumptions and properties of the estimators of the parameters. The results are motivated with examples of operational data. Results about the important case of a linear regression model with one covariate are covered in detail. This case includes analysis of time trends. The analysis is applied with two different sets of time trend data. Diagnostic procedures and tests for the adequacy of the model are discussed. Some related methods such as weighted regression and nonlinear models are also considered. A discussion of the general linear model is also included. Appendix A gives some basic SAS programs and outputs for some of the analyses discussed in the body of the report. Appendix B is a review of some of the matrix theoretic results which are useful in the development of linear models

  19. Relative controllability and null controllability of linear delay systems ...

    African Journals Online (AJOL)

    Necessary and sufficient conditions are established for the relative, absolute controllability and null controllability of the generalized linear delay system and its discrete prototype. The paper presents illuminating examples on previous controllability results by Manitius and Olbrot [7] and carries over the results of Onwuatu [8] ...

  20. Free energy calculations, enhanced by a Gaussian ansatz, for the "chemical work" distribution.

    Science.gov (United States)

    Boulougouris, Georgios C

    2014-05-15

    The evaluation of the free energy is essential in molecular simulation because it is intimately related with the existence of multiphase equilibrium. Recently, it was demonstrated that it is possible to evaluate the Helmholtz free energy using a single statistical ensemble along an entire isotherm by accounting for the "chemical work" of transforming each molecule, from an interacting one, to an ideal gas. In this work, we show that it is possible to perform such a free energy perturbation over a liquid vapor phase transition. Furthermore, we investigate the link between a general free energy perturbation scheme and the novel nonequilibrium theories of Crook's and Jarzinsky. We find that for finite systems away from the thermodynamic limit the second law of thermodynamics will always be an inequality for isothermal free energy perturbations, resulting always to a dissipated work that may tend to zero only in the thermodynamic limit. The work, the heat, and the entropy produced during a thermodynamic free energy perturbation can be viewed in the context of the Crooks and Jarzinsky formalism, revealing that for a given value of the ensemble average of the "irreversible" work, the minimum entropy production corresponded to a Gaussian distribution for the histogram of the work. We propose the evaluation of the free energy difference in any free energy perturbation based scheme on the average irreversible "chemical work" minus the dissipated work that can be calculated from the variance of the distribution of the logarithm of the work histogram, within the Gaussian approximation. As a consequence, using the Gaussian ansatz for the distribution of the "chemical work," accurate estimates for the chemical potential and the free energy of the system can be performed using much shorter simulations and avoiding the necessity of sampling the computational costly tails of the "chemical work." For a more general free energy perturbation scheme that the Gaussian ansatz may not be

  1. Dispersion relation of linearly polarized strong electromagnetic waves

    Energy Technology Data Exchange (ETDEWEB)

    Ferrari, A; Massaglia, S [Consiglio Nazionale delle Ricerche, Turin (Italy). Lab. di Cosmo-Geofisica; Dobrowolny, M [Comitato Nazionale per l' Energia Nucleaire, Frascati (Italy). Lab. Plasma Spazio

    1975-12-15

    A numerical study is presented of the dispersion relation of linearly polarized strong electromagnetic waves in a cold electron plasma. The nonlinear effects introduced by the relativistic motion of electrons are: (1) the dispersion relation depends explicitly on the field strength ..cap alpha..=eE/sub 0//mc..omega../sub 0/, and (2) the propagation of modes with frequencies below the formal electron plasma frequency is allowed.

  2. Relative Importance for Linear Regression in R: The Package relaimpo

    OpenAIRE

    Groemping, Ulrike

    2006-01-01

    Relative importance is a topic that has seen a lot of interest in recent years, particularly in applied work. The R package relaimpo implements six different metrics for assessing relative importance of regressors in the linear model, two of which are recommended - averaging over orderings of regressors and a newly proposed metric (Feldman 2005) called pmvd. Apart from delivering the metrics themselves, relaimpo also provides (exploratory) bootstrap confidence intervals. This paper offers a b...

  3. Non-Equilibrium Properties from Equilibrium Free Energy Calculations

    Science.gov (United States)

    Pohorille, Andrew; Wilson, Michael A.

    2012-01-01

    Calculating free energy in computer simulations is of central importance in statistical mechanics of condensed media and its applications to chemistry and biology not only because it is the most comprehensive and informative quantity that characterizes the eqUilibrium state, but also because it often provides an efficient route to access dynamic and kinetic properties of a system. Most of applications of equilibrium free energy calculations to non-equilibrium processes rely on a description in which a molecule or an ion diffuses in the potential of mean force. In general case this description is a simplification, but it might be satisfactorily accurate in many instances of practical interest. This hypothesis has been tested in the example of the electrodiffusion equation . Conductance of model ion channels has been calculated directly through counting the number of ion crossing events observed during long molecular dynamics simulations and has been compared with the conductance obtained from solving the generalized Nernst-Plank equation. It has been shown that under relatively modest conditions the agreement between these two approaches is excellent, thus demonstrating the assumptions underlying the diffusion equation are fulfilled. Under these conditions the electrodiffusion equation provides an efficient approach to calculating the full voltage-current dependence routinely measured in electrophysiological experiments.

  4. Flavour fields in steady state: stress tensor and free energy

    International Nuclear Information System (INIS)

    Banerjee, Avik; Kundu, Arnab; Kundu, Sandipan

    2016-01-01

    The dynamics of a probe brane in a given gravitational background is governed by the Dirac-Born-Infeld action. The corresponding open string metric arises naturally in studying the fluctuations on the probe. In Gauge-String duality, it is known that in the presence of a constant electric field on the worldvolume of the probe, the open string metric acquires an event horizon and therefore the fluctuation modes on the probe experience an effective temperature. In this article, we bring together various properties of such a system to a formal definition and a subsequent narration of the effective thermodynamics and the stress tensor of the corresponding flavour fields, also including a non-vanishing chemical potential. In doing so, we point out a potentially infinitely-degenerate scheme-dependence of regularizing the free energy, which nevertheless yields a universal contribution in certain cases. This universal piece appears as the coefficient of a log-divergence in free energy when a space-filling probe brane is embedded in AdS d+1 -background, for d=2,4, and is related to conformal anomaly. For the special case of d=2, the universal factor has a striking resemblance to the well-known heat current formula in (1+1)-dimensional conformal field theory in steady-state, which endows a plausible physical interpretation to it. Interestingly, we observe a vanishing conformal anomaly in d=6.

  5. Iterative free-energy optimization for recurrent neural networks (INFERNO)

    Science.gov (United States)

    2017-01-01

    The intra-parietal lobe coupled with the Basal Ganglia forms a working memory that demonstrates strong planning capabilities for generating robust yet flexible neuronal sequences. Neurocomputational models however, often fails to control long range neural synchrony in recurrent spiking networks due to spontaneous activity. As a novel framework based on the free-energy principle, we propose to see the problem of spikes’ synchrony as an optimization problem of the neurons sub-threshold activity for the generation of long neuronal chains. Using a stochastic gradient descent, a reinforcement signal (presumably dopaminergic) evaluates the quality of one input vector to move the recurrent neural network to a desired activity; depending on the error made, this input vector is strengthened to hill-climb the gradient or elicited to search for another solution. This vector can be learned then by one associative memory as a model of the basal-ganglia to control the recurrent neural network. Experiments on habit learning and on sequence retrieving demonstrate the capabilities of the dual system to generate very long and precise spatio-temporal sequences, above two hundred iterations. Its features are applied then to the sequential planning of arm movements. In line with neurobiological theories, we discuss its relevance for modeling the cortico-basal working memory to initiate flexible goal-directed neuronal chains of causation and its relation to novel architectures such as Deep Networks, Neural Turing Machines and the Free-Energy Principle. PMID:28282439

  6. Minimum free-energy paths for the self-organization of polymer brushes.

    Science.gov (United States)

    Gleria, Ignacio; Mocskos, Esteban; Tagliazucchi, Mario

    2017-03-22

    A methodology to calculate minimum free-energy paths based on the combination of a molecular theory and the improved string method is introduced and applied to study the self-organization of polymer brushes under poor solvent conditions. Polymer brushes in a poor solvent cannot undergo macroscopic phase separation due to the physical constraint imposed by the grafting points; therefore, they microphase separate forming aggregates. Under some conditions, the theory predicts that the homogeneous brush and the aggregates can exist as two different minima of the free energy. The theoretical methodology introduced in this work allows us to predict the minimum free-energy path connecting these two minima as well as the morphology of the system along the path. It is shown that the transition between the homogeneous brush and the aggregates may involve a free-energy barrier or be barrierless depending on the relative stability of the two morphologies and the chain length and grafting density of the polymer. In the case where a free-energy barrier exists, one of the morphologies is a metastable structure and, therefore, the properties of the brush as the quality of the solvent is cycled are expected to display hysteresis. The theory is also applied to study the adhesion/deadhesion transition between two opposing surfaces modified by identical polymer brushes and it is shown that this process may also require surpassing a free-energy barrier.

  7. Binding free energy analysis of protein-protein docking model structures by evERdock.

    Science.gov (United States)

    Takemura, Kazuhiro; Matubayasi, Nobuyuki; Kitao, Akio

    2018-03-14

    To aid the evaluation of protein-protein complex model structures generated by protein docking prediction (decoys), we previously developed a method to calculate the binding free energies for complexes. The method combines a short (2 ns) all-atom molecular dynamics simulation with explicit solvent and solution theory in the energy representation (ER). We showed that this method successfully selected structures similar to the native complex structure (near-native decoys) as the lowest binding free energy structures. In our current work, we applied this method (evERdock) to 100 or 300 model structures of four protein-protein complexes. The crystal structures and the near-native decoys showed the lowest binding free energy of all the examined structures, indicating that evERdock can successfully evaluate decoys. Several decoys that show low interface root-mean-square distance but relatively high binding free energy were also identified. Analysis of the fraction of native contacts, hydrogen bonds, and salt bridges at the protein-protein interface indicated that these decoys were insufficiently optimized at the interface. After optimizing the interactions around the interface by including interfacial water molecules, the binding free energies of these decoys were improved. We also investigated the effect of solute entropy on binding free energy and found that consideration of the entropy term does not necessarily improve the evaluations of decoys using the normal model analysis for entropy calculation.

  8. The puckering free-energy surface of proline

    Directory of Open Access Journals (Sweden)

    Di Wu

    2013-03-01

    Full Text Available Proline has two preferred puckering states, which are often characterized by the pseudorotation phase angle and amplitude. Although proline's five endocyclic torsion angles can be utilized to calculate the phase angle and amplitude, it is not clear if there is any direct correlation between each torsion angle and the proline-puckering pathway. Here we have designed five proline puckering pathways utilizing each torsion angle χj (j = 1∼5 as the reaction coordinate. By examining the free-energy surfaces of the five puckering pathways, we find they can be categorized into two groups. The χ2 pathway (χ2 is about the Cβ—Cγ bond is especially meaningful in describing proline puckering: it changes linearly with the puckering amplitude and symmetrically with the phase angle. Our results show that this conclusion applies to both trans and cis proline conformations. We have also analyzed the correlations of proline puckering and its backbone torsion angles ϕ and ψ. We show proline has preferred puckering states at the specific regions of ϕ, ψ angles. Interestingly, the shapes of ψ-χ2 free-energy surfaces are similar among the trans proline in water, cis proline in water and cis proline in the gas phase, but they differ substantially from that of the trans proline in the gas phase. Our calculations are conducted using molecular simulations; we also verify our results using the proline conformations selected from the Protein Data Bank. In addition, we have compared our results with those calculated by the quantum mechanical methods.

  9. Temperature dependence of grain boundary free energy and elastic constants

    International Nuclear Information System (INIS)

    Foiles, Stephen M.

    2010-01-01

    This work explores the suggestion that the temperature dependence of the grain boundary free energy can be estimated from the temperature dependence of the elastic constants. The temperature-dependent elastic constants and free energy of a symmetric Σ79 tilt boundary are computed for an embedded atom method model of Ni. The grain boundary free energy scales with the product of the shear modulus times the lattice constant for temperatures up to about 0.75 the melting temperature.

  10. Estimate of electrostatic solvation free energy of electron in various polar solvents by using modified born equation

    International Nuclear Information System (INIS)

    Yamashita, Kazuo; Kitamura, Mitsutaka; Imai, Hideo

    1976-01-01

    The modified Born equation was tentatively applied to estimate the electrostatic free energies of solvation of the electron in various polar solvents. The related data of halide ions and a datum of the hydration free energy of the electron obtained by radiation chemical studies were used for the numerical calculations. (auth.)

  11. A Free Energy Model for Hysteresis Ferroelectric Materials

    National Research Council Canada - National Science Library

    Smith, Ralph C; Ounaies, Zoubeida; Seelecke, Stefan; Smith, Joshua

    2003-01-01

    This paper provides a theory for quantifying the hysteresis and constitutive nonlinearities inherent to piezoceramic compounds through a combination of free energy analysis and stochastic homogenization techniques...

  12. Free-Energy Calculations. A Mathematical Perspective

    Science.gov (United States)

    Pohorille, Andrzej

    2015-01-01

    conductance, defined as the ratio of ionic current through the channel to applied voltage, can be calculated in MD simulations by way of applying an external electric field to the system and counting the number of ions that traverse the channel per unit time. If the current is small, a voltage significantly higher than the experimental one needs to be applied to collect sufficient statistics of ion crossing events. Then, the calculated conductance has to be extrapolated to the experimental voltage using procedures of unknown accuracy. Instead, we propose an alternative approach that applies if ion transport through channels can be described with sufficient accuracy by the one-dimensional diffusion equation in the potential given by the free energy profile and applied voltage. Then, it is possible to test the assumptions of the equation, recover the full voltage/current dependence, determine the reliability of the calculated conductance and reconstruct the underlying (equilibrium) free energy profile, all from MD simulations at a single voltage. We will present the underlying theory, model calculations that test this theory and simulations on ion conductance through a channel that has been extensively studied experimentally. To our knowledge this is the first case in which the complete, experimentally measured dependence of the current on applied voltage has been reconstructed from MD simulations.

  13. Relative Importance for Linear Regression in R: The Package relaimpo

    Directory of Open Access Journals (Sweden)

    Ulrike Gromping

    2006-09-01

    Full Text Available Relative importance is a topic that has seen a lot of interest in recent years, particularly in applied work. The R package relaimpo implements six different metrics for assessing relative importance of regressors in the linear model, two of which are recommended - averaging over orderings of regressors and a newly proposed metric (Feldman 2005 called pmvd. Apart from delivering the metrics themselves, relaimpo also provides (exploratory bootstrap confidence intervals. This paper offers a brief tutorial introduction to the package. The methods and relaimpo’s functionality are illustrated using the data set swiss that is generally available in R. The paper targets readers who have a basic understanding of multiple linear regression. For the background of more advanced aspects, references are provided.

  14. A linearized dispersion relation for orthorhombic pseudo-acoustic modeling

    KAUST Repository

    Song, Xiaolei

    2012-11-04

    Wavefield extrapolation in acoustic orthorhombic anisotropic media suffers from wave-mode coupling and stability limitations in the parameter range. We introduce a linearized form of the dispersion relation for acoustic orthorhombic media to model acoustic wavefields. We apply the lowrank approximation approach to handle the corresponding space-wavenumber mixed-domain operator. Numerical experiments show that the proposed wavefield extrapolator is accurate and practically free of dispersions. Further, there is no coupling of qSv and qP waves, because we use the analytical dispersion relation. No constraints on Thomsen\\'s parameters are required for stability. The linearized expression may provide useful application for parameter estimation in orthorhombic media.

  15. [Relations between biomedical variables: mathematical analysis or linear algebra?].

    Science.gov (United States)

    Hucher, M; Berlie, J; Brunet, M

    1977-01-01

    The authors, after a short reminder of one pattern's structure, stress on the possible double approach of relations uniting the variables of this pattern: use of fonctions, what is within the mathematical analysis sphere, use of linear algebra profiting by matricial calculation's development and automatiosation. They precise the respective interests on these methods, their bounds and the imperatives for utilization, according to the kind of variables, of data, and the objective for work, understanding phenomenons or helping towards decision.

  16. Canonical perturbation theory in linearized general relativity theory

    International Nuclear Information System (INIS)

    Gonzales, R.; Pavlenko, Yu.G.

    1986-01-01

    Canonical perturbation theory in linearized general relativity theory is developed. It is shown that the evolution of arbitrary dynamic value, conditioned by the interaction of particles, gravitation and electromagnetic fields, can be presented in the form of a series, each member of it corresponding to the contribution of certain spontaneous or induced process. The main concepts of the approach are presented in the approximation of a weak gravitational field

  17. Free-energy coarse-grained potential for C60

    International Nuclear Information System (INIS)

    Edmunds, D. M.; Tangney, P.; Vvedensky, D. D.; Foulkes, W. M. C.

    2015-01-01

    We propose a new deformable free energy method for generating a free-energy coarse-graining potential for C 60 . Potentials generated from this approach exhibit a strong temperature dependence and produce excellent agreement with benchmark fully atomistic molecular dynamics simulations. Parameter sets for analytical fits to this potential are provided at four different temperatures

  18. A Short Essay on the Uses of Free Energy

    Science.gov (United States)

    Koutandos, Spyridon

    2013-01-01

    In this article we examine cases of more classical and less classical nature compared to results found by quantum mechanics and attribute a form of Free Energy discontinuity for each case within a boundary layer. The concept of a boundary layer is broadened as to include areas of first or second variations of the Gibbs free energy. It is…

  19. Cosmological constant versus free energy for heterotic strings

    International Nuclear Information System (INIS)

    Alvarez, E.; Osorio, M.A.R.

    1988-01-01

    A detailed analysis is made of the modular-invariant formulation of the free energy of heterotic strings. Several instances are pointed out in which a duality formula can be obtained, and its physical implications are discussed. The interplay between the free energy of a given heterotic string and the cosmological constant of the toroidal compactification of another heterotic string is emphasized. (orig.)

  20. Calculation of molecular free energies in classical potentials

    International Nuclear Information System (INIS)

    Farhi, Asaf; Singh, Bipin

    2016-01-01

    Free energies of molecules can be calculated by quantum chemistry computations or by normal mode classical calculations. However, the first can be computationally impractical for large molecules and the second is based on the assumption of harmonic dynamics. We present a novel, accurate and complete calculation of molecular free energies in standard classical potentials. In this method we transform the molecule by relaxing potential terms which depend on the coordinates of a group of atoms in that molecule and calculate the free energy difference associated with the transformation. Then, since the transformed molecule can be treated as non-interacting systems, the free energy associated with these atoms is analytically or numerically calculated. This two-step calculation can be applied to calculate free energies of molecules or free energy difference between (possibly large) molecules in a general environment. We demonstrate the method in free energy calculations for methanethiol and butane molecules in vacuum and solvent. We suggest the potential application of free energy calculation of chemical reactions in classical molecular simulations. (paper)

  1. Free energy from molecular dynamics with multiple constraints

    NARCIS (Netherlands)

    den Otter, Wouter K.; Briels, Willem J.

    2000-01-01

    In molecular dynamics simulations of reacting systems, the key step to determining the equilibrium constant and the reaction rate is the calculation of the free energy as a function of the reaction coordinate. Intuitively the derivative of the free energy is equal to the average force needed to

  2. An exact linear dispersion relation for CRM instability

    International Nuclear Information System (INIS)

    Choyal, Y; Minami, K

    2011-01-01

    An exact self-consistent linear dispersion relation of a large orbit electron beam including two principles of cyclotron emission with oscillation frequencies above and below the relativistic electron frequency is derived and analyzed numerically for the first time in the literature. The two principles are cyclotron resonance maser (CRM) instability and Cherenkov instability in the azimuthal direction. Self-consistency in the formulation and inclusion of proper boundary conditions have removed the unphysical instability existing for infinitely large k z observed in conventional dispersion relations of CRM instability.

  3. Approximate scaling properties of RNA free energy landscapes

    Science.gov (United States)

    Baskaran, S.; Stadler, P. F.; Schuster, P.

    1996-01-01

    RNA free energy landscapes are analysed by means of "time-series" that are obtained from random walks restricted to excursion sets. The power spectra, the scaling of the jump size distribution, and the scaling of the curve length measured with different yard stick lengths are used to describe the structure of these "time series". Although they are stationary by construction, we find that their local behavior is consistent with both AR(1) and self-affine processes. Random walks confined to excursion sets (i.e., with the restriction that the fitness value exceeds a certain threshold at each step) exhibit essentially the same statistics as free random walks. We find that an AR(1) time series is in general approximately self-affine on timescales up to approximately the correlation length. We present an empirical relation between the correlation parameter rho of the AR(1) model and the exponents characterizing self-affinity.

  4. Calculation of the surface free energy of fcc copper nanoparticles

    International Nuclear Information System (INIS)

    Jia Ming; Lai Yanqing; Tian Zhongliang; Liu Yexiang

    2009-01-01

    Using molecular dynamics simulations with the modified analytic embedded-atom method we calculate the Gibbs free energy and surface free energy for fcc Cu bulk, and further obtain the Gibbs free energy of nanoparticles. Based on the Gibbs free energy of nanoparticles, we have investigated the heat capacity of copper nanoparticles. Calculation results indicate that the Gibbs free energy and the heat capacity of nanoparticles can be divided into two parts: bulk quantity and surface quantity. The molar heat capacity of the bulk sample is lower compared with the molar heat capacity of nanoparticles, and this difference increases with the decrease in the particle size. It is also observed that the size effect on the thermodynamic properties of Cu nanoparticles is not really significant until the particle is less than about 20 nm. It is the surface atoms that decide the size effect on the thermodynamic properties of nanoparticles

  5. Diabat Interpolation for Polymorph Free-Energy Differences.

    Science.gov (United States)

    Kamat, Kartik; Peters, Baron

    2017-02-02

    Existing methods to compute free-energy differences between polymorphs use harmonic approximations, advanced non-Boltzmann bias sampling techniques, and/or multistage free-energy perturbations. This work demonstrates how Bennett's diabat interpolation method ( J. Comput. Phys. 1976, 22, 245 ) can be combined with energy gaps from lattice-switch Monte Carlo techniques ( Phys. Rev. E 2000, 61, 906 ) to swiftly estimate polymorph free-energy differences. The new method requires only two unbiased molecular dynamics simulations, one for each polymorph. To illustrate the new method, we compute the free-energy difference between face-centered cubic and body-centered cubic polymorphs for a Gaussian core solid. We discuss the justification for parabolic models of the free-energy diabats and similarities to methods that have been used in studies of electron transfer.

  6. Enthalpy and interfacial free energy changes of water capillary condensed in mesoporous silica, MCM-41 and SBA-15.

    Science.gov (United States)

    Kittaka, Shigeharu; Ishimaru, Shinji; Kuranishi, Miki; Matsuda, Tomoko; Yamaguchi, Toshio

    2006-07-21

    The effect of confinement on the solid-liquid phase transitions of water was studied by using DSC and FT-IR measurements. Enthalpy changes upon melting of frozen water in MCM-41 and SBA-15 were determined as a function of pore size and found to decrease with decreasing pore size. The melting point also decreased almost monotonically with a decrease in pore size. Analysis of the Gibbs-Thomson relation on the basis of the thermodynamic data showed that there were two stages of interfacial free energy change after the constant region, i.e., below a pore size of 6.0 nm: a gradual decrease down to 3.4 nm and another decrease after a small jump upward. This fact demonstrates that the simple Gibbs-Thomson relation, i.e., a linear relation between the melting point change and the inverse pore size, is limited to the range not far from the melting point of bulk water. FT-IR measurements suggest that the decrease in enthalpy change and interfacial free energy change with decreasing pore size reflect the similarity of the structures of both liquid and solid phases of water in smaller pores at lower temperatures.

  7. Some computer simulations based on the linear relative risk model

    International Nuclear Information System (INIS)

    Gilbert, E.S.

    1991-10-01

    This report presents the results of computer simulations designed to evaluate and compare the performance of the likelihood ratio statistic and the score statistic for making inferences about the linear relative risk mode. The work was motivated by data on workers exposed to low doses of radiation, and the report includes illustration of several procedures for obtaining confidence limits for the excess relative risk coefficient based on data from three studies of nuclear workers. The computer simulations indicate that with small sample sizes and highly skewed dose distributions, asymptotic approximations to the score statistic or to the likelihood ratio statistic may not be adequate. For testing the null hypothesis that the excess relative risk is equal to zero, the asymptotic approximation to the likelihood ratio statistic was adequate, but use of the asymptotic approximation to the score statistic rejected the null hypothesis too often. Frequently the likelihood was maximized at the lower constraint, and when this occurred, the asymptotic approximations for the likelihood ratio and score statistics did not perform well in obtaining upper confidence limits. The score statistic and likelihood ratio statistics were found to perform comparably in terms of power and width of the confidence limits. It is recommended that with modest sample sizes, confidence limits be obtained using computer simulations based on the score statistic. Although nuclear worker studies are emphasized in this report, its results are relevant for any study investigating linear dose-response functions with highly skewed exposure distributions. 22 refs., 14 tabs

  8. Relating Reasoning Methodologies in Linear Logic and Process Algebra

    Directory of Open Access Journals (Sweden)

    Yuxin Deng

    2012-11-01

    Full Text Available We show that the proof-theoretic notion of logical preorder coincides with the process-theoretic notion of contextual preorder for a CCS-like calculus obtained from the formula-as-process interpretation of a fragment of linear logic. The argument makes use of other standard notions in process algebra, namely a labeled transition system and a coinductively defined simulation relation. This result establishes a connection between an approach to reason about process specifications and a method to reason about logic specifications.

  9. Relatively Inexact Proximal Point Algorithm and Linear Convergence Analysis

    Directory of Open Access Journals (Sweden)

    Ram U. Verma

    2009-01-01

    Full Text Available Based on a notion of relatively maximal (m-relaxed monotonicity, the approximation solvability of a general class of inclusion problems is discussed, while generalizing Rockafellar's theorem (1976 on linear convergence using the proximal point algorithm in a real Hilbert space setting. Convergence analysis, based on this new model, is simpler and compact than that of the celebrated technique of Rockafellar in which the Lipschitz continuity at 0 of the inverse of the set-valued mapping is applied. Furthermore, it can be used to generalize the Yosida approximation, which, in turn, can be applied to first-order evolution equations as well as evolution inclusions.

  10. Multiscale Free Energy Simulations: An Efficient Method for Connecting Classical MD Simulations to QM or QM/MM Free Energies Using Non-Boltzmann Bennett Reweighting Schemes

    Science.gov (United States)

    2015-01-01

    The reliability of free energy simulations (FES) is limited by two factors: (a) the need for correct sampling and (b) the accuracy of the computational method employed. Classical methods (e.g., force fields) are typically used for FES and present a myriad of challenges, with parametrization being a principle one. On the other hand, parameter-free quantum mechanical (QM) methods tend to be too computationally expensive for adequate sampling. One widely used approach is a combination of methods, where the free energy difference between the two end states is computed by, e.g., molecular mechanics (MM), and the end states are corrected by more accurate methods, such as QM or hybrid QM/MM techniques. Here we report two new approaches that significantly improve the aforementioned scheme; with a focus on how to compute corrections between, e.g., the MM and the more accurate QM calculations. First, a molecular dynamics trajectory that properly samples relevant conformational degrees of freedom is generated. Next, potential energies of each trajectory frame are generated with a QM or QM/MM Hamiltonian. Free energy differences are then calculated based on the QM or QM/MM energies using either a non-Boltzmann Bennett approach (QM-NBB) or non-Boltzmann free energy perturbation (NB-FEP). Both approaches are applied to calculate relative and absolute solvation free energies in explicit and implicit solvent environments. Solvation free energy differences (relative and absolute) between ethane and methanol in explicit solvent are used as the initial test case for QM-NBB. Next, implicit solvent methods are employed in conjunction with both QM-NBB and NB-FEP to compute absolute solvation free energies for 21 compounds. These compounds range from small molecules such as ethane and methanol to fairly large, flexible solutes, such as triacetyl glycerol. Several technical aspects were investigated. Ultimately some best practices are suggested for improving methods that seek to connect

  11. Guidelines for the analysis of free energy calculations.

    Science.gov (United States)

    Klimovich, Pavel V; Shirts, Michael R; Mobley, David L

    2015-05-01

    Free energy calculations based on molecular dynamics simulations show considerable promise for applications ranging from drug discovery to prediction of physical properties and structure-function studies. But these calculations are still difficult and tedious to analyze, and best practices for analysis are not well defined or propagated. Essentially, each group analyzing these calculations needs to decide how to conduct the analysis and, usually, develop its own analysis tools. Here, we review and recommend best practices for analysis yielding reliable free energies from molecular simulations. Additionally, we provide a Python tool, alchemical-analysis.py, freely available on GitHub as part of the pymbar package (located at http://github.com/choderalab/pymbar), that implements the analysis practices reviewed here for several reference simulation packages, which can be adapted to handle data from other packages. Both this review and the tool covers analysis of alchemical calculations generally, including free energy estimates via both thermodynamic integration and free energy perturbation-based estimators. Our Python tool also handles output from multiple types of free energy calculations, including expanded ensemble and Hamiltonian replica exchange, as well as standard fixed ensemble calculations. We also survey a range of statistical and graphical ways of assessing the quality of the data and free energy estimates, and provide prototypes of these in our tool. We hope this tool and discussion will serve as a foundation for more standardization of and agreement on best practices for analysis of free energy calculations.

  12. Relationship between enamel bond fatigue durability and surface free-energy characteristics with universal adhesives.

    Science.gov (United States)

    Nagura, Yuko; Tsujimoto, Akimasa; Barkmeier, Wayne W; Watanabe, Hidehiko; Johnson, William W; Takamizawa, Toshiki; Latta, Mark A; Miyazaki, Masashi

    2018-04-01

    The relationship between enamel bond fatigue durability and surface free-energy characteristics with universal adhesives was investigated. The initial shear bond strengths and shear fatigue strengths of five universal adhesives to enamel were determined with and without phosphoric acid pre-etching. The surface free-energy characteristics of adhesive-treated enamel with and without pre-etching were also determined. The initial shear bond strength and shear fatigue strength of universal adhesive to pre-etched enamel were higher than those to ground enamel. The initial shear bond strength and shear fatigue strength of universal adhesive to pre-etched enamel were material dependent, unlike those to ground enamel. The surface free-energy of the solid (γ S ) and the hydrogen-bonding force (γSh) of universal adhesive-treated enamel were different depending on the adhesive, regardless of the presence or absence of pre-etching. The bond fatigue durability of universal adhesives was higher to pre-etched enamel than to ground enamel. In addition, the bond fatigue durability to pre-etched enamel was material dependent, unlike that to ground enamel. The surface free-energy characteristics of universal adhesive-treated enamel were influenced by the adhesive type, regardless of the presence or absence of pre-etching. The surface free-energy characteristics of universal adhesive-treated enamel were related to the results of the bond fatigue durability. © 2018 Eur J Oral Sci.

  13. Methods for Efficiently and Accurately Computing Quantum Mechanical Free Energies for Enzyme Catalysis.

    Science.gov (United States)

    Kearns, F L; Hudson, P S; Boresch, S; Woodcock, H L

    2016-01-01

    Enzyme activity is inherently linked to free energies of transition states, ligand binding, protonation/deprotonation, etc.; these free energies, and thus enzyme function, can be affected by residue mutations, allosterically induced conformational changes, and much more. Therefore, being able to predict free energies associated with enzymatic processes is critical to understanding and predicting their function. Free energy simulation (FES) has historically been a computational challenge as it requires both the accurate description of inter- and intramolecular interactions and adequate sampling of all relevant conformational degrees of freedom. The hybrid quantum mechanical molecular mechanical (QM/MM) framework is the current tool of choice when accurate computations of macromolecular systems are essential. Unfortunately, robust and efficient approaches that employ the high levels of computational theory needed to accurately describe many reactive processes (ie, ab initio, DFT), while also including explicit solvation effects and accounting for extensive conformational sampling are essentially nonexistent. In this chapter, we will give a brief overview of two recently developed methods that mitigate several major challenges associated with QM/MM FES: the QM non-Boltzmann Bennett's acceptance ratio method and the QM nonequilibrium work method. We will also describe usage of these methods to calculate free energies associated with (1) relative properties and (2) along reaction paths, using simple test cases with relevance to enzymes examples. © 2016 Elsevier Inc. All rights reserved.

  14. Galerkin projection methods for solving multiple related linear systems

    Energy Technology Data Exchange (ETDEWEB)

    Chan, T.F.; Ng, M.; Wan, W.L.

    1996-12-31

    We consider using Galerkin projection methods for solving multiple related linear systems A{sup (i)}x{sup (i)} = b{sup (i)} for 1 {le} i {le} s, where A{sup (i)} and b{sup (i)} are different in general. We start with the special case where A{sup (i)} = A and A is symmetric positive definite. The method generates a Krylov subspace from a set of direction vectors obtained by solving one of the systems, called the seed system, by the CG method and then projects the residuals of other systems orthogonally onto the generated Krylov subspace to get the approximate solutions. The whole process is repeated with another unsolved system as a seed until all the systems are solved. We observe in practice a super-convergence behaviour of the CG process of the seed system when compared with the usual CG process. We also observe that only a small number of restarts is required to solve all the systems if the right-hand sides are close to each other. These two features together make the method particularly effective. In this talk, we give theoretical proof to justify these observations. Furthermore, we combine the advantages of this method and the block CG method and propose a block extension of this single seed method. The above procedure can actually be modified for solving multiple linear systems A{sup (i)}x{sup (i)} = b{sup (i)}, where A{sup (i)} are now different. We can also extend the previous analytical results to this more general case. Applications of this method to multiple related linear systems arising from image restoration and recursive least squares computations are considered as examples.

  15. Free energy evaluation in polymer translocation via Jarzynski equality

    Energy Technology Data Exchange (ETDEWEB)

    Mondaini, Felipe, E-mail: fmondaini@if.ufrj.br [Centro Federal de Educação Tecnológica Celso Suckow da Fonseca, Petrópolis, 25.620-003, RJ (Brazil); Moriconi, L., E-mail: moriconi@if.ufrj.br [Instituto de Física, Universidade Federal do Rio de Janeiro, C.P. 68528, 21945-970, Rio de Janeiro, RJ (Brazil)

    2014-05-01

    We perform, with the help of cloud computing resources, extensive Langevin simulations, which provide free energy estimates for unbiased three-dimensional polymer translocation. We employ the Jarzynski equality in its rigorous setting, to compute the variation of the free energy in single monomer translocation events. In our three-dimensional Langevin simulations, the excluded-volume and van der Waals interactions between beads (monomers and membrane atoms) are modeled through a repulsive Lennard-Jones (LJ) potential and consecutive monomers are subject to the Finite-Extension Nonlinear Elastic (FENE) potential. Analysing data for polymers with different lengths, the free energy profile is noted to have interesting finite-size scaling properties.

  16. Free energy evaluation in polymer translocation via Jarzynski equality

    International Nuclear Information System (INIS)

    Mondaini, Felipe; Moriconi, L.

    2014-01-01

    We perform, with the help of cloud computing resources, extensive Langevin simulations, which provide free energy estimates for unbiased three-dimensional polymer translocation. We employ the Jarzynski equality in its rigorous setting, to compute the variation of the free energy in single monomer translocation events. In our three-dimensional Langevin simulations, the excluded-volume and van der Waals interactions between beads (monomers and membrane atoms) are modeled through a repulsive Lennard-Jones (LJ) potential and consecutive monomers are subject to the Finite-Extension Nonlinear Elastic (FENE) potential. Analysing data for polymers with different lengths, the free energy profile is noted to have interesting finite-size scaling properties.

  17. Information-to-free-energy conversion: Utilizing thermal fluctuations.

    Science.gov (United States)

    Toyabe, Shoichi; Muneyuki, Eiro

    2013-01-01

    Maxwell's demon is a hypothetical creature that can convert information to free energy. A debate that has lasted for more than 100 years has revealed that the demon's operation does not contradict the laws of thermodynamics; hence, the demon can be realized physically. We briefly review the first experimental demonstration of Maxwell's demon of Szilard's engine type that converts information to free energy. We pump heat from an isothermal environment by using the information about the thermal fluctuations of a Brownian particle and increase the particle's free energy.

  18. Regeneralized London free energy for high-Tc vortex lattices

    Directory of Open Access Journals (Sweden)

    M. A. Shahzamanian

    2006-09-01

    Full Text Available   The London free-energy is regeneralized by the Ginsburg-Landau free-energy density in the presence of both d and s order parameters. We have shown that the strength of the s-d coupling, makes an important rule to determine the form of the lattice vortex. Appearance of the ratios of the coherence length to penetration depth in the higher order corrections of the free-energy density will truncate these corrections for even large values of .

  19. Unified interpretation of exciplex formation and marcus electron transfer on the basis of two-dimensional free energy surfaces.

    Science.gov (United States)

    Murata, Shigeo; Tachiya, M

    2007-09-27

    The mechanism of exciplex formation proposed in a previous paper has been refined to show how exciplex formation and Marcus electron transfer (ET) in fluorescence quenching are related to each other. This was done by making simple calculations of the free energies of the initial (DA*) and final (D+A-) states of ET. First it was shown that the decrease in D-A distance can induce intermolecular ET even in nonpolar solvents where solvent orientational polarization is absent, and that it leads to exciplex formation. This is consistent with experimental results that exciplex is most often observed in nonpolar solvents. The calculation was then extended to ET in polar solvents where the free energies are functions of both D-A distance and solvent orientational polarization. This enabled us to discuss both exciplex formation and Marcus ET in the same D-A pair and solvent on the basis of 2-dimensional free energy surfaces. The surfaces contain more information about the rates of these reactions, the mechanism of fluorescence quenching by ET, etc., than simple reaction schemes. By changing the parameters such as the free energy change of reaction, solvent dielectric constants, etc., one can construct the free energy surfaces for various systems. The effects of free energy change of reaction and of solvent polarity on the mechanism and relative importance of exciplex formation and Marcus ET in fluorescence quenching can be well explained. The free energy surface will also be useful for discussion of other phenomena related to ET reactions.

  20. Communication: modeling charge-sign asymmetric solvation free energies with nonlinear boundary conditions.

    Science.gov (United States)

    Bardhan, Jaydeep P; Knepley, Matthew G

    2014-10-07

    We show that charge-sign-dependent asymmetric hydration can be modeled accurately using linear Poisson theory after replacing the standard electric-displacement boundary condition with a simple nonlinear boundary condition. Using a single multiplicative scaling factor to determine atomic radii from molecular dynamics Lennard-Jones parameters, the new model accurately reproduces MD free-energy calculations of hydration asymmetries for: (i) monatomic ions, (ii) titratable amino acids in both their protonated and unprotonated states, and (iii) the Mobley "bracelet" and "rod" test problems [D. L. Mobley, A. E. Barber II, C. J. Fennell, and K. A. Dill, "Charge asymmetries in hydration of polar solutes," J. Phys. Chem. B 112, 2405-2414 (2008)]. Remarkably, the model also justifies the use of linear response expressions for charging free energies. Our boundary-element method implementation demonstrates the ease with which other continuum-electrostatic solvers can be extended to include asymmetry.

  1. Communication: Modeling charge-sign asymmetric solvation free energies with nonlinear boundary conditions

    International Nuclear Information System (INIS)

    Bardhan, Jaydeep P.; Knepley, Matthew G.

    2014-01-01

    We show that charge-sign-dependent asymmetric hydration can be modeled accurately using linear Poisson theory after replacing the standard electric-displacement boundary condition with a simple nonlinear boundary condition. Using a single multiplicative scaling factor to determine atomic radii from molecular dynamics Lennard-Jones parameters, the new model accurately reproduces MD free-energy calculations of hydration asymmetries for: (i) monatomic ions, (ii) titratable amino acids in both their protonated and unprotonated states, and (iii) the Mobley “bracelet” and “rod” test problems [D. L. Mobley, A. E. Barber II, C. J. Fennell, and K. A. Dill, “Charge asymmetries in hydration of polar solutes,” J. Phys. Chem. B 112, 2405–2414 (2008)]. Remarkably, the model also justifies the use of linear response expressions for charging free energies. Our boundary-element method implementation demonstrates the ease with which other continuum-electrostatic solvers can be extended to include asymmetry

  2. Communication: Modeling charge-sign asymmetric solvation free energies with nonlinear boundary conditions

    Science.gov (United States)

    Bardhan, Jaydeep P.; Knepley, Matthew G.

    2014-01-01

    We show that charge-sign-dependent asymmetric hydration can be modeled accurately using linear Poisson theory after replacing the standard electric-displacement boundary condition with a simple nonlinear boundary condition. Using a single multiplicative scaling factor to determine atomic radii from molecular dynamics Lennard-Jones parameters, the new model accurately reproduces MD free-energy calculations of hydration asymmetries for: (i) monatomic ions, (ii) titratable amino acids in both their protonated and unprotonated states, and (iii) the Mobley “bracelet” and “rod” test problems [D. L. Mobley, A. E. Barber II, C. J. Fennell, and K. A. Dill, “Charge asymmetries in hydration of polar solutes,” J. Phys. Chem. B 112, 2405–2414 (2008)]. Remarkably, the model also justifies the use of linear response expressions for charging free energies. Our boundary-element method implementation demonstrates the ease with which other continuum-electrostatic solvers can be extended to include asymmetry. PMID:25296776

  3. Communication: Modeling charge-sign asymmetric solvation free energies with nonlinear boundary conditions

    Energy Technology Data Exchange (ETDEWEB)

    Bardhan, Jaydeep P. [Department of Mechanical and Industrial Engineering, Northeastern University, Boston, Massachusetts 02115 (United States); Knepley, Matthew G. [Computation Institute, The University of Chicago, Chicago, Illinois 60637 (United States)

    2014-10-07

    We show that charge-sign-dependent asymmetric hydration can be modeled accurately using linear Poisson theory after replacing the standard electric-displacement boundary condition with a simple nonlinear boundary condition. Using a single multiplicative scaling factor to determine atomic radii from molecular dynamics Lennard-Jones parameters, the new model accurately reproduces MD free-energy calculations of hydration asymmetries for: (i) monatomic ions, (ii) titratable amino acids in both their protonated and unprotonated states, and (iii) the Mobley “bracelet” and “rod” test problems [D. L. Mobley, A. E. Barber II, C. J. Fennell, and K. A. Dill, “Charge asymmetries in hydration of polar solutes,” J. Phys. Chem. B 112, 2405–2414 (2008)]. Remarkably, the model also justifies the use of linear response expressions for charging free energies. Our boundary-element method implementation demonstrates the ease with which other continuum-electrostatic solvers can be extended to include asymmetry.

  4. Free Energy Reconstruction from Logarithmic Mean-Force Dynamics Using Multiple Nonequilibrium Trajectories.

    Science.gov (United States)

    Morishita, Tetsuya; Yonezawa, Yasushige; Ito, Atsushi M

    2017-07-11

    Efficient and reliable estimation of the mean force (MF), the derivatives of the free energy with respect to a set of collective variables (CVs), has been a challenging problem because free energy differences are often computed by integrating the MF. Among various methods for computing free energy differences, logarithmic mean-force dynamics (LogMFD) [ Morishita et al., Phys. Rev. E 2012 , 85 , 066702 ] invokes the conservation law in classical mechanics to integrate the MF, which allows us to estimate the free energy profile along the CVs on-the-fly. Here, we present a method called parallel dynamics, which improves the estimation of the MF by employing multiple replicas of the system and is straightforwardly incorporated in LogMFD or a related method. In the parallel dynamics, the MF is evaluated by a nonequilibrium path-ensemble using the multiple replicas based on the Crooks-Jarzynski nonequilibrium work relation. Thanks to the Crooks relation, realizing full-equilibrium states is no longer mandatory for estimating the MF. Additionally, sampling in the hidden subspace orthogonal to the CV space is highly improved with appropriate weights for each metastable state (if any), which is hardly achievable by typical free energy computational methods. We illustrate how to implement parallel dynamics by combining it with LogMFD, which we call logarithmic parallel dynamics (LogPD). Biosystems of alanine dipeptide and adenylate kinase in explicit water are employed as benchmark systems to which LogPD is applied to demonstrate the effect of multiple replicas on the accuracy and efficiency in estimating the free energy profiles using parallel dynamics.

  5. Free-energy calculations for semi-flexible macromolecules: Applications to DNA knotting and looping

    International Nuclear Information System (INIS)

    Giovan, Stefan M.; Scharein, Robert G.; Hanke, Andreas; Levene, Stephen D.

    2014-01-01

    We present a method to obtain numerically accurate values of configurational free energies of semiflexible macromolecular systems, based on the technique of thermodynamic integration combined with normal-mode analysis of a reference system subject to harmonic constraints. Compared with previous free-energy calculations that depend on a reference state, our approach introduces two innovations, namely, the use of internal coordinates to constrain the reference states and the ability to freely select these reference states. As a consequence, it is possible to explore systems that undergo substantially larger fluctuations than those considered in previous calculations, including semiflexible biopolymers having arbitrary ratios of contour length L to persistence length P. To validate the method, high accuracy is demonstrated for free energies of prime DNA knots with L/P = 20 and L/P = 40, corresponding to DNA lengths of 3000 and 6000 base pairs, respectively. We then apply the method to study the free-energy landscape for a model of a synaptic nucleoprotein complex containing a pair of looped domains, revealing a bifurcation in the location of optimal synapse (crossover) sites. This transition is relevant to target-site selection by DNA-binding proteins that occupy multiple DNA sites separated by large linear distances along the genome, a problem that arises naturally in gene regulation, DNA recombination, and the action of type-II topoisomerases

  6. Free-energy calculations for semi-flexible macromolecules: Applications to DNA knotting and looping

    Energy Technology Data Exchange (ETDEWEB)

    Giovan, Stefan M. [Department of Molecular and Cell Biology, University of Texas at Dallas, Richardson, Texas 75083 (United States); Scharein, Robert G. [Hypnagogic Software, Vancouver, British Columbia V6K 1V6 (Canada); Hanke, Andreas [Department of Physics and Astronomy, University of Texas at Brownsville, Brownsville, Texas 78520 (United States); Levene, Stephen D., E-mail: sdlevene@utdallas.edu [Department of Molecular and Cell Biology, University of Texas at Dallas, Richardson, Texas 75083 (United States); Department of Bioengineering, University of Texas at Dallas, Richardson, Texas 75083 (United States); Department of Physics, University of Texas at Dallas, Richardson, Texas 75083 (United States)

    2014-11-07

    We present a method to obtain numerically accurate values of configurational free energies of semiflexible macromolecular systems, based on the technique of thermodynamic integration combined with normal-mode analysis of a reference system subject to harmonic constraints. Compared with previous free-energy calculations that depend on a reference state, our approach introduces two innovations, namely, the use of internal coordinates to constrain the reference states and the ability to freely select these reference states. As a consequence, it is possible to explore systems that undergo substantially larger fluctuations than those considered in previous calculations, including semiflexible biopolymers having arbitrary ratios of contour length L to persistence length P. To validate the method, high accuracy is demonstrated for free energies of prime DNA knots with L/P = 20 and L/P = 40, corresponding to DNA lengths of 3000 and 6000 base pairs, respectively. We then apply the method to study the free-energy landscape for a model of a synaptic nucleoprotein complex containing a pair of looped domains, revealing a bifurcation in the location of optimal synapse (crossover) sites. This transition is relevant to target-site selection by DNA-binding proteins that occupy multiple DNA sites separated by large linear distances along the genome, a problem that arises naturally in gene regulation, DNA recombination, and the action of type-II topoisomerases.

  7. Free energy and plaquette expectation value for gluons on the lattice, in three dimensions

    International Nuclear Information System (INIS)

    Panagopoulos, H.; Skouroupathis, A.; Tsapalis, A.

    2006-01-01

    We calculate the perturbative value of the free energy in lattice QCD in three dimensions, up to three loops. Our calculation is performed using the Wilson formulation for gluons in SU(N) gauge theories. The free energy is directly related to the average plaquette. To carry out the calculation, we compute the coefficients involved in the perturbative expansion of the Free Energy up to three loops, using an automated set of procedures developed by us in Mathematica. The dependence on N is shown explicitly in our results. For purposes of comparison, we also present the individual contributions from every diagram. These have been obtained by means of two independent calculations, in order to cross check our results

  8. Accurate calculation of conformational free energy differences in explicit water: the confinement-solvation free energy approach.

    Science.gov (United States)

    Esque, Jeremy; Cecchini, Marco

    2015-04-23

    The calculation of the free energy of conformation is key to understanding the function of biomolecules and has attracted significant interest in recent years. Here, we present an improvement of the confinement method that was designed for use in the context of explicit solvent MD simulations. The development involves an additional step in which the solvation free energy of the harmonically restrained conformers is accurately determined by multistage free energy perturbation simulations. As a test-case application, the newly introduced confinement/solvation free energy (CSF) approach was used to compute differences in free energy between conformers of the alanine dipeptide in explicit water. The results are in excellent agreement with reference calculations based on both converged molecular dynamics and umbrella sampling. To illustrate the general applicability of the method, conformational equilibria of met-enkephalin (5 aa) and deca-alanine (10 aa) in solution were also analyzed. In both cases, smoothly converged free-energy results were obtained in agreement with equilibrium sampling or literature calculations. These results demonstrate that the CSF method may provide conformational free-energy differences of biomolecules with small statistical errors (below 0.5 kcal/mol) and at a moderate computational cost even with a full representation of the solvent.

  9. Modeling free energy availability from Hadean hydrothermal systems to the first metabolism.

    Science.gov (United States)

    Simoncini, E; Russell, M J; Kleidon, A

    2011-12-01

    Off-axis Hydrothermal Systems (HSs) are seen as the possible setting for the emergence of life. As the availability of free energy is a general requirement to drive any form of metabolism, we ask here under which conditions free energy generation by geologic processes is greatest and relate these to the conditions found at off-axis HSs. To do so, we present a conceptual model in which we explicitly capture the energetics of fluid motion and its interaction with exothermic reactions to maintain a state of chemical disequilibrium. Central to the interaction is the temperature at which the exothermic reactions take place. This temperature not only sets the equilibrium constant of the chemical reactions and thereby the distance of the actual state to chemical equilibrium, but these reactions also shape the temperature gradient that drives convection and thereby the advection of reactants to the reaction sites and the removal of the products that relate to geochemical free energy generation. What this conceptual model shows is that the positive feedback between convection and the chemical kinetics that is found at HSs favors a greater rate of free energy generation than in the absence of convection. Because of the lower temperatures and because the temperature of reactions is determined more strongly by these dynamics rather than an external heat flux, the conditions found at off-axis HSs should result in the greatest rates of geochemical free energy generation. Hence, we hypothesize from these thermodynamic considerations that off-axis HSs seem most conducive for the emergence of protometabolic pathways as these provide the greatest, abiotic generation rates of chemical free energy.

  10. Water droplet excess free energy determined by cluster mitosis using guided molecular dynamics

    Science.gov (United States)

    Lau, Gabriel V.; Hunt, Patricia A.; Müller, Erich A.; Jackson, George; Ford, Ian J.

    2015-12-01

    Atmospheric aerosols play a vital role in affecting climate by influencing the properties and lifetimes of clouds and precipitation. Understanding the underlying microscopic mechanisms involved in the nucleation of aerosol droplets from the vapour phase is therefore of great interest. One key thermodynamic quantity in nucleation is the excess free energy of cluster formation relative to that of the saturated vapour. In our current study, the excess free energy is extracted for clusters of pure water modelled with the TIP4P/2005 intermolecular potential using a method based on nonequilibrium molecular dynamics and the Jarzynski relation. The change in free energy associated with the "mitosis" or division of a cluster of N water molecules into two N/2 sub-clusters is evaluated. This methodology is an extension of the disassembly procedure used recently to calculate the excess free energy of argon clusters [H. Y. Tang and I. J. Ford, Phys. Rev. E 91, 023308 (2015)]. Our findings are compared to the corresponding excess free energies obtained from classical nucleation theory (CNT) as well as internally consistent classical theory (ICCT). The values of the excess free energy that we obtain with the mitosis method are consistent with CNT for large cluster sizes but for the smallest clusters, the results tend towards ICCT; for intermediate sized clusters, we obtain values between the ICCT and CNT predictions. Furthermore, the curvature-dependent surface tension which can be obtained by regarding the clusters as spherical droplets of bulk density is found to be a monotonically increasing function of cluster size for the studied range. The data are compared to other values reported in the literature, agreeing qualitatively with some but disagreeing with the values determined by Joswiak et al. [J. Phys. Chem. Lett. 4, 4267 (2013)] using a biased mitosis approach; an assessment of the differences is the main motivation for our current study.

  11. Water droplet excess free energy determined by cluster mitosis using guided molecular dynamics

    Energy Technology Data Exchange (ETDEWEB)

    Lau, Gabriel V.; Müller, Erich A.; Jackson, George [Department of Chemical Engineering, Imperial College London, South Kensington Campus, London SW7 2AZ (United Kingdom); Hunt, Patricia A. [Department of Chemistry, Imperial College London, South Kensington Campus, London SW7 2AZ (United Kingdom); Ford, Ian J. [Department of Physics and Astronomy and London Centre for Nanotechnology, University College London, Gower Street, London WC1E 6BT (United Kingdom)

    2015-12-28

    Atmospheric aerosols play a vital role in affecting climate by influencing the properties and lifetimes of clouds and precipitation. Understanding the underlying microscopic mechanisms involved in the nucleation of aerosol droplets from the vapour phase is therefore of great interest. One key thermodynamic quantity in nucleation is the excess free energy of cluster formation relative to that of the saturated vapour. In our current study, the excess free energy is extracted for clusters of pure water modelled with the TIP4P/2005 intermolecular potential using a method based on nonequilibrium molecular dynamics and the Jarzynski relation. The change in free energy associated with the “mitosis” or division of a cluster of N water molecules into two N/2 sub-clusters is evaluated. This methodology is an extension of the disassembly procedure used recently to calculate the excess free energy of argon clusters [H. Y. Tang and I. J. Ford, Phys. Rev. E 91, 023308 (2015)]. Our findings are compared to the corresponding excess free energies obtained from classical nucleation theory (CNT) as well as internally consistent classical theory (ICCT). The values of the excess free energy that we obtain with the mitosis method are consistent with CNT for large cluster sizes but for the smallest clusters, the results tend towards ICCT; for intermediate sized clusters, we obtain values between the ICCT and CNT predictions. Furthermore, the curvature-dependent surface tension which can be obtained by regarding the clusters as spherical droplets of bulk density is found to be a monotonically increasing function of cluster size for the studied range. The data are compared to other values reported in the literature, agreeing qualitatively with some but disagreeing with the values determined by Joswiak et al. [J. Phys. Chem. Lett. 4, 4267 (2013)] using a biased mitosis approach; an assessment of the differences is the main motivation for our current study.

  12. Free energy distribution function of a random Ising ferromagnet

    International Nuclear Information System (INIS)

    Dotsenko, Victor; Klumov, Boris

    2012-01-01

    We study the free energy distribution function of a weakly disordered Ising ferromagnet in terms of the D-dimensional random temperature Ginzburg–Landau Hamiltonian. It is shown that besides the usual Gaussian 'body' this distribution function exhibits non-Gaussian tails both in the paramagnetic and in the ferromagnetic phases. Explicit asymptotic expressions for these tails are derived. It is demonstrated that the tails are strongly asymmetric: the left tail (for large negative values of the free energy) is much slower than the right one (for large positive values of the free energy). It is argued that at the critical point the free energy of the random Ising ferromagnet in dimensions D < 4 is described by a non-trivial universal distribution function which is non-self-averaging

  13. The free-energy principle: a unified brain theory?

    Science.gov (United States)

    Friston, Karl

    2010-02-01

    A free-energy principle has been proposed recently that accounts for action, perception and learning. This Review looks at some key brain theories in the biological (for example, neural Darwinism) and physical (for example, information theory and optimal control theory) sciences from the free-energy perspective. Crucially, one key theme runs through each of these theories - optimization. Furthermore, if we look closely at what is optimized, the same quantity keeps emerging, namely value (expected reward, expected utility) or its complement, surprise (prediction error, expected cost). This is the quantity that is optimized under the free-energy principle, which suggests that several global brain theories might be unified within a free-energy framework.

  14. Relative null controllability of linear systems with multiple delays in ...

    African Journals Online (AJOL)

    varying multiple delays in state and control are developed. If the uncontrolled system is uniformly asymptotically stable, and if the linear system is controllable, then the linear system is null controllable. Journal of the Nigerian Association of ...

  15. New Inequalities and Uncertainty Relations on Linear Canonical Transform Revisit

    Directory of Open Access Journals (Sweden)

    Xu Guanlei

    2009-01-01

    Full Text Available The uncertainty principle plays an important role in mathematics, physics, signal processing, and so on. Firstly, based on definition of the linear canonical transform (LCT and the traditional Pitt's inequality, one novel Pitt's inequality in the LCT domains is obtained, which is connected with the LCT parameters a and b. Then one novel logarithmic uncertainty principle is derived from this novel Pitt's inequality in the LCT domains, which is associated with parameters of the two LCTs. Secondly, from the relation between the original function and LCT, one entropic uncertainty principle and one Heisenberg's uncertainty principle in the LCT domains are derived, which are associated with the LCT parameters a and b. The reason why the three lower bounds are only associated with LCT parameters a and b and independent of c and d is presented. The results show it is possible that the bounds tend to zeros.

  16. The free-energy cost of interaction between DNA loops.

    Science.gov (United States)

    Huang, Lifang; Liu, Peijiang; Yuan, Zhanjiang; Zhou, Tianshou; Yu, Jianshe

    2017-10-03

    From the viewpoint of thermodynamics, the formation of DNA loops and the interaction between them, which are all non-equilibrium processes, result in the change of free energy, affecting gene expression and further cell-to-cell variability as observed experimentally. However, how these processes dissipate free energy remains largely unclear. Here, by analyzing a mechanic model that maps three fundamental topologies of two interacting DNA loops into a 4-state model of gene transcription, we first show that a longer DNA loop needs more mean free energy consumption. Then, independent of the type of interacting two DNA loops (nested, side-by-side or alternating), the promotion between them always consumes less mean free energy whereas the suppression dissipates more mean free energy. More interestingly, we find that in contrast to the mechanism of direct looping between promoter and enhancer, the facilitated-tracking mechanism dissipates less mean free energy but enhances the mean mRNA expression, justifying the facilitated-tracking hypothesis, a long-standing debate in biology. Based on minimal energy principle, we thus speculate that organisms would utilize the mechanisms of loop-loop promotion and facilitated tracking to survive in complex environments. Our studies provide insights into the understanding of gene expression regulation mechanism from the view of energy consumption.

  17. Learning free energy landscapes using artificial neural networks.

    Science.gov (United States)

    Sidky, Hythem; Whitmer, Jonathan K

    2018-03-14

    Existing adaptive bias techniques, which seek to estimate free energies and physical properties from molecular simulations, are limited by their reliance on fixed kernels or basis sets which hinder their ability to efficiently conform to varied free energy landscapes. Further, user-specified parameters are in general non-intuitive yet significantly affect the convergence rate and accuracy of the free energy estimate. Here we propose a novel method, wherein artificial neural networks (ANNs) are used to develop an adaptive biasing potential which learns free energy landscapes. We demonstrate that this method is capable of rapidly adapting to complex free energy landscapes and is not prone to boundary or oscillation problems. The method is made robust to hyperparameters and overfitting through Bayesian regularization which penalizes network weights and auto-regulates the number of effective parameters in the network. ANN sampling represents a promising innovative approach which can resolve complex free energy landscapes in less time than conventional approaches while requiring minimal user input.

  18. Hierarchical Protein Free Energy Landscapes from Variationally Enhanced Sampling.

    Science.gov (United States)

    Shaffer, Patrick; Valsson, Omar; Parrinello, Michele

    2016-12-13

    In recent work, we demonstrated that it is possible to obtain approximate representations of high-dimensional free energy surfaces with variationally enhanced sampling ( Shaffer, P.; Valsson, O.; Parrinello, M. Proc. Natl. Acad. Sci. , 2016 , 113 , 17 ). The high-dimensional spaces considered in that work were the set of backbone dihedral angles of a small peptide, Chignolin, and the high-dimensional free energy surface was approximated as the sum of many two-dimensional terms plus an additional term which represents an initial estimate. In this paper, we build on that work and demonstrate that we can calculate high-dimensional free energy surfaces of very high accuracy by incorporating additional terms. The additional terms apply to a set of collective variables which are more coarse than the base set of collective variables. In this way, it is possible to build hierarchical free energy surfaces, which are composed of terms that act on different length scales. We test the accuracy of these free energy landscapes for the proteins Chignolin and Trp-cage by constructing simple coarse-grained models and comparing results from the coarse-grained model to results from atomistic simulations. The approach described in this paper is ideally suited for problems in which the free energy surface has important features on different length scales or in which there is some natural hierarchy.

  19. Learning free energy landscapes using artificial neural networks

    Science.gov (United States)

    Sidky, Hythem; Whitmer, Jonathan K.

    2018-03-01

    Existing adaptive bias techniques, which seek to estimate free energies and physical properties from molecular simulations, are limited by their reliance on fixed kernels or basis sets which hinder their ability to efficiently conform to varied free energy landscapes. Further, user-specified parameters are in general non-intuitive yet significantly affect the convergence rate and accuracy of the free energy estimate. Here we propose a novel method, wherein artificial neural networks (ANNs) are used to develop an adaptive biasing potential which learns free energy landscapes. We demonstrate that this method is capable of rapidly adapting to complex free energy landscapes and is not prone to boundary or oscillation problems. The method is made robust to hyperparameters and overfitting through Bayesian regularization which penalizes network weights and auto-regulates the number of effective parameters in the network. ANN sampling represents a promising innovative approach which can resolve complex free energy landscapes in less time than conventional approaches while requiring minimal user input.

  20. Gibbs Sampler-Based λ-Dynamics and Rao-Blackwell Estimator for Alchemical Free Energy Calculation.

    Science.gov (United States)

    Ding, Xinqiang; Vilseck, Jonah Z; Hayes, Ryan L; Brooks, Charles L

    2017-06-13

    λ-dynamics is a generalized ensemble method for alchemical free energy calculations. In traditional λ-dynamics, the alchemical switch variable λ is treated as a continuous variable ranging from 0 to 1 and an empirical estimator is utilized to approximate the free energy. In the present article, we describe an alternative formulation of λ-dynamics that utilizes the Gibbs sampler framework, which we call Gibbs sampler-based λ-dynamics (GSLD). GSLD, like traditional λ-dynamics, can be readily extended to calculate free energy differences between multiple ligands in one simulation. We also introduce a new free energy estimator, the Rao-Blackwell estimator (RBE), for use in conjunction with GSLD. Compared with the current empirical estimator, the advantage of RBE is that RBE is an unbiased estimator and its variance is usually smaller than the current empirical estimator. We also show that the multistate Bennett acceptance ratio equation or the unbinned weighted histogram analysis method equation can be derived using the RBE. We illustrate the use and performance of this new free energy computational framework by application to a simple harmonic system as well as relevant calculations of small molecule relative free energies of solvation and binding to a protein receptor. Our findings demonstrate consistent and improved performance compared with conventional alchemical free energy methods.

  1. Comparative assessment of computational methods for the determination of solvation free energies in alcohol-based molecules.

    Science.gov (United States)

    Martins, Silvia A; Sousa, Sergio F

    2013-06-05

    The determination of differences in solvation free energies between related drug molecules remains an important challenge in computational drug optimization, when fast and accurate calculation of differences in binding free energy are required. In this study, we have evaluated the performance of five commonly used polarized continuum model (PCM) methodologies in the determination of solvation free energies for 53 typical alcohol and alkane small molecules. In addition, the performance of these PCM methods, of a thermodynamic integration (TI) protocol and of the Poisson-Boltzmann (PB) and generalized Born (GB) methods, were tested in the determination of solvation free energies changes for 28 common alkane-alcohol transformations, by the substitution of an hydrogen atom for a hydroxyl substituent. The results show that the solvation model D (SMD) performs better among the PCM-based approaches in estimating solvation free energies for alcohol molecules, and solvation free energy changes for alkane-alcohol transformations, with an average error below 1 kcal/mol for both quantities. However, for the determination of solvation free energy changes on alkane-alcohol transformation, PB and TI yielded better results. TI was particularly accurate in the treatment of hydroxyl groups additions to aromatic rings (0.53 kcal/mol), a common transformation when optimizing drug-binding in computer-aided drug design. Copyright © 2013 Wiley Periodicals, Inc.

  2. Predicting Hydride Donor Strength via Quantum Chemical Calculations of Hydride Transfer Activation Free Energy.

    Science.gov (United States)

    Alherz, Abdulaziz; Lim, Chern-Hooi; Hynes, James T; Musgrave, Charles B

    2018-01-25

    We propose a method to approximate the kinetic properties of hydride donor species by relating the nucleophilicity (N) of a hydride to the activation free energy ΔG ⧧ of its corresponding hydride transfer reaction. N is a kinetic parameter related to the hydride transfer rate constant that quantifies a nucleophilic hydridic species' tendency to donate. Our method estimates N using quantum chemical calculations to compute ΔG ⧧ for hydride transfers from hydride donors to CO 2 in solution. A linear correlation for each class of hydrides is then established between experimentally determined N values and the computationally predicted ΔG ⧧ ; this relationship can then be used to predict nucleophilicity for different hydride donors within each class. This approach is employed to determine N for four different classes of hydride donors: two organic (carbon-based and benzimidazole-based) and two inorganic (boron and silicon) hydride classes. We argue that silicon and boron hydrides are driven by the formation of the more stable Si-O or B-O bond. In contrast, the carbon-based hydrides considered herein are driven by the stability acquired upon rearomatization, a feature making these species of particular interest, because they both exhibit catalytic behavior and can be recycled.

  3. Protein Folding Free Energy Landscape along the Committor - the Optimal Folding Coordinate.

    Science.gov (United States)

    Krivov, Sergei V

    2018-06-06

    Recent advances in simulation and experiment have led to dramatic increases in the quantity and complexity of produced data, which makes the development of automated analysis tools very important. A powerful approach to analyze dynamics contained in such data sets is to describe/approximate it by diffusion on a free energy landscape - free energy as a function of reaction coordinates (RC). For the description to be quantitatively accurate, RCs should be chosen in an optimal way. Recent theoretical results show that such an optimal RC exists; however, determining it for practical systems is a very difficult unsolved problem. Here we describe a solution to this problem. We describe an adaptive nonparametric approach to accurately determine the optimal RC (the committor) for an equilibrium trajectory of a realistic system. In contrast to alternative approaches, which require a functional form with many parameters to approximate an RC and thus extensive expertise with the system, the suggested approach is nonparametric and can approximate any RC with high accuracy without system specific information. To avoid overfitting for a realistically sampled system, the approach performs RC optimization in an adaptive manner by focusing optimization on less optimized spatiotemporal regions of the RC. The power of the approach is illustrated on a long equilibrium atomistic folding simulation of HP35 protein. We have determined the optimal folding RC - the committor, which was confirmed by passing a stringent committor validation test. It allowed us to determine a first quantitatively accurate protein folding free energy landscape. We have confirmed the recent theoretical results that diffusion on such a free energy profile can be used to compute exactly the equilibrium flux, the mean first passage times, and the mean transition path times between any two points on the profile. We have shown that the mean squared displacement along the optimal RC grows linear with time as for

  4. Connecting free energy surfaces in implicit and explicit solvent: an efficient method to compute conformational and solvation free energies.

    Science.gov (United States)

    Deng, Nanjie; Zhang, Bin W; Levy, Ronald M

    2015-06-09

    The ability to accurately model solvent effects on free energy surfaces is important for understanding many biophysical processes including protein folding and misfolding, allosteric transitions, and protein–ligand binding. Although all-atom simulations in explicit solvent can provide an accurate model for biomolecules in solution, explicit solvent simulations are hampered by the slow equilibration on rugged landscapes containing multiple basins separated by barriers. In many cases, implicit solvent models can be used to significantly speed up the conformational sampling; however, implicit solvent simulations do not fully capture the effects of a molecular solvent, and this can lead to loss of accuracy in the estimated free energies. Here we introduce a new approach to compute free energy changes in which the molecular details of explicit solvent simulations are retained while also taking advantage of the speed of the implicit solvent simulations. In this approach, the slow equilibration in explicit solvent, due to the long waiting times before barrier crossing, is avoided by using a thermodynamic cycle which connects the free energy basins in implicit solvent and explicit solvent using a localized decoupling scheme. We test this method by computing conformational free energy differences and solvation free energies of the model system alanine dipeptide in water. The free energy changes between basins in explicit solvent calculated using fully explicit solvent paths agree with the corresponding free energy differences obtained using the implicit/explicit thermodynamic cycle to within 0.3 kcal/mol out of ∼3 kcal/mol at only ∼8% of the computational cost. We note that WHAM methods can be used to further improve the efficiency and accuracy of the implicit/explicit thermodynamic cycle.

  5. From slump loss to Gibbs' free energy

    DEFF Research Database (Denmark)

    Jensen, Ole Mejlhede; Diamond, Sidney

    2006-01-01

    In its classical form, the science of construction materials is a descriptive, empirical discipline related to certain types of materials, e.g. the study of the properties of wood, steel, concrete and plastics. This traditional division of the science into the separate study of the different...

  6. Measuring excess free energies of self-assembled membrane structures.

    Science.gov (United States)

    Norizoe, Yuki; Daoulas, Kostas Ch; Müller, Marcus

    2010-01-01

    Using computer simulation of a solvent-free, coarse-grained model for amphiphilic membranes, we study the excess free energy of hourglass-shaped connections (i.e., stalks) between two apposed bilayer membranes. In order to calculate the free energy by simulation in the canonical ensemble, we reversibly transfer two apposed bilayers into a configuration with a stalk in three steps. First, we gradually replace the intermolecular interactions by an external, ordering field. The latter is chosen such that the structure of the non-interacting system in this field closely resembles the structure of the original, interacting system in the absence of the external field. The absence of structural changes along this path suggests that it is reversible; a fact which is confirmed by expanded-ensemble simulations. Second, the external, ordering field is changed as to transform the non-interacting system from the apposed bilayer structure to two-bilayers connected by a stalk. The final external field is chosen such that the structure of the non-interacting system resembles the structure of the stalk in the interacting system without a field. On the third branch of the transformation path, we reversibly replace the external, ordering field by non-bonded interactions. Using expanded-ensemble techniques, the free energy change along this reversible path can be obtained with an accuracy of 10(-3)k(B)T per molecule in the n VT-ensemble. Calculating the chemical potential, we obtain the free energy of a stalk in the grandcanonical ensemble, and employing semi-grandcanonical techniques, we calculate the change of the excess free energy upon altering the molecular architecture. This computational strategy can be applied to compute the free energy of self-assembled phases in lipid and copolymer systems, and the excess free energy of defects or interfaces.

  7. Using reweighting and free energy surface interpolation to predict solid-solid phase diagrams

    Science.gov (United States)

    Schieber, Natalie P.; Dybeck, Eric C.; Shirts, Michael R.

    2018-04-01

    Many physical properties of small organic molecules are dependent on the current crystal packing, or polymorph, of the material, including bioavailability of pharmaceuticals, optical properties of dyes, and charge transport properties of semiconductors. Predicting the most stable crystalline form at a given temperature and pressure requires determining the crystalline form with the lowest relative Gibbs free energy. Effective computational prediction of the most stable polymorph could save significant time and effort in the design of novel molecular crystalline solids or predict their behavior under new conditions. In this study, we introduce a new approach using multistate reweighting to address the problem of determining solid-solid phase diagrams and apply this approach to the phase diagram of solid benzene. For this approach, we perform sampling at a selection of temperature and pressure states in the region of interest. We use multistate reweighting methods to determine the reduced free energy differences between T and P states within a given polymorph and validate this phase diagram using several measures. The relative stability of the polymorphs at the sampled states can be successively interpolated from these points to create the phase diagram by combining these reduced free energy differences with a reference Gibbs free energy difference between polymorphs. The method also allows for straightforward estimation of uncertainties in the phase boundary. We also find that when properly implemented, multistate reweighting for phase diagram determination scales better with the size of the system than previously estimated.

  8. Free energy for protonation reaction in lithium-ion battery cathode materials

    International Nuclear Information System (INIS)

    Benedek, R.; Thackeray, M. M.; van de Walle, A.

    2008-01-01

    Calculations are performed of free energies for proton-for-lithium-ion exchange reactions in lithium-ion battery cathode materials. First-principles calculations are employed for the solid phases and tabulated ionization potential and hydration energy data for aqueous ions. Layered structures, spinel LiMn 2 O 4 , and olivine LiFePO 4 are considered. Protonation is most favorable energetically in layered systems, such as Li 2 MnO 3 and LiCoO 2 . Less favorable are ion-exchange in spinel LiMn 2 O 4 and LiV 3 O 8 . Unfavorable is the substitution of protons for Li in olivine LiFePO 4 , because of the large distortion of the Fe and P coordination polyhedra. The reaction free energy scales roughly linearly with the volume change in the reaction

  9. Quantitative prediction of solvation free energy in octanol of organic compounds.

    Science.gov (United States)

    Delgado, Eduardo J; Jaña, Gonzalo A

    2009-03-01

    The free energy of solvation, DeltaGS0, in octanol of organic compounds is quantitatively predicted from the molecular structure. The model, involving only three molecular descriptors, is obtained by multiple linear regression analysis from a data set of 147 compounds containing diverse organic functions, namely, halogenated and non-halogenated alkanes, alkenes, alkynes, aromatics, alcohols, aldehydes, ketones, amines, ethers and esters; covering a DeltaGS0 range from about -50 to 0 kJ.mol(-1). The model predicts the free energy of solvation with a squared correlation coefficient of 0.93 and a standard deviation, 2.4 kJ.mol(-1), just marginally larger than the generally accepted value of experimental uncertainty. The involved molecular descriptors have definite physical meaning corresponding to the different intermolecular interactions occurring in the bulk liquid phase. The model is validated with an external set of 36 compounds not included in the training set.

  10. Quantitative Prediction of Solvation Free Energy in Octanol of Organic Compounds

    Directory of Open Access Journals (Sweden)

    Eduardo J. Delgado

    2009-03-01

    Full Text Available The free energy of solvation, ΔGS0 , in octanol of organic compunds is quantitatively predicted from the molecular structure. The model, involving only three molecular descriptors, is obtained by multiple linear regression analysis from a data set of 147 compounds containing diverse organic functions, namely, halogenated and non-halogenated alkanes, alkenes, alkynes, aromatics, alcohols, aldehydes, ketones, amines, ethers and esters; covering a ΔGS0 range from about –50 to 0 kJ·mol-1. The model predicts the free energy of solvation with a squared correlation coefficient of 0.93 and a standard deviation, 2.4 kJ·mol-1, just marginally larger than the generally accepted value of experimental uncertainty. The involved molecular descriptors have definite physical meaning corresponding to the different intermolecular interactions occurring in the bulk liquid phase. The model is validated with an external set of 36 compounds not included in the training set.

  11. A Carbon-Free Energy Future

    Science.gov (United States)

    Linden, H. R.; Singer, S. F.

    2001-12-01

    It is generally agreed that hydrogen is an ideal energy source, both for transportation and for the generation of electric power. Through the use of fuel cells, hydrogen becomes a high-efficiency carbon-free power source for electromotive transport; with the help of regenerative braking, cars should be able to reach triple the current mileage. Many have visualized a distributed electric supply network with decentralized generation based on fuel cells. Fuel cells can provide high generation efficiencies by overcoming the fundamental thermodynamic limitation imposed by the Carnot cycle. Further, by using the heat energy of the high-temperature fuel cell in co-generation, one can achieve total thermal efficiencies approaching 100 percent, as compared to present-day average power-plant efficiencies of around 35 percent. In addition to reducing CO2 emissions, distributed generation based on fuel cells also eliminates the tremendous release of waste heat into the environment, the need for cooling water, and related limitations on siting. Manufacture of hydrogen remains a key problem, but there are many technical solutions that come into play whenever the cost equations permit . One can visualize both central and local hydrogen production. Initially, reforming of abundant natural gas into mixtures of 80% H2 and 20% CO2 provides a relatively low-emission source of hydrogen. Conventional fossil-fuel plants and nuclear plants can become hydrogen factories using both high-temperature topping cycles and electrolysis of water. Hydro-electric plants can manufacture hydrogen by electrolysis. Later, photovoltaic and wind farms could be set up at favorable locations around the world as hydrogen factories. If perfected, photovoltaic hydrogen production through catalysis would use solar photons most efficiently . For both wind and PV, hydrogen production solves some crucial problems: intermittency of wind and of solar radiation, storage of energy, and use of locations that are not

  12. Thermodynamic free energy methods to investigate shape transitions in bilayer membranes.

    Science.gov (United States)

    Ramakrishnan, N; Tourdot, Richard W; Radhakrishnan, Ravi

    2016-06-01

    The conformational free energy landscape of a system is a fundamental thermodynamic quantity of importance particularly in the study of soft matter and biological systems, in which the entropic contributions play a dominant role. While computational methods to delineate the free energy landscape are routinely used to analyze the relative stability of conformational states, to determine phase boundaries, and to compute ligand-receptor binding energies its use in problems involving the cell membrane is limited. Here, we present an overview of four different free energy methods to study morphological transitions in bilayer membranes, induced either by the action of curvature remodeling proteins or due to the application of external forces. Using a triangulated surface as a model for the cell membrane and using the framework of dynamical triangulation Monte Carlo, we have focused on the methods of Widom insertion, thermodynamic integration, Bennett acceptance scheme, and umbrella sampling and weighted histogram analysis. We have demonstrated how these methods can be employed in a variety of problems involving the cell membrane. Specifically, we have shown that the chemical potential, computed using Widom insertion, and the relative free energies, computed using thermodynamic integration and Bennett acceptance method, are excellent measures to study the transition from curvature sensing to curvature inducing behavior of membrane associated proteins. The umbrella sampling and WHAM analysis has been used to study the thermodynamics of tether formation in cell membranes and the quantitative predictions of the computational model are in excellent agreement with experimental measurements. Furthermore, we also present a method based on WHAM and thermodynamic integration to handle problems related to end-point-catastrophe that are common in most free energy methods.

  13. Using the fast fourier transform in binding free energy calculations.

    Science.gov (United States)

    Nguyen, Trung Hai; Zhou, Huan-Xiang; Minh, David D L

    2018-04-30

    According to implicit ligand theory, the standard binding free energy is an exponential average of the binding potential of mean force (BPMF), an exponential average of the interaction energy between the unbound ligand ensemble and a rigid receptor. Here, we use the fast Fourier transform (FFT) to efficiently evaluate BPMFs by calculating interaction energies when rigid ligand configurations from the unbound ensemble are discretely translated across rigid receptor conformations. Results for standard binding free energies between T4 lysozyme and 141 small organic molecules are in good agreement with previous alchemical calculations based on (1) a flexible complex ( R≈0.9 for 24 systems) and (2) flexible ligand with multiple rigid receptor configurations ( R≈0.8 for 141 systems). While the FFT is routinely used for molecular docking, to our knowledge this is the first time that the algorithm has been used for rigorous binding free energy calculations. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

  14. Computation of Hemagglutinin Free Energy Difference by the Confinement Method

    Science.gov (United States)

    2017-01-01

    Hemagglutinin (HA) mediates membrane fusion, a crucial step during influenza virus cell entry. How many HAs are needed for this process is still subject to debate. To aid in this discussion, the confinement free energy method was used to calculate the conformational free energy difference between the extended intermediate and postfusion state of HA. Special care was taken to comply with the general guidelines for free energy calculations, thereby obtaining convergence and demonstrating reliability of the results. The energy that one HA trimer contributes to fusion was found to be 34.2 ± 3.4kBT, similar to the known contributions from other fusion proteins. Although computationally expensive, the technique used is a promising tool for the further energetic characterization of fusion protein mechanisms. Knowledge of the energetic contributions per protein, and of conserved residues that are crucial for fusion, aids in the development of fusion inhibitors for antiviral drugs. PMID:29151344

  15. Standard free energy of formation of iron iodide

    Science.gov (United States)

    Khandkar, A.; Tare, V. B.; Wagner, J. B., Jr.

    1983-01-01

    An experiment is reported where silver iodide is used to determine the standard free energy of formation of iron iodide. By using silver iodide as a solid electrolyte, a galvanic cell, Ag/AgI/Fe-FeI2, is formulated. The standard free energy of formation of AgI is known, and hence it is possible to estimate the standard free energy of formation of FeI2 by measuring the open-circuit emf of the above cell as a function of temperature. The free standard energy of formation of FeI2 determined by this method is -38784 + 24.165T cal/mol. It is estimated that the maximum error associated with this method is plus or minus 2500 cal/mol.

  16. A Variational Approach to Enhanced Sampling and Free Energy Calculations

    Science.gov (United States)

    Parrinello, Michele

    2015-03-01

    The presence of kinetic bottlenecks severely hampers the ability of widely used sampling methods like molecular dynamics or Monte Carlo to explore complex free energy landscapes. One of the most popular methods for addressing this problem is umbrella sampling which is based on the addition of an external bias which helps overcoming the kinetic barriers. The bias potential is usually taken to be a function of a restricted number of collective variables. However constructing the bias is not simple, especially when the number of collective variables increases. Here we introduce a functional of the bias which, when minimized, allows us to recover the free energy. We demonstrate the usefulness and the flexibility of this approach on a number of examples which include the determination of a six dimensional free energy surface. Besides the practical advantages, the existence of such a variational principle allows us to look at the enhanced sampling problem from a rather convenient vantage point.

  17. Unsupervised Calculation of Free Energy Barriers in Large Crystalline Systems

    Science.gov (United States)

    Swinburne, Thomas D.; Marinica, Mihai-Cosmin

    2018-03-01

    The calculation of free energy differences for thermally activated mechanisms in the solid state are routinely hindered by the inability to define a set of collective variable functions that accurately describe the mechanism under study. Even when possible, the requirement of descriptors for each mechanism under study prevents implementation of free energy calculations in the growing range of automated material simulation schemes. We provide a solution, deriving a path-based, exact expression for free energy differences in the solid state which does not require a converged reaction pathway, collective variable functions, Gram matrix evaluations, or probability flux-based estimators. The generality and efficiency of our method is demonstrated on a complex transformation of C 15 interstitial defects in iron and double kink nucleation on a screw dislocation in tungsten, the latter system consisting of more than 120 000 atoms. Both cases exhibit significant anharmonicity under experimentally relevant temperatures.

  18. Inquiries into the Nature of Free Energy and Entropy in Respect to Biochemical Thermodynamics

    Directory of Open Access Journals (Sweden)

    Clinton D. Stoner

    2000-08-01

    Full Text Available Free energy and entropy are examined in detail from the standpoint of classical thermodynamics. The approach is logically based on the fact that thermodynamic work is mediated by thermal energy through the tendency for nonthermal energy to convert spontaneously into thermal energy and for thermal energy to distribute spontaneously and uniformly within the accessible space. The fact that free energy is a Second-Law, expendable energy that makes it possible for thermodynamic work to be done at finite rates is emphasized. Entropy, as originally defined, is pointed out to be the capacity factor for thermal energy that is hidden with respect to temperature; it serves to evaluate the practical quality of thermal energy and to account for changes in the amounts of latent thermal energies in systems maintained at constant temperature. With entropy thus operationally defined, it is possible to see that TDS° of the Gibbs standard free energy relation DG°= DH°-TDS° serves to account for differences or changes in nonthermal energies that do not contribute to DG° and that, since DH° serves to account for differences or changes in total energy, complete enthalpy-entropy (DH° - TDS° compensation must invariably occur in isothermal processes for which TDS° is finite. A major objective was to clarify the means by which free energy is transferred and conserved in sequences of biological reactions coupled by freely diffusible intermediates. In achieving this objective it was found necessary to distinguish between a 'characteristic free energy' possessed by all First-Law energies in amounts equivalent to the amounts of the energies themselves and a 'free energy of concentration' that is intrinsically mechanical and relatively elusive in that it can appear to be free of First-Law energy. The findings in this regard serve to clarify the fact that the transfer of chemical potential energy from one

  19. Surface free energy of alkali and transition metal nanoparticles

    International Nuclear Information System (INIS)

    Aqra, Fathi; Ayyad, Ahmed

    2014-01-01

    Graphical abstract: Size dependent surface free energy of spherical, cubic and disk Au nanoparticles. - Highlights: • A model to account for the surface free energy of metallic nanoparticles is described. • The model requires only the cohesive energy of the nanoparticle. • The surface free energy of a number of metallic nanoparticles has been calculated, and the obtained values agree well with existing data. • Surface energy falls down very fast when the number of atoms is less than hundred. • The model is applicable to any metallic nanoparticle. - Abstract: This paper addresses an interesting issue on the surface free energy of metallic nanoparticles as compared to the bulk material. Starting from a previously reported equation, a theoretical model, that involves a specific term for calculating the cohesive energy of nanoparticle, is established in a view to describe the behavior of surface free energy of metallic nanoparticles (using different shapes of particle: sphere, cube and disc). The results indicate that the behavior of surface energy is very appropriate for spherical nanoparticle, and thus, it is the most realistic shape of a nanoparticle. The surface energy of copper, silver, gold, platinum, tungsten, molybdenum, tantalum, paladium and alkali metallic nanoparticles is only prominent in the nanoscale size, and it decreases with the decrease of nanoparticle size. Thus, the surface free energy plays a more important role in determining the properties of nanoparticles than in bulk materials. It differs from shape to another, and falls down as the number of atoms (nanoparticle size) decreases. In the case of spherical nanoparticles, the onset of the sharp decrease in surface energy is observed at about 110 atom. A decrease of 16% and 45% in surface energy is found by moving from bulk to 110 atom and from bulk to 5 atom, respectively. The predictions are consistent with the reported data

  20. Conformational Transitions and Convergence of Absolute Binding Free Energy Calculations

    Science.gov (United States)

    Lapelosa, Mauro; Gallicchio, Emilio; Levy, Ronald M.

    2011-01-01

    The Binding Energy Distribution Analysis Method (BEDAM) is employed to compute the standard binding free energies of a series of ligands to a FK506 binding protein (FKBP12) with implicit solvation. Binding free energy estimates are in reasonably good agreement with experimental affinities. The conformations of the complexes identified by the simulations are in good agreement with crystallographic data, which was not used to restrain ligand orientations. The BEDAM method is based on λ -hopping Hamiltonian parallel Replica Exchange (HREM) molecular dynamics conformational sampling, the OPLS-AA/AGBNP2 effective potential, and multi-state free energy estimators (MBAR). Achieving converged and accurate results depends on all of these elements of the calculation. Convergence of the binding free energy is tied to the level of convergence of binding energy distributions at critical intermediate states where bound and unbound states are at equilibrium, and where the rate of binding/unbinding conformational transitions is maximal. This finding mirrors similar observations in the context of order/disorder transitions as for example in protein folding. Insights concerning the physical mechanism of ligand binding and unbinding are obtained. Convergence for the largest FK506 ligand is achieved only after imposing strict conformational restraints, which however require accurate prior structural knowledge of the structure of the complex. The analytical AGBNP2 model is found to underestimate the magnitude of the hydrophobic driving force towards binding in these systems characterized by loosely packed protein-ligand binding interfaces. Rescoring of the binding energies using a numerical surface area model corrects this deficiency. This study illustrates the complex interplay between energy models, exploration of conformational space, and free energy estimators needed to obtain robust estimates from binding free energy calculations. PMID:22368530

  1. A Short Essay on the Uses of Free Energy

    OpenAIRE

    Koutandos, Spyridon

    2013-01-01

    In this article we examine cases of more classical and less classical nature compared to results found by quantum mechanics and attribute a form of Free Energy discontinuity for each case within a boundary layer. The concept of a boundary layer is broadened as to include areas of first or second variations of the Gibbs free energy. It is constructive to think not only of implosions like boundary layers but also of explosion like ones. Situations such as boiling and the passage of electric cur...

  2. Free energy surfaces from nonequilibrium processes without work measurement

    Science.gov (United States)

    Adib, Artur B.

    2006-04-01

    Recent developments in statistical mechanics have allowed the estimation of equilibrium free energies from the statistics of work measurements during processes that drive the system out of equilibrium. Here a different class of processes is considered, wherein the system is prepared and released from a nonequilibrium state, and no external work is involved during its observation. For such "clamp-and-release" processes, a simple strategy for the estimation of equilibrium free energies is offered. The method is illustrated with numerical simulations and analyzed in the context of tethered single-molecule experiments.

  3. Description of quantum coherence in thermodynamic processes requires constraints beyond free energy

    Science.gov (United States)

    Lostaglio, Matteo; Jennings, David; Rudolph, Terry

    2015-01-01

    Recent studies have developed fundamental limitations on nanoscale thermodynamics, in terms of a set of independent free energy relations. Here we show that free energy relations cannot properly describe quantum coherence in thermodynamic processes. By casting time-asymmetry as a quantifiable, fundamental resource of a quantum state, we arrive at an additional, independent set of thermodynamic constraints that naturally extend the existing ones. These asymmetry relations reveal that the traditional Szilárd engine argument does not extend automatically to quantum coherences, but instead only relational coherences in a multipartite scenario can contribute to thermodynamic work. We find that coherence transformations are always irreversible. Our results also reveal additional structural parallels between thermodynamics and the theory of entanglement. PMID:25754774

  4. Description of quantum coherence in thermodynamic processes requires constraints beyond free energy

    Science.gov (United States)

    Lostaglio, Matteo; Jennings, David; Rudolph, Terry

    2015-03-01

    Recent studies have developed fundamental limitations on nanoscale thermodynamics, in terms of a set of independent free energy relations. Here we show that free energy relations cannot properly describe quantum coherence in thermodynamic processes. By casting time-asymmetry as a quantifiable, fundamental resource of a quantum state, we arrive at an additional, independent set of thermodynamic constraints that naturally extend the existing ones. These asymmetry relations reveal that the traditional Szilárd engine argument does not extend automatically to quantum coherences, but instead only relational coherences in a multipartite scenario can contribute to thermodynamic work. We find that coherence transformations are always irreversible. Our results also reveal additional structural parallels between thermodynamics and the theory of entanglement.

  5. Evaluation of the accuracy of the free-energy-minimization method

    International Nuclear Information System (INIS)

    Najafabadi, R.; Srolovitz, D.J.

    1995-01-01

    We have made a detailed comparison between three competing methods for determining the free energies of solids and their defects: the thermodynamic integration of Monte Carlo (TIMC) data, the quasiharmonic (QH) model, and the free-energy-minimization (FEM) method. The accuracy of these methods decreases from the TIMC to QH to FEM method, while the computational efficiency improves in that order. All three methods yield perfect crystal lattice parameters and free energies at finite temperatures which are in good agreement for three different Cu interatomic potentials [embedded atom method (EAM), Morse and Lennard-Jones]. The FEM error (relative to the TIMC) in the (001) surface free energy and in the vacancy formation energy were found to be much larger for the EAM potential than for the other two potentials. Part of the errors in the FEM determination of the free energies are associated with anharmonicities in the interatomic potentials, with the remainder attributed to decoupling of the atomic vibrations. The anharmonicity of the EAM potential was found to be unphysically large compared with experimental vacancy formation entropy determinations. Based upon these results, we show that the FEM method provides a reasonable compromise between accuracy and computational demands. However, the accuracy of this approach is sensitive to the choice of interatomic potential and the nature of the defect to which it is being applied. The accuracy of the FEM is best in high-symmetry environments (perfect crystal, high-symmetry defects, etc.) and when used to describe materials where the anharmonicity is not too large

  6. Free Energy Landscapes of Alanine Oligopeptides in Rigid-Body and Hybrid Water Models.

    Science.gov (United States)

    Nayar, Divya; Chakravarty, Charusita

    2015-08-27

    Replica exchange molecular dynamics is used to study the effect of different rigid-body (mTIP3P, TIP4P, SPC/E) and hybrid (H1.56, H3.00) water models on the conformational free energy landscape of the alanine oligopeptides (acAnme and acA5nme), in conjunction with the CHARMM22 force field. The free energy landscape is mapped out as a function of the Ramachandran angles. In addition, various secondary structure metrics, solvation shell properties, and the number of peptide-solvent hydrogen bonds are monitored. Alanine dipeptide is found to have similar free energy landscapes in different solvent models, an insensitivity which may be due to the absence of possibilities for forming i-(i + 4) or i-(i + 3) intrapeptide hydrogen bonds. The pentapeptide, acA5nme, where there are three intrapeptide backbone hydrogen bonds, shows a conformational free energy landscape with a much greater degree of sensitivity to the choice of solvent model, though the three rigid-body water models differ only quantitatively. The pentapeptide prefers nonhelical, non-native PPII and β-sheet populations as the solvent is changed from SPC/E to the less tetrahedral liquid (H1.56) to an LJ-like liquid (H3.00). The pentapeptide conformational order metrics indicate a preference for open, solvent-exposed, non-native structures in hybrid solvent models at all temperatures of study. The possible correlations between the properties of solvent models and secondary structure preferences of alanine oligopeptides are discussed, and the competition between intrapeptide, peptide-solvent, and solvent-solvent hydrogen bonding is shown to be crucial in the relative free energies of different conformers.

  7. Re-examining the tetraphenyl-arsonium/tetraphenyl-borate (TATB) hypothesis for single-ion solvation free energies

    Science.gov (United States)

    Pollard, Travis P.; Beck, Thomas L.

    2018-06-01

    Attempts to establish an absolute single-ion hydration free energy scale have followed multiple strategies. Two central themes consist of (1) employing bulk pair thermodynamic data and an underlying interfacial-potential-free model to partition the hydration free energy into individual contributions [Marcus, Latimer, and tetraphenyl-arsonium/tetraphenyl-borate (TATB) methods] or (2) utilizing bulk thermodynamic and cluster data to estimate the free energy to insert a proton into water, including in principle an interfacial potential contribution [the cluster pair approximation (CPA)]. While the results for the hydration free energy of the proton agree remarkably well between the three approaches in the first category, the value differs from the CPA result by roughly +10 kcal/mol, implying a value for the effective electrochemical surface potential of water of -0.4 V. This paper provides a computational re-analysis of the TATB method for single-ion free energies using quasichemical theory. A previous study indicated a significant discrepancy between the free energies of hydration for the TA cation and the TB anion. We show that the main contribution to this large computed difference is an electrostatic artifact arising from modeling interactions in periodic boundaries. No attempt is made here to develop more accurate models for the local ion/solvent interactions that may lead to further small free energy differences between the TA and TB ions, but the results clarify the primary importance of interfacial potential effects for analysis of the various free energy scales. Results are also presented, related to the TATB assumption in the organic solvents dimethyl sulfoxide and 1,2-dichloroethane.

  8. Solid-liquid interface free energies of pure bcc metals and B2 phases

    Science.gov (United States)

    Wilson, S. R.; Gunawardana, K. G. S. H.; Mendelev, M. I.

    2015-04-01

    The solid-liquid interface (SLI) free energy was determined from molecular dynamics (MD) simulation for several body centered cubic (bcc) metals and B2 metallic compounds (space group: P m 3 ¯ m ; prototype: CsCl). In order to include a bcc metal with a low melting temperature in our study, a semi-empirical potential was developed for Na. Two additional synthetic "Na" potentials were also developed to explore the effect of liquid structure and latent heat on the SLI free energy. The obtained MD data were compared with the empirical Turnbull, Laird, and Ewing relations. All three relations are found to predict the general trend observed in the MD data for bcc metals obtained within the present study. However, only the Laird and Ewing relations are able to predict the trend obtained within the sequence of "Na" potentials. The Laird relation provides the best prediction for our MD data and other MD data for bcc metals taken from the literature. Overall, the Laird relation also agrees well with our B2 data but requires a proportionality constant that is substantially different from the bcc case. It also fails to explain a considerable difference between the SLI free energies of some B2 phases which have nearly the same melting temperature. In contrast, this difference is satisfactorily described by the Ewing relation. Moreover, the Ewing relation obtained from the bcc dataset also provides a reasonable description of the B2 data.

  9. Free Energy Adjusted Peak Signal to Noise Ratio (FEA-PSNR) for Image Quality Assessment

    Science.gov (United States)

    Liu, Ning; Zhai, Guangtao

    2017-12-01

    Peak signal to noise ratio (PSNR), the de facto universal image quality metric has been widely criticized as having poor correlation with human subjective quality ratings. In this paper, it will be illustrated that the low performance of PSNR as an image quality metric is partially due to its inability of differentiating image contents. And it is revealed that the deviation between subjective score and PSNR for each type of distortions can be systematically captured by perceptual complexity of the target image. The free energy modelling technique is then introduced to simulate the human cognitive process and measure perceptual complexity of an image. Then it is shown that performance of PSNR can be effectively improved using a linear score mapping process considering image free energy and distortion type. The proposed free energy adjusted peak signal to noise ratio (FEA-PSNR) does not change computational steps the of ordinary PSNR and therefore it inherits the merits of being simple, derivable and physically meaningful. So FEA-PSNR can be easily integrated into existing PSNR based image processing systems to achieve more visually plausible results. And the proposed analysis approach can be extended to other types of image quality metrics for enhanced performance.

  10. Free energies of binding from large-scale first-principles quantum mechanical calculations: application to ligand hydration energies.

    Science.gov (United States)

    Fox, Stephen J; Pittock, Chris; Tautermann, Christofer S; Fox, Thomas; Christ, Clara; Malcolm, N O J; Essex, Jonathan W; Skylaris, Chris-Kriton

    2013-08-15

    Schemes of increasing sophistication for obtaining free energies of binding have been developed over the years, where configurational sampling is used to include the all-important entropic contributions to the free energies. However, the quality of the results will also depend on the accuracy with which the intermolecular interactions are computed at each molecular configuration. In this context, the energy change associated with the rearrangement of electrons (electronic polarization and charge transfer) upon binding is a very important effect. Classical molecular mechanics force fields do not take this effect into account explicitly, and polarizable force fields and semiempirical quantum or hybrid quantum-classical (QM/MM) calculations are increasingly employed (at higher computational cost) to compute intermolecular interactions in free-energy schemes. In this work, we investigate the use of large-scale quantum mechanical calculations from first-principles as a way of fully taking into account electronic effects in free-energy calculations. We employ a one-step free-energy perturbation (FEP) scheme from a molecular mechanical (MM) potential to a quantum mechanical (QM) potential as a correction to thermodynamic integration calculations within the MM potential. We use this approach to calculate relative free energies of hydration of small aromatic molecules. Our quantum calculations are performed on multiple configurations from classical molecular dynamics simulations. The quantum energy of each configuration is obtained from density functional theory calculations with a near-complete psinc basis set on over 600 atoms using the ONETEP program.

  11. Free energy of the Lennard-Jones solid

    NARCIS (Netherlands)

    Hoef, van der M.A.

    2000-01-01

    We have determined a simple expression for the absolute Helmholtz free energy of the fcc Lennard-Jones solid from molecular dynamics simulations. The pressure and energy data from these simulations have been fitted to a simple functional form (18 parameters) for densities ranging from around

  12. Free energy barriers to evaporation of water in hydrophobic confinement.

    Science.gov (United States)

    Sharma, Sumit; Debenedetti, Pablo G

    2012-11-08

    We use umbrella sampling Monte Carlo and forward and reverse forward flux sampling (FFS) simulation techniques to compute the free energy barriers to evaporation of water confined between two hydrophobic surfaces separated by nanoscopic gaps, as a function of the gap width, at 1 bar and 298 K. The evaporation mechanism for small (1 × 1 nm(2)) surfaces is found to be fundamentally different from that for large (3 × 3 nm(2)) surfaces. In the latter case, the evaporation proceeds via the formation of a gap-spanning tubular cavity. The 1 × 1 nm(2) surfaces, in contrast, are too small to accommodate a stable vapor cavity. Accordingly, the associated free energy barriers correspond to the formation of a critical-sized cavity for sufficiently large confining surfaces, and to complete emptying of the gap region for small confining surfaces. The free energy barriers to evaporation were found to be of O(20kT) for 14 Å gaps, and to increase by approximately ~5kT with every 1 Å increase in the gap width. The entropy contribution to the free energy of evaporation was found to be independent of the gap width.

  13. Funnel metadynamics as accurate binding free-energy method

    Science.gov (United States)

    Limongelli, Vittorio; Bonomi, Massimiliano; Parrinello, Michele

    2013-01-01

    A detailed description of the events ruling ligand/protein interaction and an accurate estimation of the drug affinity to its target is of great help in speeding drug discovery strategies. We have developed a metadynamics-based approach, named funnel metadynamics, that allows the ligand to enhance the sampling of the target binding sites and its solvated states. This method leads to an efficient characterization of the binding free-energy surface and an accurate calculation of the absolute protein–ligand binding free energy. We illustrate our protocol in two systems, benzamidine/trypsin and SC-558/cyclooxygenase 2. In both cases, the X-ray conformation has been found as the lowest free-energy pose, and the computed protein–ligand binding free energy in good agreement with experiments. Furthermore, funnel metadynamics unveils important information about the binding process, such as the presence of alternative binding modes and the role of waters. The results achieved at an affordable computational cost make funnel metadynamics a valuable method for drug discovery and for dealing with a variety of problems in chemistry, physics, and material science. PMID:23553839

  14. The Free Energy in the Derrida-Retaux Recursive Model

    Science.gov (United States)

    Hu, Yueyun; Shi, Zhan

    2018-05-01

    We are interested in a simple max-type recursive model studied by Derrida and Retaux (J Stat Phys 156:268-290, 2014) in the context of a physics problem, and find a wide range for the exponent in the free energy in the nearly supercritical regime.

  15. Calculating zeros: Non-equilibrium free energy calculations

    International Nuclear Information System (INIS)

    Oostenbrink, Chris; Gunsteren, Wilfred F. van

    2006-01-01

    Free energy calculations on three model processes with theoretically known free energy changes have been performed using short simulation times. A comparison between equilibrium (thermodynamic integration) and non-equilibrium (fast growth) methods has been made in order to assess the accuracy and precision of these methods. The three processes have been chosen to represent processes often observed in biomolecular free energy calculations. They involve a redistribution of charges, the creation and annihilation of neutral particles and conformational changes. At very short overall simulation times, the thermodynamic integration approach using discrete steps is most accurate. More importantly, reasonable accuracy can be obtained using this method which seems independent of the overall simulation time. In cases where slow conformational changes play a role, fast growth simulations might have an advantage over discrete thermodynamic integration where sufficient sampling needs to be obtained at every λ-point, but only if the initial conformations do properly represent an equilibrium ensemble. From these three test cases practical lessons can be learned that will be applicable to biomolecular free energy calculations

  16. Molecular dynamics simulations and free energy profile of ...

    Indian Academy of Sciences (India)

    aDepartment of Chemical Engineering, bDepartment of Chemistry, Amirkabir University of Technology,. 15875-4413 ... Lipid bilayers; Paracetamol; free energy; molecular dynamics simulation; membrane. 1. ..... bilayer is less favourable due to the hydrophobic nature .... Orsi M and Essex J W 2010 Soft Matter 6 3797. 54.

  17. A Simple PB/LIE Free Energy Function Accurately Predicts the Peptide Binding Specificity of the Tiam1 PDZ Domain.

    Science.gov (United States)

    Panel, Nicolas; Sun, Young Joo; Fuentes, Ernesto J; Simonson, Thomas

    2017-01-01

    PDZ domains generally bind short amino acid sequences at the C-terminus of target proteins, and short peptides can be used as inhibitors or model ligands. Here, we used experimental binding assays and molecular dynamics simulations to characterize 51 complexes involving the Tiam1 PDZ domain and to test the performance of a semi-empirical free energy function. The free energy function combined a Poisson-Boltzmann (PB) continuum electrostatic term, a van der Waals interaction energy, and a surface area term. Each term was empirically weighted, giving a Linear Interaction Energy or "PB/LIE" free energy. The model yielded a mean unsigned deviation of 0.43 kcal/mol and a Pearson correlation of 0.64 between experimental and computed free energies, which was superior to a Null model that assumes all complexes have the same affinity. Analyses of the models support several experimental observations that indicate the orientation of the α 2 helix is a critical determinant for peptide specificity. The models were also used to predict binding free energies for nine new variants, corresponding to point mutants of the Syndecan1 and Caspr4 peptides. The predictions did not reveal improved binding; however, they suggest that an unnatural amino acid could be used to increase protease resistance and peptide lifetimes in vivo . The overall performance of the model should allow its use in the design of new PDZ ligands in the future.

  18. A Simple PB/LIE Free Energy Function Accurately Predicts the Peptide Binding Specificity of the Tiam1 PDZ Domain

    Directory of Open Access Journals (Sweden)

    Nicolas Panel

    2017-09-01

    Full Text Available PDZ domains generally bind short amino acid sequences at the C-terminus of target proteins, and short peptides can be used as inhibitors or model ligands. Here, we used experimental binding assays and molecular dynamics simulations to characterize 51 complexes involving the Tiam1 PDZ domain and to test the performance of a semi-empirical free energy function. The free energy function combined a Poisson-Boltzmann (PB continuum electrostatic term, a van der Waals interaction energy, and a surface area term. Each term was empirically weighted, giving a Linear Interaction Energy or “PB/LIE” free energy. The model yielded a mean unsigned deviation of 0.43 kcal/mol and a Pearson correlation of 0.64 between experimental and computed free energies, which was superior to a Null model that assumes all complexes have the same affinity. Analyses of the models support several experimental observations that indicate the orientation of the α2 helix is a critical determinant for peptide specificity. The models were also used to predict binding free energies for nine new variants, corresponding to point mutants of the Syndecan1 and Caspr4 peptides. The predictions did not reveal improved binding; however, they suggest that an unnatural amino acid could be used to increase protease resistance and peptide lifetimes in vivo. The overall performance of the model should allow its use in the design of new PDZ ligands in the future.

  19. The Concentration Dependence of the (Delta)s Term in the Gibbs Free Energy Function: Application to Reversible Reactions in Biochemistry

    Science.gov (United States)

    Gary, Ronald K.

    2004-01-01

    The concentration dependence of (delta)S term in the Gibbs free energy function is described in relation to its application to reversible reactions in biochemistry. An intuitive and non-mathematical argument for the concentration dependence of the (delta)S term in the Gibbs free energy equation is derived and the applicability of the equation to…

  20. Towards a universal method for calculating hydration free energies: a 3D reference interaction site model with partial molar volume correction.

    Science.gov (United States)

    Palmer, David S; Frolov, Andrey I; Ratkova, Ekaterina L; Fedorov, Maxim V

    2010-12-15

    We report a simple universal method to systematically improve the accuracy of hydration free energies calculated using an integral equation theory of molecular liquids, the 3D reference interaction site model. A strong linear correlation is observed between the difference of the experimental and (uncorrected) calculated hydration free energies and the calculated partial molar volume for a data set of 185 neutral organic molecules from different chemical classes. By using the partial molar volume as a linear empirical correction to the calculated hydration free energy, we obtain predictions of hydration free energies in excellent agreement with experiment (R = 0.94, σ = 0.99 kcal mol (- 1) for a test set of 120 organic molecules).

  1. Towards a universal method for calculating hydration free energies: a 3D reference interaction site model with partial molar volume correction

    International Nuclear Information System (INIS)

    Palmer, David S; Frolov, Andrey I; Ratkova, Ekaterina L; Fedorov, Maxim V

    2010-01-01

    We report a simple universal method to systematically improve the accuracy of hydration free energies calculated using an integral equation theory of molecular liquids, the 3D reference interaction site model. A strong linear correlation is observed between the difference of the experimental and (uncorrected) calculated hydration free energies and the calculated partial molar volume for a data set of 185 neutral organic molecules from different chemical classes. By using the partial molar volume as a linear empirical correction to the calculated hydration free energy, we obtain predictions of hydration free energies in excellent agreement with experiment (R = 0.94, σ = 0.99 kcal mol -1 for a test set of 120 organic molecules). (fast track communication)

  2. Calculating solution redox free energies with ab initio quantum mechanical/molecular mechanical minimum free energy path method

    International Nuclear Information System (INIS)

    Zeng Xiancheng; Hu Hao; Hu Xiangqian; Yang Weitao

    2009-01-01

    A quantum mechanical/molecular mechanical minimum free energy path (QM/MM-MFEP) method was developed to calculate the redox free energies of large systems in solution with greatly enhanced efficiency for conformation sampling. The QM/MM-MFEP method describes the thermodynamics of a system on the potential of mean force surface of the solute degrees of freedom. The molecular dynamics (MD) sampling is only carried out with the QM subsystem fixed. It thus avoids 'on-the-fly' QM calculations and thus overcomes the high computational cost in the direct QM/MM MD sampling. In the applications to two metal complexes in aqueous solution, the new QM/MM-MFEP method yielded redox free energies in good agreement with those calculated from the direct QM/MM MD method. Two larger biologically important redox molecules, lumichrome and riboflavin, were further investigated to demonstrate the efficiency of the method. The enhanced efficiency and uncompromised accuracy are especially significant for biochemical systems. The QM/MM-MFEP method thus provides an efficient approach to free energy simulation of complex electron transfer reactions.

  3. Comparative exploration of hydrogen sulfide and water transmembrane free energy surfaces via orthogonal space tempering free energy sampling.

    Science.gov (United States)

    Lv, Chao; Aitchison, Erick W; Wu, Dongsheng; Zheng, Lianqing; Cheng, Xiaolin; Yang, Wei

    2016-03-05

    Hydrogen sulfide (H2 S), a commonly known toxic gas compound, possesses unique chemical features that allow this small solute molecule to quickly diffuse through cell membranes. Taking advantage of the recent orthogonal space tempering (OST) method, we comparatively mapped the transmembrane free energy landscapes of H2 S and its structural analogue, water (H2 O), seeking to decipher the molecular determinants that govern their drastically different permeabilities. As revealed by our OST sampling results, in contrast to the highly polar water solute, hydrogen sulfide is evidently amphipathic, and thus inside membrane is favorably localized at the interfacial region, that is, the interface between the polar head-group and nonpolar acyl chain regions. Because the membrane binding affinity of H2 S is mainly governed by its small hydrophobic moiety and the barrier height inbetween the interfacial region and the membrane center is largely determined by its moderate polarity, the transmembrane free energy barriers to encounter by this toxic molecule are very small. Moreover when H2 S diffuses from the bulk solution to the membrane center, the above two effects nearly cancel each other, so as to lead to a negligible free energy difference. This study not only explains why H2 S can quickly pass through cell membranes but also provides a practical illustration on how to use the OST free energy sampling method to conveniently analyze complex molecular processes. © 2015 Wiley Periodicals, Inc. © 2015 Wiley Periodicals, Inc.

  4. Nonlocal Free Energy of a Spatially Inhomogeneous Superconductor

    International Nuclear Information System (INIS)

    Grigorishin, K.V.; Lev, B.I.

    2012-01-01

    The microscopic approach is developed for obtaining of the free energy of a superconductor based on direct calculation of the vacuum amplitude. The free energy functional of the spatially inhomogeneous superconductor in a magnetic field is obtained with help of the developed approach. The obtained functional is generalization of Ginzburg-Landau functionals for any temperature, for arbitrary spatial variations of the order parameter and for the nonlocality of a magnetic response and the order parameter. Moreover, the nonlocality of the magnetic response is the consequence of order parameter's nonlocality. The extremals of this functional are considered in the explicit form in the low- and high-temperature limit at the condition of slowness of spatial variations of the order parameter. (condensed matter: electronic structure, electrical, magnetic, and optical properties)

  5. Solid/liquid interfacial free energies in binary systems

    Science.gov (United States)

    Nason, D.; Tiller, W. A.

    1973-01-01

    Description of a semiquantitative technique for predicting the segregation characteristics of smooth interfaces between binary solid and liquid solutions in terms of readily available thermodynamic parameters of the bulk solutions. A lattice-liquid interfacial model and a pair-bonded regular solution model are employed in the treatment with an accommodation for liquid interfacial entropy. The method is used to calculate the interfacial segregation and the free energy of segregation for solid-liquid interfaces between binary solutions for the (111) boundary of fcc crystals. The zone of compositional transition across the interface is shown to be on the order of a few atomic layers in width, being moderately narrower for ideal solutions. The free energy of the segregated interface depends primarily upon the solid composition and the heats of fusion of the component atoms, the composition difference of the solutions, and the difference of the heats of mixing of the solutions.

  6. FESetup: Automating Setup for Alchemical Free Energy Simulations.

    Science.gov (United States)

    Loeffler, Hannes H; Michel, Julien; Woods, Christopher

    2015-12-28

    FESetup is a new pipeline tool which can be used flexibly within larger workflows. The tool aims to support fast and easy setup of alchemical free energy simulations for molecular simulation packages such as AMBER, GROMACS, Sire, or NAMD. Post-processing methods like MM-PBSA and LIE can be set up as well. Ligands are automatically parametrized with AM1-BCC, and atom mappings for a single topology description are computed with a maximum common substructure search (MCSS) algorithm. An abstract molecular dynamics (MD) engine can be used for equilibration prior to free energy setup or standalone. Currently, all modern AMBER force fields are supported. Ease of use, robustness of the code, and automation where it is feasible are the main development goals. The project follows an open development model, and we welcome contributions.

  7. QCD inequalities for the nucleon mass and the free energy of baryonic matter.

    Science.gov (United States)

    Cohen, Thomas D

    2003-07-18

    The positivity of the integrand of certain Euclidean space functional integrals for two flavor QCD with degenerate quark masses implies that the free energy per unit volume for QCD with a baryon chemical potential mu(B) (and zero isospin chemical potential) is greater than the free energy with an isospin chemical potential mu(I)=(2 mu(B)/N(c)) (and zero baryon chemical potential). The same result applies to QCD with any number of heavy flavors in addition to the two light flavors so long as the chemical potential is understood as applying to the light quark contributions to the baryon number. This relation implies a bound on the nucleon mass: there exists a particle X in QCD (presumably the pion) such that M(N)> or =(N(c) m(X)/2 I(X)) where m(X) is the mass of the particle and I(X) is its isospin.

  8. Two-Dimensional Free Energy Surfaces for Electron Transfer Reactions in Solution

    Directory of Open Access Journals (Sweden)

    Shigeo Murata

    2008-01-01

    Full Text Available Change in intermolecular distance between electron donor (D and acceptor (A can induce intermolecular electron transfer (ET even in nonpolar solvent, where solvent orientational polarization is absent. This was shown by making simple calculations of the energies of the initial and final states of ET. In the case of polar solvent, the free energies are functions of both D-A distance and solvent orientational polarization. On the basis of 2-dimensional free energy surfaces, the relation of Marcus ET and exciplex formation is discussed. The transient effect in fluorescence quenching was measured for several D-A pairs in a nonpolar solvent. The results were analyzed by assuming a distance dependence of the ET rate that is consistent with the above model.

  9. Relating Cohesive Zone Model to Linear Elastic Fracture Mechanics

    Science.gov (United States)

    Wang, John T.

    2010-01-01

    The conditions required for a cohesive zone model (CZM) to predict a failure load of a cracked structure similar to that obtained by a linear elastic fracture mechanics (LEFM) analysis are investigated in this paper. This study clarifies why many different phenomenological cohesive laws can produce similar fracture predictions. Analytical results for five cohesive zone models are obtained, using five different cohesive laws that have the same cohesive work rate (CWR-area under the traction-separation curve) but different maximum tractions. The effect of the maximum traction on the predicted cohesive zone length and the remote applied load at fracture is presented. Similar to the small scale yielding condition for an LEFM analysis to be valid. the cohesive zone length also needs to be much smaller than the crack length. This is a necessary condition for a CZM to obtain a fracture prediction equivalent to an LEFM result.

  10. Peptide Free Energy Landscapes Calibrated by Molecular Orbital Calculations

    OpenAIRE

    Ono, S.; Kuroda, M.; Higo, J.; Kamiya, N.; Nakajima, N.; Nakamura, H.

    2002-01-01

    Free energy landscapes of peptide conformations werecalibrated by ab initiomolecular orbital calculations, after enhancedconformational sampling using the multicanonical molecular dynamicssimulations. Three different potentials of mean force for an isolateddipeptide were individually obtained using the conventional force fields,AMBER parm94, AMBER parm96, and CHARMm22. Each potential ofmean force was calibrated based on the umbrella sampling algorithm fromthe adiabatic energy map that was cal...

  11. Free energy landscape and molecular pathways of gas hydrate nucleation

    International Nuclear Information System (INIS)

    Bi, Yuanfei; Porras, Anna; Li, Tianshu

    2016-01-01

    Despite the significance of gas hydrates in diverse areas, a quantitative knowledge of hydrate formation at a molecular level is missing. The impediment to acquiring this understanding is primarily attributed to the stochastic nature and ultra-fine scales of nucleation events, posing a great challenge for both experiment and simulation to explore hydrate nucleation. Here we employ advanced molecular simulation methods, including forward flux sampling (FFS), p B histogram analysis, and backward flux sampling, to overcome the limit of direct molecular simulation for exploring both the free energy landscape and molecular pathways of hydrate nucleation. First we test the half-cage order parameter (H-COP) which we developed for driving FFS, through conducting the p B histogram analysis. Our results indeed show that H-COP describes well the reaction coordinates of hydrate nucleation. Through the verified order parameter, we then directly compute the free energy landscape for hydrate nucleation by combining both forward and backward flux sampling. The calculated stationary distribution density, which is obtained independently of nucleation theory, is found to fit well against the classical nucleation theory (CNT). Subsequent analysis of the obtained large ensemble of hydrate nucleation trajectories show that although on average, hydrate formation is facilitated by a two-step like mechanism involving a gradual transition from an amorphous to a crystalline structure, there also exist nucleation pathways where hydrate crystallizes directly, without going through the amorphous stage. The CNT-like free energy profile and the structural diversity suggest the existence of multiple active transition pathways for hydrate nucleation, and possibly also imply the near degeneracy in their free energy profiles among different pathways. Our results thus bring a new perspective to the long standing question of how hydrates crystallize.

  12. Free energy landscape and molecular pathways of gas hydrate nucleation.

    Science.gov (United States)

    Bi, Yuanfei; Porras, Anna; Li, Tianshu

    2016-12-07

    Despite the significance of gas hydrates in diverse areas, a quantitative knowledge of hydrate formation at a molecular level is missing. The impediment to acquiring this understanding is primarily attributed to the stochastic nature and ultra-fine scales of nucleation events, posing a great challenge for both experiment and simulation to explore hydrate nucleation. Here we employ advanced molecular simulation methods, including forward flux sampling (FFS), p B histogram analysis, and backward flux sampling, to overcome the limit of direct molecular simulation for exploring both the free energy landscape and molecular pathways of hydrate nucleation. First we test the half-cage order parameter (H-COP) which we developed for driving FFS, through conducting the p B histogram analysis. Our results indeed show that H-COP describes well the reaction coordinates of hydrate nucleation. Through the verified order parameter, we then directly compute the free energy landscape for hydrate nucleation by combining both forward and backward flux sampling. The calculated stationary distribution density, which is obtained independently of nucleation theory, is found to fit well against the classical nucleation theory (CNT). Subsequent analysis of the obtained large ensemble of hydrate nucleation trajectories show that although on average, hydrate formation is facilitated by a two-step like mechanism involving a gradual transition from an amorphous to a crystalline structure, there also exist nucleation pathways where hydrate crystallizes directly, without going through the amorphous stage. The CNT-like free energy profile and the structural diversity suggest the existence of multiple active transition pathways for hydrate nucleation, and possibly also imply the near degeneracy in their free energy profiles among different pathways. Our results thus bring a new perspective to the long standing question of how hydrates crystallize.

  13. Surface free energy analysis of adsorbents used for radioiodine adsorption

    International Nuclear Information System (INIS)

    González-García, C.M.; Román, S.; González, J.F.; Sabio, E.; Ledesma, B.

    2013-01-01

    In this work, the surface free energy of biomass-based activated carbons, both fresh and impregnated with triethylenediamine, has been evaluated. The contribution of Lifshitz van der Waals components was determined by the model proposed by van Oss et al. The results obtained allowed predicting the most probable configurations of the impregnant onto the carbon surface and its influence on the subsequent adsorption of radioactive methyl iodide.

  14. Free energy landscape and molecular pathways of gas hydrate nucleation

    Energy Technology Data Exchange (ETDEWEB)

    Bi, Yuanfei; Porras, Anna; Li, Tianshu, E-mail: tsli@gwu.edu [Department of Civil and Environmental Engineering, George Washington University, Washington DC 20052 (United States)

    2016-12-07

    Despite the significance of gas hydrates in diverse areas, a quantitative knowledge of hydrate formation at a molecular level is missing. The impediment to acquiring this understanding is primarily attributed to the stochastic nature and ultra-fine scales of nucleation events, posing a great challenge for both experiment and simulation to explore hydrate nucleation. Here we employ advanced molecular simulation methods, including forward flux sampling (FFS), p{sub B} histogram analysis, and backward flux sampling, to overcome the limit of direct molecular simulation for exploring both the free energy landscape and molecular pathways of hydrate nucleation. First we test the half-cage order parameter (H-COP) which we developed for driving FFS, through conducting the p{sub B} histogram analysis. Our results indeed show that H-COP describes well the reaction coordinates of hydrate nucleation. Through the verified order parameter, we then directly compute the free energy landscape for hydrate nucleation by combining both forward and backward flux sampling. The calculated stationary distribution density, which is obtained independently of nucleation theory, is found to fit well against the classical nucleation theory (CNT). Subsequent analysis of the obtained large ensemble of hydrate nucleation trajectories show that although on average, hydrate formation is facilitated by a two-step like mechanism involving a gradual transition from an amorphous to a crystalline structure, there also exist nucleation pathways where hydrate crystallizes directly, without going through the amorphous stage. The CNT-like free energy profile and the structural diversity suggest the existence of multiple active transition pathways for hydrate nucleation, and possibly also imply the near degeneracy in their free energy profiles among different pathways. Our results thus bring a new perspective to the long standing question of how hydrates crystallize.

  15. Optimized Free Energies from Bidirectional Single-Molecule Force Spectroscopy

    Science.gov (United States)

    Minh, David D. L.; Adib, Artur B.

    2008-05-01

    An optimized method for estimating path-ensemble averages using data from processes driven in opposite directions is presented. Based on this estimator, bidirectional expressions for reconstructing free energies and potentials of mean force from single-molecule force spectroscopy—valid for biasing potentials of arbitrary stiffness—are developed. Numerical simulations on a model potential indicate that these methods perform better than unidirectional strategies.

  16. Emotional valence and the free-energy principle.

    Science.gov (United States)

    Joffily, Mateus; Coricelli, Giorgio

    2013-01-01

    The free-energy principle has recently been proposed as a unified Bayesian account of perception, learning and action. Despite the inextricable link between emotion and cognition, emotion has not yet been formulated under this framework. A core concept that permeates many perspectives on emotion is valence, which broadly refers to the positive and negative character of emotion or some of its aspects. In the present paper, we propose a definition of emotional valence in terms of the negative rate of change of free-energy over time. If the second time-derivative of free-energy is taken into account, the dynamics of basic forms of emotion such as happiness, unhappiness, hope, fear, disappointment and relief can be explained. In this formulation, an important function of emotional valence turns out to regulate the learning rate of the causes of sensory inputs. When sensations increasingly violate the agent's expectations, valence is negative and increases the learning rate. Conversely, when sensations increasingly fulfil the agent's expectations, valence is positive and decreases the learning rate. This dynamic interaction between emotional valence and learning rate highlights the crucial role played by emotions in biological agents' adaptation to unexpected changes in their world.

  17. Emotional valence and the free-energy principle.

    Directory of Open Access Journals (Sweden)

    Mateus Joffily

    Full Text Available The free-energy principle has recently been proposed as a unified Bayesian account of perception, learning and action. Despite the inextricable link between emotion and cognition, emotion has not yet been formulated under this framework. A core concept that permeates many perspectives on emotion is valence, which broadly refers to the positive and negative character of emotion or some of its aspects. In the present paper, we propose a definition of emotional valence in terms of the negative rate of change of free-energy over time. If the second time-derivative of free-energy is taken into account, the dynamics of basic forms of emotion such as happiness, unhappiness, hope, fear, disappointment and relief can be explained. In this formulation, an important function of emotional valence turns out to regulate the learning rate of the causes of sensory inputs. When sensations increasingly violate the agent's expectations, valence is negative and increases the learning rate. Conversely, when sensations increasingly fulfil the agent's expectations, valence is positive and decreases the learning rate. This dynamic interaction between emotional valence and learning rate highlights the crucial role played by emotions in biological agents' adaptation to unexpected changes in their world.

  18. Computing conformational free energy differences in explicit solvent: An efficient thermodynamic cycle using an auxiliary potential and a free energy functional constructed from the end points.

    Science.gov (United States)

    Harris, Robert C; Deng, Nanjie; Levy, Ronald M; Ishizuka, Ryosuke; Matubayasi, Nobuyuki

    2017-06-05

    Many biomolecules undergo conformational changes associated with allostery or ligand binding. Observing these changes in computer simulations is difficult if their timescales are long. These calculations can be accelerated by observing the transition on an auxiliary free energy surface with a simpler Hamiltonian and connecting this free energy surface to the target free energy surface with free energy calculations. Here, we show that the free energy legs of the cycle can be replaced with energy representation (ER) density functional approximations. We compute: (1) The conformational free energy changes for alanine dipeptide transitioning from the right-handed free energy basin to the left-handed basin and (2) the free energy difference between the open and closed conformations of β-cyclodextrin, a "host" molecule that serves as a model for molecular recognition in host-guest binding. β-cyclodextrin contains 147 atoms compared to 22 atoms for alanine dipeptide, making β-cyclodextrin a large molecule for which to compute solvation free energies by free energy perturbation or integration methods and the largest system for which the ER method has been compared to exact free energy methods. The ER method replaced the 28 simulations to compute each coupling free energy with two endpoint simulations, reducing the computational time for the alanine dipeptide calculation by about 70% and for the β-cyclodextrin by > 95%. The method works even when the distribution of conformations on the auxiliary free energy surface differs substantially from that on the target free energy surface, although some degree of overlap between the two surfaces is required. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  19. Uncertainty relations, zero point energy and the linear canonical group

    Science.gov (United States)

    Sudarshan, E. C. G.

    1993-01-01

    The close relationship between the zero point energy, the uncertainty relations, coherent states, squeezed states, and correlated states for one mode is investigated. This group-theoretic perspective enables the parametrization and identification of their multimode generalization. In particular the generalized Schroedinger-Robertson uncertainty relations are analyzed. An elementary method of determining the canonical structure of the generalized correlated states is presented.

  20. On the normalization of the minimum free energy of RNAs by sequence length.

    Directory of Open Access Journals (Sweden)

    Edoardo Trotta

    Full Text Available The minimum free energy (MFE of ribonucleic acids (RNAs increases at an apparent linear rate with sequence length. Simple indices, obtained by dividing the MFE by the number of nucleotides, have been used for a direct comparison of the folding stability of RNAs of various sizes. Although this normalization procedure has been used in several studies, the relationship between normalized MFE and length has not yet been investigated in detail. Here, we demonstrate that the variation of MFE with sequence length is not linear and is significantly biased by the mathematical formula used for the normalization procedure. For this reason, the normalized MFEs strongly decrease as hyperbolic functions of length and produce unreliable results when applied for the comparison of sequences with different sizes. We also propose a simple modification of the normalization formula that corrects the bias enabling the use of the normalized MFE for RNAs longer than 40 nt. Using the new corrected normalized index, we analyzed the folding free energies of different human RNA families showing that most of them present an average MFE density more negative than expected for a typical genomic sequence. Furthermore, we found that a well-defined and restricted range of MFE density characterizes each RNA family, suggesting the use of our corrected normalized index to improve RNA prediction algorithms. Finally, in coding and functional human RNAs the MFE density appears scarcely correlated with sequence length, consistent with a negligible role of thermodynamic stability demands in determining RNA size.

  1. On the normalization of the minimum free energy of RNAs by sequence length.

    Science.gov (United States)

    Trotta, Edoardo

    2014-01-01

    The minimum free energy (MFE) of ribonucleic acids (RNAs) increases at an apparent linear rate with sequence length. Simple indices, obtained by dividing the MFE by the number of nucleotides, have been used for a direct comparison of the folding stability of RNAs of various sizes. Although this normalization procedure has been used in several studies, the relationship between normalized MFE and length has not yet been investigated in detail. Here, we demonstrate that the variation of MFE with sequence length is not linear and is significantly biased by the mathematical formula used for the normalization procedure. For this reason, the normalized MFEs strongly decrease as hyperbolic functions of length and produce unreliable results when applied for the comparison of sequences with different sizes. We also propose a simple modification of the normalization formula that corrects the bias enabling the use of the normalized MFE for RNAs longer than 40 nt. Using the new corrected normalized index, we analyzed the folding free energies of different human RNA families showing that most of them present an average MFE density more negative than expected for a typical genomic sequence. Furthermore, we found that a well-defined and restricted range of MFE density characterizes each RNA family, suggesting the use of our corrected normalized index to improve RNA prediction algorithms. Finally, in coding and functional human RNAs the MFE density appears scarcely correlated with sequence length, consistent with a negligible role of thermodynamic stability demands in determining RNA size.

  2. Intercellular signaling through secreted proteins induces free-energy gradient-directed cell movement.

    Science.gov (United States)

    Kravchenko-Balasha, Nataly; Shin, Young Shik; Sutherland, Alex; Levine, R D; Heath, James R

    2016-05-17

    Controlling cell migration is important in tissue engineering and medicine. Cell motility depends on factors such as nutrient concentration gradients and soluble factor signaling. In particular, cell-cell signaling can depend on cell-cell separation distance and can influence cellular arrangements in bulk cultures. Here, we seek a physical-based approach, which identifies a potential governed by cell-cell signaling that induces a directed cell-cell motion. A single-cell barcode chip (SCBC) was used to experimentally interrogate secreted proteins in hundreds of isolated glioblastoma brain cancer cell pairs and to monitor their relative motions over time. We used these trajectories to identify a range of cell-cell separation distances where the signaling was most stable. We then used a thermodynamics-motivated analysis of secreted protein levels to characterize free-energy changes for different cell-cell distances. We show that glioblastoma cell-cell movement can be described as Brownian motion biased by cell-cell potential. To demonstrate that the free-energy potential as determined by the signaling is the driver of motion, we inhibited two proteins most involved in maintaining the free-energy gradient. Following inhibition, cell pairs showed an essentially random Brownian motion, similar to the case for untreated, isolated single cells.

  3. Modifying Poisson equation for near-solute dielectric polarization and solvation free energy

    Energy Technology Data Exchange (ETDEWEB)

    Yang, Pei-Kun, E-mail: peikun@isu.edu.tw

    2016-06-15

    Highlights: • We modify the Poisson equation. • The dielectric polarization was calculated from the modified Poisson equation. • The solvation free energies of the solutes were calculated from the dielectric polarization. • The calculated solvation free energies were similar to those obtained from MD simulations. - Abstract: The dielectric polarization P is important for calculating the stability of protein conformation and the binding affinity of protein–protein/ligand interactions and for exploring the nonthermal effect of an external electric field on biomolecules. P was decomposed into the product of the electric dipole moment per molecule p; bulk solvent density N{sub bulk}; and relative solvent molecular density g. For a molecular solute, 4πr{sup 2}p(r) oscillates with the distance r to the solute, and g(r) has a large peak in the near-solute region, as observed in molecular dynamics (MD) simulations. Herein, the Poisson equation was modified for computing p based on the modified Gauss’s law of Maxwell’s equations, and the potential of the mean force was used for computing g. For one or two charged atoms in a water cluster, the solvation free energies of the solutes obtained by these equations were similar to those obtained from MD simulations.

  4. Simulations of skin barrier function: free energies of hydrophobic and hydrophilic transmembrane pores in ceramide bilayers.

    Science.gov (United States)

    Notman, Rebecca; Anwar, Jamshed; Briels, W J; Noro, Massimo G; den Otter, Wouter K

    2008-11-15

    Transmembrane pore formation is central to many biological processes such as ion transport, cell fusion, and viral infection. Furthermore, pore formation in the ceramide bilayers of the stratum corneum may be an important mechanism by which penetration enhancers such as dimethylsulfoxide (DMSO) weaken the barrier function of the skin. We have used the potential of mean constraint force (PMCF) method to calculate the free energy of pore formation in ceramide bilayers in both the innate gel phase and in the DMSO-induced fluidized state. Our simulations show that the fluid phase bilayers form archetypal water-filled hydrophilic pores similar to those observed in phospholipid bilayers. In contrast, the rigid gel-phase bilayers develop hydrophobic pores. At the relatively small pore diameters studied here, the hydrophobic pores are empty rather than filled with bulk water, suggesting that they do not compromise the barrier function of ceramide membranes. A phenomenological analysis suggests that these vapor pores are stable, below a critical radius, because the penalty of creating water-vapor and tail-vapor interfaces is lower than that of directly exposing the strongly hydrophobic tails to water. The PMCF free energy profile of the vapor pore supports this analysis. The simulations indicate that high DMSO concentrations drastically impair the barrier function of the skin by strongly reducing the free energy required for pore opening.

  5. Equation of state and Helmholtz free energy for the atomic system of the repulsive Lennard-Jones particles.

    Science.gov (United States)

    Mirzaeinia, Ali; Feyzi, Farzaneh; Hashemianzadeh, Seyed Majid

    2017-12-07

    Simple and accurate expressions are presented for the equation of state (EOS) and absolute Helmholtz free energy of a system composed of simple atomic particles interacting through the repulsive Lennard-Jones potential model in the fluid and solid phases. The introduced EOS has 17 and 22 coefficients for fluid and solid phases, respectively, which are regressed to the Monte Carlo (MC) simulation data over the reduced temperature range of 0.6≤T * ≤6.0 and the packing fraction range of 0.1 ≤ η ≤ 0.72. The average absolute relative percent deviation in fitting the EOS parameters to the MC data is 0.06 and 0.14 for the fluid and solid phases, respectively. The thermodynamic integration method is used to calculate the free energy using the MC simulation results. The Helmholtz free energy of the ideal gas is employed as the reference state for the fluid phase. For the solid phase, the values of the free energy at the reduced density equivalent to the close-packed of a hard sphere are used as the reference state. To check the validity of the predicted values of the Helmholtz free energy, the Widom particle insertion method and the Einstein crystal technique of Frenkel and Ladd are employed. The results obtained from the MC simulation approaches are well agreed to the EOS results, which show that the proposed model can reliably be utilized in the framework of thermodynamic theories.

  6. Extrapolations of nuclear binding energies from new linear mass relations

    DEFF Research Database (Denmark)

    Hove, D.; Jensen, A. S.; Riisager, K.

    2013-01-01

    We present a method to extrapolate nuclear binding energies from known values for neighboring nuclei. We select four specific mass relations constructed to eliminate smooth variation of the binding energy as function nucleon numbers. The fast odd-even variations are avoided by comparing nuclei...

  7. Trp-cage: Folding free energy landscape in explicit water

    Science.gov (United States)

    Zhou, Ruhong

    2003-11-01

    Trp-cage is a 20-residue miniprotein, which is believed to be the fastest folder known so far. In this study, the folding free energy landscape of Trp-cage has been explored in explicit solvent by using an OPLSAA force field with periodic boundary condition. A highly parallel replica exchange molecular dynamics method is used for the conformation space sampling, with the help of a recently developed efficient molecular dynamics algorithm P3ME/RESPA (particle-particle particle-mesh Ewald/reference system propagator algorithm). A two-step folding mechanism is proposed that involves an intermediate state where two correctly formed partial hydrophobic cores are separated by an essential salt-bridge between residues Asp-9 and Arg-16 near the center of the peptide. This metastable intermediate state provides an explanation for the superfast folding process. The free energy landscape is found to be rugged at low temperatures, and then becomes smooth and funnel-like above 340 K. The lowest free energy structure at 300 K is only 1.50 Å C-RMSD (C-rms deviation) from the NMR structures. The simulated nuclear Overhauser effect pair distances are in excellent agreement with the raw NMR data. The temperature dependence of the Trp-cage population, however, is found to be significantly different from experiment, with a much higher melting transition temperature above 400 K (experimental 315 K), indicating that the current force fields, parameterized at room temperature, need to be improved to correctly predict the temperature dependence.

  8. Minimal Self-Models and the Free Energy Principle

    Directory of Open Access Journals (Sweden)

    Jakub eLimanowski

    2013-09-01

    Full Text Available The term "minimal phenomenal selfhood" describes the basic, pre-reflective experience of being a self (Blanke & Metzinger, 2009. Theoretical accounts of the minimal self have long recognized the importance and the ambivalence of the body as both part of the physical world, and the enabling condition for being in this world (Gallagher, 2005; Grafton, 2009. A recent account of minimal phenomenal selfhood (MPS, Metzinger, 2004a centers on the consideration that minimal selfhood emerges as the result of basic self-modeling mechanisms, thereby being founded on pre-reflective bodily processes. The free energy principle (FEP, Friston, 2010 is a novel unified theory of cortical function that builds upon the imperative that self-organizing systems entail hierarchical generative models of the causes of their sensory input, which are optimized by minimizing free energy as an approximation of the log-likelihood of the model. The implementation of the FEP via predictive coding mechanisms and in particular the active inference principle emphasizes the role of embodiment for predictive self-modeling, which has been appreciated in recent publications. In this review, we provide an overview of these conceptions and illustrate thereby the potential power of the FEP in explaining the mechanisms underlying minimal selfhood and its key constituents, multisensory integration, interoception, agency, perspective, and the experience of mineness. We conclude that the conceptualization of MPS can be well mapped onto a hierarchical generative model furnished by the free energy principle and may constitute the basis for higher-level, cognitive forms of self-referral, as well as the understanding of other minds.

  9. Towards a fossil free energy future. The next energy transition

    Energy Technology Data Exchange (ETDEWEB)

    Lazarus, M.; Greber, L.; Hall, J.; Bartels, C.; Bernow, S.; Hansen, E.; Raskin, P.; Von Hippel, D. (Stockholm Environment Institute, Boston, MA (United States))

    1993-04-01

    The report provides technical analysis and documentation as input to the Greenpeace project 'Towards a fossil free energy future'. It presents a main scenario and several variants for reducing greenhouse gas emissions, and the technical methods and assumptions used to develop them. The goal is to investigate the technical, economic and policy feasibility to phasing out fossil fuels over the next century as part of a strategy to avert unacceptably high levels or rates of global warming. 209 refs., 42 figs., 27 tabs.

  10. Wettability and surface free energy of polarised ceramic biomaterials

    International Nuclear Information System (INIS)

    Nakamura, Miho; Hori, Naoko; Namba, Saki; Yamashita, Kimihiro; Toyama, Takeshi; Nishimiya, Nobuyuki

    2015-01-01

    The surface modification of ceramic biomaterials used for medical devices is expected to improve osteoconductivity through control of the interfaces between the materials and living tissues. Polarisation treatment induced surface charges on hydroxyapatite, β-tricalcium phosphate, carbonate-substituted hydroxyapatite and yttria-stabilized zirconia regardless of the differences in the carrier ions participating in the polarisation. Characterization of the surfaces revealed that the wettability of the polarised ceramic biomaterials was improved through the increase in the surface free energies compared with conventional ceramic surfaces. (note)

  11. Coarse-grained versus atomistic simulations : realistic interaction free energies for real proteins

    NARCIS (Netherlands)

    May, Ali; Pool, René; van Dijk, Erik; Bijlard, Jochem; Abeln, Sanne; Heringa, Jaap; Feenstra, K Anton

    2014-01-01

    MOTIVATION: To assess whether two proteins will interact under physiological conditions, information on the interaction free energy is needed. Statistical learning techniques and docking methods for predicting protein-protein interactions cannot quantitatively estimate binding free energies. Full

  12. Free energy minimization and information gain: The devil is in the details

    NARCIS (Netherlands)

    Kwisthout, J.H.P.; Rooij, I.J.E.I. van

    2015-01-01

    Contrary to Friston's previous work, this paper describes free energy minimization using categorical probability distributions over discrete states. This alternative mathematical framework exposes a fundamental, yet unnoticed challenge for the free energy principle. When considering discrete state

  13. Coarse-grained versus atomistic simulations: realistic interaction free energies for real proteins

    NARCIS (Netherlands)

    May, A.; Pool, R.; van Dijk, E.; Bijlard, J.; Abeln, S.; Heringa, J.; Feenstra, K.A.

    2014-01-01

    MOTIVATION: To assess whether two proteins will interact under physiological conditions, information on the interaction free energy is needed. Statistical learning techniques and docking methods for predicting protein-protein interactions cannot quantitatively estimate binding free energies. Full

  14. Linear relations between leaf mass per area (LMA) and seasonal climate discovered through Linear Manifold Clustering (LMC)

    Science.gov (United States)

    Kiang, N. Y.; Haralick, R. M.; Diky, A.; Kattge, J.; Su, X.

    2016-12-01

    Leaf mass per area (LMA) is a critical variable in plant carbon allocation, correlates with leaf activity traits (photosynthetic activity, respiration), and is a controller of litterfall mass and hence carbon substrate for soil biogeochemistry. Recent advances in understanding the leaf economics spectrum (LES) show that LMA has a strong correlation with leaf life span, a trait that reflects ecological strategy, whereas physiological traits that control leaf activity scale with each other when mass-normalized (Osnas et al., 2013). These functional relations help reduce the number of independent variables in quantifying leaf traits. However, LMA is an independent variable that remains a challenge to specify in dynamic global vegetation models (DGVMs), when vegetation types are classified into a limited number of plant functional types (PFTs) without clear mechanistic drivers for LMA. LMA can range orders of magnitude across plant species, as well as vary within a single plant, both vertically and seasonally. As climate relations in combination with alternative ecological strategies have yet to be well identified for LMA, we have assembled 22,000 records of LMA spanning 0.004 - 33 mg/m2 from the numerous contributors to the TRY database (Kattge et al., 2011), with observations distributed over several climate zones and plant functional categories (growth form, leaf type, phenology). We present linear relations between LMA and climate variables, including seasonal temperature, precipitation, and radiation, as derived through Linear Manifold Clustering (LMC). LMC is a stochastic search technique for identifying linear dependencies between variables in high dimensional space. We identify a set of parsimonious classes of LMA-climate groups based on a metric of minimum description to identify structure in the data set, akin to data compression. The relations in each group are compared to Köppen-Geiger climate classes, with some groups revealing continuous linear relations

  15. Free energy landscape of a minimalist salt bridge model.

    Science.gov (United States)

    Li, Xubin; Lv, Chao; Corbett, Karen M; Zheng, Lianqing; Wu, Dongsheng; Yang, Wei

    2016-01-01

    Salt bridges are essential to protein stability and dynamics. Despite the importance, there has been scarce of detailed discussion on how salt bridge partners interact with each other in distinct solvent exposed environments. In this study, employing a recent generalized orthogonal space tempering (gOST) method, we enabled efficient molecular dynamics simulation of repetitive breaking and reforming of salt bridge structures within a minimalist salt-bridge model, the Asp-Arg dipeptide and thereby were able to map its detailed free energy landscape in aqueous solution. Free energy surface analysis shows that although individually-solvated states are more favorable, salt-bridge states still occupy a noticeable portion of the overall population. Notably, the competing forces, e.g. intercharge attractions that drive the formation of salt bridges and solvation forces that pull the charged groups away from each other, are energetically comparable. As the result, the salt bridge stability is highly tunable by local environments; for instance when local water molecules are perturbed to interact more strongly with each other, the population of the salt-bridge states is likely to increase. Our results reveal the critical role of local solvent structures in modulating salt-bridge partner interactions and imply the importance of water fluctuations on conformational dynamics that involves solvent accessible salt bridge formations. © 2015 The Protein Society.

  16. Free-energy landscape of a hyperstable RNA tetraloop.

    Science.gov (United States)

    Miner, Jacob C; Chen, Alan A; García, Angel E

    2016-06-14

    We report the characterization of the energy landscape and the folding/unfolding thermodynamics of a hyperstable RNA tetraloop obtained through high-performance molecular dynamics simulations at microsecond timescales. Sampling of the configurational landscape is conducted using temperature replica exchange molecular dynamics over three isochores at high, ambient, and negative pressures to determine the thermodynamic stability and the free-energy landscape of the tetraloop. The simulations reveal reversible folding/unfolding transitions of the tetraloop into the canonical A-RNA conformation and the presence of two alternative configurations, including a left-handed Z-RNA conformation and a compact purine Triplet. Increasing hydrostatic pressure shows a stabilizing effect on the A-RNA conformation and a destabilization of the left-handed Z-RNA. Our results provide a comprehensive description of the folded free-energy landscape of a hyperstable RNA tetraloop and highlight the significant advances of all-atom molecular dynamics in describing the unbiased folding of a simple RNA secondary structure motif.

  17. Advancing Drug Discovery through Enhanced Free Energy Calculations.

    Science.gov (United States)

    Abel, Robert; Wang, Lingle; Harder, Edward D; Berne, B J; Friesner, Richard A

    2017-07-18

    A principal goal of drug discovery project is to design molecules that can tightly and selectively bind to the target protein receptor. Accurate prediction of protein-ligand binding free energies is therefore of central importance in computational chemistry and computer aided drug design. Multiple recent improvements in computing power, classical force field accuracy, enhanced sampling methods, and simulation setup have enabled accurate and reliable calculations of protein-ligands binding free energies, and position free energy calculations to play a guiding role in small molecule drug discovery. In this Account, we outline the relevant methodological advances, including the REST2 (Replica Exchange with Solute Temperting) enhanced sampling, the incorporation of REST2 sampling with convential FEP (Free Energy Perturbation) through FEP/REST, the OPLS3 force field, and the advanced simulation setup that constitute our FEP+ approach, followed by the presentation of extensive comparisons with experiment, demonstrating sufficient accuracy in potency prediction (better than 1 kcal/mol) to substantially impact lead optimization campaigns. The limitations of the current FEP+ implementation and best practices in drug discovery applications are also discussed followed by the future methodology development plans to address those limitations. We then report results from a recent drug discovery project, in which several thousand FEP+ calculations were successfully deployed to simultaneously optimize potency, selectivity, and solubility, illustrating the power of the approach to solve challenging drug design problems. The capabilities of free energy calculations to accurately predict potency and selectivity have led to the advance of ongoing drug discovery projects, in challenging situations where alternative approaches would have great difficulties. The ability to effectively carry out projects evaluating tens of thousands, or hundreds of thousands, of proposed drug candidates

  18. Prediction of binding free energy for adsorption of antimicrobial peptide lactoferricin B on a POPC membrane

    Science.gov (United States)

    Vivcharuk, Victor; Tomberli, Bruno; Tolokh, Igor S.; Gray, C. G.

    2008-03-01

    Molecular dynamics (MD) simulations are used to study the interaction of a zwitterionic palmitoyl-oleoyl-phosphatidylcholine (POPC) bilayer with the cationic antimicrobial peptide bovine lactoferricin (LFCinB) in a 100 mM NaCl solution at 310 K. The interaction of LFCinB with POPC is used as a model system for studying the details of membrane-peptide interactions, with the peptide selected because of its antimicrobial nature. Seventy-two 3 ns MD simulations, with six orientations of LFCinB at 12 different distances from a POPC membrane, are carried out to determine the potential of mean force (PMF) or free energy profile for the peptide as a function of the distance between LFCinB and the membrane surface. To calculate the PMF for this relatively large system a new variant of constrained MD and thermodynamic integration is developed. A simplified method for relating the PMF to the LFCinB-membrane binding free energy is described and used to predict a free energy of adsorption (or binding) of -1.05±0.39kcal/mol , and corresponding maximum binding force of about 20 pN, for LFCinB-POPC. The contributions of the ions-LFCinB and the water-LFCinB interactions to the PMF are discussed. The method developed will be a useful starting point for future work simulating peptides interacting with charged membranes and interactions involved in the penetration of membranes, features necessary to understand in order to rationally design peptides as potential alternatives to traditional antibiotics.

  19. Gibbs free energy of formation of UPb(s) compound

    International Nuclear Information System (INIS)

    Samui, Pradeep; Agarwal, Renu; Mishra, Ratikanta

    2012-01-01

    Liquid lead and lead-bismuth eutectic (LBE) are being explored as primary candidates for coolants in accelerator driven systems and in advanced nuclear reactors due to their favorable thermo-physical and chemical properties. They are also proposed to be used as spallation neutron source in ADS Reactor Systems. However, corrosion of structural materials (i.e. steel) presents a critical challenge for the use of liquid lead or LBE in advanced nuclear reactors. The interactions of liquid lead or LBE with clad and fuel is of great scientific and technological importance in the development of advanced nuclear reactors. Clad failure/breach can lead to reaction of coolant elements with fuel components. Thus the study of fuel-coolant interaction of U with Pb/Bi is important. The paper deals with the determination of Gibbs free energy of formation of U-rich phase i.e. UPb in Pb-U system, employing Knudsen effusion mass loss technique

  20. Exploring the free energy surfaces of clusters using reconnaissance metadynamics

    Science.gov (United States)

    Tribello, Gareth A.; Cuny, Jérôme; Eshet, Hagai; Parrinello, Michele

    2011-09-01

    A new approach is proposed for exploring the low-energy structures of small to medium-sized aggregates of atoms and molecules. This approach uses the recently proposed reconnaissance metadynamics method [G. A. Tribello, M. Ceriotti, and M. Parrinello. Proc. Natl. Acad. Sci. U.S.A. 107(41), 17509 (2010), 10.1073/pnas.1011511107] in tandem with collective variables that describe the average structure of the coordination sphere around the atoms/molecules. We demonstrate this method on both Lennard-Jones and water clusters and show how it is able to quickly find the global minimum in the potential energy surface, while exploring the finite temperature free energy surface.

  1. Hydrogen role in a carbon-free energy mix

    International Nuclear Information System (INIS)

    2014-02-01

    Among the energy storage technologies under development today, there is today an increasing interest towards the hydrogen-based ones. Hydrogen generation allows to store electricity, while its combustion can supply electrical, mechanical or heat energy. The French Atomic Energy Commission (CEA) started to work on hydrogen technologies at the end of the 1990's in order to reinforce its economical interest. The development of these technologies is one of the 34 French industrial programs presented in September 2013 by the French Minister of productive recovery. This paper aims at identifying the hydrogen stakes in a carbon-free energy mix and at highlighting the remaining technological challenges to be met before reaching an industrial development level

  2. Ising model on tangled chain - 1: Free energy and entropy

    International Nuclear Information System (INIS)

    Mejdani, R.

    1993-04-01

    In this paper we have considered an Ising model defined on tangled chain, in which more bonds have been added to those of pure Ising chain. to understand their competition, particularly between ferromagnetic and antiferromagnetic bonds, we have studied, using the transfer matrix method, some simple analytical calculations and an iterative algorithm, the behaviour of the free energy and entropy, particularly in the zero-field and zero temperature limit, for different configurations of the ferromagnetic tangled chain and different types of addition interaction (ferromagnetic or antiferromagnetic). We found that the condition J=J' between the ferromagnetic interaction J along the chain and the antiferromagnetic interaction J' across the chain is somewhat as a ''transition-region'' condition for this behaviour. Our results indicate also the existence of non-zero entropy at zero temperature. (author). 17 refs, 8 figs

  3. Calculating Free Energies Using Scaled-Force Molecular Dynamics Algorithm

    Science.gov (United States)

    Darve, Eric; Wilson, Micahel A.; Pohorille, Andrew

    2000-01-01

    One common objective of molecular simulations in chemistry and biology is to calculate the free energy difference between different states of the system of interest. Examples of problems that have such an objective are calculations of receptor-ligand or protein-drug interactions, associations of molecules in response to hydrophobic, and electrostatic interactions or partition of molecules between immiscible liquids. Another common objective is to describe evolution of the system towards a low energy (possibly the global minimum energy), 'native' state. Perhaps the best example of such a problem is folding of proteins or short RNA molecules. Both types of problems share the same difficulty. Often, different states of the system are separated by high energy barriers, which implies that transitions between these states are rare events. This, in turn, can greatly impede exploration of phase space. In some instances this can lead to 'quasi non-ergodicity', whereby a part of phase space is inaccessible on timescales of the simulation. A host of strategies has been developed to improve efficiency of sampling the phase space. For example, some Monte Carlo techniques involve large steps which move the system between low-energy regions in phase space without the need for sampling the configurations corresponding to energy barriers (J-walking). Most strategies, however, rely on modifying probabilities of sampling low and high-energy regions in phase space such that transitions between states of interest are encouraged. Perhaps the simplest implementation of this strategy is to increase the temperature of the system. This approach was successfully used to identify denaturation pathways in several proteins, but it is clearly not applicable to protein folding. It is also not a successful method for determining free energy differences. Finally, the approach is likely to fail for systems with co-existing phases, such as water-membrane systems, because it may lead to spontaneous

  4. Computational prediction of binding affinity for CYP1A2-ligand complexes using empirical free energy calculations

    DEFF Research Database (Denmark)

    Poongavanam, Vasanthanathan; Olsen, Lars; Jørgensen, Flemming Steen

    2010-01-01

    , and methods based on statistical mechanics. In the present investigation, we started from an LIE model to predict the binding free energy of structurally diverse compounds of cytochrome P450 1A2 ligands, one of the important human metabolizing isoforms of the cytochrome P450 family. The data set includes both...... substrates and inhibitors. It appears that the electrostatic contribution to the binding free energy becomes negligible in this particular protein and a simple empirical model was derived, based on a training set of eight compounds. The root mean square error for the training set was 3.7 kJ/mol. Subsequent......Predicting binding affinities for receptor-ligand complexes is still one of the challenging processes in computational structure-based ligand design. Many computational methods have been developed to achieve this goal, such as docking and scoring methods, the linear interaction energy (LIE) method...

  5. Affine-response model of molecular solvation of ions: Accurate predictions of asymmetric charging free energies.

    Science.gov (United States)

    Bardhan, Jaydeep P; Jungwirth, Pavel; Makowski, Lee

    2012-09-28

    Two mechanisms have been proposed to drive asymmetric solvent response to a solute charge: a static potential contribution similar to the liquid-vapor potential, and a steric contribution associated with a water molecule's structure and charge distribution. In this work, we use free-energy perturbation molecular-dynamics calculations in explicit water to show that these mechanisms act in complementary regimes; the large static potential (∼44 kJ/mol/e) dominates asymmetric response for deeply buried charges, and the steric contribution dominates for charges near the solute-solvent interface. Therefore, both mechanisms must be included in order to fully account for asymmetric solvation in general. Our calculations suggest that the steric contribution leads to a remarkable deviation from the popular "linear response" model in which the reaction potential changes linearly as a function of charge. In fact, the potential varies in a piecewise-linear fashion, i.e., with different proportionality constants depending on the sign of the charge. This discrepancy is significant even when the charge is completely buried, and holds for solutes larger than single atoms. Together, these mechanisms suggest that implicit-solvent models can be improved using a combination of affine response (an offset due to the static potential) and piecewise-linear response (due to the steric contribution).

  6. Affine-response model of molecular solvation of ions: Accurate predictions of asymmetric charging free energies

    Science.gov (United States)

    Bardhan, Jaydeep P.; Jungwirth, Pavel; Makowski, Lee

    2012-01-01

    Two mechanisms have been proposed to drive asymmetric solvent response to a solute charge: a static potential contribution similar to the liquid-vapor potential, and a steric contribution associated with a water molecule's structure and charge distribution. In this work, we use free-energy perturbation molecular-dynamics calculations in explicit water to show that these mechanisms act in complementary regimes; the large static potential (∼44 kJ/mol/e) dominates asymmetric response for deeply buried charges, and the steric contribution dominates for charges near the solute-solvent interface. Therefore, both mechanisms must be included in order to fully account for asymmetric solvation in general. Our calculations suggest that the steric contribution leads to a remarkable deviation from the popular “linear response” model in which the reaction potential changes linearly as a function of charge. In fact, the potential varies in a piecewise-linear fashion, i.e., with different proportionality constants depending on the sign of the charge. This discrepancy is significant even when the charge is completely buried, and holds for solutes larger than single atoms. Together, these mechanisms suggest that implicit-solvent models can be improved using a combination of affine response (an offset due to the static potential) and piecewise-linear response (due to the steric contribution). PMID:23020318

  7. A complex linear least-squares method to derive relative and absolute orientations of seismic sensors

    OpenAIRE

    F. Grigoli; Simone Cesca; Torsten Dahm; L. Krieger

    2012-01-01

    Determining the relative orientation of the horizontal components of seismic sensors is a common problem that limits data analysis and interpretation for several acquisition setups, including linear arrays of geophones deployed in borehole installations or ocean bottom seismometers deployed at the seafloor. To solve this problem we propose a new inversion method based on a complex linear algebra approach. Relative orientation angles are retrieved by minimizing, in a least-squares sense, the l...

  8. Linear relations in microbial reaction systems: a general overview of their origin, form, and use.

    Science.gov (United States)

    Noorman, H J; Heijnen, J J; Ch A M Luyben, K

    1991-09-01

    In microbial reaction systems, there are a number of linear relations among net conversion rates. These can be very useful in the analysis of experimental data. This article provides a general approach for the formation and application of the linear relations. Two type of system descriptions, one considering the biomass as a black box and the other based on metabolic pathways, are encountered. These are defined in a linear vector and matrix algebra framework. A correct a priori description can be obtained by three useful tests: the independency, consistency, and observability tests. The independency are different. The black box approach provides only conservations relations. They are derived from element, electrical charge, energy, and Gibbs energy balances. The metabolic approach provides, in addition to the conservation relations, metabolic and reaction relations. These result from component, energy, and Gibbs energy balances. Thus it is more attractive to use the metabolic description than the black box approach. A number of different types of linear relations given in the literature are reviewed. They are classified according to the different categories that result from the black box or the metabolic system description. Validation of hypotheses related to metabolic pathways can be supported by experimental validation of the linear metabolic relations. However, definite proof from biochemical evidence remains indispensable.

  9. Dissipation, generalized free energy, and a self-consistent nonequilibrium thermodynamics of chemically driven open subsystems.

    Science.gov (United States)

    Ge, Hao; Qian, Hong

    2013-06-01

    Nonequilibrium thermodynamics of a system situated in a sustained environment with influx and efflux is usually treated as a subsystem in a larger, closed "universe." A question remains with regard to what the minimally required description for the surrounding of such an open driven system is so that its nonequilibrium thermodynamics can be established solely based on the internal stochastic kinetics. We provide a solution to this problem using insights from studies of molecular motors in a chemical nonequilibrium steady state (NESS) with sustained external drive through a regenerating system or in a quasisteady state (QSS) with an excess amount of adenosine triphosphate (ATP), adenosine diphosphate (ADP), and inorganic phosphate (Pi). We introduce the key notion of minimal work that is needed, W(min), for the external regenerating system to sustain a NESS (e.g., maintaining constant concentrations of ATP, ADP and Pi for a molecular motor). Using a Markov (master-equation) description of a motor protein, we illustrate that the NESS and QSS have identical kinetics as well as the second law in terms of the same positive entropy production rate. The heat dissipation of a NESS without mechanical output is exactly the W(min). This provides a justification for introducing an ideal external regenerating system and yields a free-energy balance equation between the net free-energy input F(in) and total dissipation F(dis) in an NESS: F(in) consists of chemical input minus mechanical output; F(dis) consists of dissipative heat, i.e. the amount of useful energy becoming heat, which also equals the NESS entropy production. Furthermore, we show that for nonstationary systems, the F(dis) and F(in) correspond to the entropy production rate and housekeeping heat in stochastic thermodynamics and identify a relative entropy H as a generalized free energy. We reach a new formulation of Markovian nonequilibrium thermodynamics based on only the internal kinetic equation without further

  10. Partition coefficients of methylated DNA bases obtained from free energy calculations with molecular electron density derived atomic charges.

    Science.gov (United States)

    Lara, A; Riquelme, M; Vöhringer-Martinez, E

    2018-05-11

    Partition coefficients serve in various areas as pharmacology and environmental sciences to predict the hydrophobicity of different substances. Recently, they have also been used to address the accuracy of force fields for various organic compounds and specifically the methylated DNA bases. In this study, atomic charges were derived by different partitioning methods (Hirshfeld and Minimal Basis Iterative Stockholder) directly from the electron density obtained by electronic structure calculations in a vacuum, with an implicit solvation model or with explicit solvation taking the dynamics of the solute and the solvent into account. To test the ability of these charges to describe electrostatic interactions in force fields for condensed phases, the original atomic charges of the AMBER99 force field were replaced with the new atomic charges and combined with different solvent models to obtain the hydration and chloroform solvation free energies by molecular dynamics simulations. Chloroform-water partition coefficients derived from the obtained free energies were compared to experimental and previously reported values obtained with the GAFF or the AMBER-99 force field. The results show that good agreement with experimental data is obtained when the polarization of the electron density by the solvent has been taken into account, and when the energy needed to polarize the electron density of the solute has been considered in the transfer free energy. These results were further confirmed by hydration free energies of polar and aromatic amino acid side chain analogs. Comparison of the two partitioning methods, Hirshfeld-I and Minimal Basis Iterative Stockholder (MBIS), revealed some deficiencies in the Hirshfeld-I method related to the unstable isolated anionic nitrogen pro-atom used in the method. Hydration free energies and partitioning coefficients obtained with atomic charges from the MBIS partitioning method accounting for polarization by the implicit solvation model

  11. Encapsulation of cisplatin as an anti-cancer drug into boron-nitride and carbon nanotubes: Molecular simulation and free energy calculation

    Energy Technology Data Exchange (ETDEWEB)

    Roosta, Sara [Molecular Simulation Research Laboratory, Department of Chemistry, Iran University of Science & Technology, Tehran (Iran, Islamic Republic of); Hashemianzadeh, Seyed Majid, E-mail: hashemianzadeh@iust.ac.ir [Molecular Simulation Research Laboratory, Department of Chemistry, Iran University of Science & Technology, Tehran (Iran, Islamic Republic of); Ketabi, Sepideh, E-mail: sepidehketabi@yahoo.com [Department of Chemistry, East Tehran Branch, Islamic Azad University, Tehran (Iran, Islamic Republic of)

    2016-10-01

    Encapsulation of cisplatin anticancer drug into the single walled (10, 0) carbon nanotube and (10, 0) boron-nitride nanotube was investigated by quantum mechanical calculations and Monte Carlo Simulation in aqueous solution. Solvation free energies and complexation free energies of the cisplatin@ carbon nanotube and cisplatin@ boron-nitride nanotube complexes was determined as well as radial distribution functions of entitled compounds. Solvation free energies of cisplatin@ carbon nanotube and cisplatin@ boron-nitride nanotube were − 4.128 kcal mol{sup −1} and − 2457.124 kcal mol{sup −1} respectively. The results showed that cisplatin@ boron-nitride nanotube was more soluble species in water. In addition electrostatic contribution of the interaction of boron- nitride nanotube complex and solvent was − 281.937 kcal mol{sup −1} which really more than Van der Waals and so the electrostatic interactions play a distinctive role in the solvation free energies of boron- nitride nanotube compounds. On the other hand electrostatic part of the interaction of carbon nanotube complex and solvent were almost the same as Van der Waals contribution. Complexation free energies were also computed to study the stability of related structures and the free energies were negative (− 374.082 and − 245.766 kcal mol{sup −1}) which confirmed encapsulation of drug into abovementioned nanotubes. However, boron-nitride nanotubes were more appropriate for encapsulation due to their larger solubility in aqueous solution. - Highlights: • Solubility of cisplatin@ boron-nitride nanotube is larger than cisplatin@ carbon nanotube. • Boron- nitride nanotube complexes have larger electrostatic contribution in solvation free energy. • Complexation free energies confirm encapsulation of drug into the nanotubes in aqueous solution. • Boron- nitride nanotubes are appropriate drug delivery systems compared with carbon nanotubes.

  12. Encapsulation of cisplatin as an anti-cancer drug into boron-nitride and carbon nanotubes: Molecular simulation and free energy calculation

    International Nuclear Information System (INIS)

    Roosta, Sara; Hashemianzadeh, Seyed Majid; Ketabi, Sepideh

    2016-01-01

    Encapsulation of cisplatin anticancer drug into the single walled (10, 0) carbon nanotube and (10, 0) boron-nitride nanotube was investigated by quantum mechanical calculations and Monte Carlo Simulation in aqueous solution. Solvation free energies and complexation free energies of the cisplatin@ carbon nanotube and cisplatin@ boron-nitride nanotube complexes was determined as well as radial distribution functions of entitled compounds. Solvation free energies of cisplatin@ carbon nanotube and cisplatin@ boron-nitride nanotube were − 4.128 kcal mol"−"1 and − 2457.124 kcal mol"−"1 respectively. The results showed that cisplatin@ boron-nitride nanotube was more soluble species in water. In addition electrostatic contribution of the interaction of boron- nitride nanotube complex and solvent was − 281.937 kcal mol"−"1 which really more than Van der Waals and so the electrostatic interactions play a distinctive role in the solvation free energies of boron- nitride nanotube compounds. On the other hand electrostatic part of the interaction of carbon nanotube complex and solvent were almost the same as Van der Waals contribution. Complexation free energies were also computed to study the stability of related structures and the free energies were negative (− 374.082 and − 245.766 kcal mol"−"1) which confirmed encapsulation of drug into abovementioned nanotubes. However, boron-nitride nanotubes were more appropriate for encapsulation due to their larger solubility in aqueous solution. - Highlights: • Solubility of cisplatin@ boron-nitride nanotube is larger than cisplatin@ carbon nanotube. • Boron- nitride nanotube complexes have larger electrostatic contribution in solvation free energy. • Complexation free energies confirm encapsulation of drug into the nanotubes in aqueous solution. • Boron- nitride nanotubes are appropriate drug delivery systems compared with carbon nanotubes.

  13. From quantum chemical formation free energies to evaporation rates

    Directory of Open Access Journals (Sweden)

    I. K. Ortega

    2012-01-01

    Full Text Available Atmospheric new particle formation is an important source of atmospheric aerosols. Large efforts have been made during the past few years to identify which molecules are behind this phenomenon, but the actual birth mechanism of the particles is not yet well known. Quantum chemical calculations have proven to be a powerful tool to gain new insights into the very first steps of particle formation. In the present study we use formation free energies calculated by quantum chemical methods to estimate the evaporation rates of species from sulfuric acid clusters containing ammonia or dimethylamine. We have found that dimethylamine forms much more stable clusters with sulphuric acid than ammonia does. On the other hand, the existence of a very deep local minimum for clusters with two sulfuric acid molecules and two dimethylamine molecules hinders their growth to larger clusters. These results indicate that other compounds may be needed to make clusters grow to larger sizes (containing more than three sulfuric acid molecules.

  14. Examining ion channel properties using free-energy methods.

    Science.gov (United States)

    Domene, Carmen; Furini, Simone

    2009-01-01

    Recent advances in structural biology have revealed the architecture of a number of transmembrane channels, allowing for these complex biological systems to be understood in atomistic detail. Computational simulations are a powerful tool by which the dynamic and energetic properties, and thereby the function of these protein architectures, can be investigated. The experimentally observable properties of a system are often determined more by energetic than dynamics, and therefore understanding the underlying free energy (FE) of biophysical processes is of crucial importance. Critical to the accurate evaluation of FE values are the problems of obtaining accurate sampling of complex biological energy landscapes, and of obtaining accurate representations of the potential energy of a system, this latter problem having been addressed through the development of molecular force fields. While these challenges are common to all FE methods, depending on the system under study, and the questions being asked of it, one technique for FE calculation may be preferable to another, the choice of method and simulation protocol being crucial to achieve efficiency. Applied in a correct manner, FE calculations represent a predictive and affordable computational tool with which to make relevant contact with experiments. This chapter, therefore, aims to give an overview of the most widely implemented computational methods used to calculate the FE associated with particular biochemical or biophysical events, and to highlight their recent applications to ion channels. Copyright © 2009 Elsevier Inc. All rights reserved.

  15. Multivariable extrapolation of grand canonical free energy landscapes

    Science.gov (United States)

    Mahynski, Nathan A.; Errington, Jeffrey R.; Shen, Vincent K.

    2017-12-01

    We derive an approach for extrapolating the free energy landscape of multicomponent systems in the grand canonical ensemble, obtained from flat-histogram Monte Carlo simulations, from one set of temperature and chemical potentials to another. This is accomplished by expanding the landscape in a Taylor series at each value of the order parameter which defines its macrostate phase space. The coefficients in each Taylor polynomial are known exactly from fluctuation formulas, which may be computed by measuring the appropriate moments of extensive variables that fluctuate in this ensemble. Here we derive the expressions necessary to define these coefficients up to arbitrary order. In principle, this enables a single flat-histogram simulation to provide complete thermodynamic information over a broad range of temperatures and chemical potentials. Using this, we also show how to combine a small number of simulations, each performed at different conditions, in a thermodynamically consistent fashion to accurately compute properties at arbitrary temperatures and chemical potentials. This method may significantly increase the computational efficiency of biased grand canonical Monte Carlo simulations, especially for multicomponent mixtures. Although approximate, this approach is amenable to high-throughput and data-intensive investigations where it is preferable to have a large quantity of reasonably accurate simulation data, rather than a smaller amount with a higher accuracy.

  16. Free-energy minimization and the dark-room problem.

    Science.gov (United States)

    Friston, Karl; Thornton, Christopher; Clark, Andy

    2012-01-01

    Recent years have seen the emergence of an important new fundamental theory of brain function. This theory brings information-theoretic, Bayesian, neuroscientific, and machine learning approaches into a single framework whose overarching principle is the minimization of surprise (or, equivalently, the maximization of expectation). The most comprehensive such treatment is the "free-energy minimization" formulation due to Karl Friston (see e.g., Friston and Stephan, 2007; Friston, 2010a,b - see also Fiorillo, 2010; Thornton, 2010). A recurrent puzzle raised by critics of these models is that biological systems do not seem to avoid surprises. We do not simply seek a dark, unchanging chamber, and stay there. This is the "Dark-Room Problem." Here, we describe the problem and further unpack the issues to which it speaks. Using the same format as the prolog of Eddington's Space, Time, and Gravitation (Eddington, 1920) we present our discussion as a conversation between: an information theorist (Thornton), a physicist (Friston), and a philosopher (Clark).

  17. Effective Ginzburg–Landau free energy functional for multi-band isotropic superconductors

    International Nuclear Information System (INIS)

    Grigorishin, Konstantin V.

    2016-01-01

    Highlights: • The intergradient coupling of order parameters in a two-band superconductor plays important role and cannot be neglected. • A two-band superconductor must be characterized with a single coherence length and a single Ginzburg–Landau parameter. • Type-1.5 superconductors are impossible. • The free energy functional for a multi-band superconductor can be reduced to the effective single-band Ginzburg–Landau functional. - Abstract: It has been shown that interband mixing of gradients of two order parameters (drag effect) in an isotropic bulk two-band superconductor plays important role – such a quantity of the intergradients coupling exists that the two-band superconductor is characterized with a single coherence length and a single Ginzburg–Landau (GL) parameter. Other quantities or neglecting of the drag effect lead to existence of two coherence lengths and dynamical instability due to violation of the phase relations between the order parameters. Thus so-called type-1.5 superconductors are impossible. An approximate method for solving of set of GL equations for a multi-band superconductor has been developed: using the result about the drag effect it has been shown that the free-energy functional for a multi-band superconductor can be reduced to the GL functional for an effective single-band superconductor.

  18. Variational energy principle for compressible, baroclinic flow. 2: Free-energy form of Hamilton's principle

    Science.gov (United States)

    Schmid, L. A.

    1977-01-01

    The first and second variations are calculated for the irreducible form of Hamilton's Principle that involves the minimum number of dependent variables necessary to describe the kinetmatics and thermodynamics of inviscid, compressible, baroclinic flow in a specified gravitational field. The form of the second variation shows that, in the neighborhood of a stationary point that corresponds to physically stable flow, the action integral is a complex saddle surface in parameter space. There exists a form of Hamilton's Principle for which a direct solution of a flow problem is possible. This second form is related to the first by a Friedrichs transformation of the thermodynamic variables. This introduces an extra dependent variable, but the first and second variations are shown to have direct physical significance, namely they are equal to the free energy of fluctuations about the equilibrium flow that satisfies the equations of motion. If this equilibrium flow is physically stable, and if a very weak second order integral constraint on the correlation between the fluctuations of otherwise independent variables is satisfied, then the second variation of the action integral for this free energy form of Hamilton's Principle is positive-definite, so the action integral is a minimum, and can serve as the basis for a direct trail and error solution. The second order integral constraint states that the unavailable energy must be maximum at equilibrium, i.e. the fluctuations must be so correlated as to produce a second order decrease in the total unavailable energy.

  19. Understanding the free energy barrier and multiple timescale dynamics of charge separation in organic photovoltaic cells.

    Science.gov (United States)

    Yan, Yaming; Song, Linze; Shi, Qiang

    2018-02-28

    By employing several lattice model systems, we investigate the free energy barrier and real-time dynamics of charge separation in organic photovoltaic (OPV) cells. It is found that the combined effects of the external electric field, entropy, and charge delocalization reduce the free energy barrier significantly. The dynamic disorder reduces charge carrier delocalization and results in the increased charge separation barrier, while the effect of static disorder is more complicated. Simulation of the real-time dynamics indicates that the free charge generation process involves multiple time scales, including an ultrafast component within hundreds of femtoseconds, an intermediate component related to the relaxation of the hot charge transfer (CT) state, and a slow component on the time scale of tens of picoseconds from the thermally equilibrated CT state. Effects of hot exciton dissociation as well as its dependence on the energy offset between the Frenkel exciton and the CT state are also analyzed. The current results indicate that only a small energy offset between the band gap and the lowest energy CT state is needed to achieve efficient free charge generation in OPV devices, which agrees with recent experimental findings.

  20. Understanding the free energy barrier and multiple timescale dynamics of charge separation in organic photovoltaic cells

    Science.gov (United States)

    Yan, Yaming; Song, Linze; Shi, Qiang

    2018-02-01

    By employing several lattice model systems, we investigate the free energy barrier and real-time dynamics of charge separation in organic photovoltaic (OPV) cells. It is found that the combined effects of the external electric field, entropy, and charge delocalization reduce the free energy barrier significantly. The dynamic disorder reduces charge carrier delocalization and results in the increased charge separation barrier, while the effect of static disorder is more complicated. Simulation of the real-time dynamics indicates that the free charge generation process involves multiple time scales, including an ultrafast component within hundreds of femtoseconds, an intermediate component related to the relaxation of the hot charge transfer (CT) state, and a slow component on the time scale of tens of picoseconds from the thermally equilibrated CT state. Effects of hot exciton dissociation as well as its dependence on the energy offset between the Frenkel exciton and the CT state are also analyzed. The current results indicate that only a small energy offset between the band gap and the lowest energy CT state is needed to achieve efficient free charge generation in OPV devices, which agrees with recent experimental findings.

  1. Comparison of Dorris-Gray and Schultz methods for the calculation of surface dispersive free energy by inverse gas chromatography.

    Science.gov (United States)

    Shi, Baoli; Wang, Yue; Jia, Lina

    2011-02-11

    Inverse gas chromatography (IGC) is an important technique for the characterization of surface properties of solid materials. A standard method of surface characterization is that the surface dispersive free energy of the solid stationary phase is firstly determined by using a series of linear alkane liquids as molecular probes, and then the acid-base parameters are calculated from the dispersive parameters. However, for the calculation of surface dispersive free energy, generally, two different methods are used, which are Dorris-Gray method and Schultz method. In this paper, the results calculated from Dorris-Gray method and Schultz method are compared through calculating their ratio with their basic equations and parameters. It can be concluded that the dispersive parameters calculated with Dorris-Gray method will always be larger than the data calculated with Schultz method. When the measuring temperature increases, the ratio increases large. Compared with the parameters in solvents handbook, it seems that the traditional surface free energy parameters of n-alkanes listed in the papers using Schultz method are not enough accurate, which can be proved with a published IGC experimental result. © 2010 Elsevier B.V. All rights reserved.

  2. HYDROLYSIS OF HALOACETONITRILES: LINEAR FREE ENERGY RELATIONSHIP, KINETICS AND PRODUCTS. (R825362)

    Science.gov (United States)

    AbstractThe hydrolysis rates of mono-, di- and trihaloacetonitriles were studied in aqueous buffer solutions at different pH. The stability of haloacetonitriles decreases and the hydrolysis rate increases with increasing pH and number of halogen atoms in the molecule:...

  3. Descriptors for ions and ion-pairs for use in linear free energy relationships.

    Science.gov (United States)

    Abraham, Michael H; Acree, William E

    2016-01-22

    The determination of Abraham descriptors for single ions is reviewed, and equations are given for the partition of single ions from water to a number of solvents. These ions include permanent anions and cations and ionic species such as carboxylic acid anions, phenoxide anions and protonated base cations. Descriptors for a large number of ions and ionic species are listed, and equations for the prediction of Abraham descriptors for ionic species are given. The application of descriptors for ions and ionic species to physicochemical processes is given; these are to water-solvent partitions, HPLC retention data, immobilised artificial membranes, the Finkelstein reaction and diffusion in water. Applications to biological processes include brain permeation, microsomal degradation of drugs, skin permeation and human intestinal absorption. The review concludes with a section on the determination of descriptors for ion-pairs. Copyright © 2015 Elsevier B.V. All rights reserved.

  4. On the TAP Free Energy in the Mixed p-Spin Models

    Science.gov (United States)

    Chen, Wei-Kuo; Panchenko, Dmitry

    2018-05-01

    Thouless et al. (Phys Mag 35(3):593-601, 1977), derived a representation for the free energy of the Sherrington-Kirkpatrick model, called the TAP free energy, written as the difference of the energy and entropy on the extended configuration space of local magnetizations with an Onsager correction term. In the setting of mixed p-spin models with Ising spins, we prove that the free energy can indeed be written as the supremum of the TAP free energy over the space of local magnetizations whose Edwards-Anderson order parameter (self-overlap) is to the right of the support of the Parisi measure. Furthermore, for generic mixed p-spin models, we prove that the free energy is equal to the TAP free energy evaluated on the local magnetization of any pure state.

  5. An ab initio approach to free-energy reconstruction using logarithmic mean force dynamics

    International Nuclear Information System (INIS)

    Nakamura, Makoto; Obata, Masao; Morishita, Tetsuya; Oda, Tatsuki

    2014-01-01

    We present an ab initio approach for evaluating a free energy profile along a reaction coordinate by combining logarithmic mean force dynamics (LogMFD) and first-principles molecular dynamics. The mean force, which is the derivative of the free energy with respect to the reaction coordinate, is estimated using density functional theory (DFT) in the present approach, which is expected to provide an accurate free energy profile along the reaction coordinate. We apply this new method, first-principles LogMFD (FP-LogMFD), to a glycine dipeptide molecule and reconstruct one- and two-dimensional free energy profiles in the framework of DFT. The resultant free energy profile is compared with that obtained by the thermodynamic integration method and by the previous LogMFD calculation using an empirical force-field, showing that FP-LogMFD is a promising method to calculate free energy without empirical force-fields

  6. Qgui: A high-throughput interface for automated setup and analysis of free energy calculations and empirical valence bond simulations in biological systems.

    Science.gov (United States)

    Isaksen, Geir Villy; Andberg, Tor Arne Heim; Åqvist, Johan; Brandsdal, Bjørn Olav

    2015-07-01

    Structural information and activity data has increased rapidly for many protein targets during the last decades. In this paper, we present a high-throughput interface (Qgui) for automated free energy and empirical valence bond (EVB) calculations that use molecular dynamics (MD) simulations for conformational sampling. Applications to ligand binding using both the linear interaction energy (LIE) method and the free energy perturbation (FEP) technique are given using the estrogen receptor (ERα) as a model system. Examples of free energy profiles obtained using the EVB method for the rate-limiting step of the enzymatic reaction catalyzed by trypsin are also shown. In addition, we present calculation of high-precision Arrhenius plots to obtain the thermodynamic activation enthalpy and entropy with Qgui from running a large number of EVB simulations. Copyright © 2015 Elsevier Inc. All rights reserved.

  7. Undecidability of the Logic of Overlap Relation over Discrete Linear Orderings

    DEFF Research Database (Denmark)

    Bresolin, Davide; Della Monica, Dario; Goranko, Valentin

    2010-01-01

    . Still, decidability is the rule for the fragments of HS with only one modal operator, based on an Allen’s relation. In this paper, we show that the logic O of the Overlap relation, when interpreted over discrete linear orderings, is an exception. The proof is based on a reduction from the undecidable...

  8. On the Linear Relation between the Mean and the Standard Deviation of a Response Time Distribution

    Science.gov (United States)

    Wagenmakers, Eric-Jan; Brown, Scott

    2007-01-01

    Although it is generally accepted that the spread of a response time (RT) distribution increases with the mean, the precise nature of this relation remains relatively unexplored. The authors show that in several descriptive RT distributions, the standard deviation increases linearly with the mean. Results from a wide range of tasks from different…

  9. SAAFEC: Predicting the Effect of Single Point Mutations on Protein Folding Free Energy Using a Knowledge-Modified MM/PBSA Approach.

    Science.gov (United States)

    Getov, Ivan; Petukh, Marharyta; Alexov, Emil

    2016-04-07

    Folding free energy is an important biophysical characteristic of proteins that reflects the overall stability of the 3D structure of macromolecules. Changes in the amino acid sequence, naturally occurring or made in vitro, may affect the stability of the corresponding protein and thus could be associated with disease. Several approaches that predict the changes of the folding free energy caused by mutations have been proposed, but there is no method that is clearly superior to the others. The optimal goal is not only to accurately predict the folding free energy changes, but also to characterize the structural changes induced by mutations and the physical nature of the predicted folding free energy changes. Here we report a new method to predict the Single Amino Acid Folding free Energy Changes (SAAFEC) based on a knowledge-modified Molecular Mechanics Poisson-Boltzmann (MM/PBSA) approach. The method is comprised of two main components: a MM/PBSA component and a set of knowledge based terms delivered from a statistical study of the biophysical characteristics of proteins. The predictor utilizes a multiple linear regression model with weighted coefficients of various terms optimized against a set of experimental data. The aforementioned approach yields a correlation coefficient of 0.65 when benchmarked against 983 cases from 42 proteins in the ProTherm database. the webserver can be accessed via http://compbio.clemson.edu/SAAFEC/.

  10. Estimating Atomic Contributions to Hydration and Binding Using Free Energy Perturbation.

    Science.gov (United States)

    Irwin, Benedict W J; Huggins, David J

    2018-05-08

    We present a general method called atom-wise free energy perturbation (AFEP), which extends a conventional molecular dynamics free energy perturbation (FEP) simulation to give the contribution to a free energy change from each atom. AFEP is derived from an expansion of the Zwanzig equation used in the exponential averaging method by defining that the system total energy can be partitioned into contributions from each atom. A partitioning method is assumed and used to group terms in the expansion to correspond to individual atoms. AFEP is applied to six example free energy changes to demonstrate the method. Firstly, the hydration free energies of methane, methanol, methylamine, methanethiol, and caffeine in water. AFEP highlights the atoms in the molecules that interact favorably or unfavorably with water. Finally AFEP is applied to the binding free energy of human immunodeficiency virus type 1 protease to lopinavir, and AFEP reveals the contribution of each atom to the binding free energy, indicating candidate areas of the molecule to improve to produce a more strongly binding inhibitor. FEP gives a single value for the free energy change and is already a very useful method. AFEP gives a free energy change for each "part" of the system being simulated, where part can mean individual atoms, chemical groups, amino acids, or larger partitions depending on what the user is trying to measure. This method should have various applications in molecular dynamics studies of physical, chemical, or biochemical phenomena, specifically in the field of computational drug discovery.

  11. Reconstructing the long-term cosmic ray intensity: linear relations do not work

    Directory of Open Access Journals (Sweden)

    K. Mursula

    2003-04-01

    Full Text Available It was recently suggested (Lockwood, 2001 that the cosmic ray intensity in the neutron monitor energy range is linearly related to the coronal source flux, and can be reconstructed for the last 130 years using the long-term coronal flux estimated earlier. Moreover, Lockwood (2001 reconstructed the coronal flux for the last 500 years using a similar linear relation between the flux and the concentration of cosmogenic 10 Be isotopes in polar ice. Here we show that the applied linear relations are oversimplified and lead to unphysical results on long time scales. In particular, the cosmic ray intensity reconstructed by Lockwood (2001 for the last 130 years has a steep trend which is considerably larger than the trend estimated from observations during the last 65 years. Accordingly, the reconstructed cosmic ray intensity reaches or even exceeds the local interstellar cosmic ray flux around 1900. We argue that these unphysical results obtained when using linear relations are due to the oversimplified approach which does not take into account the complex and essentially nonlinear nature of long-term cosmic ray modulation in the heliosphere. We also compare the long-term cosmic ray intensity based on a linear treatment with the reconstruction based on a recent physical model which predicts a considerably lower cosmic ray intensity around 1900.Key words. Interplanetary physics (cosmic rays; heliopause and solar wind termination – Geomagnetism and paleomagnetism (time variations, secular and long-term

  12. Chemical Disequilibria and Sources of Gibbs Free Energy Inside Enceladus

    Science.gov (United States)

    Zolotov, M. Y.

    2010-12-01

    Non-photosynthetic organisms use chemical disequilibria in the environment to gain metabolic energy from enzyme catalyzed oxidation-reduction (redox) reactions. The presence of carbon dioxide, ammonia, formaldehyde, methanol, methane and other hydrocarbons in the eruptive plume of Enceladus [1] implies diverse redox disequilibria in the interior. In the history of the moon, redox disequilibria could have been activated through melting of a volatile-rich ice and following water-rock-organic interactions. Previous and/or present aqueous processes are consistent with the detection of NaCl and Na2CO3/NaHCO3-bearing grains emitted from Enceladus [2]. A low K/Na ratio in the grains [2] and a low upper limit for N2 in the plume [3] indicate low temperature (possibly enzymes if organisms were (are) present. The redox conditions in aqueous systems and amounts of available Gibbs free energy should have been affected by the production, consumption and escape of hydrogen. Aqueous oxidation of minerals (Fe-Ni metal, Fe-Ni phosphides, etc.) accreted on Enceladus should have led to H2 production, which is consistent with H2 detection in the plume [1]. Numerical evaluations based on concentrations of plume gases [1] reveal sufficient energy sources available to support metabolically diverse life at a wide range of activities (a) of dissolved H2 (log aH2 from 0 to -10). Formaldehyde, carbon dioxide [c.f. 4], HCN (if it is present), methanol, acetylene and other hydrocarbons have the potential to react with H2 to form methane. Aqueous hydrogenations of acetylene, HCN and formaldehyde to produce methanol are energetically favorable as well. Both favorable hydrogenation and hydration of HCN lead to formation of ammonia. Condensed organic species could also participate in redox reactions. Methane and ammonia are the final products of these putative redox transformations. Sulfates may have not formed in cold and/or short-term aqueous environments with a limited H2 escape. In contrast to

  13. The Emissions-Free Energy (EFE) Working Group

    Energy Technology Data Exchange (ETDEWEB)

    Humphries, R., E-mail: Roger.Humphries@amec.com [AMEC NSS, Toronto, Ontario (Canada)

    2014-07-01

    There has been a growing international interest in smaller, simpler reactors for generating electricity and process heat. They incorporate modern technological advances in reactor design, reactor safety, modular construction, proliferation resistance, and risk reduction. The interest in these reactors has been driven by many factors, including the need to reduce greenhouse gas emissions and provide reliable power in 'off-grid' or 'edge-of-grid' locations. Licensing these new small reactors, particularly in Canada's resource rich remote northern regions, will raises issues in a wide variety of technical, institutional, socio-economic and regulatory policy areas. The first small reactor vendor to file a license application or to engage the CNSC in its pre-licensing vendor design review process is going to have to deal with these issues. However these issues affect the entire small reactor industry and it is essential that the industry as a whole address them. Accordingly, a small reactor industry-wide Working Group has been established to identify and prioritize the issues that need to be addressed and work with the CNSC and other interested stakeholders to agree on a resolution acceptable to all parties. The objective of the small reactor industry is to introduce an economical, emissions-free source of electrical and thermal energy. It is the opinion of the WG that our emphasis ought to be on the product rather than the technology, hence the name Emissions-Free Energy Working Group. The EFE WG has initiated contact with the CNSC and has started its review of CNSC draft regulatory and guidance documents. (author)

  14. The free energy landscape of small molecule unbinding.

    Directory of Open Access Journals (Sweden)

    Danzhi Huang

    2011-02-01

    Full Text Available The spontaneous dissociation of six small ligands from the active site of FKBP (the FK506 binding protein is investigated by explicit water molecular dynamics simulations and network analysis. The ligands have between four (dimethylsulphoxide and eleven (5-diethylamino-2-pentanone non-hydrogen atoms, and an affinity for FKBP ranging from 20 to 0.2 mM. The conformations of the FKBP/ligand complex saved along multiple trajectories (50 runs at 310 K for each ligand are grouped according to a set of intermolecular distances into nodes of a network, and the direct transitions between them are the links. The network analysis reveals that the bound state consists of several subbasins, i.e., binding modes characterized by distinct intermolecular hydrogen bonds and hydrophobic contacts. The dissociation kinetics show a simple (i.e., single-exponential time dependence because the unbinding barrier is much higher than the barriers between subbasins in the bound state. The unbinding transition state is made up of heterogeneous positions and orientations of the ligand in the FKBP active site, which correspond to multiple pathways of dissociation. For the six small ligands of FKBP, the weaker the binding affinity the closer to the bound state (along the intermolecular distance are the transition state structures, which is a new manifestation of Hammond behavior. Experimental approaches to the study of fragment binding to proteins have limitations in temporal and spatial resolution. Our network analysis of the unbinding simulations of small inhibitors from an enzyme paints a clear picture of the free energy landscape (both thermodynamics and kinetics of ligand unbinding.

  15. On Sequences of Numbers and Polynomials Defined by Linear Recurrence Relations of Order 2

    Directory of Open Access Journals (Sweden)

    Tian-Xiao He

    2009-01-01

    Full Text Available Here we present a new method to construct the explicit formula of a sequence of numbers and polynomials generated by a linear recurrence relation of order 2. The applications of the method to the Fibonacci and Lucas numbers, Chebyshev polynomials, the generalized Gegenbauer-Humbert polynomials are also discussed. The derived idea provides a general method to construct identities of number or polynomial sequences defined by linear recurrence relations. The applications using the method to solve some algebraic and ordinary differential equations are presented.

  16. Relation between linear and nonlinear N=3,4 supergravity theories

    International Nuclear Information System (INIS)

    Sevrin, A.; Thielemans, K.; Troost, W.

    1993-01-01

    The effective actions for d=2, N=3,4 chiral supergravities with a linear and a nonlinear gauge algebra are related to each other by a quantum reduction; the latter is obtained from the former by putting quantum currents equal to zero. This implies that the renormalization factors for the quantum actions are identical

  17. Free energy change of off-eutectic binary alloys on solidification

    Science.gov (United States)

    Ohsaka, K.; Trinh, E. H.; Lin, J.-C.; Perepezko, J. H.

    1991-01-01

    A formula for the free energy difference between the undercooled liquid phase and the stable solid phase is derived for off-eutectic binary alloys in which the equilibrium solid/liquid transition takes place over a certain temperature range. The free energy change is then evaluated numerically for a Bi-25 at. pct Cd alloy modeled as a sub-subregular solution.

  18. A simple free energy for the isotropic-nematic phase transition of rods

    NARCIS (Netherlands)

    Tuinier, R.

    2016-01-01

    A free energy expression is proposed that describes the isotropic-nematic binodal concentrations of hard rods. A simple analytical form for this free energy was yet only available using a Gaussian trial function for the orientation distribution function (ODF), leading, however, to a significant

  19. Constructing a multidimensional free energy surface like a spider weaving a web.

    Science.gov (United States)

    Chen, Changjun

    2017-10-15

    Complete free energy surface in the collective variable space provides important information of the reaction mechanisms of the molecules. But, sufficient sampling in the collective variable space is not easy. The space expands quickly with the number of the collective variables. To solve the problem, many methods utilize artificial biasing potentials to flatten out the original free energy surface of the molecule in the simulation. Their performances are sensitive to the definitions of the biasing potentials. Fast-growing biasing potential accelerates the sampling speed but decreases the accuracy of the free energy result. Slow-growing biasing potential gives an optimized result but needs more simulation time. In this article, we propose an alternative method. It adds the biasing potential to a representative point of the molecule in the collective variable space to improve the conformational sampling. And the free energy surface is calculated from the free energy gradient in the constrained simulation, not given by the negative of the biasing potential as previous methods. So the presented method does not require the biasing potential to remove all the barriers and basins on the free energy surface exactly. Practical applications show that the method in this work is able to produce the accurate free energy surfaces for different molecules in a short time period. The free energy errors are small in the cases of various biasing potentials. © 2017 Wiley Periodicals, Inc. © 2017 Wiley Periodicals, Inc.

  20. Free energy on a cycle graph and trigonometric deformation of heat kernel traces on odd spheres

    Science.gov (United States)

    Kan, Nahomi; Shiraishi, Kiyoshi

    2018-01-01

    We consider a possible ‘deformation’ of the trace of the heat kernel on odd dimensional spheres, motivated by the calculation of the free energy of a scalar field on a discretized circle. By using an expansion in terms of the modified Bessel functions, we obtain the values of the free energies after a suitable regularization.

  1. Designed azurins show lower reorganization free energies for intraprotein electron transfer

    DEFF Research Database (Denmark)

    Farver, Ole; Marshall, Nicholas M; Wherland, Scot

    2013-01-01

    Low reorganization free energies are necessary for fast electron transfer (ET) reactions. Hence, rational design of redox proteins with lower reorganization free energies has been a long-standing challenge, promising to yield a deeper understanding of the underlying principles of ET reactivity...

  2. Incorporating the effect of ionic strength in free energy calculations using explicit ions

    NARCIS (Netherlands)

    Donnini, S; Mark, AE; Juffer, AH; Villa, Alessandra

    2005-01-01

    The incorporation of explicit ions to mimic the effect of ionic strength or to neutralize the overall charge on a system in free energy calculations using molecular dynamics simulations is investigated. The difference in the free energy of hydration between two triosephosphate isomerase inhibitors

  3. CAN THE STABILITY OF PROTEIN MUTANTS BE PREDICTED BY FREE-ENERGY CALCULATIONS

    NARCIS (Netherlands)

    YUNYU, S; MARK, AE; WANG, CX; HUANG, FH; BERENDSEN, HJC; VANGUNSTEREN, WF

    The use of free energy simulation techniques in the study of protein stability is critically evaluated. Results from two simulations of the thermostability mutation Asn218 to Ser218 in Subtilisin are presented. It is shown that components of the free energy change can be highly sensitive to the

  4. Direct evaluation of free energy for large system through structure integration approach.

    Science.gov (United States)

    Takeuchi, Kazuhito; Tanaka, Ryohei; Yuge, Koretaka

    2015-09-30

    We propose a new approach, 'structure integration', enabling direct evaluation of configurational free energy for large systems. The present approach is based on the statistical information of lattice. Through first-principles-based simulation, we find that the present method evaluates configurational free energy accurately in disorder states above critical temperature.

  5. A general approach for defining the macroscopic free energy density of saturated porous media at finite strains under non-isothermal conditions

    International Nuclear Information System (INIS)

    Gajo, A.

    2011-01-01

    A general approach is proposed for defining the macroscopic free energy density function (and its complement, the free enthalpy) of a saturated porous medium submitted to finite deformations under non-isothermal conditions, in the case of compressible fluid and solid constituents. Reference is made to an elementary volume treated as an 'open system', moving with the solid skeleton. The proposed free energy depends on the generalised strains (namely an appropriate measure of the strain of the solid skeleton and the variation in fluid mass content) and the absolute temperatures of the solid and fluid phases (which are assumed to differ from each other for the sake of generality). This macroscopic energy proves to be a potential for the generalised stresses (namely the associated measure of the total stress and the free enthalpy of the pore fluid per unit mass) and the entropies of the solid and fluid phases. In contrast with mixture theories, the resulting free energy is not the simple sum of the free energies of the single constituents. Two simplified cases are examined in detail, i.e. the semi-linear theory (originally proposed for isothermal conditions and extended here to non-isothermal problems) and the linear theory. The proposed approach paves the way to the consistent non-isothermal-hyper-elastic-plastic modelling of saturated porous media with a compressible fluid and solid constituents. (authors)

  6. A Non-linear "Inflation-Relative Prices Variability" Relationship: Evidence from Latin America

    OpenAIRE

    Mª Ángeles Caraballo Pou; Carlos Dabús; Diego Caramuta

    2006-01-01

    This paper presents evidence on a non-linear "inflation-relative prices variability" relationship in three Latin American countries with very high inflation experiences: Argentina, Brazil and Peru. More precisely, and in contrast to results found in previous literature for similar countries, we find a non-concave relation at higher inflation regimes, i.e. when inflation rate surpasses certain threshold. This non-concavity is mainly explained by the unexpected component of inflation, which sug...

  7. Thermodynamics of metabolic pathways for penicillin production: Analysis of thermodynamic feasibility and free energy changes during fed-batch cultivation

    DEFF Research Database (Denmark)

    Pissarra, P.D.; Nielsen, Jens Bredal

    1997-01-01

    This paper describes the thermodynamic analysis of pathways related to penicillin production in Penicillium chrysogenum. First a thermodynamic feasibility analysis is performed of the L-lysine pathway of which one of the precursors for penicillin biosynthesis (alpha-aminoadipic acid......) is an intermediate. It is found that the L-lysine pathway in P. chrysogenum is thermodynamically feasible and that the calculated standard Gibbs free energy values of the two enzymes controlling the pathway flux indicate that they operate far from equilibrium. It is therefore proposed that the regulation of alpha......-aminoadipate reductase by lysine is important to maintain a high concentration of alpha-aminoadipate in order to direct the carbon flux to penicillin production. Secondly the changes in Gibbs free energy in the penicillin biosynthetic pathway during fed-batch cultivation were studied. The analysis showed that all...

  8. Free energy simulations with the AMOEBA polarizable force field and metadynamics on GPU platform.

    Science.gov (United States)

    Peng, Xiangda; Zhang, Yuebin; Chu, Huiying; Li, Guohui

    2016-03-05

    The free energy calculation library PLUMED has been incorporated into the OpenMM simulation toolkit, with the purpose to perform enhanced sampling MD simulations using the AMOEBA polarizable force field on GPU platform. Two examples, (I) the free energy profile of water pair separation (II) alanine dipeptide dihedral angle free energy surface in explicit solvent, are provided here to demonstrate the accuracy and efficiency of our implementation. The converged free energy profiles could be obtained within an affordable MD simulation time when the AMOEBA polarizable force field is employed. Moreover, the free energy surfaces estimated using the AMOEBA polarizable force field are in agreement with those calculated from experimental data and ab initio methods. Hence, the implementation in this work is reliable and would be utilized to study more complicated biological phenomena in both an accurate and efficient way. © 2015 Wiley Periodicals, Inc. © 2015 Wiley Periodicals, Inc.

  9. Reply to Comment on 'On the importance of the free energy for elasticity under pressure'

    International Nuclear Information System (INIS)

    Marcus, P M; Qiu, S L

    2004-01-01

    All criticisms by Steinle-Neumann and Cohen of the correctness of our calculations of equilibrium structure and elastic constants under pressure from the Gibbs free energy are answered and the criticisms are rejected. The difference between the free energy and the internal energy as functions of structure is described to clarify the use of the free energy. The meaning of elastic constants in a system under pressure is discussed in order to derive the basic quadratic expansion of the free energy in the strains. The coefficients in the expansion are the elastic constants under pressure and are in agreement with well-known work. We give reasons why calculations based on the Gibbs free energy are simpler and more accurate than the usual calculations based on minima of the energy at constant volume. (reply)

  10. Heavy quark free energies for three quark systems at finite temperature

    International Nuclear Information System (INIS)

    Huebner, Kay; Karsch, Frithjof; Kaczmarek, Olaf; Vogt, Oliver

    2008-01-01

    We study the free energy of static three quark systems in singlet, octet, decuplet, and average color channels in the quenched approximation and in 2-flavor QCD at finite temperature. We show that in the high temperature phase singlet and decuplet free energies of three quark systems are well described by the sum of the free energies of three diquark systems plus self-energy contributions of the three quarks. In the confining low temperature phase we find evidence for a Y-shaped flux tube in SU(3) pure gauge theory, which is less evident in 2-flavor QCD due to the onset of string breaking. We also compare the short distance behavior of octet and decuplet free energies to the free energies of single static quarks in the corresponding color representations.

  11. Free energy study of H2O, N2O5, SO2, and O3 gas sorption by water droplets/slabs

    Science.gov (United States)

    Li, Wentao; Pak, Chi Yuen; Tse, Ying-Lung Steve

    2018-04-01

    Understanding gas sorption by water in the atmosphere is an active research area because the gases can significantly alter the radiation and chemical properties of the atmosphere. We attempt to elucidate the molecular details of the gas sorption of water and three common atmospheric gases (N2O5, SO2, and O3) by water droplets/slabs in molecular dynamics simulations. The system size effects are investigated, and we show that the calculated solvation free energy decreases linearly as a function of the reciprocal of the number of water molecules from 1/215 to 1/1000 in both the slab and the droplet systems. By analyzing the infinitely large system size limit by extrapolation, we find that all our droplet results are more accurate than the slab results when compared to the experimental values. We also show how the choice of restraints in umbrella sampling can affect the sampling efficiency for the droplet systems. The free energy changes were decomposed into the energetic ΔU and entropic -TΔS contributions to reveal the molecular details of the gas sorption processes. By further decomposing ΔU into Lennard-Jones and Coulombic interactions, we observe that the ΔU trends are primarily determined by local effects due to the size of the gas molecule, charge distribution, and solvation structure around the gas molecule. Moreover, we find that there is a strong correlation between the change in the entropic contribution and the mean residence time of water, which is spatially nonlocal and related to the mobility of water.

  12. Converging ligand‐binding free energies obtained with free‐energy perturbations at the quantum mechanical level

    Science.gov (United States)

    Olsson, Martin A.; Söderhjelm, Pär

    2016-01-01

    In this article, the convergence of quantum mechanical (QM) free‐energy simulations based on molecular dynamics simulations at the molecular mechanics (MM) level has been investigated. We have estimated relative free energies for the binding of nine cyclic carboxylate ligands to the octa‐acid deep‐cavity host, including the host, the ligand, and all water molecules within 4.5 Å of the ligand in the QM calculations (158–224 atoms). We use single‐step exponential averaging (ssEA) and the non‐Boltzmann Bennett acceptance ratio (NBB) methods to estimate QM/MM free energy with the semi‐empirical PM6‐DH2X method, both based on interaction energies. We show that ssEA with cumulant expansion gives a better convergence and uses half as many QM calculations as NBB, although the two methods give consistent results. With 720,000 QM calculations per transformation, QM/MM free‐energy estimates with a precision of 1 kJ/mol can be obtained for all eight relative energies with ssEA, showing that this approach can be used to calculate converged QM/MM binding free energies for realistic systems and large QM partitions. © 2016 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc. PMID:27117350

  13. Computing the Free Energy along a Reaction Coordinate Using Rigid Body Dynamics.

    Science.gov (United States)

    Tao, Peng; Sodt, Alexander J; Shao, Yihan; König, Gerhard; Brooks, Bernard R

    2014-10-14

    The calculations of potential of mean force along complex chemical reactions or rare events pathways are of great interest because of their importance for many areas in chemistry, molecular biology, and material science. The major difficulty for free energy calculations comes from the great computational cost for adequate sampling of the system in high-energy regions, especially close to the reaction transition state. Here, we present a method, called FEG-RBD, in which the free energy gradients were obtained from rigid body dynamics simulations. Then the free energy gradients were integrated along a reference reaction pathway to calculate free energy profiles. In a given system, the reaction coordinates defining a subset of atoms (e.g., a solute, or the quantum mechanics (QM) region of a quantum mechanics/molecular mechanics simulation) are selected to form a rigid body during the simulation. The first-order derivatives (gradients) of the free energy with respect to the reaction coordinates are obtained through the integration of constraint forces within the rigid body. Each structure along the reference reaction path is separately subjected to such a rigid body simulation. The individual free energy gradients are integrated along the reference pathway to obtain the free energy profile. Test cases provided demonstrate both the strengths and weaknesses of the FEG-RBD method. The most significant benefit of this method comes from the fast convergence rate of the free energy gradient using rigid-body constraints instead of restraints. A correction to the free energy due to approximate relaxation of the rigid-body constraint is estimated and discussed. A comparison with umbrella sampling using a simple test case revealed the improved sampling efficiency of FEG-RBD by a factor of 4 on average. The enhanced efficiency makes this method effective for calculating the free energy of complex chemical reactions when the reaction coordinate can be unambiguously defined by a

  14. Solvent-assisted multistage nonequilibrium electron transfer in rigid supramolecular systems: Diabatic free energy surfaces and algorithms for numerical simulations

    Science.gov (United States)

    Feskov, Serguei V.; Ivanov, Anatoly I.

    2018-03-01

    An approach to the construction of diabatic free energy surfaces (FESs) for ultrafast electron transfer (ET) in a supramolecule with an arbitrary number of electron localization centers (redox sites) is developed, supposing that the reorganization energies for the charge transfers and shifts between all these centers are known. Dimensionality of the coordinate space required for the description of multistage ET in this supramolecular system is shown to be equal to N - 1, where N is the number of the molecular centers involved in the reaction. The proposed algorithm of FES construction employs metric properties of the coordinate space, namely, relation between the solvent reorganization energy and the distance between the two FES minima. In this space, the ET reaction coordinate zn n' associated with electron transfer between the nth and n'th centers is calculated through the projection to the direction, connecting the FES minima. The energy-gap reaction coordinates zn n' corresponding to different ET processes are not in general orthogonal so that ET between two molecular centers can create nonequilibrium distribution, not only along its own reaction coordinate but along other reaction coordinates too. This results in the influence of the preceding ET steps on the kinetics of the ensuing ET. It is important for the ensuing reaction to be ultrafast to proceed in parallel with relaxation along the ET reaction coordinates. Efficient algorithms for numerical simulation of multistage ET within the stochastic point-transition model are developed. The algorithms are based on the Brownian simulation technique with the recrossing-event detection procedure. The main advantages of the numerical method are (i) its computational complexity is linear with respect to the number of electronic states involved and (ii) calculations can be naturally parallelized up to the level of individual trajectories. The efficiency of the proposed approach is demonstrated for a model

  15. Using docking and alchemical free energy approach to determine the binding mechanism of eEF2K inhibitors and prioritizing the compound synthesis.

    Science.gov (United States)

    Wang, Qiantao; Edupuganti, Ramakrishna; Tavares, Clint D J; Dalby, Kevin N; Ren, Pengyu

    2015-01-01

    A-484954 is a known eEF2K inhibitor with submicromolar IC50 potency. However, the binding mechanism and the crystal structure of the kinase remains unknown. Here, we employ a homology eEF2K model, docking and alchemical free energy simulations to probe the binding mechanism of eEF2K, and in turn, guide the optimization of potential lead compounds. The inhibitor was docked into the ATP-binding site of a homology model first. Three different binding poses, hypothesis 1, 2, and 3, were obtained and subsequently applied to molecular dynamics (MD) based alchemical free energy simulations. The calculated relative binding free energy of the analogs of A-484954 using the binding pose of hypothesis 1 show a good correlation with the experimental IC50 values, yielding an r (2) coefficient of 0.96 after removing an outlier (compound 5). Calculations using another two poses show little correlation with experimental data, (r (2) of less than 0.5 with or without removing any outliers). Based on hypothesis 1, the calculated relative free energy suggests that bigger cyclic groups, at R1 e.g., cyclobutyl and cyclopentyl promote more favorable binding than smaller groups, such as cyclopropyl and hydrogen. Moreover, this study also demonstrates the ability of the alchemical free energy approach in combination with docking and homology modeling to prioritize compound synthesis. This can be an effective means of facilitating structure-based drug design when crystal structures are not available.

  16. Surfing the free energy landscape of flavodoxin folding

    NARCIS (Netherlands)

    Bollen, Y.J.M.

    2004-01-01

    The research described in this thesis has been carried out to obtain a better understanding of the fundamental rules describing protein folding. Protein folding is the process in which a linear chain of amino acids contracts to a compact state in which it is active. Flavodoxin from Azotobacter

  17. An approximate but efficient method to calculate free energy trends by computer simulation: Application to dihydrofolate reductase-inhibitor complexes

    Science.gov (United States)

    Gerber, Paul R.; Mark, Alan E.; van Gunsteren, Wilfred F.

    1993-06-01

    Derivatives of free energy differences have been calculated by molecular dynamics techniques. The systems under study were ternary complexes of Trimethoprim (TMP) with dihydrofolate reductases of E. coli and chicken liver, containing the cofactor NADPH. Derivatives are taken with respect to modification of TMP, with emphasis on altering the 3-, 4- and 5-substituents of the phenyl ring. A linear approximation allows the encompassing of a whole set of modifications in a single simulation, as opposed to a full perturbation calculation, which requires a separate simulation for each modification. In the case considered here, the proposed technique requires a factor of 1000 less computing effort than a full free energy perturbation calculation. For the linear approximation to yield a significant result, one has to find ways of choosing the perturbation evolution, such that the initial trend mirrors the full calculation. The generation of new atoms requires a careful treatment of the singular terms in the non-bonded interaction. The result can be represented by maps of the changed molecule, which indicate whether complex formation is favoured under movement of partial charges and change in atom polarizabilities. Comparison with experimental measurements of inhibition constants reveals fair agreement in the range of values covered. However, detailed comparison fails to show a significant correlation. Possible reasons for the most pronounced deviations are given.

  18. Surface free energy of TiC layers deposited by electrophoretic deposition (EPD)

    Science.gov (United States)

    Gorji, Mohammad Reza; Sanjabi, Sohrab

    2018-01-01

    In this study porous structure coatings of bare TiC (i.e. 20 nm, 0.7 µm and 5/45 µm) and core-shell structures of TiC/NiP synthesized through electroless plating were deposited by EPD. Room temperature surface free energy (i.e. γs) of TiC and TiC/NiP coatings were determined via measuring contact angles of distilled water and diiodemethane liquids. The effect of Ni-P shell on spreading behavior of pure copper on porous EPD structures was also investigated by high temperature wetting experiments. According to the results existence of a Ni-P layer around the TiC particles has led to roughness (i.e. at least 0.1 µm), and porosity mean length (i.e. at least 1 µm) increase. This might be related to various sizes of TiC agglomerates formed during electroless plating. It has been observed that room temperature γs changed from 44.49 to 54.12 mJ.m-2 as a consequence of particle size enlargement for TiC. The highest and lowest (67.25 and 44.49 mJ.m-2) γs were measured for TiC nanoparticles which showed 1.5 times increase in surface free energy after being plated with Ni-P. It was also observed that plating Ni-P altered non-spreading (θs > 100 o) behavior of TiC to full-spreading ((θs 0o)) which can be useful for preparation of hard coatings by infiltration sintering phenomenon. Zeta potential of EPD suspensions, morphology, phase structure and topography of as-EPD layers were investigated through Zetasizer, field emission scanning electron microscopy (FESEM), X-ray diffraction (XRD) and atomic force microscopy (AFM) instruments respectively.

  19. Effects of different cropping systems and weed management methods on free energy and content of pigments in maize

    Directory of Open Access Journals (Sweden)

    Igor Spasojević

    2014-03-01

    Full Text Available Rotation is a cropping system that has many advantages and ensures better crop growth and yielding. Its combinination with other cropping measures can ensure optimal crop density for maximal growth and photosynthesis efficiency. The aim of this study was to investigate the influence of different cropping systems: monoculture and two rotations, including maize, wheat and soybean (MSW and MWS, and different weed management methods (weed removal by hoeing, application of a full recommended herbicide dose (RD and half that dose (0.5 RD, and weedy check on weed biomass and maize growth parameters - leaf area index (LAI, free energy, contents of chlorophyll and carotenoids, grain yield, and their possible relationships in two fields of the maize hybrids ZP 677 (H1 and ZP 606 (H2. The lowest LAI and grain yield were found in monoculture, particularly in weedy check, which had relatively high weed infestation. Higher weed biomass was also observed in herbicide treated plots in monoculture. Such high competition pressure indicates a stress reflected on reduced LAI and chlorophyll content, and increased free energy and content of carotenoids. On the other hand, rotation, particularly if it is combined with the application of herbicides or hoeing, had a positive impact on yielding potential by increasing LAI and the contents of chlorophyll and carotenoids, and decreasing free energy.

  20. Exact results in nonequilibrium statistical mechanics: Formalism and applications in chemical kinetics and single-molecule free energy estimation

    Science.gov (United States)

    Adib, Artur B.

    In the last two decades or so, a collection of results in nonequilibrium statistical mechanics that departs from the traditional near-equilibrium framework introduced by Lars Onsager in 1931 has been derived, yielding new fundamental insights into far-from-equilibrium processes in general. Apart from offering a more quantitative statement of the second law of thermodynamics, some of these results---typified by the so-called "Jarzynski equality"---have also offered novel means of estimating equilibrium quantities from nonequilibrium processes, such as free energy differences from single-molecule "pulling" experiments. This thesis contributes to such efforts by offering three novel results in nonequilibrium statistical mechanics: (a) The entropic analog of the Jarzynski equality; (b) A methodology for estimating free energies from "clamp-and-release" nonequilibrium processes; and (c) A directly measurable symmetry relation in chemical kinetics similar to (but more general than) chemical detailed balance. These results share in common the feature of remaining valid outside Onsager's near-equilibrium regime, and bear direct applicability in protein folding kinetics as well as in single-molecule free energy estimation.

  1. Competing quantum effects in the free energy profiles and diffusion rates of hydrogen and deuterium molecules through clathrate hydrates.

    Science.gov (United States)

    Cendagorta, Joseph R; Powers, Anna; Hele, Timothy J H; Marsalek, Ondrej; Bačić, Zlatko; Tuckerman, Mark E

    2016-11-30

    Clathrate hydrates hold considerable promise as safe and economical materials for hydrogen storage. Here we present a quantum mechanical study of H 2 and D 2 diffusion through a hexagonal face shared by two large cages of clathrate hydrates over a wide range of temperatures. Path integral molecular dynamics simulations are used to compute the free-energy profiles for the diffusion of H 2 and D 2 as a function of temperature. Ring polymer molecular dynamics rate theory, incorporating both exact quantum statistics and approximate quantum dynamical effects, is utilized in the calculations of the H 2 and D 2 diffusion rates in a broad temperature interval. We find that the shape of the quantum free-energy profiles and their height relative to the classical free energy barriers at a given temperature, as well as the rate of diffusion, are strongly affected by competing quantum effects: above 25 K, zero-point energy (ZPE) perpendicular to the reaction path for diffusion between cavities decreases the quantum rate compared to the classical rate, whereas at lower temperatures tunneling outcompetes the ZPE and as a result the quantum rate is greater than the classical rate.

  2. Computational Study of Geometry, Solvation Free Energy, Dipole Moment, Polarizability, Hyperpolarizability and Molecular Properties of 2-Methylimidazole

    Directory of Open Access Journals (Sweden)

    Mohammad Firoz Khan

    2016-12-01

    Full Text Available Ab initio calculations were carried out to study the geometry, solvation free energy, dipole moment, molecular electrostatic potential (MESP, Mulliken and Natural charge distribution, polarizability, hyperpolarizability, Natural Bond Orbital (NBO energetic and different molecular properties like global reactivity descriptors (chemical hardness, softness, chemical potential, electronegativity, electrophilicity index of 2-methylimidazole. B3LYP/6-31G(d,p level of theory was used to optimize the structure both in the gas phase and in solution. The solvation free energy, dipole moment and molecular properties were calculated by applying the Solvation Model on Density (SMD in four solvent systems, namely water, dimethylsulfoxide (DMSO, n-octanol and chloroform. The computed bond distances, bond angles and dihedral angles of 2-methylimidazole agreed reasonably well with the experimental data except for C(2-N(1, C(4-C(5 and N(1-H(7 bond lengths and N(1-C(5-C(4 bond angle. The solvation free energy, dipole moment, polarizability, first order hyperpolarizability, chemical potential, electronegativity and electrophilicity index of 2-methylimidazole increased on going from non-polar to polar solvents. Chemical hardness also increased with increasing polarity of the solvent and the opposite relation was found in the case of softness. These results provide better understanding of the stability and reactivity of 2-methylimidazole in different solvent systems.

  3. Magnon specific heat and free energy of Heisenberg ferromagnetic single-walled nanotubes: Green's function approach

    Energy Technology Data Exchange (ETDEWEB)

    Mi, Bin-Zhou, E-mail: mbzfjerry2008@126.com [Department of Basic Curriculum, North China Institute of Science and Technology, Beijing 101601 (China); Department of Physics, School of Mathematics and Physics, University of Science and Technology Beijing, Beijing 100083 (China); Zhai, Liang-Jun [The School of Mathematics and Physics, Jiangsu University of Technology, Changzhou 213001 (China); Hua, Ling-Ling [Department of Basic Curriculum, North China Institute of Science and Technology, Beijing 101601 (China)

    2016-01-15

    The effect of magnetic spin correlation on the thermodynamic properties of Heisenberg ferromagnetic single-walled nanotubes are comprehensively investigated by use of the double-time Green's function method. The influence of temperature, spin quantum number, diameter of the tube, anisotropy strength and external magnetic field to internal energy, free energy, and magnon specific heat are carefully calculated. Compared to the mean field approximation, the consideration of the magnetic correlation effect significantly improves the internal energy values at finite temperature, while it does not so near zero temperature, and this effect is related to the diameter of the tube, anisotropy strength, and spin quantum number. The magnetic correlation effect lowers the internal energy at finite temperature. As a natural consequence of the reduction of the internal energy, the specific heat is reduced, and the free energy is elevated. - Highlights: • Magnon specific heat and free energy of Heisenberg ferromagnetic single-walled nanotubes (HFM-SWNTs) are investigated. • The magnetic correlations effect has a considerable contribution to the thermodynamics properties of HFM-SWNTs. • Magnetic correlation effects are always to lower the internal energy at finite temperature. • At Curie point, magnetic correlation energy is much less than zero. • The peak values of magnon specific heat curves rise and shift right towards higher temperatures with the diameter of tubes, the anisotropy strength, and the spin quantum number rising.

  4. Computational Approach to Explore the B/A Junction Free Energy in DNA.

    Science.gov (United States)

    Kulkarni, Mandar; Mukherjee, Arnab

    2016-01-04

    Protein-DNA interactions induce conformational changes in DNA such as B- to A-form transitions at a local level. Such transitions are associated with a junction free energy cost at the boundary of two different conformations in a DNA molecule. In this study, we performed umbrella sampling simulations to find the free energy values of the B-A transition at the dinucleotide and trinucleotide level of DNA. Using a combination of dinucleotide and trinucleotide free energy costs obtained from simulations, we calculated the B/A junction free energy. Our study shows that the B/A junction free energy is 0.52 kcal mol(-1) for the A-philic GG step and 1.59 kcal mol(-1) for the B-philic AA step. This observation is in agreement with experimentally derived values. After excluding junction effects, we obtained an absolute free energy cost for the B- to A-form conversion for all the dinucleotide steps. These absolute free energies may be used for predicting the propensity of structural transitions in DNA. © 2016 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  5. The inverted free energy landscape of an intrinsically disordered peptide by simulations and experiments.

    Science.gov (United States)

    Granata, Daniele; Baftizadeh, Fahimeh; Habchi, Johnny; Galvagnion, Celine; De Simone, Alfonso; Camilloni, Carlo; Laio, Alessandro; Vendruscolo, Michele

    2015-10-26

    The free energy landscape theory has been very successful in rationalizing the folding behaviour of globular proteins, as this representation provides intuitive information on the number of states involved in the folding process, their populations and pathways of interconversion. We extend here this formalism to the case of the Aβ40 peptide, a 40-residue intrinsically disordered protein fragment associated with Alzheimer's disease. By using an advanced sampling technique that enables free energy calculations to reach convergence also in the case of highly disordered states of proteins, we provide a precise structural characterization of the free energy landscape of this peptide. We find that such landscape has inverted features with respect to those typical of folded proteins. While the global free energy minimum consists of highly disordered structures, higher free energy regions correspond to a large variety of transiently structured conformations with secondary structure elements arranged in several different manners, and are not separated from each other by sizeable free energy barriers. From this peculiar structure of the free energy landscape we predict that this peptide should become more structured and not only more compact, with increasing temperatures, and we show that this is the case through a series of biophysical measurements.

  6. The elastic free energy of a tandem modular protein under force.

    Science.gov (United States)

    Valle-Orero, Jessica; Eckels, Edward C; Stirnemann, Guillaume; Popa, Ionel; Berkovich, Ronen; Fernandez, Julio M

    2015-05-01

    Recent studies have provided a theoretical framework for including entropic elasticity in the free energy landscape of proteins under mechanical force. Accounting for entropic elasticity using polymer physics models has helped explain the hopping behavior seen in single molecule experiments in the low force regime. Here, we expand on the construction of the free energy of a single protein domain under force proposed by Berkovich et al. to provide a free energy landscape for N tandem domains along a continuous polypeptide. Calculation of the free energy of individual domains followed by their concatenation provides a continuous free energy landscape whose curvature is dominated by the worm-like chain at forces below 20 pN. We have validated our free energy model using Brownian dynamics and reproduce key features of protein folding. This free energy model can predict the effects of changes in the elastic properties of a multidomain protein as a consequence of biological modifications such as phosphorylation or the formation of disulfide bonds. This work lays the foundations for the modeling of tissue elasticity, which is largely determined by the properties of tandem polyproteins. Copyright © 2015. Published by Elsevier Inc.

  7. Inequalities for magnetic-flux free energies and confinement in lattice gauge theories

    International Nuclear Information System (INIS)

    Yoneya, T.

    1982-01-01

    Rigorous inequalities among magnetic-flux free energies of tori with varying diameters are derived in lattice gauge theories. From the inequalities, it follows that if the magnetic-flux free energy vanishes in the limit of large uniform dilatation of a torus, the free energy must always decrease exponentially with the area of the cross section of the torus. The latter property is known to be sufficient for permanent confinement of static quarks. As a consequence of this property, a lower bound V(R) >= const x R for the static quark-antiquark potential is obtained in three-dimensional U(n) lattice gauge theory for sufficiently large R. (orig.)

  8. Quantifying the linear and nonlinear relations between the urban form fragmentation and the carbon emission distribution

    Science.gov (United States)

    Zuo, S.; Dai, S.; Ren, Y.; Yu, Z.

    2017-12-01

    Scientifically revealing the spatial heterogeneity and the relationship between the fragmentation of urban landscape and the direct carbon emissions are of great significance to land management and urban planning. In fact, the linear and nonlinear effects among the various factors resulted in the carbon emission spatial map. However, there is lack of the studies on the direct and indirect relations between the carbon emission and the city functional spatial form changes, which could not be reflected by the land use change. The linear strength and direction of the single factor could be calculated through the correlation and Geographically Weighted Regression (GWR) analysis, the nonlinear power of one factor and the interaction power of each two factors could be quantified by the Geodetector analysis. Therefore, we compared the landscape fragmentation metrics of the urban land cover and functional district patches to characterize the landscape form and then revealed the relations between the landscape fragmentation level and the direct the carbon emissions based on the three methods. The results showed that fragmentation decreased and the fragmented patches clustered at the coarser resolution. The direct CO2 emission density and the population density increased when the fragmentation level aggregated. The correlation analysis indicated the weak linear relation between them. The spatial variation of GWR output indicated the fragmentation indicator (MESH) had the positive influence on the carbon emission located in the relatively high emission region, and the negative effects regions accounted for the small part of the area. The Geodetector which explores the nonlinear relation identified the DIVISION and MESH as the most powerful direct factor for the land cover patches, NP and PD for the functional district patches, and the interactions between fragmentation indicator (MESH) and urban sprawl metrics (PUA and DIS) had the greatly increased explanation powers on the

  9. Catchment organisation, free energy dynamics and network control on critical zone water flows

    Science.gov (United States)

    Zehe, E.; Ehret, U.; Kleidon, A.; Jackisch, C.; Scherer, U.; Blume, T.

    2012-04-01

    processes using the behavioural system architecture and small perturbations and compare them with respect to their efficiency to dissipate free energy which is equivalent to produce entropy. The study will present the underlying theory and discuss simulation results with respect to the following core hypotheses: H1: A macro scale configuration of a hydro-geo-ecosystem, is in stationary non equilibrium closer to a functional optimum as other possible configurations, if it "dissipates" more of the available free energy to maintain the stationary cycles that redistribute and export mass and energy within/from the system. This implies (I1) that the system approaches faster a dynamic equilibrium state characterised by a minimum in free energy, and less free energy from persistent gradients is available to perform work in the system. H2: Macroscopically connected flow networks enhance redistribution of mass against macroscale gradients and thus dissipation of free energy, because they minimise local energy dissipation per unit mass flow along the flow path. This implies (I2) mechanic stability of the flow network, of the textural storage elements and thus of the entire system against frequent disturbances under stationary conditions.

  10. Linear and nonlinear physics of the magnetoacoustic cyclotron instability of fusion-born ions in relation to ion cyclotron emission

    Energy Technology Data Exchange (ETDEWEB)

    Carbajal, L., E-mail: L.Carbajal-Gomez@warwick.ac.uk; Cook, J. W. S. [Centre for Fusion, Space and Astrophysics, Department of Physics, The University of Warwick, Coventry CV4 7AL (United Kingdom); Dendy, R. O. [EURATOM/CCFE Fusion Association, Culham Science Centre, Abingdon OX14 3DB, Oxfordshire (United Kingdom); Centre for Fusion, Space and Astrophysics, Department of Physics, The University of Warwick, Coventry CV4 7AL (United Kingdom); Chapman, S. C. [Centre for Fusion, Space and Astrophysics, Department of Physics, The University of Warwick, Coventry CV4 7AL (United Kingdom); Department of Mathematics and Statistics, University of Tromsø, N-9037, Tromsø (Norway); Max Planck Institute for the Physics of Complex Systems, D-01187, Dresden (Germany)

    2014-01-15

    The magnetoacoustic cyclotron instability (MCI) probably underlies observations of ion cyclotron emission (ICE) from energetic ion populations in tokamak plasmas, including fusion-born alpha-particles in JET and TFTR [Dendy et al., Nucl. Fusion 35, 1733 (1995)]. ICE is a potential diagnostic for lost alpha-particles in ITER; furthermore, the MCI is representative of a class of collective instabilities, which may result in the partial channelling of the free energy of energetic ions into radiation, and away from collisional heating of the plasma. Deep understanding of the MCI is thus of substantial practical interest for fusion, and the hybrid approximation for the plasma, where ions are treated as particles and electrons as a neutralising massless fluid, offers an attractive way forward. The hybrid simulations presented here access MCI physics that arises on timescales longer than can be addressed by fully kinetic particle-in-cell simulations and by analytical linear theory, which the present simulations largely corroborate. Our results go further than previous studies by entering into the nonlinear stage of the MCI, which shows novel features. These include stronger drive at low cyclotron harmonics, the re-energisation of the alpha-particle population, self-modulation of the phase shift between the electrostatic and electromagnetic components, and coupling between low and high frequency modes of the excited electromagnetic field.

  11. A GPU-Accelerated Parameter Interpolation Thermodynamic Integration Free Energy Method.

    Science.gov (United States)

    Giese, Timothy J; York, Darrin M

    2018-03-13

    There has been a resurgence of interest in free energy methods motivated by the performance enhancements offered by molecular dynamics (MD) software written for specialized hardware, such as graphics processing units (GPUs). In this work, we exploit the properties of a parameter-interpolated thermodynamic integration (PI-TI) method to connect states by their molecular mechanical (MM) parameter values. This pathway is shown to be better behaved for Mg 2+ → Ca 2+ transformations than traditional linear alchemical pathways (with and without soft-core potentials). The PI-TI method has the practical advantage that no modification of the MD code is required to propagate the dynamics, and unlike with linear alchemical mixing, only one electrostatic evaluation is needed (e.g., single call to particle-mesh Ewald) leading to better performance. In the case of AMBER, this enables all the performance benefits of GPU-acceleration to be realized, in addition to unlocking the full spectrum of features available within the MD software, such as Hamiltonian replica exchange (HREM). The TI derivative evaluation can be accomplished efficiently in a post-processing step by reanalyzing the statistically independent trajectory frames in parallel for high throughput. We also show how one can evaluate the particle mesh Ewald contribution to the TI derivative evaluation without needing to perform two reciprocal space calculations. We apply the PI-TI method with HREM on GPUs in AMBER to predict p K a values in double stranded RNA molecules and make comparison with experiments. Convergence to under 0.25 units for these systems required 100 ns or more of sampling per window and coupling of windows with HREM. We find that MM charges derived from ab initio QM/MM fragment calculations improve the agreement between calculation and experimental results.

  12. Enchanced total dose damage in junction field effect transistors and related linear integrated circuits

    International Nuclear Information System (INIS)

    Flament, O.; Autran, J.L.; Roche, P.; Leray, J.L.; Musseau, O.

    1996-01-01

    Enhanced total dose damage of Junction Field-effect Transistors (JFETs) due to low dose rate and/or elevated temperature has been investigated for elementary p-channel structures fabricated on bulk and SOI substrates as well as for related linear integrated circuits. All these devices were fabricated with conventional junction isolation (field oxide). Large increases in damage have been revealed by performing high temperature and/or low dose rate irradiations. These results are consistent with previous studies concerning bipolar field oxides under low-field conditions. They suggest that the transport of radiation-induced holes through the oxide is the underlying mechanism. Such an enhanced degradation must be taken into account for low dose rate effects on linear integrated circuits

  13. Modeling Loop Reorganization Free Energies of Acetylcholinesterase: A Comparison of Explicit and Implicit Solvent Models

    National Research Council Canada - National Science Library

    Olson, Mark

    2004-01-01

    ... screening of charge-charge interactions. This paper compares different solvent models applied to the problem of estimating the free-energy difference between two loop conformations in acetylcholinesterase...

  14. Relationship between wave energy and free energy from pickup ions in the Comet Halley environment

    Science.gov (United States)

    Huddleston, D. E.; Johnstone, A. D.

    1992-01-01

    The free energy available from the implanted heavy ion population at Comet Halley is calculated by assuming that the initial unstable velocity space ring distribution of the ions evolves toward a bispherical shell. Ultimately this free energy adds to the turbulence in the solar wind. Upstream and downstream free energies are obtained separately for the conditions observed along the Giotto spacecraft trajectory. The results indicate that the waves are mostly upstream propagating in the solar wind frame. The total free energy density always exceeds the measured wave energy density because, as expected in the nonlinear process of ion scattering, the available energy is not all immediately released. An estimate of the amount which has been released can be obtained from the measured oxygen ion distributions and again it exceeds that observed. The theoretical analysis is extended to calculate the k spectrum of the cometary-ion-generated turbulence.

  15. The free energy of locking a ring: Changing a deoxyribonucleoside to a locked nucleic acid.

    Science.gov (United States)

    Xu, You; Villa, Alessandra; Nilsson, Lennart

    2017-06-05

    Locked nucleic acid (LNA), a modified nucleoside which contains a bridging group across the ribose ring, improves the stability of DNA/RNA duplexes significantly, and therefore is of interest in biotechnology and gene therapy applications. In this study, we investigate the free energy change between LNA and DNA nucleosides. The transformation requires the breaking of the bridging group across the ribose ring, a problematic transformation in free energy calculations. To address this, we have developed a 3-step (easy to implement) and a 1-step protocol (more efficient, but more complicated to setup), for single and dual topologies in classical molecular dynamics simulations, using the Bennett Acceptance Ratio method to calculate the free energy. We validate the approach on the solvation free energy difference for the nucleosides thymidine, cytosine, and 5-methyl-cytosine. © 2017 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc. © 2017 The Authors. Journal of Computational Chemistry Published by Wiley Periodicals, Inc.

  16. The calculation of surface free energy based on embedded atom method for solid nickel

    International Nuclear Information System (INIS)

    Luo Wenhua; Hu Wangyu; Su Kalin; Liu Fusheng

    2013-01-01

    Highlights: ► A new solution for accurate prediction of surface free energy based on embedded atom method was proposed. ► The temperature dependent anisotropic surface energy of solid nickel was obtained. ► In isotropic environment, the approach does not change most predictions of bulk material properties. - Abstract: Accurate prediction of surface free energy of crystalline metals is a challenging task. The theory calculations based on embedded atom method potentials often underestimate surface free energy of metals. With an analytical charge density correction to the argument of the embedding energy of embedded atom method, an approach to improve the prediction for surface free energy is presented. This approach is applied to calculate the temperature dependent anisotropic surface energy of bulk nickel and surface energies of nickel nanoparticles, and the obtained results are in good agreement with available experimental data.

  17. An asymptotic formula for the free energy density of ideal quantum gases

    International Nuclear Information System (INIS)

    Mackowiak, J.

    1988-01-01

    It is shown that the expressions for the free energy density of ideal quantum gases in the canonical and grand canonical ensembles, are identical up to additive terms which vanish in the thermodynamic limit. (orig.)

  18. Efficient free energy calculations for compounds with multiple stable conformations separated by high energy barriers

    NARCIS (Netherlands)

    Hritz, J.; Oostenbrink, C.

    2009-01-01

    Compounds with high intramolecular energy barriers represent challenging targets for free energy calculations because of the difficulty to obtain sufficient conformational sampling. Existing approaches are therefore computationally very demanding, thus preventing practical applications for such

  19. A free energy study of the liquid-liquid phase transition of the Jagla ...

    Indian Academy of Sciences (India)

    Appendix” preliminary free energy surface calculations for select parameterizations of the generalized family of Jagla potentials spanning from the original (anomalous,water-like) Jagla model to the Lennard-Jones model. These calculations ...

  20. Free Energy Minimization Calculation of Complex Chemical Equilibria. Reduction of Silicon Dioxide with Carbon at High Temperature.

    Science.gov (United States)

    Wai, C. M.; Hutchinson, S. G.

    1989-01-01

    Discusses the calculation of free energy in reactions between silicon dioxide and carbon. Describes several computer programs for calculating the free energy minimization and their uses in chemistry classrooms. Lists 16 references. (YP)

  1. Assignment of Side-Chain Conformation Using Adiabatic Energy Mapping, Free Energy Perturbation, and Molecular Dynamic Simulations

    DEFF Research Database (Denmark)

    Frimurer, Thomas M.; Günther, Peter H.; Sørensen, Morten Dahl

    1999-01-01

    adiabatic mapping, conformational change, essentialdynamics, free energy simulations, Kunitz type inhibitor *ga3(VI)......adiabatic mapping, conformational change, essentialdynamics, free energy simulations, Kunitz type inhibitor *ga3(VI)...

  2. Free energy diagram for the heterogeneous enzymatic hydrolysis of glycosidic bonds in cellulose

    DEFF Research Database (Denmark)

    Westh, Peter; Cruys-Bagger, Nicolaj; Sørensen, Trine Holst

    2015-01-01

    for all stable and activated complexes defined by the reaction scheme, and hence propose a free energy diagram for the full heterogeneous process. For other Cel7A enzymes, including variants with and without carbohydrate binding module (CBM), we obtained activation parameters for the association...... no influence on the transition state for association, but increased the free energy barrier for dissociation. Hence, the CBM appeared to promote the stability of the complex by delaying dissociation rather than accelerating association....

  3. Phase field modelling of precipitate morphologies in systems with tetragonal interfacial free energy anisotropy

    OpenAIRE

    Roy, Arijit; Gururajan, M P

    2017-01-01

    A wide variety of morphologies arise due to the tetragonal anisotropy in interfacial free energy. In this paper, we report on a family of Extended Cahn-Hilliard (ECH) models for incorporating tetragonal anisotropy in interfacial free energy. We list the non-zero and independent parameters that are introduced in our model and list the constraints on them. For appropriate choice of these parameters, our model can produce a many of the morphologies seen in tetragonal systems such as di-pyramids,...

  4. Calculation of the Local Free Energy Landscape in the Restricted Region by the Modified Tomographic Method.

    Science.gov (United States)

    Chen, Changjun

    2016-03-31

    The free energy landscape is the most important information in the study of the reaction mechanisms of the molecules. However, it is difficult to calculate. In a large collective variable space, a molecule must take a long time to obtain the sufficient sampling during the simulation. To save the calculation quantity, decreasing the sampling region and constructing the local free energy landscape is required in practice. However, the restricted region in the collective variable space may have an irregular shape. Simply restricting one or more collective variables of the molecule cannot satisfy the requirement. In this paper, we propose a modified tomographic method to perform the simulation. First, it divides the restricted region by some hyperplanes and connects the centers of hyperplanes together by a curve. Second, it forces the molecule to sample on the curve and the hyperplanes in the simulation and calculates the free energy data on them. Finally, all the free energy data are combined together to form the local free energy landscape. Without consideration of the area outside the restricted region, this free energy calculation can be more efficient. By this method, one can further optimize the path quickly in the collective variable space.

  5. Chemical Denaturants Smoothen Ruggedness on the Free Energy Landscape of Protein Folding.

    Science.gov (United States)

    Malhotra, Pooja; Jethva, Prashant N; Udgaonkar, Jayant B

    2017-08-08

    To characterize experimentally the ruggedness of the free energy landscape of protein folding is challenging, because the distributed small free energy barriers are usually dominated by one, or a few, large activation free energy barriers. This study delineates changes in the roughness of the free energy landscape by making use of the observation that a decrease in ruggedness is accompanied invariably by an increase in folding cooperativity. Hydrogen exchange (HX) coupled to mass spectrometry was used to detect transient sampling of local energy minima and the global unfolded state on the free energy landscape of the small protein single-chain monellin. Under native conditions, local noncooperative openings result in interconversions between Boltzmann-distributed intermediate states, populated on an extremely rugged "uphill" energy landscape. The cooperativity of these interconversions was increased by selectively destabilizing the native state via mutations, and further by the addition of a chemical denaturant. The perturbation of stability alone resulted in seven backbone amide sites exchanging cooperatively. The size of the cooperatively exchanging and/or unfolding unit did not depend on the extent of protein destabilization. Only upon the addition of a denaturant to a destabilized mutant variant did seven additional backbone amide sites exchange cooperatively. Segmentwise analysis of the HX kinetics of the mutant variants further confirmed that the observed increase in cooperativity was due to the smoothing of the ruggedness of the free energy landscape of folding of the protein by the chemical denaturant.

  6. Metadyn View: Fast web-based viewer of free energy surfaces calculated by metadynamics

    Science.gov (United States)

    Hošek, Petr; Spiwok, Vojtěch

    2016-01-01

    Metadynamics is a highly successful enhanced sampling technique for simulation of molecular processes and prediction of their free energy surfaces. An in-depth analysis of data obtained by this method is as important as the simulation itself. Although there are several tools to compute free energy surfaces from metadynamics data, they usually lack user friendliness and a build-in visualization part. Here we introduce Metadyn View as a fast and user friendly viewer of bias potential/free energy surfaces calculated by metadynamics in Plumed package. It is based on modern web technologies including HTML5, JavaScript and Cascade Style Sheets (CSS). It can be used by visiting the web site and uploading a HILLS file. It calculates the bias potential/free energy surface on the client-side, so it can run online or offline without necessity to install additional web engines. Moreover, it includes tools for measurement of free energies and free energy differences and data/image export.

  7. Origin of parameter degeneracy and molecular shape relationships in geometric-flow calculations of solvation free energies

    Energy Technology Data Exchange (ETDEWEB)

    Daily, Michael D. [Fundamental and Computational Sciences Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352 (United States); Chun, Jaehun [Energy and Environment Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352 (United States); Heredia-Langner, Alejandro [National Security Directorate, Pacific Northwest National Laboratory, Richland, Washington 99352 (United States); Wei, Guowei [Department of Mathematics, Michigan State University, East Lansing, Michigan 48824 (United States); Baker, Nathan A. [Computational and Statistical Analytics Division, Pacific Northwest National Laboratory, Richland, Washington 99352 (United States)

    2013-11-28

    Implicit solvent models are important tools for calculating solvation free energies for chemical and biophysical studies since they require fewer computational resources but can achieve accuracy comparable to that of explicit-solvent models. In past papers, geometric flow-based solvation models have been established for solvation analysis of small and large compounds. In the present work, the use of realistic experiment-based parameter choices for the geometric flow models is studied. We find that the experimental parameters of solvent internal pressure p = 172 MPa and surface tension γ = 72 mN/m produce solvation free energies within 1 RT of the global minimum root-mean-squared deviation from experimental data over the expanded set. Our results demonstrate that experimental values can be used for geometric flow solvent model parameters, thus eliminating the need for additional parameterization. We also examine the correlations between optimal values of p and γ which are strongly anti-correlated. Geometric analysis of the small molecule test set shows that these results are inter-connected with an approximately linear relationship between area and volume in the range of molecular sizes spanned by the data set. In spite of this considerable degeneracy between the surface tension and pressure terms in the model, both terms are important for the broader applicability of the model.

  8. No evidence that mRNAs have lower folding free energies than random sequences with the same dinucleotide distribution

    DEFF Research Database (Denmark)

    Workman, Christopher; Krogh, Anders Stærmose

    1999-01-01

    This work investigates whether mRNA has a lower estimated folding free energy than random sequences. The free energy estimates are calculated by the mfold program for prediction of RNA secondary structures. For a set of 46 mRNAs it is shown that the predicted free energy is not significantly diff...

  9. Exact asymptotic relations for the effective response of linear viscoelastic heterogeneous media

    Science.gov (United States)

    Gallican, Valentin; Brenner, Renald; Suquet, Pierre

    2017-11-01

    This article addresses the asymptotic response of viscoelastic heterogeneous media in the frequency domain, at high and low frequencies, for different types of elementary linear viscoelastic constituents. By resorting to stationary principles for complex viscoelasticity and adopting a classification of the viscoelastic behaviours based on the nature of their asymptotic regimes, either elastic or viscous, four exact relations are obtained on the overall viscoelastic complex moduli in each case. Two relations are related to the asymptotic uncoupled heterogeneous problems, while the two remaining ones result from the viscoelastic coupling that manifests itself in the transient regime. These results also provide exact conditions on certain integrals in time of the effective relaxation spectrum. This general setting encompasses the results obtained in preceding studies on mixtures of Maxwell constituents [1,2]. xml:lang="fr"

  10. General formulae for polarization observables in deuteron electrodisintegration and linear relations

    International Nuclear Information System (INIS)

    Arenhoevel, H.; Leidemann, W.; Tomusiak, E.L.

    1993-01-01

    Formal expressions are derived for all possible polarization observables in deuteron electrodisintegration with longitudinally polarized incoming electrons, oriented deuteron targets and polarization analysis of outgoing nucleons. They are given in terms of general structure functions which can be determined experimentally. These structure functions are Hermitean forms of the T-matrix elements which, in principle, allow the determination of all T-matrix elements up to an arbitrary common phase. Since the set of structure functions is overcomplete, linear relations among various structure functions exist which are derived explicitly

  11. Assessing the stability of free-energy perturbation calculations by performing variations in the method

    Science.gov (United States)

    Manzoni, Francesco; Ryde, Ulf

    2018-03-01

    We have calculated relative binding affinities for eight tetrafluorophenyl-triazole-thiogalactoside inhibitors of galectin-3 with the alchemical free-energy perturbation approach. We obtain a mean absolute deviation from experimental estimates of only 2-3 kJ/mol and a correlation coefficient (R 2) of 0.5-0.8 for seven relative affinities spanning a range of up to 11 kJ/mol. We also studied the effect of using different methods to calculate the charges of the inhibitor and different sizes of the perturbed group (the atoms that are described by soft-core potentials and are allowed to have differing coordinates). However, the various approaches gave rather similar results and it is not possible to point out one approach as consistently and significantly better than the others. Instead, we suggest that such small and reasonable variations in the computational method can be used to check how stable the calculated results are and to obtain a more accurate estimate of the uncertainty than if performing only one calculation with a single computational setup.

  12. A new approach to the estimation of surface free energy based on Vickers microhardness data

    Directory of Open Access Journals (Sweden)

    2009-03-01

    Full Text Available A relation between surface free energy (σMHV and Meyer’s lines cut-values has been established using Vickers microhardness (MHV method and empirical physical laws. This relation allows the calculation of σMHV only from MHV data. The parameters required are Meyer’s lines cut-values and the mean value of diagonal length of the impression at different loads applied (drealmean. Our study of 12 samples of ultra high molecular weight polyethylene (PE-UHMW showed that the new approach is applicable when the slope value of Meyer’s lines equals 2 (i.e. n = 2. A γ-60Co source was used for the irradiation of 11 samples (one of the samples investigated is un-irradiated at room temperature in air. Doses of 1, 2, 5, 10, 20, 50, 100, 200, 500, 1000 and 1500 kGy were applied. The values of σMHV obtained are in a good agreement with the literature. The dependence of σMHV on the dose applied strictly corresponds to the radiation effects theory. MHV was measured at seven different loads – 0.0123, 0.0245, 0.049, 0.098, 0.196, 0.392, 0.785 N at a loading time of 30 s.

  13. Computational scheme for pH-dependent binding free energy calculation with explicit solvent.

    Science.gov (United States)

    Lee, Juyong; Miller, Benjamin T; Brooks, Bernard R

    2016-01-01

    We present a computational scheme to compute the pH-dependence of binding free energy with explicit solvent. Despite the importance of pH, the effect of pH has been generally neglected in binding free energy calculations because of a lack of accurate methods to model it. To address this limitation, we use a constant-pH methodology to obtain a true ensemble of multiple protonation states of a titratable system at a given pH and analyze the ensemble using the Bennett acceptance ratio (BAR) method. The constant pH method is based on the combination of enveloping distribution sampling (EDS) with the Hamiltonian replica exchange method (HREM), which yields an accurate semi-grand canonical ensemble of a titratable system. By considering the free energy change of constraining multiple protonation states to a single state or releasing a single protonation state to multiple states, the pH dependent binding free energy profile can be obtained. We perform benchmark simulations of a host-guest system: cucurbit[7]uril (CB[7]) and benzimidazole (BZ). BZ experiences a large pKa shift upon complex formation. The pH-dependent binding free energy profiles of the benchmark system are obtained with three different long-range interaction calculation schemes: a cutoff, the particle mesh Ewald (PME), and the isotropic periodic sum (IPS) method. Our scheme captures the pH-dependent behavior of binding free energy successfully. Absolute binding free energy values obtained with the PME and IPS methods are consistent, while cutoff method results are off by 2 kcal mol(-1) . We also discuss the characteristics of three long-range interaction calculation methods for constant-pH simulations. © 2015 The Protein Society.

  14. Improved free-energy landscape reconstruction of bacteriorhodopsin highlights local variations in unfolding energy.

    Science.gov (United States)

    Heenan, Patrick R; Yu, Hao; Siewny, Matthew G W; Perkins, Thomas T

    2018-03-28

    Precisely quantifying the energetics that drive the folding of membrane proteins into a lipid bilayer remains challenging. More than 15 years ago, atomic force microscopy (AFM) emerged as a powerful tool to mechanically extract individual membrane proteins from a lipid bilayer. Concurrently, fluctuation theorems, such as the Jarzynski equality, were applied to deduce equilibrium free energies (ΔG 0 ) from non-equilibrium single-molecule force spectroscopy records. The combination of these two advances in single-molecule studies deduced the free-energy of the model membrane protein bacteriorhodopsin in its native lipid bilayer. To elucidate this free-energy landscape at a higher resolution, we applied two recent developments. First, as an input to the reconstruction, we used force-extension curves acquired with a 100-fold higher time resolution and 10-fold higher force precision than traditional AFM studies of membrane proteins. Next, by using an inverse Weierstrass transform and the Jarzynski equality, we removed the free energy associated with the force probe and determined the molecular free-energy landscape of the molecule under study, bacteriorhodopsin. The resulting landscape yielded an average unfolding free energy per amino acid (aa) of 1.0 ± 0.1 kcal/mol, in agreement with past single-molecule studies. Moreover, on a smaller spatial scale, this high-resolution landscape also agreed with an equilibrium measurement of a particular three-aa transition in bacteriorhodopsin that yielded 2.7 kcal/mol/aa, an unexpectedly high value. Hence, while average unfolding ΔG 0 per aa is a useful metric, the derived high-resolution landscape details significant local variation from the mean. More generally, we demonstrated that, as anticipated, the inverse Weierstrass transform is an efficient means to reconstruct free-energy landscapes from AFM data.

  15. Properties of linear integral equations related to the six-vertex model with disorder parameter II

    International Nuclear Information System (INIS)

    Boos, Hermann; Göhmann, Frank

    2012-01-01

    We study certain functions arising in the context of the calculation of correlation functions of the XXZ spin chain and of integrable field theories related to various scaling limits of the underlying six-vertex model. We show that several of these functions that are related to linear integral equations can be obtained by acting with (deformed) difference operators on a master function Φ. The latter is defined in terms of a functional equation and of its asymptotic behavior. Concentrating on the so-called temperature case, we show that these conditions uniquely determine the high-temperature series expansions of the master function. This provides an efficient calculation scheme for the high-temperature expansions of the derived functions as well. (paper)

  16. Binding free energy and counterion release for adsorption of the antimicrobial peptide lactoferricin B on a POPG membrane

    Science.gov (United States)

    Tolokh, Igor S.; Vivcharuk, Victor; Tomberli, Bruno; Gray, C. G.

    2009-09-01

    Molecular dynamics (MD) simulations are used to study the interaction of an anionic palmitoyl-oleoyl-phosphatidylglycerol (POPG) bilayer with the cationic antimicrobial peptide bovine lactoferricin (LFCinB) in a 100 mM NaCl solution at 310 K. The interaction of LFCinB with a POPG bilayer is employed as a model system for studying the details of membrane adsorption selectivity of cationic antimicrobial peptides. Seventy eight 4 ns MD production run trajectories of the equilibrated system, with six restrained orientations of LFCinB at 13 different separations from the POPG membrane, are generated to determine the free energy profile for the peptide as a function of the distance between LFCinB and the membrane surface. To calculate the profile for this relatively large system, a variant of constrained MD and thermodynamic integration is used. A simplified method for relating the free energy profile to the LFCinB-POPG membrane binding constant is employed to predict a free energy of adsorption of -5.4±1.3kcal/mol and a corresponding maximum adsorption binding force of about 58 pN. We analyze the results using Poisson-Boltzmann theory. We find the peptide-membrane attraction to be dominated by the entropy increase due to the release of counterions and polarized water from the region between the charged membrane and peptide, as the two approach each other. We contrast these results with those found earlier for adsorption of LFCinB on the mammalianlike palmitoyl-oleoyl-phosphatidylcholine membrane.

  17. Comment on "Inference with minimal Gibbs free energy in information field theory".

    Science.gov (United States)

    Iatsenko, D; Stefanovska, A; McClintock, P V E

    2012-03-01

    Enßlin and Weig [Phys. Rev. E 82, 051112 (2010)] have introduced a "minimum Gibbs free energy" (MGFE) approach for estimation of the mean signal and signal uncertainty in Bayesian inference problems: it aims to combine the maximum a posteriori (MAP) and maximum entropy (ME) principles. We point out, however, that there are some important questions to be clarified before the new approach can be considered fully justified, and therefore able to be used with confidence. In particular, after obtaining a Gaussian approximation to the posterior in terms of the MGFE at some temperature T, this approximation should always be raised to the power of T to yield a reliable estimate. In addition, we show explicitly that MGFE indeed incorporates the MAP principle, as well as the MDI (minimum discrimination information) approach, but not the well-known ME principle of Jaynes [E.T. Jaynes, Phys. Rev. 106, 620 (1957)]. We also illuminate some related issues and resolve apparent discrepancies. Finally, we investigate the performance of MGFE estimation for different values of T, and we discuss the advantages and shortcomings of the approach.

  18. Parsing of the free energy of aromatic-aromatic stacking interactions in solution

    Energy Technology Data Exchange (ETDEWEB)

    Kostjukov, Viktor V.; Khomytova, Nina M. [Department of Physics, Sevastopol National Technical University, Sevastopol 99053, Crimea (Ukraine); Hernandez Santiago, Adrian A.; Tavera, Anna-Maria Cervantes; Alvarado, Julieta Salas [Faculty of Chemical Sciences, Autonomous University of Puebla, Puebla (Mexico); Evstigneev, Maxim P., E-mail: max_evstigneev@mail.ru [Department of Physics, Sevastopol National Technical University, Sevastopol 99053, Crimea (Ukraine)

    2011-10-15

    Graphical abstract: Highlights: > A protocol for decomposition of the free energy of aromatic stacking is developed. > The factors stabilizing/destabilizing stacking of aromatic molecules are defined. > Hydrophobic contribution is found to be dominant. - Abstract: We report an analysis of the energetics of aromatic-aromatic stacking interactions for 39 non-covalent reactions of self- and hetero-association of 12 aromatic molecules with different structures and charge states. A protocol for computation of the contributions to the total energy from various energetic terms has been developed and the results are consistent with experiment in 92% of all the systems studied. It is found that the contributions from hydrogen bonds and entropic factors are always unfavorable, whereas contributions from van-der-Waals, electrostatic and/or hydrophobic effects may lead to stabilizing or destabilizing factors depending on the system studied. The analysis carried out in this work provides an answer to the questions 'What forces stabilize/destabilize the stacking of aromatic molecules in aqueous-salt solution and what are their relative importance?'

  19. Parsing of the free energy of aromatic-aromatic stacking interactions in solution

    International Nuclear Information System (INIS)

    Kostjukov, Viktor V.; Khomytova, Nina M.; Hernandez Santiago, Adrian A.; Tavera, Anna-Maria Cervantes; Alvarado, Julieta Salas; Evstigneev, Maxim P.

    2011-01-01

    Graphical abstract: Highlights: → A protocol for decomposition of the free energy of aromatic stacking is developed. → The factors stabilizing/destabilizing stacking of aromatic molecules are defined. → Hydrophobic contribution is found to be dominant. - Abstract: We report an analysis of the energetics of aromatic-aromatic stacking interactions for 39 non-covalent reactions of self- and hetero-association of 12 aromatic molecules with different structures and charge states. A protocol for computation of the contributions to the total energy from various energetic terms has been developed and the results are consistent with experiment in 92% of all the systems studied. It is found that the contributions from hydrogen bonds and entropic factors are always unfavorable, whereas contributions from van-der-Waals, electrostatic and/or hydrophobic effects may lead to stabilizing or destabilizing factors depending on the system studied. The analysis carried out in this work provides an answer to the questions 'What forces stabilize/destabilize the stacking of aromatic molecules in aqueous-salt solution and what are their relative importance?'

  20. Cluster expansion of the solvation free energy difference: Systematic improvements in the solvation of single ions

    Science.gov (United States)

    Pliego, Josefredo R.

    2017-07-01

    The cluster expansion method has been used in the imperfect gas theory for several decades. This paper proposes a cluster expansion of the solvation free energy difference. This difference, which results from a change in the solute-solvent potential energy, can be written as the logarithm of a finite series. Similar to the Mayer function, the terms in the series are related to configurational integrals, which makes the integrand relevant only for configurations of the solvent molecules close to the solute. In addition, the terms involve interaction of solute with one, two, and so on solvent molecules. The approach could be used for hybrid quantum mechanical and molecular mechanics methods or mixed cluster-continuum approximation. A simple form of the theory was applied for prediction of pKa in methanol; the results indicated that three explicit methanol molecules and the dielectric continuum lead to a root of mean squared error (RMSE) of only 1.3 pKa units, whereas the pure continuum solvation model based on density method leads to a RMSE of 6.6 pKa units.

  1. Critique of pure free energy principle. Comment on "Answering Schrödinger's question: A free-energy formulation" by Maxwell James Désormeau Ramstead et al.

    Science.gov (United States)

    Tozzi, Arturo; Peters, James F.

    2018-03-01

    The paper by Ramstead et al. [1] [in this issue] reminds us the efforts of eminent scientists such as Whitehead and Godel. After having produced influential manuscripts, they turned to more philosophical issues, understanding the need for a larger formalization of their bounteous scientific results [2,3]. In a similar way, the successful free-energy principle has been generalized, in order to encompass not only the brain activity of the original formulation, but also the whole spectrum of life [1]. The final result is of prominent importance, because, in touch with Quine's naturalized epistemology [4] and Badiou's account of set theory [5], provides philosophical significance to otherwise purely scientific matters. The free energy principle becomes a novel paradigm that attempts to explain general physical/biological mechanisms in the light of a novel scientific ontology, the "variational neuroethology". The latter, seemingly grounded in a recursive multilevel reductionistic/emergentistic approach à la Bechtel [6], has also its roots in a rationalistic top-down approach that, starting from mathematical/physical general concepts (von Helmholtz's free energy), formulates experimentally testable (and falsifiable) theories.

  2. Quantum mechanical free energy profiles with post-quantization restraints: Binding free energy of the water dimer over a broad range of temperatures.

    Science.gov (United States)

    Bishop, Kevin P; Roy, Pierre-Nicholas

    2018-03-14

    Free energy calculations are a crucial part of understanding chemical systems but are often computationally expensive for all but the simplest of systems. Various enhanced sampling techniques have been developed to improve the efficiency of these calculations in numerical simulations. However, the majority of these approaches have been applied using classical molecular dynamics. There are many situations where nuclear quantum effects impact the system of interest and a classical description fails to capture these details. In this work, path integral molecular dynamics has been used in conjunction with umbrella sampling, and it has been observed that correct results are only obtained when the umbrella sampling potential is applied to a single path integral bead post quantization. This method has been validated against a Lennard-Jones benchmark system before being applied to the more complicated water dimer system over a broad range of temperatures. Free energy profiles are obtained, and these are utilized in the calculation of the second virial coefficient as well as the change in free energy from the separated water monomers to the dimer. Comparisons to experimental and ground state calculation values from the literature are made for the second virial coefficient at higher temperature and the dissociation energy of the dimer in the ground state.

  3. Crystal–liquid interfacial free energy and thermophysical properties of pure liquid Ti using electrostatic levitation: Hypercooling limit, specific heat, total hemispherical emissivity, density, and interfacial free energy

    International Nuclear Information System (INIS)

    Lee, Geun Woo; Jeon, Sangho; Park, Cheolmin; Kang, Dong-Hee

    2013-01-01

    Highlights: • Thermophysical properties of liquid Ti are obtained by electrostatic levitation. • How to measure the thermophysical properties is shown with non-contact method. • Hypercooling limit of liquid Ti guarantying homogeneous nucleation is 341 K. • Accurate ratio C p /ε T of the liquid Ti is obtained with weak temperature dependence. • Interfacial free energy of Ti is estimated with the thermophysical parameters. -- Abstract: Thermophysical properties of liquid Ti are measured by a newly developed electrostatic levitation. In this study, we measure a hypercooling limit (ΔT hyp ), specific heat (C p ), total hemispherical emissivity (ε T ), and density (ρ) of liquid Ti. The ΔT hyp of the liquid Ti is 341 K. The C p of the liquid Ti shows very weak temperature dependence during supercooling. The ε T and ρ of the liquid Ti are given by 0.329 and ρ(T) (g/cm 3 ) = (4.16 − 2.36) · 10 −4 (T − T m ). Finally, the interfacial free energy is estimated with the measured thermophysical parameters. The interfacial free energy is 0.164 J/m 2 , and Turnbull’s coefficient is 0.48

  4. The Gibbs free energy of homogeneous nucleation: From atomistic nuclei to the planar limit.

    Science.gov (United States)

    Cheng, Bingqing; Tribello, Gareth A; Ceriotti, Michele

    2017-09-14

    In this paper we discuss how the information contained in atomistic simulations of homogeneous nucleation should be used when fitting the parameters in macroscopic nucleation models. We show how the number of solid and liquid atoms in such simulations can be determined unambiguously by using a Gibbs dividing surface and how the free energy as a function of the number of solid atoms in the nucleus can thus be extracted. We then show that the parameters (the chemical potential, the interfacial free energy, and a Tolman correction) of a model based on classical nucleation theory can be fitted using the information contained in these free-energy profiles but that the parameters in such models are highly correlated. This correlation is unfortunate as it ensures that small errors in the computed free energy surface can give rise to large errors in the extrapolated properties of the fitted model. To resolve this problem we thus propose a method for fitting macroscopic nucleation models that uses simulations of planar interfaces and simulations of three-dimensional nuclei in tandem. We show that when the chemical potentials and the interface energy are pinned to their planar-interface values, more precise estimates for the Tolman length are obtained. Extrapolating the free energy profile obtained from small simulation boxes to larger nuclei is thus more reliable.

  5. SAAMBE: Webserver to Predict the Charge of Binding Free Energy Caused by Amino Acids Mutations.

    Science.gov (United States)

    Petukh, Marharyta; Dai, Luogeng; Alexov, Emil

    2016-04-12

    Predicting the effect of amino acid substitutions on protein-protein affinity (typically evaluated via the change of protein binding free energy) is important for both understanding the disease-causing mechanism of missense mutations and guiding protein engineering. In addition, researchers are also interested in understanding which energy components are mostly affected by the mutation and how the mutation affects the overall structure of the corresponding protein. Here we report a webserver, the Single Amino Acid Mutation based change in Binding free Energy (SAAMBE) webserver, which addresses the demand for tools for predicting the change of protein binding free energy. SAAMBE is an easy to use webserver, which only requires that a coordinate file be inputted and the user is provided with various, but easy to navigate, options. The user specifies the mutation position, wild type residue and type of mutation to be made. The server predicts the binding free energy change, the changes of the corresponding energy components and provides the energy minimized 3D structure of the wild type and mutant proteins for download. The SAAMBE protocol performance was tested by benchmarking the predictions against over 1300 experimentally determined changes of binding free energy and a Pearson correlation coefficient of 0.62 was obtained. How the predictions can be used for discriminating disease-causing from harmless mutations is discussed. The webserver can be accessed via http://compbio.clemson.edu/saambe_webserver/.

  6. Effect of Atomic Charges on Octanol–Water Partition Coefficient Using Alchemical Free Energy Calculation

    Directory of Open Access Journals (Sweden)

    Koji Ogata

    2018-02-01

    Full Text Available The octanol–water partition coefficient (logPow is an important index for measuring solubility, membrane permeability, and bioavailability in the drug discovery field. In this paper, the logPow values of 58 compounds were predicted by alchemical free energy calculation using molecular dynamics simulation. In free energy calculations, the atomic charges of the compounds are always fixed. However, they must be recalculated for each solvent. Therefore, three different sets of atomic charges were tested using quantum chemical calculations, taking into account vacuum, octanol, and water environments. The calculated atomic charges in the different environments do not necessarily influence the correlation between calculated and experimentally measured ∆Gwater values. The largest correlation coefficient values of the solvation free energy in water and octanol were 0.93 and 0.90, respectively. On the other hand, the correlation coefficient of logPow values calculated from free energies, the largest of which was 0.92, was sensitive to the combination of the solvation free energies calculated from the calculated atomic charges. These results reveal that the solvent assumed in the atomic charge calculation is an important factor determining the accuracy of predicted logPow values.

  7. AlaScan: A Graphical User Interface for Alanine Scanning Free-Energy Calculations.

    Science.gov (United States)

    Ramadoss, Vijayaraj; Dehez, François; Chipot, Christophe

    2016-06-27

    Computation of the free-energy changes that underlie molecular recognition and association has gained significant importance due to its considerable potential in drug discovery. The massive increase of computational power in recent years substantiates the application of more accurate theoretical methods for the calculation of binding free energies. The impact of such advances is the application of parent approaches, like computational alanine scanning, to investigate in silico the effect of amino-acid replacement in protein-ligand and protein-protein complexes, or probe the thermostability of individual proteins. Because human effort represents a significant cost that precludes the routine use of this form of free-energy calculations, minimizing manual intervention constitutes a stringent prerequisite for any such systematic computation. With this objective in mind, we propose a new plug-in, referred to as AlaScan, developed within the popular visualization program VMD to automate the major steps in alanine-scanning calculations, employing free-energy perturbation as implemented in the widely used molecular dynamics code NAMD. The AlaScan plug-in can be utilized upstream, to prepare input files for selected alanine mutations. It can also be utilized downstream to perform the analysis of different alanine-scanning calculations and to report the free-energy estimates in a user-friendly graphical user interface, allowing favorable mutations to be identified at a glance. The plug-in also assists the end-user in assessing the reliability of the calculation through rapid visual inspection.

  8. BFEE: A User-Friendly Graphical Interface Facilitating Absolute Binding Free-Energy Calculations.

    Science.gov (United States)

    Fu, Haohao; Gumbart, James C; Chen, Haochuan; Shao, Xueguang; Cai, Wensheng; Chipot, Christophe

    2018-03-26

    Quantifying protein-ligand binding has attracted the attention of both theorists and experimentalists for decades. Many methods for estimating binding free energies in silico have been reported in recent years. Proper use of the proposed strategies requires, however, adequate knowledge of the protein-ligand complex, the mathematical background for deriving the underlying theory, and time for setting up the simulations, bookkeeping, and postprocessing. Here, to minimize human intervention, we propose a toolkit aimed at facilitating the accurate estimation of standard binding free energies using a geometrical route, coined the binding free-energy estimator (BFEE), and introduced it as a plug-in of the popular visualization program VMD. Benefitting from recent developments in new collective variables, BFEE can be used to generate the simulation input files, based solely on the structure of the complex. Once the simulations are completed, BFEE can also be utilized to perform the post-treatment of the free-energy calculations, allowing the absolute binding free energy to be estimated directly from the one-dimensional potentials of mean force in simulation outputs. The minimal amount of human intervention required during the whole process combined with the ergonomic graphical interface makes BFEE a very effective and practical tool for the end-user.

  9. Work fluctuation theorems and free energy from kinetic theory

    Science.gov (United States)

    Brey, J. Javier; Ruiz-Montero, M. J.; Domínguez, Álvaro

    2018-01-01

    The formulation of the first and second principles of thermodynamics for a particle in contact with a heat bath and submitted to an external force is analyzed, by means of the Boltzmann-Lorentz kinetic equation. The possible definitions of the thermodynamic quantities are discussed in the light of the H theorem verified by the distribution of the particle. The work fluctuation relations formulated by Bochkov and Kuzovlev, and by Jarzynski, respectively, are derived from the kinetic equation. In addition, particle simulations using both the direct simulation Monte Carlo method and molecular dynamics, are used to investigate the practical accuracy of the results. Work distributions are also measured, and they turn out to be rather complex. On the other hand, they seem to depend very little, if any, on the interaction potential between the intruder and the bath.

  10. The free energy barrier for arginine gating charge translation is altered by mutations in the voltage sensor domain.

    Directory of Open Access Journals (Sweden)

    Christine S Schwaiger

    Full Text Available The gating of voltage-gated ion channels is controlled by the arginine-rich S4 helix of the voltage-sensor domain moving in response to an external potential. Recent studies have suggested that S4 moves in three to four steps to open the conducting pore, thus visiting several intermediate conformations during gating. However, the exact conformational changes are not known in detail. For instance, it has been suggested that there is a local rotation in the helix corresponding to short segments of a 3(10-helix moving along S4 during opening and closing. Here, we have explored the energetics of the transition between the fully open state (based on the X-ray structure and the first intermediate state towards channel closing (C1, modeled from experimental constraints. We show that conformations within 3 Å of the X-ray structure are obtained in simulations starting from the C1 model, and directly observe the previously suggested sliding 3(10-helix region in S4. Through systematic free energy calculations, we show that the C1 state is a stable intermediate conformation and determine free energy profiles for moving between the states without constraints. Mutations indicate several residues in a narrow hydrophobic band in the voltage sensor contribute to the barrier between the open and C1 states, with F233 in the S2 helix having the largest influence. Substitution for smaller amino acids reduces the transition cost, while introduction of a larger ring increases it, largely confirming experimental activation shift results. There is a systematic correlation between the local aromatic ring rotation, the arginine barrier crossing, and the corresponding relative free energy. In particular, it appears to be more advantageous for the F233 side chain to rotate towards the extracellular side when arginines cross the hydrophobic region.

  11. Elucidation of the conformational free energy landscape in H.pylori LuxS and its implications to catalysis

    Directory of Open Access Journals (Sweden)

    Bhattacharyya Moitrayee

    2010-08-01

    Full Text Available Abstract Background One of the major challenges in understanding enzyme catalysis is to identify the different conformations and their populations at detailed molecular level in response to ligand binding/environment. A detail description of the ligand induced conformational changes provides meaningful insights into the mechanism of action of enzymes and thus its function. Results In this study, we have explored the ligand induced conformational changes in H.pylori LuxS and the associated mechanistic features. LuxS, a dimeric protein, produces the precursor (4,5-dihydroxy-2,3-pentanedione for autoinducer-2 production which is a signalling molecule for bacterial quorum sensing. We have performed molecular dynamics simulations on H.pylori LuxS in its various ligand bound forms and analyzed the simulation trajectories using various techniques including the structure network analysis, free energy evaluation and water dynamics at the active site. The results bring out the mechanistic details such as co-operativity and asymmetry between the two subunits, subtle changes in the conformation as a response to the binding of active and inactive forms of ligands and the population distribution of different conformations in equilibrium. These investigations have enabled us to probe the free energy landscape and identify the corresponding conformations in terms of network parameters. In addition, we have also elucidated the variations in the dynamics of water co-ordination to the Zn2+ ion in LuxS and its relation to the rigidity at the active sites. Conclusions In this article, we provide details of a novel method for the identification of conformational changes in the different ligand bound states of the protein, evaluation of ligand-induced free energy changes and the biological relevance of our results in the context of LuxS structure-function. The methodology outlined here is highly generalized to illuminate the linkage between structure and function in

  12. Associations of infant feeding and timing of linear growth and relative weight gain during early life with childhood body composition

    NARCIS (Netherlands)

    de Beer, M.; Vrijkotte, T.G.M.; Fall, C.H.D.; Eijsden, M.; Osmond, C.; Gemke, R.J.B.J.

    2015-01-01

    Background:Growth and feeding during infancy have been associated with later life body mass index. However, the associations of infant feeding, linear growth and weight gain relative to linear growth with separate components of body composition remain unclear.Methods:Of 5551 children with collected

  13. Associations of infant feeding and timing of linear growth and relative weight gain during early life with childhood body composition

    NARCIS (Netherlands)

    de Beer, M.; Vrijkotte, T. G. M.; Fall, C. H. D.; van Eijsden, M.; Osmond, C.; Gemke, R. J. B. J.

    2015-01-01

    Growth and feeding during infancy have been associated with later life body mass index. However, the associations of infant feeding, linear growth and weight gain relative to linear growth with separate components of body composition remain unclear. Of 5551 children with collected growth and

  14. Characterization of the order relation on the set of completely n-positive linear maps between C*-algebras

    Directory of Open Access Journals (Sweden)

    Maria Joita

    2007-12-01

    Full Text Available In this paper we characterize the order relation on the set of all nondegenerate completely n-positive linear maps between C*-algebras in terms of a self-dual Hilbert module induced by each completely n-positive linear map.

  15. Towards abundant and pollution-free energy. Laser nuclear fusion

    International Nuclear Information System (INIS)

    Robieux, J.

    2008-01-01

    This book shows that it is now practically certain that by the year 2080 laser nuclear fusion will allow to produce an abundant and relatively cheap energy. Thanks to this energy, it will be possible to convert a mixture of CO 2 , H 2 and water into an automotive fuel or a food product. Laser nuclear fusion will use deuterium as fuel and thus oil and gas will become useless. Also, thanks to this new energy source, global warming and starvation will be overcome. The laser fusion concept was introduced by J. Robieux in 1962 just after the discovery of the laser. This idea was immediately accepted and sustained by the French President De Gaulle. The research on laser fusion was initially undertaken at the Marcoussis research centre from the Compagnie Generale d'Electricite (General Electricity Company - CGE). In 1967, the lasers built at Marcoussis were 30 times more powerful than any other laser in the rest of world. A cooperation with the USA started at that time and is still going on today. In 1969, the CEA centre of Limeil realized the world premiere experiments of laser fusion. This book presents the historical aspects and the state-of-the-art of this technology today. It is written in two parts, the first part does not require any scientific knowledge and is accessible to everybody, while the second part can be understood only by readers having a basic scientific background. (J.S.)

  16. 78 FR 21149 - Certain Linear Actuators; Notice of Receipt of Complaint; Solicitation of Comments Relating to...

    Science.gov (United States)

    2013-04-09

    ... INTERNATIONAL TRADE COMMISSION [Docket No. 2949] Certain Linear Actuators; Notice of Receipt of... received a complaint entitled Certain Linear Actuators, DN 2949; the Commission is soliciting comments on... States after importation of certain linear actuators. The complaint names as respondents Changzhou Kaidi...

  17. Tangent Orbital Rendezvous Using Linear Relative Motion with J2 Perturbations

    Directory of Open Access Journals (Sweden)

    Gang Zhang

    2013-01-01

    Full Text Available The tangent-impulse coplanar orbit rendezvous problem is studied based on the linear relative motion for J2-perturbed elliptic orbits. There are three cases: (1 only the first impulse is tangent; (2 only the second impulse is tangent; (3 both impulses are tangent. For a given initial impulse point, the first two problems can be transformed into finding all roots of a single variable function about the transfer time, which can be done by the secant method. The bitangent rendezvous problem requires the same solution for the first two problems. By considering the initial coasting time, the bitangent rendezvous solution is obtained with a difference function. A numerical example for two coplanar elliptic orbits with J2 perturbations is given to verify the efficiency of these proposed techniques.

  18. Equilibrium fluctuation relations for voltage coupling in membrane proteins.

    Science.gov (United States)

    Kim, Ilsoo; Warshel, Arieh

    2015-11-01

    A general theoretical framework is developed to account for the effects of an external potential on the energetics of membrane proteins. The framework is based on the free energy relation between two (forward/backward) probability densities, which was recently generalized to non-equilibrium processes, culminating in the work-fluctuation theorem. Starting from the probability densities of the conformational states along the "voltage coupling" reaction coordinate, we investigate several interconnected free energy relations between these two conformational states, considering voltage activation of ion channels. The free energy difference between the two conformational states at zero (depolarization) membrane potential (i.e., known as the chemical component of free energy change in ion channels) is shown to be equivalent to the free energy difference between the two "equilibrium" (resting and activated) conformational states along the one-dimensional voltage couplin reaction coordinate. Furthermore, the requirement that the application of linear response approximation to the free energy functionals of voltage coupling should satisfy the general free energy relations, yields a novel closed-form expression for the gating charge in terms of other basic properties of ion channels. This connection is familiar in statistical mechanics, known as the equilibrium fluctuation-response relation. The theory is illustrated by considering the coupling of a unit charge to the external voltage in the two sites near the surface of membrane, representing the activated and resting states. This is done using a coarse-graining (CG) model of membrane proteins, which includes the membrane, the electrolytes and the electrodes. The CG model yields Marcus-type voltage dependent free energy parabolas for the response of the electrostatic environment (electrolytes etc.) to the transition from the initial to the final configuratinal states, leading to equilibrium free energy difference and free

  19. Consequences of Laughter Upon Trunk Compression and Cortical Activation: Linear and Polynomial Relations

    Science.gov (United States)

    Svebak, Sven

    2016-01-01

    Results from two studies of biological consequences of laughter are reported. A proposed inhibitory brain mechanism was tested in Study 1. It aims to protect against trunk compression that can cause health hazards during vigorous laughter. Compression may be maximal during moderate durations and, for protective reasons, moderate in enduring vigorous laughs. Twenty-five university students volunteered to see a candid camera film. Laughter responses (LR) and the superimposed ha-responses were operationally assessed by mercury-filled strain gauges strapped around the trunk. On average, the thorax compression amplitudes exceeded those of the abdomen, and greater amplitudes were seen in the males than in the females after correction for resting trunk circumference. Regression analyses supported polynomial relations because medium LR durations were associated with particularly high thorax amplitudes. In Study 2, power changes were computed in the beta and alpha EEG frequency bands of the parietal cortex from before to after exposure to the comedy “Dinner for one” in 56 university students. Highly significant linear relations were calculated between the number of laughs and post-exposure cortical activation (increase of beta, decrease of alpha) due to high activation after frequent laughter. The results from Study 1 supported the hypothesis of a protective brain mechanism that is activated during long LRs to reduce the risk of harm to vital organs in the trunk cavity. The results in Study 2 supported a linear cortical activation and, thus, provided evidence for a biological correlate to the subjective experience of mental refreshment after laughter. PMID:27547260

  20. Absolute Hydration Free Energy of Proton from First Principles Electronic Structure Calculations

    International Nuclear Information System (INIS)

    Zhan, Chang-Guo; Dixon, David A.

    2001-01-01

    The absolute hydration free energy of the proton, DGhyd298(H+), is one of the fundamental quantities for the thermodynamics of aqueous systems. Its exact value remains unknown despite extensive experimental and computational efforts. We report a first-principles determination of DGhyd298(H+) by using the latest developments in electronic structure theory and massively parallel computers. DGhyd298(H+) is accurately predicted to be -262.4 kcal/mol based on high-level, first-principles solvation-included electronic structure calculations. The absolute hydration free energies of other cations can be obtained by using appropriate available thermodynamic data in combination with this value. The high accuracy of the predicted absolute hydration free energy of proton is confirmed by applying the same protocol to predict DGhyd298(Li+)

  1. The vortex free energy in the screening phase of the Z(2) Higgs model

    International Nuclear Information System (INIS)

    Meyer, H.

    1983-06-01

    The vortex free energy was proposed to distinguish between the confinement - and the Higgs phase (in the sense of 't Hooft) in lattice gauge theory, when matter fields are present that transform according to an arbitrary representation of the gauge group. In this paper I consider the Z(2) Higgs model and calculate the vortex free energy in the screening part of the confining/screening phase of Fradkin and Shenker. The result does not agree with the expected behavior that corresponds to the structure of the phase diagram. Therefore the vortex free energy is no longer a good indicator for confinement when matter fields transform nontrivially under the center of the gauge group (such as Z(2) Higgs scalars). (orig.)

  2. Free energies of stable and metastable pores in lipid membranes under tension.

    Science.gov (United States)

    den Otter, Wouter K

    2009-11-28

    The free energy profile of pore formation in a lipid membrane, covering the entire range from a density fluctuation in an intact bilayer to a large tension-stabilized pore, has been calculated by molecular dynamics simulations with a coarse-grained lipid model. Several fixed elongations are used to obtain the Helmholtz free energy as a function of pore size for thermodynamically stable, metastable, and unstable pores, and the system-size dependence of these elongations is discussed. A link to the Gibbs free energy at constant tension, commonly known as the Litster model, is established by a Legendre transformation. The change of genus upon pore formation is exploited to estimate the saddle-splay modulus or Gaussian curvature modulus of the membrane leaflets. Details are provided of the simulation approach, which combines the potential of mean constraint force method with a reaction coordinate based on the local lipid density.

  3. Free energy calculations along entropic pathways. III. Nucleation of capillary bridges and bubbles

    Science.gov (United States)

    Desgranges, Caroline; Delhommelle, Jerome

    2017-05-01

    Using molecular simulation, we analyze the capillary condensation and evaporation processes for argon confined in a cylindrical nanopore. For this purpose, we define the entropy of the adsorbed fluid as a reaction coordinate and determine the free energy associated with both processes along entropic pathways. For capillary condensation, we identify a complex free energy profile resulting from the multi-stage nature of this phenomenon. We find capillary condensation to proceed through the nucleation of a liquid bridge across the nanopore, followed by its expansion throughout the pore to give rise to the stable phase of high density. In the case of capillary evaporation, the free energy profile along the entropy pathway also exhibits different regimes, corresponding to the initial destabilization of the layered structure of the fluid followed by the formation, and subsequent expansion, of a bubble across the nanopore.

  4. Extrapolation procedures for calculating high-temperature gibbs free energies of aqueous electrolytes

    International Nuclear Information System (INIS)

    Tremaine, P.R.

    1979-01-01

    Methods for calculating high-temprature Gibbs free energies of mononuclear cations and anions from room-temperature data are reviewed. Emphasis is given to species required for oxide solubility calculations relevant to mass transport situations in the nuclear industry. Free energies predicted by each method are compared to selected values calculated from recently reported solubility studies and other literature data. Values for monatomic ions estimated using the assumption anti C 0 p(T) = anti C 0 p(298) agree best with experiment to 423 K. From 423 K to 523 K, free energies from an electrostatic model for ion hydration are more accurate. Extrapolations for hydrolyzed species are limited by a lack of room-temperature entropy data and expressions for estimating these entropies are discussed. (orig.) [de

  5. Grain-boundary free energy in an assembly of elastic disks.

    Science.gov (United States)

    Lusk, Mark T; Beale, Paul D

    2004-02-01

    Grain-boundary free energy is estimated as a function of misoriention for symmetric tilt boundaries in an assembly of nearly hard disks. Fluctuating cell theory is used to accomplish this since the most common techniques for calculating interfacial free energy cannot be applied to such assemblies. The results are analogous to those obtained using a Leonard-Jones potential, but in this case the interfacial energy is dominated by an entropic contribution. Disk assemblies colorized with free and specific volume elucidate differences between these two characteristics of boundary structure. Profiles are also provided of the Helmholtz and Gibbs free energies as a function of distance from the grain boundaries. Low angle grain boundaries are shown to follow the classical relationship between dislocation orientation/spacing and misorientation angle.

  6. Control of the Effective Free-Energy Landscape in a Frustrated Magnet by a Field Pulse

    Science.gov (United States)

    Wan, Yuan; Moessner, Roderich

    2017-10-01

    Thermal fluctuations can lift the degeneracy of a ground state manifold, producing a free-energy landscape without accidentally degenerate minima. In a process known as order by disorder, a subset of states incorporating symmetry breaking may be selected. Here, we show that such a free-energy landscape can be controlled in a nonequilibrium setting as the slow motion within the ground state manifold is governed by the fast modes out of it. For the paradigmatic case of the classical pyrochlore X Y antiferromagnet, we show that a uniform magnetic field pulse can excite these fast modes to generate a tunable effective free-energy landscape with minima at thermodynamically unstable portions of the ground state manifold.

  7. Development of a group contribution method for estimating free energy of peptides in a dodecane-water system via molecular dynamic simulations.

    Science.gov (United States)

    Mora Osorio, Camilo Andrés; González Barrios, Andrés Fernando

    2016-12-07

    Calculation of the Gibbs free energy changes of biological molecules at the oil-water interface is commonly performed with Molecular Dynamics simulations (MD). It is a process that could be performed repeatedly in order to find some molecules of high stability in this medium. Here, an alternative method of calculation has been proposed: a group contribution method (GCM) for peptides based on MD of the twenty classic amino acids to obtain free energy change during the insertion of any peptide chain in water-dodecane interfaces. Multiple MD of the twenty classic amino acids located at the interface of rectangular simulation boxes with a dodecane-water medium were performed. A GCM to calculate the free energy of entire peptides is then proposed. The method uses the summation of the Gibbs free energy of each amino acid adjusted in function of its presence or absence in the chain as well as its hydrophobic characteristics. Validation of the equation was performed with twenty-one peptides all simulated using MD in dodecane-water rectangular boxes in previous work, obtaining an average relative error of 16%.

  8. Free Energy Self-Averaging in Protein-Sized Random Heteropolymers

    International Nuclear Information System (INIS)

    Chuang, Jeffrey; Grosberg, Alexander Yu.; Kardar, Mehran

    2001-01-01

    Current theories of heteropolymers are inherently macroscopic, but are applied to mesoscopic proteins. To compute the free energy over sequences, one assumes self-averaging -- a property established only in the macroscopic limit. By enumerating the states and energies of compact 18, 27, and 36mers on a lattice with an ensemble of random sequences, we test the self-averaging approximation. We find that fluctuations in the free energy between sequences are weak, and that self-averaging is valid at the scale of real proteins. The results validate sequence design methods which exponentially speed up computational design and simplify experimental realizations

  9. Interaction Free Energies of Eight Sodium Salts and a Phosphatidylcholine Membrane

    DEFF Research Database (Denmark)

    Wang, C. H.; Ge, Y.; Mortensen, J.

    2011-01-01

    Many recent reports have discussed specific effects of anions on the properties of lipid membranes and possible roles of such effects within biochemistry. One key parameter in both theoretical and experimental treatments of membrane-salt interactions is the net affinity, that is, the free energy...... salts by dialysis equilibrium measurements. This method provides model free thermodynamic data and allows investigations in the dilute concentration range where solution nonideality and perturbation of membrane structure is limited. The transfer free energy of DMPC from water to salt solutions, Delta mu...

  10. Merging Belief Propagation and the Mean Field Approximation: A Free Energy Approach

    DEFF Research Database (Denmark)

    Riegler, Erwin; Kirkelund, Gunvor Elisabeth; Manchón, Carles Navarro

    2013-01-01

    We present a joint message passing approach that combines belief propagation and the mean field approximation. Our analysis is based on the region-based free energy approximation method proposed by Yedidia et al. We show that the message passing fixed-point equations obtained with this combination...... correspond to stationary points of a constrained region-based free energy approximation. Moreover, we present a convergent implementation of these message passing fixed-point equations provided that the underlying factor graph fulfills certain technical conditions. In addition, we show how to include hard...

  11. Efficiency of free-energy calculations of spin lattices by spectral quantum algorithms

    International Nuclear Information System (INIS)

    Master, Cyrus P.; Yamaguchi, Fumiko; Yamamoto, Yoshihisa

    2003-01-01

    Ensemble quantum algorithms are well suited to calculate estimates of the energy spectra for spin-lattice systems. Based on the phase estimation algorithm, these algorithms efficiently estimate discrete Fourier coefficients of the density of states. Their efficiency in calculating the free energy per spin of general spin lattices to bounded error is examined. We find that the number of Fourier components required to bound the error in the free energy due to the broadening of the density of states scales polynomially with the number of spins in the lattice. However, the precision with which the Fourier components must be calculated is found to be an exponential function of the system size

  12. Size and shape dependent Gibbs free energy and phase stability of titanium and zirconium nanoparticles

    International Nuclear Information System (INIS)

    Xiong Shiyun; Qi Weihong; Huang Baiyun; Wang Mingpu; Li Yejun

    2010-01-01

    The Debye model of Helmholtz free energy for bulk material is generalized to Gibbs free energy (GFE) model for nanomaterial, while a shape factor is introduced to characterize the shape effect on GFE. The structural transitions of Ti and Zr nanoparticles are predicted based on GFE. It is further found that GFE decreases with the shape factor and increases with decreasing of the particle size. The critical size of structural transformation for nanoparticles goes up as temperature increases in the absence of change in shape factor. For specified temperature, the critical size climbs up with the increase of shape factor. The present predictions agree well with experiment values.

  13. Polymer in a pore: Effect of confinement on the free energy barrier

    Science.gov (United States)

    Kumar, Sanjiv; Kumar, Sanjay

    2018-06-01

    We investigate the transfer of a polymer chain from cis- side to trans- side through two types of pores: cone-shaped channel and flat-channel. Using the exact enumeration technique, we obtain the free energy landscapes of a polymer chain for such systems. We have also calculated the free-energy barrier of a polymer chain attached to the edge of the pore. The model system allows us to calculate the force required to pull polymer from the pore and stall-force to confine polymer within the pore.

  14. Free energy

    International Nuclear Information System (INIS)

    Holm, Oeystein B.

    2006-01-01

    Norway has fallen behind in the development of district heating and use of solar energy compared to Sweden and Denmark. It is a myth that Norway has less hours of sun than its neighbours; southern and eastern Norway has equally good conditions as areas in Sweden and Denmark that have large solar collector installations used for district heating. Benefits of the solar energy technology are highlighted, especially environmental aspects (ml)

  15. Role of size on the relative importance of fluid dynamic losses in linear cryocoolers

    Science.gov (United States)

    Kirkconnell, Carl; Ghavami, Ali; Ghiaasiaan, S. Mostafa; Perrella, Matthew

    2017-12-01

    Thermodynamic modeling results for a novel small satellite (SmallSat) Stirling Cryocooler, capable of delivering over 200 mW net cooling power at 80 K for less than 6 W DC input power, are used in this paper as the basis for related pulse tube computational fluid dynamics (CFD) analysis. Industry and government requirements for SmallSat infrared sensors are driving the development of ever-more miniaturized cryocooler systems. Such cryocoolers must be extremely compact and lightweight, a challenge met by this research team through operating a Stirling cryocooler at a frequency of approximately 300 Hz. The primary advantage of operating at such a high frequency is that the required compression and expansion swept volumes are reduced relative to linear coolers operating at lower frequencies, which evidently reduces the size of the motor mechanisms and the thermodynamic components. In the case of a pulse tube cryocooler, this includes a reduction in diameter of the pulse tube itself. This unfortunately leads to high boundary layer losses, as the presented results demonstrate. Using a Stirling approach with a mechanical moving expander piston eliminates this small pulse tube loss mechanism, but other challenges are introduced, such as maintaining very tight clearance gaps between moving and stationary elements. This paper focuses on CFD modelling results for a highly miniaturized pulse tube cooler.

  16. cgDNA: a software package for the prediction of sequence-dependent coarse-grain free energies of B-form DNA.

    Science.gov (United States)

    Petkevičiūtė, D; Pasi, M; Gonzalez, O; Maddocks, J H

    2014-11-10

    cgDNA is a package for the prediction of sequence-dependent configuration-space free energies for B-form DNA at the coarse-grain level of rigid bases. For a fragment of any given length and sequence, cgDNA calculates the configuration of the associated free energy minimizer, i.e. the relative positions and orientations of each base, along with a stiffness matrix, which together govern differences in free energies. The model predicts non-local (i.e. beyond base-pair step) sequence dependence of the free energy minimizer. Configurations can be input or output in either the Curves+ definition of the usual helical DNA structural variables, or as a PDB file of coordinates of base atoms. We illustrate the cgDNA package by comparing predictions of free energy minimizers from (a) the cgDNA model, (b) time-averaged atomistic molecular dynamics (or MD) simulations, and (c) NMR or X-ray experimental observation, for (i) the Dickerson-Drew dodecamer and (ii) three oligomers containing A-tracts. The cgDNA predictions are rather close to those of the MD simulations, but many orders of magnitude faster to compute. Both the cgDNA and MD predictions are in reasonable agreement with the available experimental data. Our conclusion is that cgDNA can serve as a highly efficient tool for studying structural variations in B-form DNA over a wide range of sequences. © The Author(s) 2014. Published by Oxford University Press on behalf of Nucleic Acids Research.

  17. Tracking development paths: Monitoring driving forces and the impact of carbon-free energy sources in Spain

    International Nuclear Information System (INIS)

    O’ Mahony, Tadhg; Dufour, Javier

    2015-01-01

    Highlights: • The development path of Spain is analysed using an extended Kaya identity. • Effect of carbon free energy sources separated. • Nuclear energy acted to increase emissions as it declined in share. • Renewable energy penetration recently began to reduce carbon emissions. • Future policy must address wider factors of sustainable development. - Abstract: The evolution of the national development path has gravity in determining the future emissions outcomes of all nations. Deep reductions in emissions require a focus not just on energy and mitigation policy but on factors underlying this development. The Kaya identity has been recommended to track national progress with respect to sustainability and carbon emissions in the development path. This study applies an extended Kaya identity to the energy-related carbon emissions of Spain. Implemented through a divisia index decomposition annually from 1990 to 2011, it highlights the impact of factors such as affluence and energy intensity. A marked departure from previous studies is the separation of the effects of the carbon-free energy sources; both renewables and nuclear as fundamental mitigation measures. The results show that affluence and population have acted to increase emissions and energy intensity was increasing until recent years. Fuel substitution has acted to decrease emissions but while renewable energy has reduced emissions with the increasing importance of biomass, wind and solar, the decline in share of nuclear has acted to increase emissions. Implications for the development path and policy are discussed and lessons are relevant both for industrialised and industrialising nations

  18. Machine learning of single molecule free energy surfaces and the impact of chemistry and environment upon structure and dynamics.

    Science.gov (United States)

    Mansbach, Rachael A; Ferguson, Andrew L

    2015-03-14

    The conformational states explored by polymers and proteins can be controlled by environmental conditions (e.g., temperature, pressure, and solvent) and molecular chemistry (e.g., molecular weight and side chain identity). We introduce an approach employing the diffusion map nonlinear machine learning technique to recover single molecule free energy landscapes from molecular simulations, quantify changes to the landscape as a function of external conditions and molecular chemistry, and relate these changes to modifications of molecular structure and dynamics. In an application to an n-eicosane chain, we quantify the thermally accessible chain configurations as a function of temperature and solvent conditions. In an application to a family of polyglutamate-derivative homopeptides, we quantify helical stability as a function of side chain length, resolve the critical side chain length for the helix-coil transition, and expose the molecular mechanisms underpinning side chain-mediated helix stability. By quantifying single molecule responses through perturbations to the underlying free energy surface, our approach provides a quantitative bridge between experimentally controllable variables and microscopic molecular behavior, guiding and informing rational engineering of desirable molecular structure and function.

  19. Free energy landscape of siRNA-polycation complexation: Elucidating the effect of molecular geometry, polymer flexibility, and charge neutralization.

    Directory of Open Access Journals (Sweden)

    Gianvito Grasso

    Full Text Available The success of medical threatments with DNA and silencing interference RNA is strongly related to the design of efficient delivery technologies. Cationic polymers represent an attractive strategy to serve as nucleic-acid carriers with the envisioned advantages of efficient complexation, low cost, ease of production, well-defined size, and low polydispersity index. However, the balance between efficacy and toxicity (safety of these polymers is a challenge and in need of improvement. With the aim of designing more effective polycationic-based gene carriers, many parameters such as carrier morphology, size, molecular weight, surface chemistry, and flexibility/rigidity ratio need to be taken into consideration. In the present work, the binding mechanism of three cationic polymers (polyarginine, polylysine and polyethyleneimine to a model siRNA target is computationally investigated at the atomistic level. In order to better understand the polycationic carrier-siRNA interactions, replica exchange molecular dynamic simulations were carried out to provide an exhaustive exploration of all the possible binding sites, taking fully into account the siRNA flexibility together with the presence of explicit solvent and ions. Moreover, well-tempered metadynamics simulations were employed to elucidate how molecular geometry, polycation flexibility, and charge neutralization affect the siRNA-polycations free energy landscape in term of low-energy binding modes and unbinding free energy barriers. Significant differences among polymer binding modes have been detected, revealing the advantageous binding properties of polyarginine and polylysine compared to polyethyleneimine.

  20. Entropic and Electrostatic Effects on the Folding Free Energy of a Surface-Attached Biomolecule: An Experimental and Theoretical Study

    Science.gov (United States)

    Watkins, Herschel M.; Vallée-Bélisle, Alexis; Ricci, Francesco; Makarov, Dmitrii E.; Plaxco, Kevin W.

    2012-01-01

    Surface-tethered biomolecules play key roles in many biological processes and biotechnologies. However, while the physical consequences of such surface attachment have seen significant theoretical study, to date this issue has seen relatively little experimental investigation. In response we present here a quantitative experimental and theoretical study of the extent to which attachment to a charged –but otherwise apparently inert– surface alters the folding free energy of a simple biomolecule. Specifically, we have measured the folding free energy of a DNA stem loop both in solution and when site-specifically attached to a negatively charged, hydroxyl-alkane-coated gold surface. We find that, whereas surface attachment is destabilizing at low ionic strength it becomes stabilizing at ionic strengths above ~130 mM. This behavior presumably reflects two competing mechanisms: excluded volume effects, which stabilize the folded conformation by reducing the entropy of the unfolded state, and electrostatics, which, at lower ionic strengths, destabilizes the more compact folded state via repulsion from the negatively charged surface. To test this hypothesis we have employed existing theories of the electrostatics of surface-bound polyelectrolytes and the entropy of surface-bound polymers to model both effects. Despite lacking any fitted parameters, these theoretical models quantitatively fit our experimental results, suggesting that, for this system, current knowledge of both surface electrostatics and excluded volume effects is reasonably complete and accurate. PMID:22239220

  1. Review of relative biological effectiveness dependence on linear energy transfer for low-LET radiations

    International Nuclear Information System (INIS)

    Hunter, Nezahat; Muirhead, Colin R

    2009-01-01

    Information on Japanese A-bomb survivors exposed to gamma radiation has been used to estimate cancer risks for the whole range of photon (x-rays) and electron energies which are commonly encountered by radiation workers in the work place or by patients and workers in diagnostic radiology. However, there is some uncertainty regarding the radiation effectiveness of various low-linear energy transfer (low-LET) radiations (x-rays, gamma radiation and electrons). In this paper we review information on the effectiveness of low-LET radiations on the basis of epidemiological and in vitro radiobiological studies. Data from various experimental studies for chromosome aberrations and cell transformation in human lymphocytes and from epidemiological studies of the Japanese A-bomb survivors, patients medically exposed to radiation for diagnostic and therapeutic procedures, and occupational exposures of nuclear workers are considered. On the basis of in vitro cellular radiobiology, there is considerable evidence that the relative biological effectiveness (RBE) of high-energy low-LET radiation (gamma radiation, electrons) is less than that of low-energy low-LET radiation (x-rays, betas). This is a factor of about 3 to 4 for 29 kVp x-rays (e.g. as in diagnostic radiation exposures of the female breast) and for tritium beta-rays (encountered in parts of the nuclear industry) relative to Co-60 gamma radiation and 2-5 MeV gamma-rays (as received by the Japanese A-bomb survivors). In epidemiological studies, although for thyroid and breast cancer there appears to be a small tendency for the excess relative risks to decrease as the radiation energy increases for low-LET radiations, it is not statistically feasible to draw any conclusion regarding an underlying dependence of cancer risk on LET for the nominally low-LET radiations. (review)

  2. Diagrams of the variations in the free energy of formation of metallic compounds (1960)

    International Nuclear Information System (INIS)

    Darras, R.; Loriers, H.

    1960-01-01

    The variations in the standard free energy ΔG produced during the formation of the principal simple metallic compounds have been calculated as a function of the temperature from recently published data, and are presented in convenient diagram form. Their usefulness in metallurgy is illustrated by some possible applications. (author) [fr

  3. Enhanced conformational sampling to visualize a free-energy landscape of protein complex formation.

    Science.gov (United States)

    Iida, Shinji; Nakamura, Haruki; Higo, Junichi

    2016-06-15

    We introduce various, recently developed, generalized ensemble methods, which are useful to sample various molecular configurations emerging in the process of protein-protein or protein-ligand binding. The methods introduced here are those that have been or will be applied to biomolecular binding, where the biomolecules are treated as flexible molecules expressed by an all-atom model in an explicit solvent. Sampling produces an ensemble of conformations (snapshots) that are thermodynamically probable at room temperature. Then, projection of those conformations to an abstract low-dimensional space generates a free-energy landscape. As an example, we show a landscape of homo-dimer formation of an endothelin-1-like molecule computed using a generalized ensemble method. The lowest free-energy cluster at room temperature coincided precisely with the experimentally determined complex structure. Two minor clusters were also found in the landscape, which were largely different from the native complex form. Although those clusters were isolated at room temperature, with rising temperature a pathway emerged linking the lowest and second-lowest free-energy clusters, and a further temperature increment connected all the clusters. This exemplifies that the generalized ensemble method is a powerful tool for computing the free-energy landscape, by which one can discuss the thermodynamic stability of clusters and the temperature dependence of the cluster networks. © 2016 The Author(s).

  4. Hydration free energies of cyanide and hydroxide ions from molecular dynamics simulations with accurate force fields

    Science.gov (United States)

    Lee, M.W.; Meuwly, M.

    2013-01-01

    The evaluation of hydration free energies is a sensitive test to assess force fields used in atomistic simulations. We showed recently that the vibrational relaxation times, 1D- and 2D-infrared spectroscopies for CN(-) in water can be quantitatively described from molecular dynamics (MD) simulations with multipolar force fields and slightly enlarged van der Waals radii for the C- and N-atoms. To validate such an approach, the present work investigates the solvation free energy of cyanide in water using MD simulations with accurate multipolar electrostatics. It is found that larger van der Waals radii are indeed necessary to obtain results close to the experimental values when a multipolar force field is used. For CN(-), the van der Waals ranges refined in our previous work yield hydration free energy between -72.0 and -77.2 kcal mol(-1), which is in excellent agreement with the experimental data. In addition to the cyanide ion, we also study the hydroxide ion to show that the method used here is readily applicable to similar systems. Hydration free energies are found to sensitively depend on the intermolecular interactions, while bonded interactions are less important, as expected. We also investigate in the present work the possibility of applying the multipolar force field in scoring trajectories generated using computationally inexpensive methods, which should be useful in broader parametrization studies with reduced computational resources, as scoring is much faster than the generation of the trajectories.

  5. Experimental Determination of Third Derivative of the Gibbs Free Energy, G II

    DEFF Research Database (Denmark)

    Koga, Yoshikata; Westh, Peter; Inaba, Akira

    2010-01-01

    We have been evaluating third derivative quantities of the Gibbs free energy, G, by graphically differentiating the second derivatives that are accessible experimentally, and demonstrated their power in elucidating the mixing schemes in aqueous solutions. Here we determine directly one of the third...

  6. Gamma-point lattice free energy estimates from O(1) force calculations

    DEFF Research Database (Denmark)

    Voss, Johannes; Vegge, Tejs

    2008-01-01

    We present a new method for estimating the vibrational free energy of crystal (and molecular) structures employing only a single force calculation, for a particularly displaced configuration, in addition to the calculation of the ground state configuration. This displacement vector is the sum...

  7. Fast exploration of an optimal path on the multidimensional free energy surface

    Science.gov (United States)

    Chen, Changjun

    2017-01-01

    In a reaction, determination of an optimal path with a high reaction rate (or a low free energy barrier) is important for the study of the reaction mechanism. This is a complicated problem that involves lots of degrees of freedom. For simple models, one can build an initial path in the collective variable space by the interpolation method first and then update the whole path constantly in the optimization. However, such interpolation method could be risky in the high dimensional space for large molecules. On the path, steric clashes between neighboring atoms could cause extremely high energy barriers and thus fail the optimization. Moreover, performing simulations for all the snapshots on the path is also time-consuming. In this paper, we build and optimize the path by a growing method on the free energy surface. The method grows a path from the reactant and extends its length in the collective variable space step by step. The growing direction is determined by both the free energy gradient at the end of the path and the direction vector pointing at the product. With fewer snapshots on the path, this strategy can let the path avoid the high energy states in the growing process and save the precious simulation time at each iteration step. Applications show that the presented method is efficient enough to produce optimal paths on either the two-dimensional or the twelve-dimensional free energy surfaces of different small molecules. PMID:28542475

  8. Free energy minimization to predict RNA secondary structures and computational RNA design.

    Science.gov (United States)

    Churkin, Alexander; Weinbrand, Lina; Barash, Danny

    2015-01-01

    Determining the RNA secondary structure from sequence data by computational predictions is a long-standing problem. Its solution has been approached in two distinctive ways. If a multiple sequence alignment of a collection of homologous sequences is available, the comparative method uses phylogeny to determine conserved base pairs that are more likely to form as a result of billions of years of evolution than by chance. In the case of single sequences, recursive algorithms that compute free energy structures by using empirically derived energy parameters have been developed. This latter approach of RNA folding prediction by energy minimization is widely used to predict RNA secondary structure from sequence. For a significant number of RNA molecules, the secondary structure of the RNA molecule is indicative of its function and its computational prediction by minimizing its free energy is important for its functional analysis. A general method for free energy minimization to predict RNA secondary structures is dynamic programming, although other optimization methods have been developed as well along with empirically derived energy parameters. In this chapter, we introduce and illustrate by examples the approach of free energy minimization to predict RNA secondary structures.

  9. 3D Printed Potential and Free Energy Surfaces for Teaching Fundamental Concepts in Physical Chemistry

    Science.gov (United States)

    Kaliakin, Danil S.; Zaari, Ryan R.; Varganov, Sergey A.

    2015-01-01

    Teaching fundamental physical chemistry concepts such as the potential energy surface, transition state, and reaction path is a challenging task. The traditionally used oversimplified 2D representation of potential and free energy surfaces makes this task even more difficult and often confuses students. We show how this 2D representation can be…

  10. Free energies of stable and metastable pores in lipid membranes under tension

    NARCIS (Netherlands)

    den Otter, Wouter K.

    2009-01-01

    The free energy profile of pore formation in a lipid membrane, covering the entire range from a density fluctuation in an intact bilayer to a large tension-stabilized pore, has been calculated by molecular dynamics simulations with a coarse-grained lipid model. Several fixed elongations are used to

  11. Spontaneous symmetry breaking and self-consistent equations for the free-energy

    International Nuclear Information System (INIS)

    Lovesey, S.W.

    1980-03-01

    A variational procedure for the free-energy is used to derive self-consistent equations that allow for spontaneous symmetry breaking. For an N-component phi 4 -model the equations are identical to those obtained by summing all loops to order 1/N. (author)

  12. Interfacial free energy of the NaCl crystal-melt interface from capillary wave fluctuations.

    Science.gov (United States)

    Benet, Jorge; MacDowell, Luis G; Sanz, Eduardo

    2015-04-07

    In this work we study, by means of molecular dynamics simulations, the solid-liquid interface of NaCl under coexistence conditions. By analysing capillary waves, we obtain the stiffness for different orientations of the solid and calculate the interfacial free energy by expanding the dependency of the interfacial free energy with the solid orientation in terms of cubic harmonics. We obtain an average value for the solid-fluid interfacial free energy of 89 ± 6 mN m(-1) that is consistent with previous results based on the measure of nucleation free energy barriers [Valeriani et al., J. Chem. Phys. 122, 194501 (2005)]. We analyse the influence of the simulation setup on interfacial properties and find that facets prepared as an elongated rectangular stripe give the same results as those prepared as squares for all cases but the 111 face. For some crystal orientations, we observe at small wave-vectors a behaviour not consistent with capillary wave theory and show that this behavior does not depend on the simulation setup.

  13. Statistical mechanical perturbation theory of solid-vapor interfacial free energy

    NARCIS (Netherlands)

    Kalikmanov, Vitalij Iosifovitsj; Hagmeijer, Rob; Venner, Cornelis H.

    2017-01-01

    The solid–vapor interfacial free energy γsv plays an important role in a number of physical phenomena, such as adsorption, wetting, and adhesion. We propose a closed form expression for the orientation averaged value of this quantity using a statistical mechanical perturbation approach developed in

  14. Statistical Mechanical Perturbation Theory of Solid−Vapor Interfacial Free Energy

    NARCIS (Netherlands)

    Kalikmanov, V.I.; Hagmeijer, R.; Venner, C.H.

    2017-01-01

    The solid–vapor interfacial free energy γsv plays an important role in a number of physical phenomena, such as adsorption, wetting, and adhesion. We propose a closed form expression for the orientation averaged value of this quantity using a statistical mechanical perturbation approach developed in

  15. Probing the Free Energy Landscape of the FBP28 WW Domain Using Multiple Techniques

    NARCIS (Netherlands)

    Periole, Xavier; Allen, Lucy R.; Tamiola, Kamil; Mark, Alan E.; Paci, Emanuele

    The free-energy landscape of a small protein, the FBP 28 WW domain, has been explored using molecular dynamics (MD) simulations with alternative descriptions of the molecule. The molecular models used range from coarse-grained to all-atom with either an implicit or explicit treatment of the solvent.

  16. Generating Converged Accurate Free Energy Surfaces for Chemical Reactions with a Force-Matched Semiempirical Model.

    Science.gov (United States)

    Kroonblawd, Matthew P; Pietrucci, Fabio; Saitta, Antonino Marco; Goldman, Nir

    2018-04-10

    We demonstrate the capability of creating robust density functional tight binding (DFTB) models for chemical reactivity in prebiotic mixtures through force matching to short time scale quantum free energy estimates. Molecular dynamics using density functional theory (DFT) is a highly accurate approach to generate free energy surfaces for chemical reactions, but the extreme computational cost often limits the time scales and range of thermodynamic states that can feasibly be studied. In contrast, DFTB is a semiempirical quantum method that affords up to a thousandfold reduction in cost and can recover DFT-level accuracy. Here, we show that a force-matched DFTB model for aqueous glycine condensation reactions yields free energy surfaces that are consistent with experimental observations of reaction energetics. Convergence analysis reveals that multiple nanoseconds of combined trajectory are needed to reach a steady-fluctuating free energy estimate for glycine condensation. Predictive accuracy of force-matched DFTB is demonstrated by direct comparison to DFT, with the two approaches yielding surfaces with large regions that differ by only a few kcal mol -1 .

  17. Estimates of Gibbs free energies of formation of chlorinated aliphatic compounds

    NARCIS (Netherlands)

    Dolfing, Jan; Janssen, Dick B.

    1994-01-01

    The Gibbs free energy of formation of chlorinated aliphatic compounds was estimated with Mavrovouniotis' group contribution method. The group contribution of chlorine was estimated from the scarce data available on chlorinated aliphatics in the literature, and found to vary somewhat according to the

  18. Free energy and structure of dislocation cores in two-dimensional crystals

    NARCIS (Netherlands)

    Bladon, P.B.; Frenkel, D.

    2004-01-01

    The nature of the melting transition in two dimensions is critically dependent on the core energy of dislocations. In this paper, we report calculations of the core free energy and the core size of dislocations in two-dimensional solids of systems interacting via square well, hard disk, and r-12

  19. Minimizing the Free Energy: A Computer Method for Teaching Chemical Equilibrium Concepts.

    Science.gov (United States)

    Heald, Emerson F.

    1978-01-01

    Presents a computer method for teaching chemical equilibrium concepts using material balance conditions and the minimization of the free energy. Method for the calculation of chemical equilibrium, the computer program used to solve equilibrium problems and applications of the method are also included. (HM)

  20. Direct measurement of free-energy barrier to nucleation of crystallites in amorphous silicon thin films

    Science.gov (United States)

    Shi, Frank G.

    1994-01-01

    A method is introduced to measure the free-energy barrier W(sup *), the activation energy, and activation entropy to nucleation of crystallites in amorphous solids, independent of the energy barrier to growth. The method allows one to determine the temperature dependence of W(sup *), and the effect of the preparation conditions of the initial amorphous phase, the dopants, and the crystallization methds on W(sup *). The method is applied to determine the free-energy barrier to nucleation of crystallites in amorphous silicon (a-Si) thin films. For thermally induced nucleation in a-Si thin films with annealing temperatures in the range of from 824 to 983 K, the free-energy barrier W(sup *) to nucleation of silicon crystals is about 2.0 - 2.1 eV regardless of the preparation conditions of the films. The observation supports the idea that a-Si transforms into an intermediate amorphous state through the structural relaxation prior to the onset of nucleation of crystallites in a-Si. The observation also indicates that the activation entropy may be an insignificant part of the free-energy barrier for the nucleation of crystallites in a-Si. Compared with the free-energy barrier to nucleation of crystallites in undoped a-Si films, a significant reduction is observed in the free-energy barrier to nucleation in Cu-doped a-Si films. For a-Si under irradiation of Xe(2+) at 10(exp 5) eV, the free-energy barrier to ion-induced nucleation of crystallites is shown to be about half of the value associated with thermal-induced nucleation of crystallites in a-Si under the otherwise same conditions, which is much more significant than previously expected. The present method has a general kinetic basis; it thus should be equally applicable to nucleation of crystallites in any amorphous elemental semiconductors and semiconductor alloys, metallic and polymeric glasses, and to nucleation of crystallites in melts and solutions.

  1. Gibbs free energy of transfer of a methylene group on {UCON + (sodium or potassium) phosphate salts} aqueous two-phase systems: Hydrophobicity effects

    International Nuclear Information System (INIS)

    Silverio, Sara C.; Rodriguez, Oscar; Teixeira, Jose A.; Macedo, Eugenia A.

    2010-01-01

    The Gibbs free energy of transfer of a suitable hydrophobic probe can be regarded as a measure of the relative hydrophobicity of the different phases. The methylene group (CH 2 ) can be considered hydrophobic, and thus be a suitable probe for hydrophobicity. In this work, the partition coefficients of a series of five dinitrophenylated-amino acids were experimentally determined, at 23 o C, in three different tie-lines of the biphasic systems: (UCON + K 2 HPO 4 ), (UCON + potassium phosphate buffer, pH 7), (UCON + KH 2 PO 4 ), (UCON + Na 2 HPO 4 ), (UCON + sodium phosphate buffer, pH 7), and (UCON + NaH 2 PO 4 ). The Gibbs free energy of transfer of CH 2 units were calculated from the partition coefficients and used to compare the relative hydrophobicity of the equilibrium phases. The largest relative hydrophobicity was found for the ATPS formed by dihydrogen phosphate salts.

  2. Living systems do not minimize free energy. Comment on "Answering Schrödinger's question: A free-energy formulation" by Maxwell James Dèsormeau Ramstead et al.

    Science.gov (United States)

    Martyushev, Leonid M.

    2018-03-01

    The paper [1] is certainly very useful and important for understanding living systems (e.g. brain) as adaptive, self-organizing patterns. There is no need to enumerate all advantages of the paper, they are obvious. The purpose of my brief comment is to discuss one issue which, as I see it, was not thought out by the authors well enough. As a consequence, their ideas do not find as wide distribution as they otherwise could have found. This issue is related to the name selected for the principle forming the basis of their approach: free-energy principle (FEP). According to the sec. 2.1 [1]: "It asserts that all biological systems maintain their integrity by actively reducing the disorder or dispersion (i.e., entropy) of their sensory and physiological states by minimizing their variational free energy." Let us note that the authors suggested different names for the principle in their earlier works (an objective function, a function of the ensemble density encoded by the organism's configuration and the sensory data to which it is exposed, etc.), and explicitly and correctly mentioned that the free energy and entropy considered by them had nothing in common with the quantities employed in physics [2,3]. It is also obvious that a purely information-theoretic approach used by the authors with regard to the problems under study allows many other wordings and interpretations. However, in spite of this fact, in their last papers as well as in the present paper, the authors choose specifically FEP. Apparently, it may be explained by the intent to additionally base their approach on the foundation of statistical thermodynamics and therefore to demonstrate the universality of the described method. However, this is exactly what might cause misunderstandings specifically among physicists and consequently in their rejection and ignoring of FEP. The physical analogy employed by the authors has the following fundamental inconsistencies: In physics, free energy is used to describe

  3. Electron-related linear and nonlinear optical responses in vertically coupled triangular quantum dots

    International Nuclear Information System (INIS)

    Martínez-Orozco, J.C.; Mora-Ramos, M.E.; Duque, C.A.

    2014-01-01

    The conduction band states of GaAs-based vertically coupled double triangular quantum dots in two dimensions are investigated within the effective mass and parabolic approximation, using a diagonalization procedure to solve the corresponding Schrödinger-like equation. The effect of an externally applied static electric field is included in the calculation, and the variation of the lowest confined energy levels as a result of the change of the field strength is reported for different geometrical setups. The linear and nonlinear optical absorptions and the relative change of the refractive index, associated with the energy transition between the ground and the first excited state in the system, are studied as a function of the incident light frequency for distinct configurations of inter-dot distance and electric field intensities. The blueshift of the resonant absorption peaks is detected as a consequence of the increment in the field intensity, whereas the opposite effect is obtained from the increase of inter-dot vertical distance. It is also shown that for large enough values of the electric field there is a quenching of the optical absorption due to field-induced change of symmetry of the first excited state wavefunction, in the case of triangular dots of equal shape and size

  4. Electron-related linear and nonlinear optical responses in vertically coupled triangular quantum dots

    Energy Technology Data Exchange (ETDEWEB)

    Martínez-Orozco, J.C. [Unidad Académica de Física. Universidad Autónoma de Zacatecas, Calzada Solidaridad esquina con Paseo la Bufa S/N, C.P. 98060. Zacatecas, Zac. (Mexico); Grupo de Materia Condensada-UdeA, Instituto de Física, Facultad de Ciencias Exactas y Naturales, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín (Colombia); Mora-Ramos, M.E. [Facultad de Ciencias, Universidad Autónoma del Estado de Morelos, Ave. Universidad 1001, CP 62209, Cuernavaca, Morelos (Mexico); Duque, C.A., E-mail: cduque@fisica.udea.edu.co [Grupo de Materia Condensada-UdeA, Instituto de Física, Facultad de Ciencias Exactas y Naturales, Universidad de Antioquia UdeA, Calle 70 No. 52-21, Medellín (Colombia)

    2014-11-01

    The conduction band states of GaAs-based vertically coupled double triangular quantum dots in two dimensions are investigated within the effective mass and parabolic approximation, using a diagonalization procedure to solve the corresponding Schrödinger-like equation. The effect of an externally applied static electric field is included in the calculation, and the variation of the lowest confined energy levels as a result of the change of the field strength is reported for different geometrical setups. The linear and nonlinear optical absorptions and the relative change of the refractive index, associated with the energy transition between the ground and the first excited state in the system, are studied as a function of the incident light frequency for distinct configurations of inter-dot distance and electric field intensities. The blueshift of the resonant absorption peaks is detected as a consequence of the increment in the field intensity, whereas the opposite effect is obtained from the increase of inter-dot vertical distance. It is also shown that for large enough values of the electric field there is a quenching of the optical absorption due to field-induced change of symmetry of the first excited state wavefunction, in the case of triangular dots of equal shape and size.

  5. Molybdenum carbide nanoparticles as catalysts for oil sands upgrading: Dynamics and free-energy profiles

    International Nuclear Information System (INIS)

    Liu, Xingchen; Salahub, Dennis R.

    2015-01-01

    There is no doubt that a huge gap exists in understanding heterogeneous catalysis between a cluster model of a few atoms and a bulk model of periodic slabs. Nanoparticles, which are crucial in heterogeneous catalysis in industry, lie in the middle of the gap. We present here our work on the computational modelling of molybdenum carbide nanoparticles (MCNPs) as the catalysts for the upgrading of oil sands in the in-situ environment, using benzene hydrogenation as a model reaction. With a cluster model, efforts were first made to understand the mechanism of the reaction with a density functional theory (DFT) study on the adsorption of benzene and its hydrogenation product – cyclohexane, as well as the cyclic hydrogenation reaction intermediates on the Mo 2 C(0001) surface. From the thermodynamic data, along with literature information, it was found that the benzene hydrogenation reaction on molybdenum carbide happens most likely through a Langmuir-Hinshelwood mechanism with the gradual lifting up of the benzene molecule. The electron localization function (ELF) was then used to help understand the nature of the interactions between the MCNPs, identifying strong multi-center interactions between the adsorbates and the MCNPs. To enable the treatment of larger nanoparticles, a fast semi-empirical density functional tight-binding (DFTB) method was parameterized. With this method, the potential energy profiles of benzene hydrogenation reactions on different sizes of MCNPs are calculated. The study was then extended to consider a MCNP embedded in solvent (benzene), using a quantum mechanical (DFTB) / molecular mechanical approach. Calculations on the free energies profiles with the umbrella sampling method show that the entropy of the MCNPs and the solvent are essential in understanding the catalytic activity of the transition metal related nanoparticles for solid/liquid heterogeneous catalysis

  6. Free energy and stability of macromolecules studied by the double scanning simulation procedure

    International Nuclear Information System (INIS)

    Meirovitch, H.; Vasquez, M.; Scheraga, H.A.

    1990-01-01

    The double scanning method (DSM) is a computer simulation technique suggested recently by Meirovitch [J. Chem. Phys. 89, 2514 (1988)]. This method is a variant of the usual or ''single'' scanning method (SSM) of the same author, which was extended by us to polypeptides [Biopolymers 27, 1189 (1988); this paper is designated here as paper II]. The two methods are step-by-step construction procedures from which the entropy and the free energy can be estimated. The transition probabilities are obtained by scanning the so-called ''future'' chains, which are continuations of the chain in future steps up to a maximum of b steps. With the SSM, the process is carried out by exact enumeration of the future chains; this is time consuming, and therefore b is limited to small values. With the DSM, on the other hand, only a relatively small sample of the future chains is generated by applying an additional scanning procedure. This enables one to increase b at the expense of approximating the transition probabilities. Increasing of b, however, is important in order to treat medium- and long-range interactions more properly. In this paper (as in our paper II), we apply the DSM to a model of decaglycine without solvent, described by the potential energy function ECEPP at 100 and 300 K. Using the SSM with the maximal value, b=4, we found in paper II that, at 100 K, the α helix rather than the statistical coil is the most stable state. The present DSM simulation at T=100 K (based on b=5) is more efficient than the SSM, and a structure with significantly lower energy than that of the α helix is found. It is argued that b can be increased further to 7 at this temperature. At 300 K the DSM, like the SSM, shows that the statistical coil is the most stable state of decaglycine. However, the DSM is found to be less efficient than the SSM

  7. Molybdenum carbide nanoparticles as catalysts for oil sands upgrading: Dynamics and free-energy profiles

    Energy Technology Data Exchange (ETDEWEB)

    Liu, Xingchen; Salahub, Dennis R. [Department of Chemistry, Institute for Quantum Science and Technology, and Centre for Molecular Simulation, University of Calgary, 2500 University Drive NW, Calgary, Alberta, Canada T2N 1N4 (Canada)

    2015-12-31

    There is no doubt that a huge gap exists in understanding heterogeneous catalysis between a cluster model of a few atoms and a bulk model of periodic slabs. Nanoparticles, which are crucial in heterogeneous catalysis in industry, lie in the middle of the gap. We present here our work on the computational modelling of molybdenum carbide nanoparticles (MCNPs) as the catalysts for the upgrading of oil sands in the in-situ environment, using benzene hydrogenation as a model reaction. With a cluster model, efforts were first made to understand the mechanism of the reaction with a density functional theory (DFT) study on the adsorption of benzene and its hydrogenation product – cyclohexane, as well as the cyclic hydrogenation reaction intermediates on the Mo{sub 2}C(0001) surface. From the thermodynamic data, along with literature information, it was found that the benzene hydrogenation reaction on molybdenum carbide happens most likely through a Langmuir-Hinshelwood mechanism with the gradual lifting up of the benzene molecule. The electron localization function (ELF) was then used to help understand the nature of the interactions between the MCNPs, identifying strong multi-center interactions between the adsorbates and the MCNPs. To enable the treatment of larger nanoparticles, a fast semi-empirical density functional tight-binding (DFTB) method was parameterized. With this method, the potential energy profiles of benzene hydrogenation reactions on different sizes of MCNPs are calculated. The study was then extended to consider a MCNP embedded in solvent (benzene), using a quantum mechanical (DFTB) / molecular mechanical approach. Calculations on the free energies profiles with the umbrella sampling method show that the entropy of the MCNPs and the solvent are essential in understanding the catalytic activity of the transition metal related nanoparticles for solid/liquid heterogeneous catalysis.

  8. Towards accurate free energy calculations in ligand protein-binding studies.

    Science.gov (United States)

    Steinbrecher, Thomas; Labahn, Andreas

    2010-01-01

    Cells contain a multitude of different chemical reaction paths running simultaneously and quite independently next to each other. This amazing feat is enabled by molecular recognition, the ability of biomolecules to form stable and specific complexes with each other and with their substrates. A better understanding of this process, i.e. of the kinetics, structures and thermodynamic properties of biomolecule binding, would be invaluable in the study of biological systems. In addition, as the mode of action of many pharmaceuticals is based upon their inhibition or activation of biomolecule targets, predictive models of small molecule receptor binding are very helpful tools in rational drug design. Since the goal here is normally to design a new compound with a high inhibition strength, one of the most important thermodynamic properties is the binding free energy DeltaG(0). The prediction of binding constants has always been one of the major goals in the field of computational chemistry, because the ability to reliably assess a hypothetical compound's binding properties without having to synthesize it first would save a tremendous amount of work. The different approaches to this question range from fast and simple empirical descriptor methods to elaborate simulation protocols aimed at putting the computation of free energies onto a solid foundation of statistical thermodynamics. While the later methods are still not suited for the screenings of thousands of compounds that are routinely performed in computational drug design studies, they are increasingly put to use for the detailed study of protein ligand interactions. This review will focus on molecular mechanics force field based free energy calculations and their application to the study of protein ligand interactions. After a brief overview of other popular methods for the calculation of free energies, we will describe recent advances in methodology and a variety of exemplary studies of molecular dynamics

  9. Designing molecular complexes using free-energy derivatives from liquid-state integral equation theory

    International Nuclear Information System (INIS)

    Mrugalla, Florian; Kast, Stefan M

    2016-01-01

    Complex formation between molecules in solution is the key process by which molecular interactions are translated into functional systems. These processes are governed by the binding or free energy of association which depends on both direct molecular interactions and the solvation contribution. A design goal frequently addressed in pharmaceutical sciences is the optimization of chemical properties of the complex partners in the sense of minimizing their binding free energy with respect to a change in chemical structure. Here, we demonstrate that liquid-state theory in the form of the solute–solute equation of the reference interaction site model provides all necessary information for such a task with high efficiency. In particular, computing derivatives of the potential of mean force (PMF), which defines the free-energy surface of complex formation, with respect to potential parameters can be viewed as a means to define a direction in chemical space toward better binders. We illustrate the methodology in the benchmark case of alkali ion binding to the crown ether 18-crown-6 in aqueous solution. In order to examine the validity of the underlying solute–solute theory, we first compare PMFs computed by different approaches, including explicit free-energy molecular dynamics simulations as a reference. Predictions of an optimally binding ion radius based on free-energy derivatives are then shown to yield consistent results for different ion parameter sets and to compare well with earlier, orders-of-magnitude more costly explicit simulation results. This proof-of-principle study, therefore, demonstrates the potential of liquid-state theory for molecular design problems. (paper)

  10. Sampling free energy surfaces as slices by combining umbrella sampling and metadynamics.

    Science.gov (United States)

    Awasthi, Shalini; Kapil, Venkat; Nair, Nisanth N

    2016-06-15

    Metadynamics (MTD) is a very powerful technique to sample high-dimensional free energy landscapes, and due to its self-guiding property, the method has been successful in studying complex reactions and conformational changes. MTD sampling is based on filling the free energy basins by biasing potentials and thus for cases with flat, broad, and unbound free energy wells, the computational time to sample them becomes very large. To alleviate this problem, we combine the standard Umbrella Sampling (US) technique with MTD to sample orthogonal collective variables (CVs) in a simultaneous way. Within this scheme, we construct the equilibrium distribution of CVs from biased distributions obtained from independent MTD simulations with umbrella potentials. Reweighting is carried out by a procedure that combines US reweighting and Tiwary-Parrinello MTD reweighting within the Weighted Histogram Analysis Method (WHAM). The approach is ideal for a controlled sampling of a CV in a MTD simulation, making it computationally efficient in sampling flat, broad, and unbound free energy surfaces. This technique also allows for a distributed sampling of a high-dimensional free energy surface, further increasing the computational efficiency in sampling. We demonstrate the application of this technique in sampling high-dimensional surface for various chemical reactions using ab initio and QM/MM hybrid molecular dynamics simulations. Further, to carry out MTD bias reweighting for computing forward reaction barriers in ab initio or QM/MM simulations, we propose a computationally affordable approach that does not require recrossing trajectories. © 2016 Wiley Periodicals, Inc. © 2016 Wiley Periodicals, Inc.

  11. Casimir free energy of dielectric films: classical limit, low-temperature behavior and control.

    Science.gov (United States)

    Klimchitskaya, G L; Mostepanenko, V M

    2017-07-12

    The Casimir free energy of dielectric films, both free-standing in vacuum and deposited on metallic or dielectric plates, is investigated. It is shown that the values of the free energy depend considerably on whether the calculation approach used neglects or takes into account the dc conductivity of film material. We demonstrate that there are material-dependent and universal classical limits in the former and latter cases, respectively. The analytic behavior of the Casimir free energy and entropy for a free-standing dielectric film at low temperature is found. According to our results, the Casimir entropy goes to zero when the temperature vanishes if the calculation approach with neglected dc conductivity of a film is employed. If the dc conductivity is taken into account, the Casimir entropy takes the positive value at zero temperature, depending on the parameters of a film, i.e. the Nernst heat theorem is violated. By considering the Casimir free energy of SiO 2 and Al 2 O 3 films deposited on a Au plate in the framework of two calculation approaches, we argue that physically correct values are obtained by disregarding the role of dc conductivity. A comparison with the well known results for the configuration of two parallel plates is made. Finally, we compute the Casimir free energy of SiO 2 , Al 2 O 3 and Ge films deposited on high-resistivity Si plates of different thicknesses and demonstrate that it can be positive, negative and equal to zero. The effect of illumination of a Si plate with laser light is considered. Possible applications of the obtained results to thin films used in microelectronics are discussed.

  12. Casimir free energy of dielectric films: classical limit, low-temperature behavior and control

    Science.gov (United States)

    Klimchitskaya, G. L.; Mostepanenko, V. M.

    2017-07-01

    The Casimir free energy of dielectric films, both free-standing in vacuum and deposited on metallic or dielectric plates, is investigated. It is shown that the values of the free energy depend considerably on whether the calculation approach used neglects or takes into account the dc conductivity of film material. We demonstrate that there are material-dependent and universal classical limits in the former and latter cases, respectively. The analytic behavior of the Casimir free energy and entropy for a free-standing dielectric film at low temperature is found. According to our results, the Casimir entropy goes to zero when the temperature vanishes if the calculation approach with neglected dc conductivity of a film is employed. If the dc conductivity is taken into account, the Casimir entropy takes the positive value at zero temperature, depending on the parameters of a film, i.e. the Nernst heat theorem is violated. By considering the Casimir free energy of SiO2 and Al2O3 films deposited on a Au plate in the framework of two calculation approaches, we argue that physically correct values are obtained by disregarding the role of dc conductivity. A comparison with the well known results for the configuration of two parallel plates is made. Finally, we compute the Casimir free energy of SiO2, Al2O3 and Ge films deposited on high-resistivity Si plates of different thicknesses and demonstrate that it can be positive, negative and equal to zero. The effect of illumination of a Si plate with laser light is considered. Possible applications of the obtained results to thin films used in microelectronics are discussed.

  13. Accuracy of free energies of hydration using CM1 and CM3 atomic charges.

    Science.gov (United States)

    Udier-Blagović, Marina; Morales De Tirado, Patricia; Pearlman, Shoshannah A; Jorgensen, William L

    2004-08-01

    Absolute free energies of hydration (DeltaGhyd) have been computed for 25 diverse organic molecules using partial atomic charges derived from AM1 and PM3 wave functions via the CM1 and CM3 procedures of Cramer, Truhlar, and coworkers. Comparisons are made with results using charges fit to the electrostatic potential surface (EPS) from ab initio 6-31G* wave functions and from the OPLS-AA force field. OPLS Lennard-Jones parameters for the organic molecules were used together with the TIP4P water model in Monte Carlo simulations with free energy perturbation theory. Absolute free energies of hydration were computed for OPLS united-atom and all-atom methane by annihilating the solutes in water and in the gas phase, and absolute DeltaGhyd values for all other molecules were computed via transformation to one of these references. Optimal charge scaling factors were determined by minimizing the unsigned average error between experimental and calculated hydration free energies. The PM3-based charge models do not lead to lower average errors than obtained with the EPS charges for the subset of 13 molecules in the original study. However, improvement is obtained by scaling the CM1A partial charges by 1.14 and the CM3A charges by 1.15, which leads to average errors of 1.0 and 1.1 kcal/mol for the full set of 25 molecules. The scaled CM1A charges also yield the best results for the hydration of amides including the E/Z free-energy difference for N-methylacetamide in water. Copyright 2004 Wiley Periodicals, Inc.

  14. Extending the Solvation-Layer Interface Condition Continum Electrostatic Model to a Linearized Poisson-Boltzmann Solvent.

    Science.gov (United States)

    Molavi Tabrizi, Amirhossein; Goossens, Spencer; Mehdizadeh Rahimi, Ali; Cooper, Christopher D; Knepley, Matthew G; Bardhan, Jaydeep P

    2017-06-13

    We extend the linearized Poisson-Boltzmann (LPB) continuum electrostatic model for molecular solvation to address charge-hydration asymmetry. Our new solvation-layer interface condition (SLIC)/LPB corrects for first-shell response by perturbing the traditional continuum-theory interface conditions at the protein-solvent and the Stern-layer interfaces. We also present a GPU-accelerated treecode implementation capable of simulating large proteins, and our results demonstrate that the new model exhibits significant accuracy improvements over traditional LPB models, while reducing the number of fitting parameters from dozens (atomic radii) to just five parameters, which have physical meanings related to first-shell water behavior at an uncharged interface. In particular, atom radii in the SLIC model are not optimized but uniformly scaled from their Lennard-Jones radii. Compared to explicit-solvent free-energy calculations of individual atoms in small molecules, SLIC/LPB is significantly more accurate than standard parametrizations (RMS error 0.55 kcal/mol for SLIC, compared to RMS error of 3.05 kcal/mol for standard LPB). On parametrizing the electrostatic model with a simple nonpolar component for total molecular solvation free energies, our model predicts octanol/water transfer free energies with an RMS error 1.07 kcal/mol. A more detailed assessment illustrates that standard continuum electrostatic models reproduce total charging free energies via a compensation of significant errors in atomic self-energies; this finding offers a window into improving the accuracy of Generalized-Born theories and other coarse-grained models. Most remarkably, the SLIC model also reproduces positive charging free energies for atoms in hydrophobic groups, whereas standard PB models are unable to generate positive charging free energies regardless of the parametrized radii. The GPU-accelerated solver is freely available online, as is a MATLAB implementation.

  15. Statistical distributions of earthquakes and related non-linear features in seismic waves

    International Nuclear Information System (INIS)

    Apostol, B.-F.

    2006-01-01

    A few basic facts in the science of the earthquakes are briefly reviewed. An accumulation, or growth, model is put forward for the focal mechanisms and the critical focal zone of the earthquakes, which relates the earthquake average recurrence time to the released seismic energy. The temporal statistical distribution for average recurrence time is introduced for earthquakes, and, on this basis, the Omori-type distribution in energy is derived, as well as the distribution in magnitude, by making use of the semi-empirical Gutenberg-Richter law relating seismic energy to earthquake magnitude. On geometric grounds, the accumulation model suggests the value r = 1/3 for the Omori parameter in the power-law of energy distribution, which leads to β = 1,17 for the coefficient in the Gutenberg-Richter recurrence law, in fair agreement with the statistical analysis of the empirical data. Making use of this value, the empirical Bath's law is discussed for the average magnitude of the aftershocks (which is 1.2 less than the magnitude of the main seismic shock), by assuming that the aftershocks are relaxation events of the seismic zone. The time distribution of the earthquakes with a fixed average recurrence time is also derived, the earthquake occurrence prediction is discussed by means of the average recurrence time and the seismicity rate, and application of this discussion to the seismic region Vrancea, Romania, is outlined. Finally, a special effect of non-linear behaviour of the seismic waves is discussed, by describing an exact solution derived recently for the elastic waves equation with cubic anharmonicities, its relevance, and its connection to the approximate quasi-plane waves picture. The properties of the seismic activity accompanying a main seismic shock, both like foreshocks and aftershocks, are relegated to forthcoming publications. (author)

  16. Acquisition of rheological and calorimetric properties of borosilicate glass to determine the free energy of formation

    International Nuclear Information System (INIS)

    Linard, Y.; Advocat, Th.

    2000-01-01

    measure low viscosities at up to 1700 K. The Adam-Gibbs theory of the entropy of relaxation processes allowed the calculation of S conf (T g ) from the various viscosity measurements. The enthalpy of formation for each glass composition was determined from experimental measurements of the enthalpy of dissolution Δ s H(T s ) of a glass sample in a molten salt ( 2 PbO.B 2 O 3 ) at 970 K using a Tian-Calvet calorimeter. Figure 3 shows some of the results obtained with simple glass compositions. The heat capacity C p , measured within 0.7% uncertainty, gradually increased with temperature, with a sharp rise at the glass transition point T g , and then remained constant at higher temperatures. The measured viscosities are shown in Figure 4, revealing the strong influence of the composition on the viscosity at temperatures near T g between 800 and 1000 K. The temperature plot does not follow a classic Arrhenius relation-hence the use of (Eqn(5)) to calculate S conf (T g ), which ranged from 10 to 17 J.mol-1 K -1 (±3 5%) for the test compositions. A narrow range of values was obtained for the enthalpy of glass dissolution in lead borate at 970 K: -0.62 to 0.37 kJ.moL -1 with relatively high (50-100%) uncertainty. All the basic parameters needed to determine the free energy of formation Δ f G T) are thus available; the results calculated using Eqns (3), (4,) and (1) are given in Table I at room temperature (298 K). In the final step, the free energy of dissolution in water was calculated for the glass compositions by integrating the thermodynamic properties obtained from the previously described experimental methods. Major differences were observed with respect to the free energy of dissolution determined by a simple model from the sum of the thermodynamic properties of simple binary silicates. These experimental determinations will allow an assessment of glass thermodynamic stability in water. This step will notably involve the correlation of aqueous leaching results with the

  17. SOME STATISTICAL ISSUES RELATED TO MULTIPLE LINEAR REGRESSION MODELING OF BEACH BACTERIA CONCENTRATIONS

    Science.gov (United States)

    As a fast and effective technique, the multiple linear regression (MLR) method has been widely used in modeling and prediction of beach bacteria concentrations. Among previous works on this subject, however, several issues were insufficiently or inconsistently addressed. Those is...

  18. A Maple package for computing Groebner bases for linear recurrence relations

    International Nuclear Information System (INIS)

    Gerdt, Vladimir P.; Robertz, Daniel

    2006-01-01

    A Maple package for computing Groebner bases of linear difference ideals is described. The underlying algorithm is based on Janet and Janet-like monomial divisions associated with finite difference operators. The package can be used, for example, for automatic generation of difference schemes for linear partial differential equations and for reduction of multiloop Feynman integrals. These two possible applications are illustrated by simple examples of the Laplace equation and a one-loop scalar integral of propagator type

  19. A Maple package for computing Groebner bases for linear recurrence relations

    Energy Technology Data Exchange (ETDEWEB)

    Gerdt, Vladimir P. [Laboratory of Information Technologies, Joint Institute for Nuclear Research, 141980 Dubna (Russian Federation)]. E-mail: gerdt@jinr.ru; Robertz, Daniel [Lehrstuhl B fuer Mathematik, RWTH Aachen, Templergraben 64, D-52062 Aachen (Germany)]. E-mail: daniel@momo.math.rwth-aachen.de

    2006-04-01

    A Maple package for computing Groebner bases of linear difference ideals is described. The underlying algorithm is based on Janet and Janet-like monomial divisions associated with finite difference operators. The package can be used, for example, for automatic generation of difference schemes for linear partial differential equations and for reduction of multiloop Feynman integrals. These two possible applications are illustrated by simple examples of the Laplace equation and a one-loop scalar integral of propagator type.

  20. EEG sensorimotor rhythms' variation and functional connectivity measures during motor imagery: linear relations and classification approaches.

    Science.gov (United States)

    Stefano Filho, Carlos A; Attux, Romis; Castellano, Gabriela

    2017-01-01

    Hands motor imagery (MI) has been reported to alter synchronization patterns amongst neurons, yielding variations in the mu and beta bands' power spectral density (PSD) of the electroencephalography (EEG) signal. These alterations have been used in the field of brain-computer interfaces (BCI), in an attempt to assign distinct MI tasks to commands of such a system. Recent studies have highlighted that information may be missing if knowledge about brain functional connectivity is not considered. In this work, we modeled the brain as a graph in which each EEG electrode represents a node. Our goal was to understand if there exists any linear correlation between variations in the synchronization patterns-that is, variations in the PSD of mu and beta bands-induced by MI and alterations in the corresponding functional networks. Moreover, we (1) explored the feasibility of using functional connectivity parameters as features for a classifier in the context of an MI-BCI; (2) investigated three different types of feature selection (FS) techniques; and (3) compared our approach to a more traditional method using the signal PSD as classifier inputs. Ten healthy subjects participated in this study. We observed significant correlations ( p  < 0.05) with values ranging from 0.4 to 0.9 between PSD variations and functional network alterations for some electrodes, prominently in the beta band. The PSD method performed better for data classification, with mean accuracies of (90 ± 8)% and (87 ± 7)% for the mu and beta band, respectively, versus (83 ± 8)% and (83 ± 7)% for the same bands for the graph method. Moreover, the number of features for the graph method was considerably larger. However, results for both methods were relatively close, and even overlapped when the uncertainties of the accuracy rates were considered. Further investigation regarding a careful exploration of other graph metrics may provide better alternatives.

  1. lme4qtl: linear mixed models with flexible covariance structure for genetic studies of related individuals.

    Science.gov (United States)

    Ziyatdinov, Andrey; Vázquez-Santiago, Miquel; Brunel, Helena; Martinez-Perez, Angel; Aschard, Hugues; Soria, Jose Manuel

    2018-02-27

    Quantitative trait locus (QTL) mapping in genetic data often involves analysis of correlated observations, which need to be accounted for to avoid false association signals. This is commonly performed by modeling such correlations as random effects in linear mixed models (LMMs). The R package lme4 is a well-established tool that implements major LMM features using sparse matrix methods; however, it is not fully adapted for QTL mapping association and linkage studies. In particular, two LMM features are lacking in the base version of lme4: the definition of random effects by custom covariance matrices; and parameter constraints, which are essential in advanced QTL models. Apart from applications in linkage studies of related individuals, such functionalities are of high interest for association studies in situations where multiple covariance matrices need to be modeled, a scenario not covered by many genome-wide association study (GWAS) software. To address the aforementioned limitations, we developed a new R package lme4qtl as an extension of lme4. First, lme4qtl contributes new models for genetic studies within a single tool integrated with lme4 and its companion packages. Second, lme4qtl offers a flexible framework for scenarios with multiple levels of relatedness and becomes efficient when covariance matrices are sparse. We showed the value of our package using real family-based data in the Genetic Analysis of Idiopathic Thrombophilia 2 (GAIT2) project. Our software lme4qtl enables QTL mapping models with a versatile structure of random effects and efficient computation for sparse covariances. lme4qtl is available at https://github.com/variani/lme4qtl .

  2. Breaking the polar-nonpolar division in solvation free energy prediction.

    Science.gov (United States)

    Wang, Bao; Wang, Chengzhang; Wu, Kedi; Wei, Guo-Wei

    2018-02-05

    Implicit solvent models divide solvation free energies into polar and nonpolar additive contributions, whereas polar and nonpolar interactions are inseparable and nonadditive. We present a feature functional theory (FFT) framework to break this ad hoc division. The essential ideas of FFT are as follows: (i) representability assumption: there exists a microscopic feature vector that can uniquely characterize and distinguish one molecule from another; (ii) feature-function relationship assumption: the macroscopic features, including solvation free energy, of a molecule is a functional of microscopic feature vectors; and (iii) similarity assumption: molecules with similar microscopic features have similar macroscopic properties, such as solvation free energies. Based on these assumptions, solvation free energy prediction is carried out in the following protocol. First, we construct a molecular microscopic feature vector that is efficient in characterizing the solvation process using quantum mechanics and Poisson-Boltzmann theory. Microscopic feature vectors are combined with macroscopic features, that is, physical observable, to form extended feature vectors. Additionally, we partition a solvation dataset into queries according to molecular compositions. Moreover, for each target molecule, we adopt a machine learning algorithm for its nearest neighbor search, based on the selected microscopic feature vectors. Finally, from the extended feature vectors of obtained nearest neighbors, we construct a functional of solvation free energy, which is employed to predict the solvation free energy of the target molecule. The proposed FFT model has been extensively validated via a large dataset of 668 molecules. The leave-one-out test gives an optimal root-mean-square error (RMSE) of 1.05 kcal/mol. FFT predictions of SAMPL0, SAMPL1, SAMPL2, SAMPL3, and SAMPL4 challenge sets deliver the RMSEs of 0.61, 1.86, 1.64, 0.86, and 1.14 kcal/mol, respectively. Using a test set of 94

  3. Incorporation of Hydrogen Bond Angle Dependency into the Generalized Solvation Free Energy Density Model.

    Science.gov (United States)

    Ma, Songling; Hwang, Sungbo; Lee, Sehan; Acree, William E; No, Kyoung Tai

    2018-04-23

    To describe the physically realistic solvation free energy surface of a molecule in a solvent, a generalized version of the solvation free energy density (G-SFED) calculation method has been developed. In the G-SFED model, the contribution from the hydrogen bond (HB) between a solute and a solvent to the solvation free energy was calculated as the product of the acidity of the donor and the basicity of the acceptor of an HB pair. The acidity and basicity parameters of a solute were derived using the summation of acidities and basicities of the respective acidic and basic functional groups of the solute, and that of the solvent was experimentally determined. Although the contribution of HBs to the solvation free energy could be evenly distributed to grid points on the surface of a molecule, the G-SFED model was still inadequate to describe the angle dependency of the HB of a solute with a polarizable continuum solvent. To overcome this shortcoming of the G-SFED model, the contribution of HBs was formulated using the geometric parameters of the grid points described in the HB coordinate system of the solute. We propose an HB angle dependency incorporated into the G-SFED model, i.e., the G-SFED-HB model, where the angular-dependent acidity and basicity densities are defined and parametrized with experimental data. The G-SFED-HB model was then applied to calculate the solvation free energies of organic molecules in water, various alcohols and ethers, and the log P values of diverse organic molecules, including peptides and a protein. Both the G-SFED model and the G-SFED-HB model reproduced the experimental solvation free energies with similar accuracy, whereas the distributions of the SFED on the molecular surface calculated by the G-SFED and G-SFED-HB models were quite different, especially for molecules having HB donors or acceptors. Since the angle dependency of HBs was included in the G-SFED-HB model, the SFED distribution of the G-SFED-HB model is well described

  4. Linear versus non-linear measures of temporal variability in finger tapping and their relation to performance on open- versus closed-loop motor tasks: comparing standard deviations to Lyapunov exponents.

    Science.gov (United States)

    Christman, Stephen D; Weaver, Ryan

    2008-05-01

    The nature of temporal variability during speeded finger tapping was examined using linear (standard deviation) and non-linear (Lyapunov exponent) measures. Experiment 1 found that right hand tapping was characterised by lower amounts of both linear and non-linear measures of variability than left hand tapping, and that linear and non-linear measures of variability were often negatively correlated with one another. Experiment 2 found that increased non-linear variability was associated with relatively enhanced performance on a closed-loop motor task (mirror tracing) and relatively impaired performance on an open-loop motor task (pointing in a dark room), especially for left hand performance. The potential uses and significance of measures of non-linear variability are discussed.

  5. The role of the concentration scale in the definition of transfer free energies.

    Science.gov (United States)

    Moeser, Beate; Horinek, Dominik

    2015-01-01

    The Gibbs free energy of transferring a solute at infinite dilution between two solvents quantifies differences in solute-solvent interactions - if the transfer takes place at constant molarity of the solute. Yet, many calculation formulae and measuring instructions that are commonly used to quantify solute-solvent interactions correspond to transfer processes in which not the molarity of the solute but its concentration measured in another concentration scale is constant. Here, we demonstrate that in this case, not only the change in solute-solvent interactions is quantified but also the entropic effect of a volume change during the transfer. Consequently, the "phenomenon" which is known as "concentration-scale dependence" of transfer free energies is simply explained by a volume-entropy effect. Our explanations are of high importance for the study of cosolvent effects on protein stability. Copyright © 2014 Elsevier B.V. All rights reserved.

  6. Gibbs free energy of formation of lanthanum rhodate by quadrupole mass spectrometer

    International Nuclear Information System (INIS)

    Prasad, R.; Banerjee, Aparna; Venugopal, V.

    2003-01-01

    The ternary oxide in the system La-Rh-O is of considerable importance because of its application in catalysis. Phase equilibria in the pseudo-binary system La 2 O 3 -Rh 2 O 3 has been investigated by Shevyakov et. al. Gibbs free energy of LaRhO 3 (s) was determined by Jacob et. al. using a solid state Galvanic cell in the temperature range 890 to 1310 K. No other thermodynamic data were available in the literature. Hence it was decided to determine Gibbs free energy of formation of LaRhO 3 (s) by an independent technique, viz. quadrupole mass spectrometer (QMS) coupled with a Knudsen effusion cell and the results are presented

  7. Efficient approach to obtain free energy gradient using QM/MM MD simulation

    International Nuclear Information System (INIS)

    Asada, Toshio; Koseki, Shiro; Ando, Kanta

    2015-01-01

    The efficient computational approach denoted as charge and atom dipole response kernel (CDRK) model to consider polarization effects of the quantum mechanical (QM) region is described using the charge response and the atom dipole response kernels for free energy gradient (FEG) calculations in the quantum mechanical/molecular mechanical (QM/MM) method. CDRK model can reasonably reproduce energies and also energy gradients of QM and MM atoms obtained by expensive QM/MM calculations in a drastically reduced computational time. This model is applied on the acylation reaction in hydrated trypsin-BPTI complex to optimize the reaction path on the free energy surface by means of FEG and the nudged elastic band (NEB) method

  8. Bespoke Bias for Obtaining Free Energy Differences within Variationally Enhanced Sampling.

    Science.gov (United States)

    McCarty, James; Valsson, Omar; Parrinello, Michele

    2016-05-10

    Obtaining efficient sampling of multiple metastable states through molecular dynamics and hence determining free energy differences is central for understanding many important phenomena. Here we present a new biasing strategy, which employs the recent variationally enhanced sampling approach (Valsson and Parrinello Phys. Rev. Lett. 2014, 113, 090601). The bias is constructed from an intuitive model of the local free energy surface describing fluctuations around metastable minima and depends on only a few parameters which are determined variationally such that efficient sampling between states is obtained. The bias constructed in this manner largely reduces the need of finding a set of collective variables that completely spans the conformational space of interest, as they only need to be a locally valid descriptor of the system about its local minimum. We introduce the method and demonstrate its power on two representative examples.

  9. Unbiased free energy estimates in fast nonequilibrium transformations using Gaussian mixtures

    International Nuclear Information System (INIS)

    Procacci, Piero

    2015-01-01

    In this paper, we present an improved method for obtaining unbiased estimates of the free energy difference between two thermodynamic states using the work distribution measured in nonequilibrium driven experiments connecting these states. The method is based on the assumption that any observed work distribution is given by a mixture of Gaussian distributions, whose normal components are identical in either direction of the nonequilibrium process, with weights regulated by the Crooks theorem. Using the prototypical example for the driven unfolding/folding of deca-alanine, we show that the predicted behavior of the forward and reverse work distributions, assuming a combination of only two Gaussian components with Crooks derived weights, explains surprisingly well the striking asymmetry in the observed distributions at fast pulling speeds. The proposed methodology opens the way for a perfectly parallel implementation of Jarzynski-based free energy calculations in complex systems

  10. Free energy correlation of rate constants for electron transfer between organic systems in aqueous solutions

    Energy Technology Data Exchange (ETDEWEB)

    Meisel, D

    1975-07-15

    Recent experimental data concerning the rate constants for electron transfer reactions of organic systems in aqueous solutions and their equilibrium constants is examined for possible correlation. The data is correlated quite well by the Marcus theory, if a reorganization parameter, lambda, of 18 kcal/mole is used. Assuming that the only contribution to lambda is the free energy of rearrangement of the water molecules, an effective radius of 5 A for the reacting entities is estimated. For the zero free energy change reaction, i.e., electron exchange between a radical ion and its parent molecule, a rate constant of about 5 X 10/sup 7/ M/sup -1/ s/sup -1/ is predicted. (auth)

  11. Tsallis’ non-extensive free energy as a subjective value of an uncertain reward

    Science.gov (United States)

    Takahashi, Taiki

    2009-03-01

    Recent studies in neuroeconomics and econophysics revealed the importance of reward expectation in decision under uncertainty. Behavioral neuroeconomic studies have proposed that the unpredictability and the probability of an uncertain reward are distinctly encoded as entropy and a distorted probability weight, respectively, in the separate neural systems. However, previous behavioral economic and decision-theoretic models could not quantify reward-seeking and uncertainty aversion in a theoretically consistent manner. In this paper, we have: (i) proposed that generalized Helmholtz free energy in Tsallis’ non-extensive thermostatistics can be utilized to quantify a perceived value of an uncertain reward, and (ii) empirically examined the explanatory powers of the models. Future study directions in neuroeconomics and econophysics by utilizing the Tsallis’ free energy model are discussed.

  12. Testing Convergence of Different Free-Energy Methods in a Simple Analytical System with Hidden Barriers

    Directory of Open Access Journals (Sweden)

    S. Alexis Paz

    2018-03-01

    Full Text Available In this work, we study the influence of hidden barriers on the convergence behavior of three free-energy calculation methods: well-tempered metadynamics (WTMD, adaptive-biasing forces (ABF, and on-the-fly parameterization (OTFP. We construct a simple two-dimensional potential-energy surfaces (PES that allows for an exact analytical result for the free-energy in any one-dimensional order parameter. Then we chose different CV definitions and PES parameters to create three different systems with increasing sampling challenges. We find that all three methods are not greatly affected by the hidden-barriers in the simplest case considered. The adaptive sampling methods show faster sampling while the auxiliary high-friction requirement of OTFP makes it slower for this case. However, a slight change in the CV definition has a strong impact in the ABF and WTMD performance, illustrating the importance of choosing suitable collective variables.

  13. Free energy option and its relevance to improve domestic energy demands in southern Nigeria

    Directory of Open Access Journals (Sweden)

    Moses Eterigho Emetere

    2016-11-01

    Full Text Available The aim of this paper is to seek an energy option that would benefit the growing energy demands. Domestic energy demands in southern Nigeria had increased greatly due to failing power programs and seasonal migrations. The fossil fuel option is gradually fading away due to environmental pollution and recent dynamic cost. The renewable energy option had been celebrated with little success in the coastal area of southern Nigeria. At the moment, the renewable energy option is very expensive with little guarantee on its efficiency with time. The data set used for this study was obtained from the Davis weather installation in Covenant University. The free energy option was considered. The cost and its environmental implication for domestic use were comparatively discussed alongside other energy options — using the Life cycle cost analysis. It was found out that free energy option is more affordable and efficient for domestic use.

  14. Communication: Theoretical prediction of free-energy landscapes for complex self-assembly

    Energy Technology Data Exchange (ETDEWEB)

    Jacobs, William M.; Reinhardt, Aleks; Frenkel, Daan [Department of Chemistry, University of Cambridge, Lensfield Road, Cambridge CB2 1EW (United Kingdom)

    2015-01-14

    We present a technique for calculating free-energy profiles for the nucleation of multicomponent structures that contain as many species as building blocks. We find that a key factor is the topology of the graph describing the connectivity of the target assembly. By considering the designed interactions separately from weaker, incidental interactions, our approach yields predictions for the equilibrium yield and nucleation barriers. These predictions are in good agreement with corresponding Monte Carlo simulations. We show that a few fundamental properties of the connectivity graph determine the most prominent features of the assembly thermodynamics. Surprisingly, we find that polydispersity in the strengths of the designed interactions stabilizes intermediate structures and can be used to sculpt the free-energy landscape for self-assembly. Finally, we demonstrate that weak incidental interactions can preclude assembly at equilibrium due to the combinatorial possibilities for incorrect association.

  15. The thermodynamic properties of the upper continental crust: Exergy, Gibbs free energy and enthalpy

    International Nuclear Information System (INIS)

    Valero, Alicia; Valero, Antonio; Vieillard, Philippe

    2012-01-01

    This paper shows a comprehensive database of the thermodynamic properties of the most abundant minerals of the upper continental crust. For those substances whose thermodynamic properties are not listed in the literature, their enthalpy and Gibbs free energy are calculated with 11 different estimation methods described in this study, with associated errors of up to 10% with respect to values published in the literature. Thanks to this procedure we have been able to make a first estimation of the enthalpy, Gibbs free energy and exergy of the bulk upper continental crust and of each of the nearly 300 most abundant minerals contained in it. Finally, the chemical exergy of the continental crust is compared to the exergy of the concentrated mineral resources. The numbers obtained indicate the huge chemical exergy wealth of the crust: 6 × 10 6 Gtoe. However, this study shows that approximately only 0.01% of that amount can be effectively used by man.

  16. Molecular dynamics simulations and free energy calculations on the enzyme 4-hydroxyphenylpyruvate dioxygenase.

    Science.gov (United States)

    De Beer, Stephanie B A; Glättli, Alice; Hutzler, Johannes; Vermeulen, Nico P E; Oostenbrink, Chris

    2011-07-30

    4-Hydroxyphenylpyruvate dioxygenase is a relevant target in both pharmaceutical and agricultural research. We report on molecular dynamics simulations and free energy calculations on this enzyme, in complex with 12 inhibitors for which experimental affinities were determined. We applied the thermodynamic integration approach and the more efficient one-step perturbation. Even though simulations seem well converged and both methods show excellent agreement between them, the correlation with the experimental values remains poor. We investigate the effect of slight modifications on the charge distribution of these highly conjugated systems and find that accurate models can be obtained when using improved force field parameters. This study gives insight into the applicability of free energy methods and current limitations in force field parameterization. Copyright © 2011 Wiley Periodicals, Inc.

  17. Effect of Collagen Matrix Saturation on the Surface Free Energy of Dentin using Different Agents.

    Science.gov (United States)

    de Almeida, Leopoldina de Fátima Dantas; Souza, Samilly Evangelista; Sampaio, Aline Araújo; Cavalcanti, Yuri Wanderley; da Silva, Wander José; Del Bel Cur, Altair A; Hebling, Josimeri

    2015-07-01

    The surface free energy of conditioned-dentin is one of the factors that interfere with monomeric infiltration of the interfibrillar spaces. Saturation of the tooth matrix with different substances may modulate this energy and, consequently, the wettability of the dentin. To evaluate the influence of different substances used to saturate conditioned-dentin on surface free energy (SFE) of this substrate. Dentin blocks (4 × 7 × 1 mm, n = 6/ group), obtained from the roots of bovine incisors, were etched using phosphoric acid for 15 seconds, rinsed and gently dried. The surfaces were treated for 60 seconds with: ultra-purified water (H20-control); ethanol (EtOH), acetone (ACT), chlorhexidine (CHX), ethylenediaminetetraacetic acid (EDTA); or sodium hypochlorite (NaOCl). The tooth surfaces were once again dried with absorbent paper and prepared for SFE evaluation using three standards: water, formamide and bromonaphthalene. Analysis of variance (ANOVA) and Dunnet's tests (a = 0.05) were applied to the data. Ethylenediaminetetraacetic acid was the only substance that caused a change to the contact angle for the standards water and formamide, while only EtOH influenced the angles formed between formamide and the dentin surface. None of the substances exerted a significant effect for bromonaphtha-lene. In comparison to the control, only EDTA and NaOCl altered both polar components of the SFE. Total SFE was increased by saturation of the collagen matrix by EDTA and reduced when NaOCl was used. Saturation of the collagen matrix by EDTA and EtOH changed the surface free energy of the dentin. In addition, the use of NaOCl negatively interfered with the properties evaluated. The increase of surface free energy and wettability of the dentin surface would allow higher penetration of the the adhesive system, which would be of importance to the clinical success of resin-dentin union.

  18. Direct measurements of the Gibbs free energy of OH using a CW tunable laser

    Science.gov (United States)

    Killinger, D. K.; Wang, C. C.

    1979-01-01

    The paper describes an absorption measurement for determining the Gibbs free energy of OH generated in a mixture of water and oxygen vapor. These measurements afford a direct verification of the accuracy of thermochemical data of H2O at high temperatures and pressures. The results indicate that values for the heat capacity of H2O obtained through numerical computations are correct within an experimental uncertainty of 0.15 cal/mole K.

  19. Standard Gibbs free energies for transfer of actinyl ions at the aqueous/organic solution interface

    International Nuclear Information System (INIS)

    Kitatsuji, Yoshihiro; Okugaki, Tomohiko; Kasuno, Megumi; Kubota, Hiroki; Maeda, Kohji; Kimura, Takaumi; Yoshida, Zenko; Kihara, Sorin

    2011-01-01

    Research highlights: → Standard Gibbs free energies for ion-transfer of tri- to hexavalent actinide ions. → Determination is based on distribution method combined with ion-transfer voltammetry. → Organic solvents examined are nitrobenzene, DCE, benzonitrile, acetophenone and NPOE. → Gibbs free energies of U(VI), Np(VI) and Pu(VI) are similar to each other. → Gibbs free energies of Np(V) is very large, comparing with ordinary monovalent cations. - Abstract: Standard Gibbs free energies for transfer (ΔG tr 0 ) of actinyl ions (AnO 2 z+ ; z = 2 or 1; An: U, Np, or Pu) between an aqueous solution and an organic solution were determined based on distribution method combined with voltammetry for ion transfer at the interface of two immiscible electrolyte solutions. The organic solutions examined were nitrobenzene, 1,2-dichloroethane, benzonitrile, acetophenone, and 2-nitrophenyl octyl ether. Irrespective of the type of organic solutions, ΔG tr 0 of UO 2 2+ ,NpO 2 2+ , and PuO 2 2+ were nearly equal to each other and slightly larger than that of Mg 2+ . The ΔG tr 0 of NpO 2 + was extraordinary large compared with those of ordinary monovalent cations. The dependence of ΔG tr 0 of AnO 2 z+ on the type of organic solutions was similar to that of H + or Mg 2+ . The ΔG tr 0 of An 3+ and An 4+ were also discussed briefly.

  20. Gibbs Free-Energy Gradient along the Path of Glucose Transport through Human Glucose Transporter 3.

    Science.gov (United States)

    Liang, Huiyun; Bourdon, Allen K; Chen, Liao Y; Phelix, Clyde F; Perry, George

    2018-06-11

    Fourteen glucose transporters (GLUTs) play essential roles in human physiology by facilitating glucose diffusion across the cell membrane. Due to its central role in the energy metabolism of the central nervous system, GLUT3 has been thoroughly investigated. However, the Gibbs free-energy gradient (what drives the facilitated diffusion of glucose) has not been mapped out along the transport path. Some fundamental questions remain. Here we present a molecular dynamics study of GLUT3 embedded in a lipid bilayer to quantify the free-energy profile along the entire transport path of attracting a β-d-glucose from the interstitium to the inside of GLUT3 and, from there, releasing it to the cytoplasm by Arrhenius thermal activation. From the free-energy profile, we elucidate the unique Michaelis-Menten characteristics of GLUT3, low K M and high V MAX , specifically suitable for neurons' high and constant demand of energy from their low-glucose environments. We compute GLUT3's binding free energy for β-d-glucose to be -4.6 kcal/mol in agreement with the experimental value of -4.4 kcal/mol ( K M = 1.4 mM). We also compute the hydration energy of β-d-glucose, -18.0 kcal/mol vs the experimental data, -17.8 kcal/mol. In this, we establish a dynamics-based connection from GLUT3's crystal structure to its cellular thermodynamics with quantitative accuracy. We predict equal Arrhenius barriers for glucose uptake and efflux through GLUT3 to be tested in future experiments.

  1. Free Energy Rate Density and Self-organization in Complex Systems

    OpenAIRE

    Georgiev, Georgi Yordanov; Gombos, Erin; Bates, Timothy; Henry, Kaitlin; Casey, Alexander; Daly, Michael

    2015-01-01

    One of the most important tasks in science is to understand the self-organization's arrow of time. To attempt this we utilize the connection between self-organization and non-equilibrium thermodynamics. Eric Chaisson calculated an exponential increase of Free Energy Rate Density (FERD) in Cosmic Evolution, from the Big Bang until now, paralleling the increase of system's structure. We term these studies "Devology". We connect FERD to the principle of least action for complex systems, driving ...

  2. Surface free energy of CrN x films deposited using closed field unbalanced magnetron sputtering

    International Nuclear Information System (INIS)

    Sun, C.-C.; Lee, S.-C.; Dai, S.-B.; Fu, Y.-S.; Wang, Y.-C.; Lee, Y.-H.

    2006-01-01

    CrN x thin films have attracted much attention for semiconductor IC packaging molding dies and forming tools due to their excellent hardness, thermal stability and non-sticking properties (low surface free energy). However, few data has been published on the surface free energy (SFE) of CrN x films at temperatures in the range 20-170 deg. C. In this study CrN x thin films with CrN, Cr(N), Cr 2 N (and mixture of these phases) were prepared using closed field unbalanced magnetron sputtering at a wide range of Cr +2 emission intensity. The contact angles of water, di-iodomethane and ethylene glycol on the coated surfaces were measured at temperatures in the range 20-170 deg. C using a Dataphysics OCA-20 contact angle analyzer. The surface free energy of the CrN x films and their components (e.g., dispersion, polar) were calculated using the Owens-Wendt geometric mean approach. The influences of CrN x film surface roughness and microstructure on the surface free energy were investigated by atomic force microscopy (AFM) and X-ray diffraction (XRD), respectively. The experimental results showed that the lowest total SFE was obtained corresponding to CrN at temperature in 20 deg. C. This is lower than that of Cr(N), Cr 2 N (and mixture of these phases). The total SFE, dispersive SFE and polar SFE of CrN x films decreased with increasing surface temperature. The film roughness has an obvious effect on the SFE and there is tendency for the SFE to increase with increasing film surface roughness

  3. Simulations of Skin Barrier Function: Free Energies of Hydrophobic and Hydrophilic Transmembrane Pores in Ceramide Bilayers

    OpenAIRE

    Notman, Rebecca; Anwar, Jamshed; Briels, W. J.; Noro, Massimo G.; den Otter, Wouter K.

    2008-01-01

    Transmembrane pore formation is central to many biological processes such as ion transport, cell fusion, and viral infection. Furthermore, pore formation in the ceramide bilayers of the stratum corneum may be an important mechanism by which penetration enhancers such as dimethylsulfoxide (DMSO) weaken the barrier function of the skin. We have used the potential of mean constraint force (PMCF) method to calculate the free energy of pore formation in ceramide bilayers in both the innate gel pha...

  4. On the free-energy of three-dimensional CFTs and polylogarithms

    International Nuclear Information System (INIS)

    Petkou, Anastasios C.

    1998-12-01

    We discuss the O(N) vector model and the U(N) Gross-Neveu model with fixed total fermion number, for large-N in three dimensions. Using non-trivial polylogarithmic identities, we calculate the renormalized free-energy density of these models at their conformal points in a 'slab' geometry with one finite dimension of length L. We briefly comment on the possible implications of our results. (author)

  5. On the free-energy of three-dimensional CFTs and polylogarithms

    Energy Technology Data Exchange (ETDEWEB)

    Petkou, Anastasios C. [Dortmund Univ. (Germany). Inst. fuer Physik; Silva Neto, Marcello B. [Centro Brasileiro de Pesquisas Fisicas (CBPF), Rio de Janeiro, RJ (Brazil)

    1998-12-01

    We discuss the O(N) vector model and the U(N) Gross-Neveu model with fixed total fermion number, for large-N in three dimensions. Using non-trivial polylogarithmic identities, we calculate the renormalized free-energy density of these models at their conformal points in a 'slab' geometry with one finite dimension of length L. We briefly comment on the possible implications of our results. (author)

  6. The Role of Shearing Energy and Interfacial Gibbs Free Energy in the Emulsification Mechanism of Waxy Crude Oil

    Directory of Open Access Journals (Sweden)

    Zhihua Wang

    2017-05-01

    Full Text Available Crude oil is generally produced with water, and the water cut produced by oil wells is increasingly common over their lifetime, so it is inevitable to create emulsions during oil production. However, the formation of emulsions presents a costly problem in surface process particularly, both in terms of transportation energy consumption and separation efficiency. To deal with the production and operational problems which are related to crude oil emulsions, especially to ensure the separation and transportation of crude oil-water systems, it is necessary to better understand the emulsification mechanism of crude oil under different conditions from the aspects of bulk and interfacial properties. The concept of shearing energy was introduced in this study to reveal the driving force for emulsification. The relationship between shearing stress in the flow field and interfacial tension (IFT was established, and the correlation between shearing energy and interfacial Gibbs free energy was developed. The potential of the developed correlation model was validated using the experimental and field data on emulsification behavior. It was also shown how droplet deformation could be predicted from a random deformation degree and orientation angle. The results indicated that shearing energy as the energy produced by shearing stress working in the flow field is the driving force activating the emulsification behavior. The deformation degree and orientation angle of dispersed phase droplet are associated with the interfacial properties, rheological properties and the experienced turbulence degree. The correlation between shearing stress and IFT can be quantified if droplet deformation degree vs. droplet orientation angle data is available. When the water cut is close to the inversion point of waxy crude oil emulsion, the interfacial Gibbs free energy change decreased and the shearing energy increased. This feature is also presented in the special regions where

  7. Binding free energy calculations to rationalize the interactions of huprines with acetylcholinesterase.

    Science.gov (United States)

    Nascimento, Érica C M; Oliva, Mónica; Andrés, Juan

    2018-05-01

    In the present study, the binding free energy of a family of huprines with acetylcholinesterase (AChE) is calculated by means of the free energy perturbation method, based on hybrid quantum mechanics and molecular mechanics potentials. Binding free energy calculations and the analysis of the geometrical parameters highlight the importance of the stereochemistry of huprines in AChE inhibition. Binding isotope effects are calculated to unravel the interactions between ligands and the gorge of AChE. New chemical insights are provided to explain and rationalize the experimental results. A good correlation with the experimental data is found for a family of inhibitors with moderate differences in the enzyme affinity. The analysis of the geometrical parameters and interaction energy per residue reveals that Asp72, Glu199, and His440 contribute significantly to the network of interactions between active site residues, which stabilize the inhibitors in the gorge. It seems that a cooperative effect of the residues of the gorge determines the affinity of the enzyme for these inhibitors, where Asp72, Glu199, and His440 make a prominent contribution.

  8. Free Energy Calculations using a Swarm-Enhanced Sampling Molecular Dynamics Approach.

    Science.gov (United States)

    Burusco, Kepa K; Bruce, Neil J; Alibay, Irfan; Bryce, Richard A

    2015-10-26

    Free energy simulations are an established computational tool in modelling chemical change in the condensed phase. However, sampling of kinetically distinct substates remains a challenge to these approaches. As a route to addressing this, we link the methods of thermodynamic integration (TI) and swarm-enhanced sampling molecular dynamics (sesMD), where simulation replicas interact cooperatively to aid transitions over energy barriers. We illustrate the approach by using alchemical alkane transformations in solution, comparing them with the multiple independent trajectory TI (IT-TI) method. Free energy changes for transitions computed by using IT-TI grew increasingly inaccurate as the intramolecular barrier was heightened. By contrast, swarm-enhanced sampling TI (sesTI) calculations showed clear improvements in sampling efficiency, leading to more accurate computed free energy differences, even in the case of the highest barrier height. The sesTI approach, therefore, has potential in addressing chemical change in systems where conformations exist in slow exchange. © 2015 WILEY-VCH Verlag GmbH & Co. KGaA, Weinheim.

  9. Improved Model for Predicting the Free Energy Contribution of Dinucleotide Bulges to RNA Duplex Stability.

    Science.gov (United States)

    Tomcho, Jeremy C; Tillman, Magdalena R; Znosko, Brent M

    2015-09-01

    Predicting the secondary structure of RNA is an intermediate in predicting RNA three-dimensional structure. Commonly, determining RNA secondary structure from sequence uses free energy minimization and nearest neighbor parameters. Current algorithms utilize a sequence-independent model to predict free energy contributions of dinucleotide bulges. To determine if a sequence-dependent model would be more accurate, short RNA duplexes containing dinucleotide bulges with different sequences and nearest neighbor combinations were optically melted to derive thermodynamic parameters. These data suggested energy contributions of dinucleotide bulges were sequence-dependent, and a sequence-dependent model was derived. This model assigns free energy penalties based on the identity of nucleotides in the bulge (3.06 kcal/mol for two purines, 2.93 kcal/mol for two pyrimidines, 2.71 kcal/mol for 5'-purine-pyrimidine-3', and 2.41 kcal/mol for 5'-pyrimidine-purine-3'). The predictive model also includes a 0.45 kcal/mol penalty for an A-U pair adjacent to the bulge and a -0.28 kcal/mol bonus for a G-U pair adjacent to the bulge. The new sequence-dependent model results in predicted values within, on average, 0.17 kcal/mol of experimental values, a significant improvement over the sequence-independent model. This model and new experimental values can be incorporated into algorithms that predict RNA stability and secondary structure from sequence.

  10. Analysis of the free-energy surface of proteins from reversible folding simulations.

    Directory of Open Access Journals (Sweden)

    Lucy R Allen

    2009-07-01

    Full Text Available Computer generated trajectories can, in principle, reveal the folding pathways of a protein at atomic resolution and possibly suggest general and simple rules for predicting the folded structure of a given sequence. While such reversible folding trajectories can only be determined ab initio using all-atom transferable force-fields for a few small proteins, they can be determined for a large number of proteins using coarse-grained and structure-based force-fields, in which a known folded structure is by construction the absolute energy and free-energy minimum. Here we use a model of the fast folding helical lambda-repressor protein to generate trajectories in which native and non-native states are in equilibrium and transitions are accurately sampled. Yet, representation of the free-energy surface, which underlies the thermodynamic and dynamic properties of the protein model, from such a trajectory remains a challenge. Projections over one or a small number of arbitrarily chosen progress variables often hide the most important features of such surfaces. The results unequivocally show that an unprojected representation of the free-energy surface provides important and unbiased information and allows a simple and meaningful description of many-dimensional, heterogeneous trajectories, providing new insight into the possible mechanisms of fast-folding proteins.

  11. Cultured Cortical Neurons Can Perform Blind Source Separation According to the Free-Energy Principle

    Science.gov (United States)

    Isomura, Takuya; Kotani, Kiyoshi; Jimbo, Yasuhiko

    2015-01-01

    Blind source separation is the computation underlying the cocktail party effect––a partygoer can distinguish a particular talker’s voice from the ambient noise. Early studies indicated that the brain might use blind source separation as a signal processing strategy for sensory perception and numerous mathematical models have been proposed; however, it remains unclear how the neural networks extract particular sources from a complex mixture of inputs. We discovered that neurons in cultures of dissociated rat cortical cells could learn to represent particular sources while filtering out other signals. Specifically, the distinct classes of neurons in the culture learned to respond to the distinct sources after repeating training stimulation. Moreover, the neural network structures changed to reduce free energy, as predicted by the free-energy principle, a candidate unified theory of learning and memory, and by Jaynes’ principle of maximum entropy. This implicit learning can only be explained by some form of Hebbian plasticity. These results are the first in vitro (as opposed to in silico) demonstration of neural networks performing blind source separation, and the first formal demonstration of neuronal self-organization under the free energy principle. PMID:26690814

  12. Exploring the free energy landscape: from dynamics to networks and back.

    Directory of Open Access Journals (Sweden)

    Diego Prada-Gracia

    2009-06-01

    Full Text Available Knowledge of the Free Energy Landscape topology is the essential key to understanding many biochemical processes. The determination of the conformers of a protein and their basins of attraction takes a central role for studying molecular isomerization reactions. In this work, we present a novel framework to unveil the features of a Free Energy Landscape answering questions such as how many meta-stable conformers there are, what the hierarchical relationship among them is, or what the structure and kinetics of the transition paths are. Exploring the landscape by molecular dynamics simulations, the microscopic data of the trajectory are encoded into a Conformational Markov Network. The structure of this graph reveals the regions of the conformational space corresponding to the basins of attraction. In addition, handling the Conformational Markov Network, relevant kinetic magnitudes as dwell times and rate constants, or hierarchical relationships among basins, completes the global picture of the landscape. We show the power of the analysis studying a toy model of a funnel-like potential and computing efficiently the conformers of a short peptide, dialanine, paving the way to a systematic study of the Free Energy Landscape in large peptides.

  13. Cultured Cortical Neurons Can Perform Blind Source Separation According to the Free-Energy Principle.

    Directory of Open Access Journals (Sweden)

    Takuya Isomura

    2015-12-01

    Full Text Available Blind source separation is the computation underlying the cocktail party effect--a partygoer can distinguish a particular talker's voice from the ambient noise. Early studies indicated that the brain might use blind source separation as a signal processing strategy for sensory perception and numerous mathematical models have been proposed; however, it remains unclear how the neural networks extract particular sources from a complex mixture of inputs. We discovered that neurons in cultures of dissociated rat cortical cells could learn to represent particular sources while filtering out other signals. Specifically, the distinct classes of neurons in the culture learned to respond to the distinct sources after repeating training stimulation. Moreover, the neural network structures changed to reduce free energy, as predicted by the free-energy principle, a candidate unified theory of learning and memory, and by Jaynes' principle of maximum entropy. This implicit learning can only be explained by some form of Hebbian plasticity. These results are the first in vitro (as opposed to in silico demonstration of neural networks performing blind source separation, and the first formal demonstration of neuronal self-organization under the free energy principle.

  14. Binding free energy calculations to rationalize the interactions of huprines with acetylcholinesterase

    Science.gov (United States)

    Nascimento, Érica C. M.; Oliva, Mónica; Andrés, Juan

    2018-05-01

    In the present study, the binding free energy of a family of huprines with acetylcholinesterase (AChE) is calculated by means of the free energy perturbation method, based on hybrid quantum mechanics and molecular mechanics potentials. Binding free energy calculations and the analysis of the geometrical parameters highlight the importance of the stereochemistry of huprines in AChE inhibition. Binding isotope effects are calculated to unravel the interactions between ligands and the gorge of AChE. New chemical insights are provided to explain and rationalize the experimental results. A good correlation with the experimental data is found for a family of inhibitors with moderate differences in the enzyme affinity. The analysis of the geometrical parameters and interaction energy per residue reveals that Asp72, Glu199, and His440 contribute significantly to the network of interactions between active site residues, which stabilize the inhibitors in the gorge. It seems that a cooperative effect of the residues of the gorge determines the affinity of the enzyme for these inhibitors, where Asp72, Glu199, and His440 make a prominent contribution.

  15. Impact of domain knowledge on blinded predictions of binding energies by alchemical free energy calculations

    Science.gov (United States)

    Mey, Antonia S. J. S.; Jiménez, Jordi Juárez; Michel, Julien

    2018-01-01

    The Drug Design Data Resource (D3R) consortium organises blinded challenges to address the latest advances in computational methods for ligand pose prediction, affinity ranking, and free energy calculations. Within the context of the second D3R Grand Challenge several blinded binding free energies predictions were made for two congeneric series of Farsenoid X Receptor (FXR) inhibitors with a semi-automated alchemical free energy calculation workflow featuring FESetup and SOMD software tools. Reasonable performance was observed in retrospective analyses of literature datasets. Nevertheless, blinded predictions on the full D3R datasets were poor due to difficulties encountered with the ranking of compounds that vary in their net-charge. Performance increased for predictions that were restricted to subsets of compounds carrying the same net-charge. Disclosure of X-ray crystallography derived binding modes maintained or improved the correlation with experiment in a subsequent rounds of predictions. The best performing protocols on D3R set1 and set2 were comparable or superior to predictions made on the basis of analysis of literature structure activity relationships (SAR)s only, and comparable or slightly inferior, to the best submissions from other groups.

  16. Solvent density inhomogeneities and solvation free energies in supercritical diatomic fluids: a density functional approach.

    Science.gov (United States)

    Husowitz, B; Talanquer, V

    2007-02-07

    Density functional theory is used to explore the solvation properties of a spherical solute immersed in a supercritical diatomic fluid. The solute is modeled as a hard core Yukawa particle surrounded by a diatomic Lennard-Jones fluid represented by two fused tangent spheres using an interaction site approximation. The authors' approach is particularly suitable for thoroughly exploring the effect of different interaction parameters, such as solute-solvent interaction strength and range, solvent-solvent long-range interactions, and particle size, on the local solvent structure and the solvation free energy under supercritical conditions. Their results indicate that the behavior of the local coordination number in homonuclear diatomic fluids follows trends similar to those reported in previous studies for monatomic fluids. The local density augmentation is particularly sensitive to changes in solute size and is affected to a lesser degree by variations in the solute-solvent interaction strength and range. The associated solvation free energies exhibit a nonmonotonous behavior as a function of density for systems with weak solute-solvent interactions. The authors' results suggest that solute-solvent interaction anisotropies have a major influence on the nature and extent of local solvent density inhomogeneities and on the value of the solvation free energies in supercritical solutions of heteronuclear molecules.

  17. Adhesion Evaluation of Asphalt-Aggregate Interface Using Surface Free Energy Method

    Directory of Open Access Journals (Sweden)

    Jie Ji

    2017-02-01

    Full Text Available The influence of organic additives (Sasobit and RH and water on the adhesion of the asphalt-aggregate interface was studied according to the surface free energy theory. Two asphalt binders (SK-70 and SK-90, and two aggregate types (limestone and basalt were used in this study. The sessile drop method was employed to test surface free energy components of asphalt, organic additives and aggregates. The adhesion models of the asphalt-aggregate interface in dry and wet conditions were established, and the adhesion work was calculated subsequently. The energy ratios were built to evaluate the effect of organic additives and water on the adhesiveness of the asphalt-aggregate interface. The results indicate that the addition of organic additives can enhance the adhesion of the asphalt-aggregate interface in dry conditions, because organic additives reduced the surface free energy of asphalt. However, the organic additives have hydrophobic characteristics and are sensitive to water. As a result, the adhesiveness of the asphalt-aggregate interface of the asphalt containing organic additives in wet conditions sharply decreased due to water damage to asphalt and organic additives. Furthermore, the compatibility of asphalt, aggregate with organic additive was noted and discussed.

  18. Log-correlated random-energy models with extensive free-energy fluctuations: Pathologies caused by rare events as signatures of phase transitions

    Science.gov (United States)

    Cao, Xiangyu; Fyodorov, Yan V.; Le Doussal, Pierre

    2018-02-01

    We address systematically an apparent nonphysical behavior of the free-energy moment generating function for several instances of the logarithmically correlated models: the fractional Brownian motion with Hurst index H =0 (fBm0) (and its bridge version), a one-dimensional model appearing in decaying Burgers turbulence with log-correlated initial conditions and, finally, the two-dimensional log-correlated random-energy model (logREM) introduced in Cao et al. [Phys. Rev. Lett. 118, 090601 (2017), 10.1103/PhysRevLett.118.090601] based on the two-dimensional Gaussian free field with background charges and directly related to the Liouville field theory. All these models share anomalously large fluctuations of the associated free energy, with a variance proportional to the log of the system size. We argue that a seemingly nonphysical vanishing of the moment generating function for some values of parameters is related to the termination point transition (i.e., prefreezing). We study the associated universal log corrections in the frozen phase, both for logREMs and for the standard REM, filling a gap in the literature. For the above mentioned integrable instances of logREMs, we predict the nontrivial free-energy cumulants describing non-Gaussian fluctuations on the top of the Gaussian with extensive variance. Some of the predictions are tested numerically.

  19. On the rank 1 convexity of stored energy functions of physically linear stress-strain relations

    Czech Academy of Sciences Publication Activity Database

    Šilhavý, Miroslav; Bertram, A.; Böhlke, T.

    2007-01-01

    Roč. 86, č. 3 (2007), s. 235-243 ISSN 0374-3535 Institutional research plan: CEZ:AV0Z10190503 Keywords : generalized linear elastic law s * generalized strain measures * rank 1 convexity Subject RIV: BA - General Mathematics Impact factor: 0.743, year: 2007

  20. Fundamental Insights into Proton-Coupled Electron Transfer in Soybean Lipoxygenase from Quantum Mechanical/Molecular Mechanical Free Energy Simulations.

    Science.gov (United States)

    Li, Pengfei; Soudackov, Alexander V; Hammes-Schiffer, Sharon

    2018-02-28

    The proton-coupled electron transfer (PCET) reaction catalyzed by soybean lipoxygenase has served as a prototype for understanding hydrogen tunneling in enzymes. Herein this PCET reaction is studied with mixed quantum mechanical/molecular mechanical (QM/MM) free energy simulations. The free energy surfaces are computed as functions of the proton donor-acceptor (C-O) distance and the proton coordinate, and the potential of mean force is computed as a function of the C-O distance, inherently including anharmonicity. The simulation results are used to calculate the kinetic isotope effects for the wild-type enzyme (WT) and the L546A/L754A double mutant (DM), which have been measured experimentally to be ∼80 and ∼700, respectively. The PCET reaction is found to be exoergic for WT and slightly endoergic for the DM, and the equilibrium C-O distance for the reactant is found to be ∼0.2 Å greater for the DM than for WT. The larger equilibrium distance for the DM, which is due mainly to less optimal substrate binding in the expanded binding cavity, is primarily responsible for its higher kinetic isotope effect. The calculated potentials of mean force are anharmonic and relatively soft at shorter C-O distances, allowing efficient thermal sampling of the shorter distances required for effective hydrogen tunneling. The primarily local electrostatic field at the transferring hydrogen is ∼100 MV/cm in the direction to facilitate proton transfer and increases dramatically as the C-O distance decreases. These simulations suggest that the overall protein environment is important for conformational sampling of active substrate configurations aligned for proton transfer, but the PCET reaction is influenced primarily by local electrostatic effects that facilitate conformational sampling of shorter proton donor-acceptor distances required for effective hydrogen tunneling.

  1. Substitution Effects and Linear Free Energy Relationships During Reduction of 4- Benzoyl-n-(4-substituted Benzyl)pyridinium Cations

    Science.gov (United States)

    Leventis, Nicholas; Zhang, Guo-Hui; Rawashdeh, Abdel-Monem M.; Sotiriou-Leventis, Chariklia; Gray, Hugh R. (Technical Monitor)

    2003-01-01

    In analogy to 4-(para-substituted benzoyl)-N-methylpyridinium cations (1-X's), the title species (2-X's, -X = -OCH3, -CH3, -H, -Br, -COCH3, -NO2) undergo two reversible, well-separated (E(sub 1/2) greater than or equal to 650 mV) one-electron reductions. The effect of substitution on the reduction potentials of 2-X's is much weaker than the effect of the same substituents on 1-X's: the Hammett rho-values are 0.80 and 0.93 for the 1st- and 2nd-e reduction of 2-X's vs. 2.3 and 3.3 for the same reductions of 1-X's, respectively. Importantly, the nitro group of 2-NO2 undergoes reduction before the 2nd-e reduction of the 4-benzoylpyridinium system. These results suggest that the redox potentials of the 4-benzoylpyridinium system can be course-tuned via p-benzoyl substitution and fine-tuned via para-benzyl substitution. Introducing the recently derived substituent constant of the -NO2(sup)- group (sigma para-NO2(sup)- = -0.97) yields an excellent correlation for the 3rd-e reduction of 2- NO2 (corresponding to the reduction of the carbonyl group) with the 2nd-e reduction of the other 2-X's, and confirms the electron donating properties of -NO2(sup)-.

  2. Econometric testing on linear and nonlinear dynamic relation between stock prices and macroeconomy in China

    Science.gov (United States)

    Borjigin, Sumuya; Yang, Yating; Yang, Xiaoguang; Sun, Leilei

    2018-03-01

    Many researchers have realized that there is a strong correlation between stock prices and macroeconomy. In order to make this relationship clear, a lot of studies have been done. However, the causal relationship between stock prices and macroeconomy has still not been well explained. A key point is that, most of the existing research adopts linear and stable models to investigate the correlation of stock prices and macroeconomy, while the real causality of that may be nonlinear and dynamic. To fill this research gap, we investigate the nonlinear and dynamic causal relationships between stock prices and macroeconomy. Based on the case of China's stock prices and acroeconomy measures from January 1992 to March 2017, we compare the linear Granger causality test models with nonlinear ones. Results demonstrate that the nonlinear dynamic Granger causality is much stronger than linear Granger causality. From the perspective of nonlinear dynamic Granger causality, China's stock prices can be viewed as "national economic barometer". On the one hand, this study will encourage researchers to take nonlinearity and dynamics into account when they investigate the correlation of stock prices and macroeconomy; on the other hand, our research can guide regulators and investors to make better decisions.

  3. Estimating relative stability of polymorphs by generation of configurational free energy phase diagram

    DEFF Research Database (Denmark)

    Upadhyay, Pratik Pankaj; Dantuluri, Ajay K; Kumar, Lokesh

    2012-01-01

    , namely, carbamazepine and nateglinide. This method was also compared with the previous methodologies. Deduced T(t) of carbamazepine using this methodology was compared with previously reported values and was found to be in good agreement. A monotropic relationship was established between nateglinide...

  4. On a partial differential equation method for determining the free energies and coexisting phase compositions of ternary mixtures from light scattering data.

    Science.gov (United States)

    Ross, David S; Thurston, George M; Lutzer, Carl V

    2008-08-14

    In this paper we present a method for determining the free energies of ternary mixtures from light scattering data. We use an approximation that is appropriate for liquid mixtures, which we formulate as a second-order nonlinear partial differential equation. This partial differential equation (PDE) relates the Hessian of the intensive free energy to the efficiency of light scattering in the forward direction. This basic equation applies in regions of the phase diagram in which the mixtures are thermodynamically stable. In regions in which the mixtures are unstable or metastable, the appropriate PDE is the nonlinear equation for the convex hull. We formulate this equation along with continuity conditions for the transition between the two equations at cloud point loci. We show how to discretize this problem to obtain a finite-difference approximation to it, and we present an iterative method for solving the discretized problem. We present the results of calculations that were done with a computer program that implements our method. These calculations show that our method is capable of reconstructing test free energy functions from simulated light scattering data. If the cloud point loci are known, the method also finds the tie lines and tie triangles that describe thermodynamic equilibrium between two or among three liquid phases. A robust method for solving this PDE problem, such as the one presented here, can be a basis for optical, noninvasive means of characterizing the thermodynamics of multicomponent mixtures.

  5. Binding affinities of the farnesoid X receptor in the D3R Grand Challenge 2 estimated by free-energy perturbation and docking

    Science.gov (United States)

    Olsson, Martin A.; García-Sosa, Alfonso T.; Ryde, Ulf

    2018-01-01

    We have studied the binding of 102 ligands to the farnesoid X receptor within the D3R Grand Challenge 2016 blind-prediction competition. First, we employed docking with five different docking software and scoring functions. The selected docked poses gave an average root-mean-squared deviation of 4.2 Å. Consensus scoring gave decent results with a Kendall's τ of 0.26 ± 0.06 and a Spearman's ρ of 0.41 ± 0.08. For a subset of 33 ligands, we calculated relative binding free energies with free-energy perturbation. Five transformations between the ligands involved a change of the net charge and we implemented and benchmarked a semi-analytic correction (Rocklin et al., J Chem Phys 139:184103, 2013) for artifacts caused by the periodic boundary conditions and Ewald summation. The results gave a mean absolute deviation of 7.5 kJ/mol compared to the experimental estimates and a correlation coefficient of R 2 = 0.1. These results were among the four best in this competition out of 22 submissions. The charge corrections were significant (7-8 kJ/mol) and always improved the results. By employing 23 intermediate states in the free-energy perturbation, there was a proper overlap between all states and the precision was 0.1-0.7 kJ/mol. However, thermodynamic cycles indicate that the sampling was insufficient in some of the perturbations.

  6. Free energy profiles of cocaine esterase-cocaine binding process by molecular dynamics and potential of mean force simulations.

    Science.gov (United States)

    Zhang, Yuxin; Huang, Xiaoqin; Han, Keli; Zheng, Fang; Zhan, Chang-Guo

    2016-11-25

    The combined molecular dynamics (MD) and potential of mean force (PMF) simulations have been performed to determine the free energy profile of the CocE)-(+)-cocaine binding process in comparison with that of the corresponding CocE-(-)-cocaine binding process. According to the MD simulations, the equilibrium CocE-(+)-cocaine binding mode is similar to the CocE-(-)-cocaine binding mode. However, based on the simulated free energy profiles, a significant free energy barrier (∼5 kcal/mol) exists in the CocE-(+)-cocaine binding process whereas no obvious free energy barrier exists in the CocE-(-)-cocaine binding process, although the free energy barrier of ∼5 kcal/mol is not high enough to really slow down the CocE-(+)-cocaine binding process. In addition, the obtained free energy profiles also demonstrate that (+)-cocaine and (-)-cocaine have very close binding free energies with CocE, with a negligible difference (∼0.2 kcal/mol), which is qualitatively consistent with the nearly same experimental K M values of the CocE enzyme for (+)-cocaine and (-)-cocaine. The consistency between the computational results and available experimental data suggests that the mechanistic insights obtained from this study are reasonable. Copyright © 2016 Elsevier Ireland Ltd. All rights reserved.

  7. Ab initio calculation of the migration free energy of oxygen diffusion in pure and samarium-doped ceria

    Science.gov (United States)

    Koettgen, Julius; Schmidt, Peter C.; Bučko, Tomáš; Martin, Manfred

    2018-01-01

    We have studied the free energy migration barriers Δ F‡ for oxygen diffusion in pure ceria and Sm-doped ceria for the temperatures 300, 700, and 1000 K. We used the density functional theory in the generalized gradient approximation and an additional Hubbard U parameter for the Ce 4 f electronic states. We compare the results for the free energy deduced from three different methods. First, a static harmonic approach is applied in which the temperature dependent vibrational contributions to energy and entropy are deduced from the phonon frequencies of supercells with a fixed volume. Second, a static quasiharmonic approach is used in which a part of the anharmonicity effect is introduced via an implicit dependence of the harmonic frequencies on the thermally expanding cell volume. Third, the free energy barriers are calculated using metadynamics and molecular dynamics in which anharmonicity effects are naturally taken into account. The three methods examined in this study lead to distinctly different results. According to the harmonic approximation, the migration free energy difference Δ F‡ increases with increasing temperature due to an increasing entropic contribution. According to the quasiharmonic approximation, the migration free energy is independent of temperature. Finally, molecular dynamics predicts a thermally induced increase in the migration free energy. We conclude that temperature dependent experimental lattice constants cancel out the increasing entropic contribution with increasing temperature in the static quasiharmonic approach. The full consideration of anharmonicity effects in the metadynamics method again leads to a temperature dependent migration free energy.

  8. Ab initio study on stacking sequences, free energy, dynamical stability and potential energy surfaces of graphite structures

    International Nuclear Information System (INIS)

    Anees, P; Valsakumar, M C; Chandra, Sharat; Panigrahi, B K

    2014-01-01

    Ab initio simulations have been performed to study the structure, energetics and stability of several plausible stacking sequences in graphite. These calculations suggest that in addition to the standard structures, graphite can also exist in AA-simple hexagonal, AB-orthorhombic and ABC-hexagonal type stacking. The free energy difference between these structures is very small (∼1 meV/atom), and hence all the structures can coexist from purely energetic considerations. Calculated x-ray diffraction patterns are similar to those of the standard structures for 2θ ⩽ 70°. Shear elastic constant C 44 is negative in AA-simple hexagonal, AB-orthorhombic and ABC-hexagonal structures, suggesting that these structures are mechanically unstable. Phonon dispersions show that the frequencies of some modes along the Γ–A direction in the Brillouin zone are imaginary in all of the new structures, implying that these structures are dynamically unstable. Incorporation of zero point vibrational energy via the quasi-harmonic approximation does not result in the restoration of dynamical stability. Potential energy surfaces for the unstable normal modes are seen to have the topography of a potential hill for all the new structures, confirming that all of the new structures are inherently unstable. The fact that the potential energy surface is not in the form of a double well implies that the structures are linearly as well as globally unstable. (paper)

  9. Model linear absolute and relative risk estimates for cancer induced by ionizing radiation in Mexican cohort of occupationally exposed

    International Nuclear Information System (INIS)

    Alvarez, R.J.T.; Trovar, M.V.M; González, J.F.

    2015-01-01

    From the rate of natural mortality m s cancer (t) for every 100 thousand habitants, modeled by a fourth-degree polynomial function of the age data of the Mexican population (2008), and assuming: a) a relationship 1: 5 of cancer induced radiation respect to presented spontaneously, b) a size of initial cohort No = 100 k SOPs, c) a speed of H E = (2 ± 1) mSv / received by the SOPs from 18 to 65 years, d) a latency of 8 years for cancer induction after irradiation, e) a time tracking cohort to 75 years, f) and taking the coefficients absolute and relative risk BEIRs induction of cancer models II and VII (excluding leukemia); It determined: BEIR II for a total of 125 and 400 deaths from cancer for absolute and relative linear models respectively. For BEIR VII has a number of fatal cases of 345 and 927 deaths respectively for absolute and relative linear model cancer. [es

  10. On the number of free energy extremums of a solid solution with two long-range order parameters

    International Nuclear Information System (INIS)

    Dateshidze, N.A.; Ratishvili, I.G.

    1977-01-01

    The free energy of ordering f.c.c. lattice solid solution is investigated. The ordering is regarded as homogeneous in the whole bulk of the crystal (i.e. resistant towards formation of antiphase domains). It is described by one of the appropriate distribution functions which contains two long-range order parameters. The calculations have revealed the extrema of the free energy function, and their shape and behaviour upon variations of temperature are analyzed. It is shown that under certain circumstances the system can display more than one minimum of free energy within the ordered phase

  11. Sparse RNA folding revisited: space-efficient minimum free energy structure prediction.

    Science.gov (United States)

    Will, Sebastian; Jabbari, Hosna

    2016-01-01

    RNA secondary structure prediction by energy minimization is the central computational tool for the analysis of structural non-coding RNAs and their interactions. Sparsification has been successfully applied to improve the time efficiency of various structure prediction algorithms while guaranteeing the same result; however, for many such folding problems, space efficiency is of even greater concern, particularly for long RNA sequences. So far, space-efficient sparsified RNA folding with fold reconstruction was solved only for simple base-pair-based pseudo-energy models. Here, we revisit the problem of space-efficient free energy minimization. Whereas the space-efficient minimization of the free energy has been sketched before, the reconstruction of the optimum structure has not even been discussed. We show that this reconstruction is not possible in trivial extension of the method for simple energy models. Then, we present the time- and space-efficient sparsified free energy minimization algorithm SparseMFEFold that guarantees MFE structure prediction. In particular, this novel algorithm provides efficient fold reconstruction based on dynamically garbage-collected trace arrows. The complexity of our algorithm depends on two parameters, the number of candidates Z and the number of trace arrows T; both are bounded by [Formula: see text], but are typically much smaller. The time complexity of RNA folding is reduced from [Formula: see text] to [Formula: see text]; the space complexity, from [Formula: see text] to [Formula: see text]. Our empirical results show more than 80 % space savings over RNAfold [Vienna RNA package] on the long RNAs from the RNA STRAND database (≥2500 bases). The presented technique is intentionally generalizable to complex prediction algorithms; due to their high space demands, algorithms like pseudoknot prediction and RNA-RNA-interaction prediction are expected to profit even stronger than "standard" MFE folding. SparseMFEFold is free

  12. Dependence of Interaction Free Energy between Solutes on an External Electrostatic Field

    Directory of Open Access Journals (Sweden)

    Pei-Kun Yang

    2013-07-01

    Full Text Available To explore the athermal effect of an external electrostatic field on the stabilities of protein conformations and the binding affinities of protein-protein/ligand interactions, the dependences of the polar and hydrophobic interactions on the external electrostatic field, −Eext, were studied using molecular dynamics (MD simulations. By decomposing Eext into, along, and perpendicular to the direction formed by the two solutes, the effect of Eext on the interactions between these two solutes can be estimated based on the effects from these two components. Eext was applied along the direction of the electric dipole formed by two solutes with opposite charges. The attractive interaction free energy between these two solutes decreased for solutes treated as point charges. In contrast, the attractive interaction free energy between these two solutes increased, as observed by MD simulations, for Eext = 40 or 60 MV/cm. Eext was applied perpendicular to the direction of the electric dipole formed by these two solutes. The attractive interaction free energy was increased for Eext = 100 MV/cm as a result of dielectric saturation. The force on the solutes along the direction of Eext computed from MD simulations was greater than that estimated from a continuum solvent in which the solutes were treated as point charges. To explore the hydrophobic interactions, Eext was applied to a water cluster containing two neutral solutes. The repulsive force between these solutes was decreased/increased for Eext along/perpendicular to the direction of the electric dipole formed by these two solutes.

  13. CALCULATING SEPARATE MAGNETIC FREE ENERGY ESTIMATES FOR ACTIVE REGIONS PRODUCING MULTIPLE FLARES: NOAA AR11158

    Energy Technology Data Exchange (ETDEWEB)

    Tarr, Lucas; Longcope, Dana; Millhouse, Margaret [Department of Physics, Montana State University, Bozeman, MT 59717 (United States)

    2013-06-10

    It is well known that photospheric flux emergence is an important process for stressing coronal fields and storing magnetic free energy, which may then be released during a flare. The Helioseismic and Magnetic Imager (HMI) on board the Solar Dynamics Observatory (SDO) captured the entire emergence of NOAA AR 11158. This region emerged as two distinct bipoles, possibly connected underneath the photosphere, yet characterized by different photospheric field evolutions and fluxes. The combined active region complex produced 15 GOES C-class, two M-class, and the X2.2 Valentine's Day Flare during the four days after initial emergence on 2011 February 12. The M and X class flares are of particular interest because they are nonhomologous, involving different subregions of the active region. We use a Magnetic Charge Topology together with the Minimum Current Corona model of the coronal field to model field evolution of the complex. Combining this with observations of flare ribbons in the 1600 A channel of the Atmospheric Imaging Assembly on board SDO, we propose a minimization algorithm for estimating the amount of reconnected flux and resulting drop in magnetic free energy during a flare. For the M6.6, M2.2, and X2.2 flares, we find a flux exchange of 4.2 Multiplication-Sign 10{sup 20} Mx, 2.0 Multiplication-Sign 10{sup 20} Mx, and 21.0 Multiplication-Sign 10{sup 20} Mx, respectively, resulting in free energy drops of 3.89 Multiplication-Sign 10{sup 30} erg, 2.62 Multiplication-Sign 10{sup 30} erg, and 1.68 Multiplication-Sign 10{sup 32} erg.

  14. Free energy landscape and cooperatively rearranging region in a hard sphere glass

    Science.gov (United States)

    Yoshidome, Takashi; Yoshimori, Akira; Odagaki, Takashi

    2007-08-01

    Exploiting the density functional theory, we calculate the free energy landscape (FEL) of the hard sphere glass in three dimensions. From the FEL, we estimate the number of the particles in the cooperatively rearranging region (CRR). We find that the density dependence of the number of the particles in the CRR is expressed as a power law function of the density. Analyzing the relaxation process in the CRR, we also find that the string motion is the elementary process for the structural relaxation, which leads to the natural definition of the simultaneously rearranging region as the particles displaced in the string motion.

  15. Ligand Conformational and Solvation/Desolvation Free Energy in Protein-Ligand Complex Formation

    Czech Academy of Sciences Publication Activity Database

    Kolář, Michal; Fanfrlík, Jindřich; Hobza, Pavel

    2011-01-01

    Roč. 115, č. 16 (2011), s. 4718-4724 ISSN 1520-6106 R&D Projects: GA MŠk LC512; GA ČR GAP208/11/0295 Grant - others:Korea Science and Engineering Foundation(KR) R32-2008-000-10180-0; European Science Fund(XE) CZ.1.05/2.1.00/03.0058 Institutional research plan: CEZ:AV0Z40550506 Keywords : solvation free energy * SMD * HIV protease inhibitors Subject RIV: CF - Physical ; Theoretical Chemistry Impact factor: 3.696, year: 2011

  16. Similarity Laws for the Lines of Ideal Free Energy and Chemical Potential in Supercritical Fluids.

    Science.gov (United States)

    Apfelbaum, E M; Vorob'ev, V S

    2017-09-21

    We have found the curves on the density-temperature plane, along which the values of free energy and chemical potential correspond to ideal gas quantities. At first, we have applied the van der Waals equation to construct them and to derive their equations. Then we have shown that the same lines for real substances (Ar, N 2 , CH 4 , SF 6 , H 2 , H 2 O) and for the model Lennard-Jones system constructed on the basis of the measurements data and calculations are well matched with the derived equations. The validity and deviations from the obtained similarity laws are discussed.

  17. Analytical free energy gradient for the molecular Ornstein-Zernike self-consistent-field method

    Directory of Open Access Journals (Sweden)

    N.Yoshida

    2007-09-01

    Full Text Available An analytical free energy gradient for the molecular Ornstein-Zernike self-consistent-field (MOZ-SCF method is presented. MOZ-SCF theory is one of the theories to considering the solvent effects on the solute electronic structure in solution. [Yoshida N. et al., J. Chem. Phys., 2000, 113, 4974] Molecular geometries of water, formaldehyde, acetonitrile and acetone in water are optimized by analytical energy gradient formula. The results are compared with those from the polarizable continuum model (PCM, the reference interaction site model (RISM-SCF and the three dimensional (3D RISM-SCF.

  18. Heavy-quark free energies, internal-energy and entropy contributions

    International Nuclear Information System (INIS)

    Kaczmarek, O.

    2009-01-01

    We present lattice QCD results on heavy-quark free energies, extract from its temperature dependence the entropy and internal-energy contributions, and discuss the onset of medium effects that lead to screening of static quark-antiquark sources in a thermal medium. The detailed analysis of the temperature and distance dependence of the different contributions indicate the complex non-perturbative nature of strongly interacting matter. We shall discuss the necessity to include those effects in studies on the behavior of heavy quarks, heavy-quark bound states and their dissociation in the quark-gluon plasma phase. (orig.)

  19. Free energy calculations on Transthyretin dissociation and ligand binding from Molecular Dynamics Simulations

    DEFF Research Database (Denmark)

    Sørensen, Jesper; Hamelberg, Donald; McCammon, J. Andrew

    experimental results have helped to explain this aberrant behavior of TTR, however, structural insights of the amyloidgenic process are still lacking. Therefore, we have used all-atom molecular dynamics simulation and free energy calculations to study the initial phase of this process. We have calculated......Many questions about the nature of aggregation and the proteins that are involved in these events are still left unanswered. One of the proteins that is known to form amyloids is Transthyretine (TTR), the secondary transporter of thyroxine and transporter of retinol-binding-protein. Several...

  20. Relating Linear and Volumetric Variables Through Body Scanning to Improve Human Interfaces in Space

    Science.gov (United States)

    Margerum, Sarah E.; Ferrer, Mike A.; Young, Karen S.; Rajulu, Sudhakar

    2010-01-01

    Designing space suits and vehicles for the diverse human population present unique challenges for the methods of traditional anthropometry. Space suits are bulky and allow the operator to shift position within the suit and inhibit the ability to identify body landmarks. Limited suit sizing options also cause variability in fit and performance between similarly sized individuals. Space vehicles are restrictive in volume in both the fit and the ability to collect data. NASA's Anthropometric and Biomechanics Facility (ABF) has utilized 3D scanning to shift from traditional linear anthropometry to explore and examine volumetric capabilities to provide anthropometric solutions for design. Overall, the key goals are to improve the human-system performance and develop new processes to aid in the design and evaluation of space systems. Four case studies are presented that illustrate the shift from purely linear analyses to an augmented volumetric toolset to predict and analyze the human within the space suit and vehicle. The first case study involves the calculation of maximal head volume to estimate total free volume in the helmet for proper air exchange. Traditional linear measurements resulted in an inaccurate representation of the head shape, yet limited data exists for the determination of a large head volume. Steps were first taken to identify and classify a maximum head volume and the resulting comparisons to the estimate are presented in this paper. This study illustrates the gap between linear components of anthropometry and the need for overall volume metrics in order to provide solutions. A second case study examines the overlay of the space suit scans and components onto scanned individuals to quantify fit and clearance to aid in sizing the suit to the individual. Restrictions in space suit size availability present unique challenges to optimally fit the individual within a limited sizing range while maintaining performance. Quantification of the clearance and